Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 144 of 187
Found at i:42993814 original size:19 final size:19
Alignment explanation
Indices: 42993769--42993816 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
42993759 TCAAAATAAT
* *
42993769 AATATATT-ATAATATTGA
1 AATATATTAATAAAATTAA
42993787 AATAGTATTAATAAAATTAA
1 AATA-TATTAATAAAATTAA
42993807 AATATATTAA
1 AATATATTAA
42993817 ACTTAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 4 0.15
19 10 0.38
20 12 0.46
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
AATATATTAATAAAATTAA
Found at i:42996598 original size:23 final size:23
Alignment explanation
Indices: 42996571--42996621 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
42996561 GAAGATTTTG
42996571 GCATATTCCCTGAAGCGAATATT
1 GCATATTCCCTGAAGCGAATATT
*
42996594 GCATA-TCCCTGAAGTGAATATT
1 GCATATTCCCTGAAGCGAATATT
*
42996616 ACATAT
1 GCATAT
42996622 AATTATTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (23 bp):
GCATATTCCCTGAAGCGAATATT
Found at i:43002919 original size:12 final size:12
Alignment explanation
Indices: 43002886--43002936 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
43002876 ATGACATACT
43002886 TAAAAA-AAGAA
1 TAAAAAGAAGAA
* * *
43002897 TAATAACAAGAG
1 TAAAAAGAAGAA
*
43002909 TAAGAAGAAGAA
1 TAAAAAGAAGAA
*
43002921 TAAAAAGAATAA
1 TAAAAAGAAGAA
43002933 TAAA
1 TAAA
43002937 GTATATAGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
11 5 0.16
12 27 0.84
ACGTcount: A:0.71, C:0.02, G:0.14, T:0.14
Consensus pattern (12 bp):
TAAAAAGAAGAA
Found at i:43003140 original size:6 final size:6
Alignment explanation
Indices: 43003123--43003201 Score: 72
Period size: 6 Copynumber: 12.7 Consensus size: 6
43003113 AAAAGAAATG
* * *
43003123 AAAT-A AAATAA TAATAA TAAATAGA AAATAA CAAACAA AAATAA TAAT-A
1 AAATAA AAATAA AAATAA -AAATA-A AAATAA -AAATAA AAATAA AAATAA
43003172 AAATAA AAATAA AAATAA AGAACTAA AAAT
1 AAATAA AAATAA AAATAA A-AA-TAA AAAT
43003202 GGGAAAATAG
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
5 8 0.13
6 30 0.49
7 18 0.30
8 5 0.08
ACGTcount: A:0.75, C:0.04, G:0.03, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:43003198 original size:20 final size:19
Alignment explanation
Indices: 43003123--43003201 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 19
43003113 AAAAGAAATG
*
43003123 AAAT-AAAATAATAA-TAA
1 AAATAAAAATAAAAACTAA
43003140 TAAATAGAAAATAACAAAC-AA
1 -AAATA-AAAATAA-AAACTAA
*
43003161 AAATAATAAT-AAAA-TAA
1 AAATAAAAATAAAAACTAA
43003178 AAATAAAAATAAAGAACTAA
1 AAATAAAAATAAA-AACTAA
43003198 AAAT
1 AAAT
43003202 GGGAAAATAG
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
17 14 0.28
18 7 0.14
19 6 0.12
20 19 0.38
21 4 0.08
ACGTcount: A:0.75, C:0.04, G:0.03, T:0.19
Consensus pattern (19 bp):
AAATAAAAATAAAAACTAA
Found at i:43006435 original size:31 final size:30
Alignment explanation
Indices: 43006407--43006483 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
43006397 TCAAAATTCA
*
43006407 AAAAGTATAGGGATTAAAATTGA-CAAATTT
1 AAAAGTATAGAGATTAAAATTGATCAAA-TT
* *
43006437 GAAAAG-ATAGAAACTAAAATTGATCAAATT
1 -AAAAGTATAGAGATTAAAATTGATCAAATT
43006467 AAAA-TATAGAGATTAAA
1 AAAAGTATAGAGATTAAA
43006484 TCCATAACTC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 14 0.36
30 16 0.41
31 9 0.23
ACGTcount: A:0.56, C:0.04, G:0.14, T:0.26
Consensus pattern (30 bp):
AAAAGTATAGAGATTAAAATTGATCAAATT
Found at i:43006606 original size:20 final size:20
Alignment explanation
Indices: 43006583--43006621 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
43006573 ATATTAACAC
*
43006583 ATTAAAATGTATAAAATACG
1 ATTAAAATGAATAAAATACG
*
43006603 ATTATAATGAATAAAATAC
1 ATTAAAATGAATAAAATAC
43006622 ATCAACGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (20 bp):
ATTAAAATGAATAAAATACG
Found at i:43008038 original size:18 final size:19
Alignment explanation
Indices: 43008001--43008041 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
43007991 AGTAAAATAT
43008001 TTTTCGGAAAATGATTTAC
1 TTTTCGGAAAATGATTTAC
*
43008020 TTTTCTGAAAATG-TTTAC
1 TTTTCGGAAAATGATTTAC
43008038 TTTT
1 TTTT
43008042 TTAGTGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (19 bp):
TTTTCGGAAAATGATTTAC
Found at i:43009406 original size:20 final size:23
Alignment explanation
Indices: 43009376--43009417 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
43009366 TCCGCGTTTC
43009376 TGCTCTTCAAG-AAGA-GATCAA
1 TGCTCTTCAAGCAAGATGATCAA
43009397 TGCT-TTCAAGCAAGATGATCA
1 TGCTCTTCAAGCAAGATGATCA
43009418 CTCCGTCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (23 bp):
TGCTCTTCAAGCAAGATGATCAA
Found at i:43021040 original size:24 final size:22
Alignment explanation
Indices: 43020988--43021040 Score: 52
Period size: 24 Copynumber: 2.3 Consensus size: 22
43020978 GTTTTAATTG
43020988 TTTAATTACGGTTTATGGTTTA
1 TTTAATTACGGTTTATGGTTTA
** * *
43021010 TGAAATTACGATTTTAGTGTTTTA
1 TTTAATTACG-GTTTA-TGGTTTA
43021034 TTTAATT
1 TTTAATT
43021041 TTTAAGTGTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
22 8 0.35
23 4 0.17
24 11 0.48
ACGTcount: A:0.26, C:0.04, G:0.15, T:0.55
Consensus pattern (22 bp):
TTTAATTACGGTTTATGGTTTA
Found at i:43021052 original size:19 final size:18
Alignment explanation
Indices: 43021021--43021058 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
43021011 GAAATTACGA
43021021 TTTTAGTGTTTTATTTAAT
1 TTTTAGTGTTTTA-TTAAT
43021040 TTTTAAGTG-TTTATTAAT
1 TTTT-AGTGTTTTATTAAT
43021058 T
1 T
43021059 AGTGTTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 8 0.44
20 4 0.22
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.66
Consensus pattern (18 bp):
TTTTAGTGTTTTATTAAT
Found at i:43021138 original size:19 final size:21
Alignment explanation
Indices: 43021114--43021163 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
43021104 GGTGTGTTAA
43021114 TTAGGGTTTTTGG-TTTATT-
1 TTAGGGTTTTTGGATTTATTG
43021133 TTAGGG-TTTTGGATTTTATTG
1 TTAGGGTTTTTGGA-TTTATTG
43021154 TTA-GGTTTTT
1 TTAGGGTTTTT
43021164 AGTGTTTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 6 0.22
19 6 0.22
20 8 0.30
21 7 0.26
ACGTcount: A:0.12, C:0.00, G:0.26, T:0.62
Consensus pattern (21 bp):
TTAGGGTTTTTGGATTTATTG
Found at i:43031926 original size:34 final size:34
Alignment explanation
Indices: 43031859--43031926 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
43031849 GTAAGTAATT
*
43031859 TATCCTCTTTCCTATTTGACAATACATGTTTTTA
1 TATCCTCTTTCCTATTTGACAATACATGGTTTTA
* **
43031893 TATCCTCTTTCTTATTTGACAATTTATGGTTTTA
1 TATCCTCTTTCCTATTTGACAATACATGGTTTTA
43031927 ATTTGATATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.22, C:0.18, G:0.07, T:0.53
Consensus pattern (34 bp):
TATCCTCTTTCCTATTTGACAATACATGGTTTTA
Found at i:43033952 original size:32 final size:32
Alignment explanation
Indices: 43033916--43033998 Score: 112
Period size: 38 Copynumber: 2.4 Consensus size: 32
43033906 TCTATTTACA
43033916 AGGGATTCCAACAGATTTCTATCCTTAATTAT
1 AGGGATTCCAACAGATTTCTATCCTTAATTAT
43033948 AGGGATTCCAATACCATCAGATTTCTATCCTTAATTAT
1 AGGGATTCC---A--A-CAGATTTCTATCCTTAATTAT
43033986 AGGGATTCCAACA
1 AGGGATTCCAACA
43033999 CTCCCCCTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
32 11 0.24
33 1 0.02
35 2 0.04
37 1 0.02
38 30 0.67
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (32 bp):
AGGGATTCCAACAGATTTCTATCCTTAATTAT
Found at i:43059355 original size:31 final size:31
Alignment explanation
Indices: 43059317--43059382 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
43059307 GGCTAGGTAT
**
43059317 CAAATTGAACATTGAAGGCAAACTCAAATAC
1 CAAATTGAACATTGAAACCAAACTCAAATAC
* **
43059348 CAAATTGAATATTGAAACCAAACTCAGGTAC
1 CAAATTGAACATTGAAACCAAACTCAAATAC
43059379 CAAA
1 CAAA
43059383 ATAGTTTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.48, C:0.20, G:0.12, T:0.20
Consensus pattern (31 bp):
CAAATTGAACATTGAAACCAAACTCAAATAC
Found at i:43060148 original size:20 final size:20
Alignment explanation
Indices: 43060115--43060154 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
43060105 TCTCTCCCAA
*
43060115 AGTAATTATGAAAGTAAAAT
1 AGTAATTATAAAAGTAAAAT
* *
43060135 AGTAATTTTAAAAGTCAAAT
1 AGTAATTATAAAAGTAAAAT
43060155 TCAACGAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.33
Consensus pattern (20 bp):
AGTAATTATAAAAGTAAAAT
Found at i:43063702 original size:31 final size:31
Alignment explanation
Indices: 43063664--43063729 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
43063654 GTCTGGGTAT
43063664 CAAATTGAACATTGAAACCAAACTCAAGTAC
1 CAAATTGAACATTGAAACCAAACTCAAGTAC
* **
43063695 CAAATTGAATATTGAAGTCAAACTCAAGTAC
1 CAAATTGAACATTGAAACCAAACTCAAGTAC
43063726 CAAA
1 CAAA
43063730 ATAGTTTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.21
Consensus pattern (31 bp):
CAAATTGAACATTGAAACCAAACTCAAGTAC
Found at i:43066690 original size:20 final size:20
Alignment explanation
Indices: 43066657--43066696 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
43066647 TCTCTCCCAA
*
43066657 AGTAATTATGAAAGTAAAAT
1 AGTAATTATAAAAGTAAAAT
* *
43066677 AGTAATTTTAAAAGTCAAAT
1 AGTAATTATAAAAGTAAAAT
43066697 TCAATGAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.33
Consensus pattern (20 bp):
AGTAATTATAAAAGTAAAAT
Found at i:43071909 original size:31 final size:31
Alignment explanation
Indices: 43071871--43071936 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
43071861 GTCTGGGTAT
* * **
43071871 CAAATTGAGCGTTGAAGGCAAACTCAAGTAC
1 CAAATTGAACATTGAAACCAAACTCAAGTAC
*
43071902 CAAATTGAATATTGAAACCAAACTCAAGTAC
1 CAAATTGAACATTGAAACCAAACTCAAGTAC
43071933 CAAA
1 CAAA
43071937 ATAGTTTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (31 bp):
CAAATTGAACATTGAAACCAAACTCAAGTAC
Found at i:43079067 original size:36 final size:36
Alignment explanation
Indices: 43079018--43079089 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
43079008 CTTAGACCCC
43079018 ATGTGATGATGTGACTACCATGCATTATTCCACATT
1 ATGTGATGATGTGACTACCATGCATTATTCCACATT
*
43079054 ATGTGATGTTGTGACTACCATGCATTATTCCACATT
1 ATGTGATGATGTGACTACCATGCATTATTCCACATT
43079090 TTCAGCGTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (36 bp):
ATGTGATGATGTGACTACCATGCATTATTCCACATT
Found at i:43088956 original size:41 final size:41
Alignment explanation
Indices: 43088898--43089093 Score: 236
Period size: 41 Copynumber: 4.8 Consensus size: 41
43088888 TTTTTAAACC
43088898 TTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGATA
1 TTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGATA
* * * **
43088939 TTTAGCGGCGTTGTTATCCGAGCGCCGCTAATTCTCTGG-CC
1 TTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTC-GGATA
*
43088980 TTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGGATA
1 TTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGATA
* * **
43089021 TTTAGTGGCGTTTTTATCTGAGCGCCGCTAATTCTCTGG-CC
1 TTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTC-GGATA
* *
43089062 TTTAGCGGCGTTTTT-GCCGAAGCGCCGCTAAT
1 TTTAGCGGCGTTTTTATCTG-AGCGCCGCTAAT
43089094 AGTAACAAAA
Statistics
Matches: 132, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
40 4 0.03
41 124 0.94
42 4 0.03
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.34
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGATA
Found at i:43089038 original size:82 final size:82
Alignment explanation
Indices: 43088896--43089093 Score: 333
Period size: 82 Copynumber: 2.4 Consensus size: 82
43088886 GATTTTTAAA
*
43088896 CCTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGATATTTAGCGGCGTTGTTATCCGAG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGGATATTTAGCGGCGTTGTTATCCGAG
43088961 CGCCGCTAATTCTCTGG
66 CGCCGCTAATTCTCTGG
* * *
43088978 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGGATATTTAGTGGCGTTTTTATCTGAG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGGATATTTAGCGGCGTTGTTATCCGAG
43089043 CGCCGCTAATTCTCTGG
66 CGCCGCTAATTCTCTGG
** *
43089060 CCTTTAGCGGCGTTTTTGCCGAAGCGCCGCTAAT
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAAT
43089094 AGTAACAAAA
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 109 1.00
ACGTcount: A:0.15, C:0.25, G:0.26, T:0.34
Consensus pattern (82 bp):
CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGGATATTTAGCGGCGTTGTTATCCGAG
CGCCGCTAATTCTCTGG
Found at i:43090328 original size:2 final size:2
Alignment explanation
Indices: 43090321--43090351 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43090311 TAATTAATAG
43090321 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43090352 ATAGGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43090898 original size:7 final size:7
Alignment explanation
Indices: 43090886--43091002 Score: 72
Period size: 7 Copynumber: 15.9 Consensus size: 7
43090876 GATATAAGGT
43090886 TTAGGGG
1 TTAGGGG
*
43090893 TTAGGGA
1 TTAGGGG
**
43090900 TTAGAGAT
1 TTAG-GGG
43090908 TTAGGGG
1 TTAGGGG
43090915 TTAGGGG
1 TTAGGGG
*
43090922 TTAGGGAT
1 TTAGGG-G
43090930 TTAGGGG
1 TTAGGGG
*
43090937 TTAAGGG
1 TTAGGGG
**
43090944 TTAGGAAT
1 TTAGG-GG
*
43090952 TTAGTGG
1 TTAGGGG
* *
43090959 CTAGGAGAT
1 TTAGG-G-G
43090968 TTAGGGG
1 TTAGGGG
43090975 TTAGGGG
1 TTAGGGG
*
43090982 TTAGGGAT
1 TTAGGG-G
*
43090990 TTAGGGT
1 TTAGGGG
43090997 TTAGGG
1 TTAGGG
43091003 TGTCAAGGGT
Statistics
Matches: 84, Mismatches: 20, Indels: 12
0.72 0.17 0.10
Matches are distributed among these distances:
7 57 0.68
8 23 0.27
9 4 0.05
ACGTcount: A:0.22, C:0.01, G:0.44, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:43090899 original size:22 final size:21
Alignment explanation
Indices: 43090868--43091002 Score: 94
Period size: 22 Copynumber: 6.1 Consensus size: 21
43090858 TACTCTATTA
*
43090868 GGGTTTGGGATATAAGGTTTAG
1 GGGTTAGGGAT-TAAGGTTTAG
*
43090890 GGGTTAGGGATTAGAGATTTAG
1 GGGTTAGGGATTA-AGGTTTAG
* *
43090912 GGGTTAGGGGTTAGGGATTTAG
1 GGGTTAGGGATTAAGG-TTTAG
43090934 GGGTTAAGGG-TT-AGGAATTTAG
1 GGGTT-AGGGATTAAGG--TTTAG
* * * *
43090956 TGGCTAGGAGATTTAGGGGTTAG
1 GGGTTAGG-GA-TTAAGGTTTAG
*
43090979 GGGTTAGGGATTTAGGGTTTAG
1 GGGTTAGGGA-TTAAGGTTTAG
43091001 GG
1 GG
43091003 TGTCAAGGGT
Statistics
Matches: 92, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
21 8 0.09
22 66 0.72
23 14 0.15
24 2 0.02
25 2 0.02
ACGTcount: A:0.22, C:0.01, G:0.44, T:0.33
Consensus pattern (21 bp):
GGGTTAGGGATTAAGGTTTAG
Found at i:43091003 original size:7 final size:7
Alignment explanation
Indices: 43090865--43091003 Score: 68
Period size: 7 Copynumber: 19.0 Consensus size: 7
43090855 ATGTACTCTA
43090865 TTAGGGT
1 TTAGGGT
43090872 TT-GGGAT
1 TTAGGG-T
* *
43090879 ATAAGGT
1 TTAGGGT
*
43090886 TTAGGGG
1 TTAGGGT
*
43090893 TTAGGGA
1 TTAGGGT
*
43090900 TTAGAGAT
1 TTAG-GGT
*
43090908 TTAGGGG
1 TTAGGGT
*
43090915 TTAGGGG
1 TTAGGGT
43090922 TTAGGGAT
1 TTAGGG-T
43090930 TTAGGGGT
1 TTA-GGGT
*
43090938 TAAGGG-
1 TTAGGGT
*
43090944 TTAGGAAT
1 TTAGG-GT
43090952 TTAGTGG-
1 TTAG-GGT
*
43090959 CTAGGAGAT
1 TTAGG-G-T
*
43090968 TTAGGGG
1 TTAGGGT
*
43090975 TTAGGGG
1 TTAGGGT
43090982 TTAGGGAT
1 TTAGGG-T
43090990 TTAGGGT
1 TTAGGGT
43090997 TTAGGGT
1 TTAGGGT
43091004 GTCAAGGGTA
Statistics
Matches: 101, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
6 8 0.08
7 61 0.60
8 24 0.24
9 8 0.08
ACGTcount: A:0.22, C:0.01, G:0.43, T:0.34
Consensus pattern (7 bp):
TTAGGGT
Found at i:43094713 original size:13 final size:13
Alignment explanation
Indices: 43094667--43094758 Score: 91
Period size: 13 Copynumber: 6.9 Consensus size: 13
43094657 TATAACTTAC
43094667 ATTACTTAAATAT
1 ATTACTTAAATAT
* *
43094680 ATTAATTACTAAAAT
1 ATTACTTA--AATAT
43094695 -TTACTTAAATAT
1 ATTACTTAAATAT
*
43094707 ATTACTTAAATAC
1 ATTACTTAAATAT
43094720 ATTACTTACTAGA-AT
1 ATTACTTA--A-ATAT
43094735 -TTACTTAAATAT
1 ATTACTTAAATAT
43094747 ATTACTTAAATA
1 ATTACTTAAATA
43094759 CATGACTTAC
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
11 1 0.02
12 7 0.11
13 37 0.57
14 13 0.20
15 6 0.09
16 1 0.02
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (13 bp):
ATTACTTAAATAT
Found at i:43094729 original size:40 final size:38
Alignment explanation
Indices: 43094650--43094901 Score: 217
Period size: 40 Copynumber: 6.5 Consensus size: 38
43094640 TATATATTTT
* * * *
43094650 TAAAATTTATAACTTACATTACTTAAATATATTAATTAC
1 TAAAATTTATAA-ATATATTACTTAAATACATTACTTAC
43094689 TAAAATTTACTTAAATATATTACTTAAATACATTACTTAC
1 TAAAATTTA--TAAATATATTACTTAAATACATTACTTAC
* *
43094729 TAGAATTTACTTAAATATATTACTTAAATACATGACTTAC
1 TAAAATTTA--TAAATATATTACTTAAATACATTACTTAC
**
43094769 TAAAA-TTA-AAGTATATATTACATTACTTACATTACTTAC
1 TAAAATTTATAA--ATATATTAC-TTAAATACATTACTTAC
* * **
43094808 TAAAA--TAT-ATTACATTACTTAAATTTATTACTTAC
1 TAAAATTTATAAATATATTACTTAAATACATTACTTAC
* * * *
43094843 AAAAATTTATAACTTACATTACTTAAATATATTACATTAC
1 TAAAATTTATAA-ATATATTACTTAAATACATTAC-TTAC
*
43094883 TTAAAATTTATATATATAT
1 -TAAAATTTATAAATATAT
43094902 ATTTAAAATT
Statistics
Matches: 179, Mismatches: 22, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
35 17 0.09
36 9 0.05
37 3 0.02
38 13 0.07
39 52 0.29
40 72 0.40
41 13 0.07
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.43
Consensus pattern (38 bp):
TAAAATTTATAAATATATTACTTAAATACATTACTTAC
Found at i:43094766 original size:13 final size:13
Alignment explanation
Indices: 43094664--43094767 Score: 79
Period size: 13 Copynumber: 7.8 Consensus size: 13
43094654 ATTTATAACT
43094664 TACATTACTTAAA
1 TACATTACTTAAA
* *
43094677 TATATTAATTACTAA
1 TACATTACTTA--AA
43094692 -A-ATTTACTTAAA
1 TACA-TTACTTAAA
*
43094704 TATATTACTTAAA
1 TACATTACTTAAA
*
43094717 TACATTACTT-AC
1 TACATTACTTAAA
*
43094729 TAGAATTTACTTAAA
1 TA-CA-TTACTTAAA
*
43094744 TATATTACTTAAA
1 TACATTACTTAAA
*
43094757 TACATGACTTA
1 TACATTACTTA
43094768 CTAAAATTAA
Statistics
Matches: 73, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
12 5 0.07
13 48 0.66
14 15 0.21
15 5 0.07
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (13 bp):
TACATTACTTAAA
Found at i:43094825 original size:18 final size:18
Alignment explanation
Indices: 43094799--43094889 Score: 87
Period size: 18 Copynumber: 4.9 Consensus size: 18
43094789 CATTACTTAC
43094799 ATTAC-TTACTAAAATAT
1 ATTACATTACTAAAATAT
* *
43094816 ATTACATTACTTAAATTT
1 ATTACATTACTAAAATAT
*
43094834 ATTAC-TTACAAAAATTTAT
1 ATTACATTACTAAAA--TAT
*
43094853 AACTTACATTACTTAAATAT
1 -A-TTACATTACTAAAATAT
43094873 ATTACATTACTTAAAAT
1 ATTACATTAC-TAAAAT
43094890 TTATATATAT
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
17 12 0.20
18 24 0.41
19 8 0.14
20 4 0.07
21 4 0.07
22 7 0.12
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTACATTACTAAAATAT
Found at i:43094842 original size:22 final size:22
Alignment explanation
Indices: 43094790--43094893 Score: 77
Period size: 22 Copynumber: 5.1 Consensus size: 22
43094780 TATATATTAC
**
43094790 ATTACTTACATTACTTACTAAAAT
1 ATTACTTACATTACTTA--AATTT
43094814 A-TA-TTACATTACTTAAATTT
1 ATTACTTACATTACTTAAATTT
43094834 ATTACTTACA--A---AAATTT
1 ATTACTTACATTACTTAAATTT
*
43094851 ATAACTTACATTACTTAAA--T
1 ATTACTTACATTACTTAAATTT
43094871 A-TA-TTACATTACTTAAAATTT
1 ATTACTTACATTACTT-AAATTT
43094892 AT
1 AT
43094894 ATATATATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 24
0.70 0.04 0.26
Matches are distributed among these distances:
17 15 0.23
18 11 0.17
19 5 0.08
20 7 0.11
21 4 0.06
22 20 0.31
23 2 0.03
24 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTACTTACATTACTTAAATTT
Found at i:43094848 original size:17 final size:17
Alignment explanation
Indices: 43094799--43094860 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
43094789 CATTACTTAC
* *
43094799 ATTACTTACTAAAATAT
1 ATTACTTACAAAAATTT
**
43094816 ATTACATTACTTAAATTT
1 ATTAC-TTACAAAAATTT
43094834 ATTACTTACAAAAATTT
1 ATTACTTACAAAAATTT
*
43094851 ATAACTTACA
1 ATTACTTACA
43094861 TTACTTAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
17 24 0.62
18 15 0.38
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTACTTACAAAAATTT
Found at i:43095191 original size:20 final size:19
Alignment explanation
Indices: 43095166--43095204 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
43095156 ATAAACTTGC
43095166 ATAACTTACATAATAACATA
1 ATAACTTACATAAT-ACATA
43095186 ATAACTTACATAATACATA
1 ATAACTTACATAATACATA
43095205 GCCTACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAACTTACATAATACATA
Found at i:43095216 original size:25 final size:24
Alignment explanation
Indices: 43095165--43095385 Score: 119
Period size: 25 Copynumber: 9.3 Consensus size: 24
43095155 TATAAACTTG
*
43095165 CATAACTTACATAAT--A-ACATA
1 CATAACTTACATAATACATACCTA
43095186 -ATAACTTACATAATACATAGCCTA
1 CATAACTTACATAATACATA-CCTA
* *
43095210 CATAACTTACATAATACACAACTTA
1 CATAACTTACATAATACA-TACCTA
* *
43095235 CATAACTTAAATAACTTACATAAC-A
1 CATAACTTACATAA--TACATACCTA
**
43095260 CATAACTTTGATAACTAACATTA--TA
1 CATAACTTACATAA-T-ACA-TACCTA
*
43095285 CACAACTTACATAATACAT---TA
1 CATAACTTACATAATACATACCTA
* *
43095306 C-TTACTTA-A-CATACATAGCCTA
1 CATAACTTACATAATACATA-CCTA
* *
43095328 CATAACTTACATAATACACAACTTA
1 CATAACTTACATAATACA-TACCTA
* *
43095353 CATAACTTAAATAACTTACATA-ATA
1 CATAACTTACATAA--TACATACCTA
43095378 CATAACTT
1 CATAACTT
43095386 TGATGAAGCT
Statistics
Matches: 156, Mismatches: 23, Indels: 38
0.72 0.11 0.18
Matches are distributed among these distances:
18 6 0.04
19 1 0.01
20 19 0.12
21 3 0.02
22 5 0.03
23 10 0.06
24 6 0.04
25 92 0.59
26 6 0.04
27 8 0.05
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.30
Consensus pattern (24 bp):
CATAACTTACATAATACATACCTA
Found at i:43095249 original size:34 final size:35
Alignment explanation
Indices: 43095211--43095385 Score: 131
Period size: 34 Copynumber: 4.7 Consensus size: 35
43095201 CATAGCCTAC
43095211 ATAACTTACATAATACACAACTT-ACATAACTTAA
1 ATAACTTACATAATACACAACTTAACATAACTTAA
* *
43095245 ATAACTTACATAACACATAACTTTGATA-ACTAACATTATA
1 ATAACTTACATAATACACAAC-TT-A-ACA-TAAC-TTA-A
* * * *
43095285 CACAACTTACATAATACATTACTTACTTAACATACATAGCCTAC
1 -ATAACTTACATAATAC---AC-AACTTAACAT--A-A-CTTAA
43095329 ATAACTTACATAATACACAACTT-ACATAACTTAA
1 ATAACTTACATAATACACAACTTAACATAACTTAA
*
43095363 ATAACTTACATAATACATAACTT
1 ATAACTTACATAATACACAACTT
43095386 TGATGAAGCT
Statistics
Matches: 111, Mismatches: 13, Indels: 34
0.70 0.08 0.22
Matches are distributed among these distances:
34 44 0.40
35 3 0.03
36 1 0.01
37 1 0.01
38 9 0.08
39 7 0.06
40 3 0.03
41 14 0.13
42 2 0.02
43 17 0.15
44 4 0.04
45 5 0.05
46 1 0.01
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (35 bp):
ATAACTTACATAATACACAACTTAACATAACTTAA
Found at i:43095254 original size:59 final size:59
Alignment explanation
Indices: 43095185--43095381 Score: 272
Period size: 59 Copynumber: 3.3 Consensus size: 59
43095175 ATAATAACAT
43095185 AATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACTTACATAACTTA
1 AATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACTTACATAACTTA
* * * ** * *
43095244 AATAACTTACATAACACATAACTTTGATAACTAACATTATACACAACTTACATAA--TA
1 AATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACTTACATAACTTA
* * *
43095301 CATTACTTACTTAACATACATAGCCTACATAACTTACATAATACACAACTTACATAACTTA
1 AATAACTTACAT-A-ATACATAGCCTACATAACTTACATAATACACAACTTACATAACTTA
43095362 AATAACTTACATAATACATA
1 AATAACTTACATAATACATA
43095382 ACTTTGATGA
Statistics
Matches: 114, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
57 11 0.10
58 1 0.01
59 90 0.79
60 1 0.01
61 11 0.10
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (59 bp):
AATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACTTACATAACTTA
Found at i:43095321 original size:84 final size:84
Alignment explanation
Indices: 43095233--43095546 Score: 297
Period size: 84 Copynumber: 3.7 Consensus size: 84
43095223 ATACACAACT
* * * * *
43095233 TACATAACTTAAATAACTTACATAACACATAACTTTGATAACTAACATTATACACAACTTACATA
1 TACATAACCTACATAACTTACATAATACACAACTTTGATAACTAACATTATACATAACTTACATA
43095298 ATACATTACTTACTTAACA
66 ATACATTACTTACTTAACA
* *
43095317 TACATAGCCTACATAACTTACATAATACACAAC-TT-A-CA-TAAC-TTA-A-ATAACTTACATA
1 TACATAACCTACATAACTTACATAATACACAACTTTGATAACTAACATTATACATAACTTACATA
* *
43095375 ATACATAACTTTGA-TGAAGCTGATTA
66 ATACATTAC-TT-ACTTAA-C-----A
* * * *
43095401 TACACAACTTACATAACTTACATAATACATAACTTTGATGAAGCT--GATTATACATAACTTACA
1 TACATAACCTACATAACTTACATAATACACAACTTTGAT-AA-CTAACATTATACATAACTTACA
43095464 TAATACATTACTTACTTAACA
64 TAATACATTACTTACTTAACA
* ** * * *
43095485 TACATAGCCTACATAACTTACATAATACACAACTTACATAGCTTACATAATACATAACTTAC
1 TACATAACCTACATAACTTACATAATACACAACTTTGATAACTAACATTATACATAACTTAC
43095547 TTGTGCAATT
Statistics
Matches: 184, Mismatches: 26, Indels: 40
0.74 0.10 0.16
Matches are distributed among these distances:
77 19 0.10
78 6 0.03
79 5 0.03
80 4 0.02
81 1 0.01
82 3 0.02
83 3 0.02
84 107 0.58
85 2 0.01
86 1 0.01
88 1 0.01
89 5 0.03
90 7 0.04
91 20 0.11
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.32
Consensus pattern (84 bp):
TACATAACCTACATAACTTACATAATACACAACTTTGATAACTAACATTATACATAACTTACATA
ATACATTACTTACTTAACA
Found at i:43095333 original size:118 final size:119
Alignment explanation
Indices: 43095168--43095416 Score: 391
Period size: 118 Copynumber: 2.1 Consensus size: 119
43095158 AAACTTGCAT
43095168 AACTTACATAATAACATAATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACT
1 AACTTACATAATAACAT-ATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACT
43095233 TACATAACTTAAATAACTTACATAACACATAACTTTGAT-AA-CTAACATTATACAC
65 TACATAACTTAAATAACTTACATAACACATAACTTTGATGAAGCT--CATTATACAC
*
43095288 AACTTACATAAT-ACAT-T-ACTTACTTAACATACATAGCCTACATAACTTACATAATACACAAC
1 AACTTACATAATAACATATAACTTACAT-A-ATACATAGCCTACATAACTTACATAATACACAAC
* *
43095350 TTACATAACTTAAATAACTTACATAATACATAACTTTGATGAAGCTGATTATACAC
64 TTACATAACTTAAATAACTTACATAACACATAACTTTGATGAAGCTCATTATACAC
43095406 AACTTACATAA
1 AACTTACATAA
43095417 CTTACATAAT
Statistics
Matches: 122, Mismatches: 3, Indels: 10
0.90 0.02 0.07
Matches are distributed among these distances:
116 7 0.06
117 2 0.02
118 93 0.76
119 6 0.05
120 14 0.11
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (119 bp):
AACTTACATAATAACATATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACTT
ACATAACTTAAATAACTTACATAACACATAACTTTGATGAAGCTCATTATACAC
Found at i:43095403 original size:25 final size:25
Alignment explanation
Indices: 43095375--43095460 Score: 95
Period size: 25 Copynumber: 3.4 Consensus size: 25
43095365 AACTTACATA
43095375 ATACATAACTTTGATGAAGCTGATT
1 ATACATAACTTTGATGAAGCTGATT
* ** * *
43095400 ATACACAACTTACAT-AA-CTTACATA
1 ATACATAACTTTGATGAAGC-T-GATT
43095425 ATACATAACTTTGATGAAGCTGATT
1 ATACATAACTTTGATGAAGCTGATT
43095450 ATACATAACTT
1 ATACATAACTT
43095461 ACATAATACA
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
23 1 0.02
24 3 0.06
25 39 0.83
26 3 0.06
27 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (25 bp):
ATACATAACTTTGATGAAGCTGATT
Found at i:43095410 original size:50 final size:50
Alignment explanation
Indices: 43095351--43095466 Score: 214
Period size: 50 Copynumber: 2.3 Consensus size: 50
43095341 ATACACAACT
*
43095351 TACATAACTTAAATAACTTACATAATACATAACTTTGATGAAGCTGATTA
1 TACATAACTTACATAACTTACATAATACATAACTTTGATGAAGCTGATTA
*
43095401 TACACAACTTACATAACTTACATAATACATAACTTTGATGAAGCTGATTA
1 TACATAACTTACATAACTTACATAATACATAACTTTGATGAAGCTGATTA
43095451 TACATAACTTACATAA
1 TACATAACTTACATAA
43095467 TACATTACTT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (50 bp):
TACATAACTTACATAACTTACATAATACATAACTTTGATGAAGCTGATTA
Found at i:43095436 original size:168 final size:166
Alignment explanation
Indices: 43095233--43095541 Score: 505
Period size: 168 Copynumber: 1.8 Consensus size: 166
43095223 ATACACAACT
*
43095233 TACATAACTTAAATAACTTACATAACACATAACTTTGAT-AA-CTAACATTATACACAACTTACA
1 TACACAACTTAAATAACTTACATAACACATAACTTTGATGAAGCT--CATTATACACAACTTACA
43095296 TAATACATTACTTACTTAACATACATAGCCTACATAACTTACATAATACACAACTTACATAACTT
64 TAATACATTACTTACTTAACATACATAGCCTACATAACTTACATAATACACAACTTACATAACTT
43095361 AAATAACTTACATAATACATAACTTTGATGAAGCTGATTA
129 AAATAA--TACATAATACATAACTTTGATGAAGCTGATTA
* * * *
43095401 TACACAACTTACATAACTTACATAATACATAACTTTGATGAAGCTGATTATACATAACTTACATA
1 TACACAACTTAAATAACTTACATAACACATAACTTTGATGAAGCTCATTATACACAACTTACATA
* *
43095466 ATACATTACTTACTTAACATACATAGCCTACATAACTTACATAATACACAACTTACATAGCTTAC
66 ATACATTACTTACTTAACATACATAGCCTACATAACTTACATAATACACAACTTACATAACTTAA
43095531 ATAATACATAA
131 ATAATACATAA
43095542 CTTACTTGTG
Statistics
Matches: 132, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
166 7 0.05
168 121 0.92
169 2 0.02
170 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.31
Consensus pattern (166 bp):
TACACAACTTAAATAACTTACATAACACATAACTTTGATGAAGCTCATTATACACAACTTACATA
ATACATTACTTACTTAACATACATAGCCTACATAACTTACATAATACACAACTTACATAACTTAA
ATAATACATAATACATAACTTTGATGAAGCTGATTA
Found at i:43095543 original size:25 final size:25
Alignment explanation
Indices: 43095484--43095546 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
43095474 CTTACTTAAC
* *
43095484 ATACATAGCCTACATAACTTACATA
1 ATACATAACTTACATAACTTACATA
* *
43095509 ATACACAACTTACATAGCTTACATA
1 ATACATAACTTACATAACTTACATA
43095534 ATACATAACTTAC
1 ATACATAACTTAC
43095547 TTGTGCAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.44, C:0.24, G:0.03, T:0.29
Consensus pattern (25 bp):
ATACATAACTTACATAACTTACATA
Found at i:43100152 original size:43 final size:42
Alignment explanation
Indices: 43100080--43100225 Score: 161
Period size: 43 Copynumber: 3.4 Consensus size: 42
43100070 CTAAAGAACA
* *
43100080 CTAAACGCCGCTATAGAACATT-A-CTTTTAGCGGCGTTTTCTTC
1 CTAAGCGCCGCTAAAGAAC-TTGATC-TTTAGCGGCGTTTT-TTC
43100123 CTAAGCGCCGCTAAAGAACTTGATCTTTAGCGGCGTTTATTTC
1 CTAAGCGCCGCTAAAGAACTTGATCTTTAGCGGCGTTT-TTTC
* * *
43100166 CTTAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTC
1 CTAAGCGCCGCTAAAGAACTTGATCTTTAGCGGC-GTTTTTTC
* *
43100209 TGTAAGCGCCGCAAAAG
1 -CTAAGCGCCGCTAAAG
43100226 TTAGCAACGT
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
42 2 0.02
43 70 0.78
44 18 0.20
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.32
Consensus pattern (42 bp):
CTAAGCGCCGCTAAAGAACTTGATCTTTAGCGGCGTTTTTTC
Found at i:43100602 original size:3 final size:3
Alignment explanation
Indices: 43100594--43100628 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
43100584 AGGGTTATGG
43100594 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
43100629 TCATTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:43101985 original size:14 final size:15
Alignment explanation
Indices: 43101956--43101990 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
43101946 GTTTTTTTTT
*
43101956 TTTTGTTGTTGTTTA
1 TTTTGTTGTGGTTTA
43101971 TTTTGTT-TGGTTTA
1 TTTTGTTGTGGTTTA
43101985 TTTTGT
1 TTTTGT
43101991 GTTTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.06, C:0.00, G:0.20, T:0.74
Consensus pattern (15 bp):
TTTTGTTGTGGTTTA
Found at i:43104282 original size:4 final size:4
Alignment explanation
Indices: 43104273--43104311 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
43104263 TTCTGGCAGA
*
43104273 ATAC ATAC ATAC ATAC ATAC ATGC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
43104312 GAGGTCATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.49, C:0.23, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:43107396 original size:21 final size:22
Alignment explanation
Indices: 43107372--43107413 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
43107362 AAGTTTGACA
*
43107372 ACAAATTAA-CAAGGCTATAAG
1 ACAAATTAACCAAGCCTATAAG
*
43107393 ACAATTTAACCAAGCCTATAA
1 ACAAATTAACCAAGCCTATAA
43107414 ATATGTAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.50, C:0.19, G:0.10, T:0.21
Consensus pattern (22 bp):
ACAAATTAACCAAGCCTATAAG
Found at i:43108509 original size:6 final size:6
Alignment explanation
Indices: 43108468--43108511 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
43108458 GGCCAAGACC
* *
43108468 GAGGTC GAGGTCA -AGGTC GAGGTA GAGGTA GAGGTA GAGGTA GA
1 GAGGTA GAGGT-A GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA GA
43108512 TTTCAACAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.30, C:0.07, G:0.48, T:0.16
Consensus pattern (6 bp):
GAGGTA
Found at i:43114306 original size:12 final size:12
Alignment explanation
Indices: 43114289--43114334 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
43114279 TGGGGGTAAG
*
43114289 ATTTGTATCTGC
1 ATTTGTATCTGA
43114301 ATTTGTATCTGA
1 ATTTGTATCTGA
* *
43114313 ATTTGTGTCTAA
1 ATTTGTATCTGA
*
43114325 ATCTGTATCT
1 ATTTGTATCT
43114335 AAACCTGTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.22, C:0.13, G:0.15, T:0.50
Consensus pattern (12 bp):
ATTTGTATCTGA
Found at i:43118746 original size:22 final size:22
Alignment explanation
Indices: 43118684--43118747 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
43118674 CTTTTAAAAT
**
43118684 TTAAAAATTATTAAAAAAAATCA
1 TTAAAAATTA-TAAAAAATTTCA
* *
43118707 -TAAAAAGTATAAACAAATTTTA
1 TTAAAAATTATAAA-AAATTTCA
43118729 TTAAAAATTATAAAAAATT
1 TTAAAAATTATAAAAAATT
43118748 AAAATTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 4 0.12
22 18 0.53
23 12 0.35
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (22 bp):
TTAAAAATTATAAAAAATTTCA
Found at i:43126618 original size:6 final size:6
Alignment explanation
Indices: 43126604--43126635 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
43126594 ATTGGGTAAA
43126604 AAAAT- AAAATC AAAATC AAAATC AAAATC AAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAA
43126636 TCGAAGTCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATC
Found at i:43139237 original size:37 final size:37
Alignment explanation
Indices: 43139180--43139317 Score: 168
Period size: 37 Copynumber: 3.7 Consensus size: 37
43139170 AGCGGATGTA
* * * *
43139180 TAGCTCGTATGATCGTTTGGCGTGTTTTCAGTTGGAT
1 TAGCTCTTATGAGCATTTGGCATGTTTTCAGTTGGAT
* *
43139217 TAACTCTTATGAGCATTTGGCATGTTATCAGTTGGAT
1 TAGCTCTTATGAGCATTTGGCATGTTTTCAGTTGGAT
** * **
43139254 TAGCTCTTCGGAGCACTTGGCATGTTTTTGGTTGGAT
1 TAGCTCTTATGAGCATTTGGCATGTTTTCAGTTGGAT
*
43139291 TAGCTCTTATGAGCATTTGGCGTGTTT
1 TAGCTCTTATGAGCATTTGGCATGTTT
43139318 CGAGTGGATT
Statistics
Matches: 84, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 84 1.00
ACGTcount: A:0.17, C:0.14, G:0.27, T:0.42
Consensus pattern (37 bp):
TAGCTCTTATGAGCATTTGGCATGTTTTCAGTTGGAT
Found at i:43143610 original size:16 final size:18
Alignment explanation
Indices: 43143583--43143616 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
43143573 TAGAATTGGT
43143583 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
43143600 TTGAG-AAATTAATTTAA
1 TTGAGAAAATTAATTTAA
43143617 GATATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:43144776 original size:19 final size:18
Alignment explanation
Indices: 43144749--43144784 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
43144739 AGTAATGATA
43144749 TTAAAAATATATAAATATT
1 TTAAAAATATA-AAATATT
*
43144768 TTAATAATATAAAATAT
1 TTAAAAATATAAAATAT
43144785 AAAAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAAAATATAAAATATT
Found at i:43152634 original size:21 final size:19
Alignment explanation
Indices: 43152586--43152634 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
43152576 TACAAACTCT
43152586 TAAA-TAAAACCAGAATTA
1 TAAATTAAAACCAGAATTA
* *
43152604 TAAATAAAAACCATAGATTA
1 TAAATTAAAACCAGA-ATTA
43152624 CTAAATTAAAA
1 -TAAATTAAAA
43152635 TAGTTCTCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 4 0.16
19 8 0.32
20 4 0.16
21 9 0.36
ACGTcount: A:0.61, C:0.10, G:0.04, T:0.24
Consensus pattern (19 bp):
TAAATTAAAACCAGAATTA
Found at i:43153274 original size:17 final size:17
Alignment explanation
Indices: 43153252--43153290 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
43153242 AGAATTGAGG
43153252 GCCCACATGCCCGTGTA
1 GCCCACATGCCCGTGTA
*
43153269 GCCCACATGCCCGTGTG
1 GCCCACATGCCCGTGTA
43153286 GCCCA
1 GCCCA
43153291 GACTCCCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.44, G:0.26, T:0.15
Consensus pattern (17 bp):
GCCCACATGCCCGTGTA
Found at i:43158127 original size:22 final size:22
Alignment explanation
Indices: 43158081--43158129 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
43158071 TACAGGTTGT
*
43158081 TGTCTTAAGACAAAAGCCTGCA
1 TGTCTTAAGACAAAAGCCTACA
* *
43158103 TGTCTTAAGATAAAAGCCTATA
1 TGTCTTAAGACAAAAGCCTACA
43158125 TGTCT
1 TGTCT
43158130 CGATACATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (22 bp):
TGTCTTAAGACAAAAGCCTACA
Found at i:43159825 original size:30 final size:30
Alignment explanation
Indices: 43159783--43159843 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
43159773 GCCCAGACGT
43159783 GTAACCTCGATATAATGTCAGCTTGTGTGA
1 GTAACCTCGATATAATGTCAGCTTGTGTGA
*
43159813 GTAACC-CTGATATATTGTCAGCTTGTGTGA
1 GTAACCTC-GATATAATGTCAGCTTGTGTGA
43159843 G
1 G
43159844 CAACGTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (30 bp):
GTAACCTCGATATAATGTCAGCTTGTGTGA
Found at i:43162167 original size:18 final size:17
Alignment explanation
Indices: 43162134--43162172 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
43162124 TTTTATAAAT
43162134 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
43162152 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
43162169 TGTG
1 TGTG
43162173 GAAGAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:43162496 original size:23 final size:23
Alignment explanation
Indices: 43162386--43162489 Score: 172
Period size: 23 Copynumber: 4.5 Consensus size: 23
43162376 GTGGACATTT
*
43162386 CTTCGGCTACATTTCAGCGGTAG
1 CTTCGGCTACATTTCAGTGGTAG
43162409 CTTCGGCTACATTTCAGTGGTAG
1 CTTCGGCTACATTTCAGTGGTAG
*
43162432 CTACGGCTACATTTCAGTGGTAG
1 CTTCGGCTACATTTCAGTGGTAG
* *
43162455 CTACGGCTACATATCAGTGGTAG
1 CTTCGGCTACATTTCAGTGGTAG
43162478 CTTCGGCTACAT
1 CTTCGGCTACAT
43162490 ATTAGTGTGG
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 77 1.00
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (23 bp):
CTTCGGCTACATTTCAGTGGTAG
Found at i:43164173 original size:26 final size:26
Alignment explanation
Indices: 43164137--43164191 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
43164127 TTCAATCCCT
43164137 ATTTTACCCCTAACAAAATTTTGACG
1 ATTTTACCCCTAACAAAATTTTGACG
*** *
43164163 ATTTTACCCCTTGTAAATTTTTGACG
1 ATTTTACCCCTAACAAAATTTTGACG
43164189 ATT
1 ATT
43164192 CTGCCCTTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.42
Consensus pattern (26 bp):
ATTTTACCCCTAACAAAATTTTGACG
Found at i:43164198 original size:25 final size:27
Alignment explanation
Indices: 43164151--43164210 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
43164141 TACCCCTAAC
*
43164151 AAAATTTTGACGATTTTACCCCTT-GT
1 AAAATTTTGACGATTCTACCCCTTGGT
* *
43164177 AAATTTTTGACGATTCT-GCCCTTGGT
1 AAAATTTTGACGATTCTACCCCTTGGT
43164203 AAAATTTT
1 AAAATTTT
43164211 AATTATTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (27 bp):
AAAATTTTGACGATTCTACCCCTTGGT
Found at i:43171663 original size:30 final size:31
Alignment explanation
Indices: 43171624--43171683 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
43171614 AGAGGTGGGA
*
43171624 TGGGCAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGCAGGGAATAAAAATTTTAGGGGAAAAG
* *
43171655 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGCAGGGAATAAAAATTTTAGGGGAAAA
43171684 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.38, C:0.02, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGCAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:43171853 original size:21 final size:21
Alignment explanation
Indices: 43171819--43171859 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43171809 GGGGAAAAGT
*
43171819 GGGAAAGAGTAAAAGTTTTGA
1 GGGAAAGAGTAAAAGGTTTGA
43171840 GGGAAA-AGTAAAAAGGTTTG
1 GGGAAAGAGT-AAAAGGTTTG
43171860 GGAGTTTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.44, C:0.00, G:0.34, T:0.22
Consensus pattern (21 bp):
GGGAAAGAGTAAAAGGTTTGA
Found at i:43171903 original size:9 final size:9
Alignment explanation
Indices: 43171889--43171925 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
43171879 TATAGTTTGA
43171889 TATTCGAAT
1 TATTCGAAT
43171898 TATTCGAAT
1 TATTCGAAT
*
43171907 TATTCGAGT
1 TATTCGAAT
43171916 TATTCGAAT
1 TATTCGAAT
43171925 T
1 T
43171926 CGAAAACTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:43176824 original size:42 final size:42
Alignment explanation
Indices: 43176765--43176850 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
43176755 AGGCAGCATA
43176765 AATTGGTACAAAGAGAGCACCAAAAGGTTGTAGCAAATCTAC
1 AATTGGTACAAAGAGAGCACCAAAAGGTTGTAGCAAATCTAC
43176807 AATTGGTACAAAGAGAGCACCAAAAGGTTGTAGCAAATCTAC
1 AATTGGTACAAAGAGAGCACCAAAAGGTTGTAGCAAATCTAC
43176849 AA
1 AA
43176851 CAAACACAGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (42 bp):
AATTGGTACAAAGAGAGCACCAAAAGGTTGTAGCAAATCTAC
Found at i:43186428 original size:21 final size:20
Alignment explanation
Indices: 43186404--43186446 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
43186394 GAAACCGTAG
43186404 AAATTGTAATTCCT-AGAAAAT
1 AAATT-TAATT-CTAAGAAAAT
*
43186425 AAATTTTATTCTAAGAAAAT
1 AAATTTAATTCTAAGAAAAT
43186445 AA
1 AA
43186447 TTTCCACTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 13 0.65
21 5 0.25
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (20 bp):
AAATTTAATTCTAAGAAAAT
Found at i:43186839 original size:17 final size:16
Alignment explanation
Indices: 43186819--43186852 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43186809 TTAATTTAAT
43186819 TAATCAAATTAATTTTC
1 TAATCAAA-TAATTTTC
*
43186836 TAATTAAATAATTTTC
1 TAATCAAATAATTTTC
43186852 T
1 T
43186853 CAACCCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATCAAATAATTTTC
Found at i:43187960 original size:31 final size:31
Alignment explanation
Indices: 43187895--43187953 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
43187885 AGACGGAATG
43187895 TTAGTCTTTCAATCGACTTGCTCATTTTCGA
1 TTAGTCTTTCAATCGACTTGCTCATTTTCGA
43187926 TTAGTCTTTCAATCGACTTGCTCATTTT
1 TTAGTCTTTCAATCGACTTGCTCATTTT
43187954 TTATTAGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.19, C:0.22, G:0.12, T:0.47
Consensus pattern (31 bp):
TTAGTCTTTCAATCGACTTGCTCATTTTCGA
Found at i:43193190 original size:31 final size:29
Alignment explanation
Indices: 43193120--43193193 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
43193110 GGCTCTGGTT
* *
43193120 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
43193149 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
43193180 ACATTTTAGTCACT
1 ACATTTTAGTCACT
43193194 GAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:43195606 original size:7 final size:7
Alignment explanation
Indices: 43195578--43195626 Score: 57
Period size: 7 Copynumber: 7.0 Consensus size: 7
43195568 TCCAATCTTA
43195578 TTTCAAT
1 TTTCAAT
*
43195585 CTTCAAAT
1 TTTC-AAT
43195593 TTT-AAT
1 TTTCAAT
43195599 TTTCAAT
1 TTTCAAT
43195606 TTTCAA-
1 TTTCAAT
43195612 TTTCGAAT
1 TTTC-AAT
43195620 TTTCAAT
1 TTTCAAT
43195627 CCTCAATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
6 10 0.28
7 17 0.47
8 9 0.25
ACGTcount: A:0.31, C:0.14, G:0.02, T:0.53
Consensus pattern (7 bp):
TTTCAAT
Found at i:43195633 original size:21 final size:20
Alignment explanation
Indices: 43195578--43195634 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
43195568 TCCAATCTTA
*
43195578 TTTCAATCTTCAAATTTTAAT
1 TTTCAATCTTC-AATTTGAAT
*
43195599 TTTCAATTTTCAATTTCGAAT
1 TTTCAATCTTCAATTT-GAAT
*
43195620 TTTCAATCCTCAATT
1 TTTCAATCTTCAATT
43195635 ATTTTTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.16
21 26 0.84
ACGTcount: A:0.30, C:0.18, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTCAATCTTCAATTTGAAT
Found at i:43195634 original size:14 final size:15
Alignment explanation
Indices: 43195578--43195632 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 15
43195568 TCCAATCTTA
43195578 TTTCAATCTTCAAAT
1 TTTCAATCTTCAAAT
*
43195593 TTT-AATTTTC-AAT
1 TTTCAATCTTCAAAT
*
43195606 TTTCAAT-TTCGAAT
1 TTTCAATCTTCAAAT
*
43195620 TTTCAATCCTCAA
1 TTTCAATCTTCAA
43195633 TTATTTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 19 0.56
15 6 0.18
ACGTcount: A:0.31, C:0.18, G:0.02, T:0.49
Consensus pattern (15 bp):
TTTCAATCTTCAAAT
Found at i:43195811 original size:24 final size:24
Alignment explanation
Indices: 43195784--43195830 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
43195774 ATTATTTTAA
43195784 TTTA-AATAGTTAATTATTATGTTG
1 TTTAGAATA-TTAATTATTATGTTG
* *
43195808 TTTAGATTATTAATTTTTATGTT
1 TTTAGAATATTAATTATTATGTT
43195831 TATATACTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (24 bp):
TTTAGAATATTAATTATTATGTTG
Found at i:43197158 original size:18 final size:20
Alignment explanation
Indices: 43197120--43197162 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
43197110 GTCATAAGTG
43197120 TTTATTTTGTTTATATATAT
1 TTTATTTTGTTTATATATAT
*
43197140 TTTATTTT-TTTA-CTATAT
1 TTTATTTTGTTTATATATAT
43197158 TTTAT
1 TTTAT
43197163 AGAACACGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 4 0.18
20 8 0.36
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTATTTTGTTTATATATAT
Found at i:43205407 original size:69 final size:69
Alignment explanation
Indices: 43205294--43207245 Score: 442
Period size: 69 Copynumber: 28.3 Consensus size: 69
43205284 GGTATGTCGA
* * * * * * *
43205294 TTTAAGATCGCAACCTCCAAAACAACTAGAGAACCTACATTCCCAGCTGATACTCTAAAGGCTTA
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAACTGATACTCTAAAGGCTTA
43205359 TCGG
66 TCGG
* ** * * * ** * *
43205363 TTTATGATCTCAACCTCTGACATAGCTAGCAAACCTATGCTCCCAGTTGAT-GTCATAAAAG-TT
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAACTGATACTC-TAAAGGCTT
* *
43205426 TTCCGA
65 AT-CGG
* * * * * *
43205432 TTTGA-GATCGCAACCTCCGGA-ATAGCTACCAAACATACATTTCCAACTGATACTCTAAAGGCT
1 TTT-ATGATCGCAACCTCC-AACATAGCTAGCGAACCTACGTTCCCAACTGATACTCTAAAGGCT
** *
43205495 CGTCGA
64 TATCGG
* * * * * * * *
43205501 TTTATAATCCCAGCCTCCAACACAACTAGTGAACCTACGCTCCCAACTGAT-GTCATAAAGG-TT
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAACTGATACTC-TAAAGGCTT
**
43205564 -TGCCA
65 AT-CGG
* * * * * * * * * * *
43205569 ATTAAGATAGCAAACTCCAAAATAGCTAGCGAACCAACATTCCCAGCCGATACTCCAAAGGCTCA
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAACTGATACTCTAAAGGCTTA
43205634 TCGG
66 TCGG
* * * * * *
43205638 TTTATGATCGCAGCCTCCAATACAGCTAGCGAACCTATGCTT-CCAACTGAT-GTCAAAAAGG--
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACG-TTCCCAACTGATACTC-TAAAGGCT
43205699 TAGGTCGG
64 TA--TCGG
* * ** ** *
43205707 TTTAAGATTGCAACCTTTGAA-ATAGCTAGC-AGACCTATATTCCCAATTGATACTCTAAAGGCT
1 TTTATGATCGCAACC-TCCAACATAGCTAGCGA-ACCTACGTTCCCAACTGATACTCTAAAGGCT
**
43205770 CGTCGG
64 TATCGG
* * * * * * * * *
43205776 TTTATAATCACAACCTCTAACATAGCTAGTGGACCTATGGTCCCAACTGAT-GTCATAAAGGTTT
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAACTGATACTC-TAAAGGCTT
** *
43205840 GCCAG
65 ATCGG
* * * * * * * *
43205845 TTTAAGATCACAACCTCCAAAATAGTTAGC-AGACCTACGTTCCTAGCTAATACTCTAAAGGCTC
1 TTTATGATCGCAACCTCCAACATAGCTAGCGA-ACCTACGTTCCCAACTGATACTCTAAAGGCTT
* *
43205909 ACCGA
65 ATCGG
* * * ** * *
43205914 TTTATGATC-CTAGCCTCTAACATAGCTAGCGAACCTACACTT-CCAA-TCGATGTTATAAAGGT
1 TTTATGATCGC-AACCTCCAACATAGCTAGCGAACCTAC-GTTCCCAACT-GATACTCTAAAGGC
43205976 TTA-CTGG
63 TTATC-GG
* * * * * ** * * *
43205983 TTTAAGATCGCAACCTCTAAAATAGCTAACGAACCTATGTT-TTAAGTTGATACTTTAAAGGCTC
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAA-CTGATACTCTAAAGGCTT
*
43206047 ACCGG
65 ATCGG
* ** * ** * * * * * *
43206052 TTTATGATTGCAACCTCCGGCACAGCTAATGGACCTACGCTCCCAGCTGAT-GTCATAAAAGTTT
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAACTGATACTC-TAAAGGCTT
**
43206116 GGCGG
65 ATCGG
* * * * ** * *
43206121 TTTAAGATCACAACCTCCAAAATAGCTAGTGGTCCTACGTTCCGAACTGATA-TGCTAAAGGCTC
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAACTGATACT-CTAAAGGCTT
* *
43206185 ACCGA
65 ATCGG
* * * * * * * * * *
43206190 TTTATGATCACAACCTTCAACACAACTAACAAACCTATGCTCCTAGCTG--ACGTCATAAA-GCT
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAACTGATAC-TC-TAAAGGCT
*
43206252 T-TGCTGA
64 TAT-C-GG
* * * * * * * * *
43206259 TTTAAGATCGCAACCTCTAAAATAGCTAGC-AGTCCTATGTTCCGAGCCGATACTCTAAAGGCTC
1 TTTATGATCGCAACCTCCAACATAGCTAGCGA-ACCTACGTTCCCAACTGATACTCTAAAGGCTT
* *
43206323 ACCAG
65 ATCGG
* * * * * * * * *
43206328 TTTATGATCGGAGCCTCTAACACAACTAGCGGAA-CTACGCTCCCAAATGAT-GTCATAAAGGTT
1 TTTATGATCGCAACCTCCAACATAGCTAGC-GAACCTACGTTCCCAACTGATACTC-TAAAGGCT
* *
43206391 TGTCAG
64 TATCGG
* * * * * * * * **** * *
43206397 TTTAAGATTGCAACCTTCAAAACAGTTAGC-AGACCCACTTTCCTTGTTGATAATCTAAAGGCTC
1 TTTATGATCGCAACCTCCAACATAGCTAGCGA-ACCTACGTTCCCAACTGATACTCTAAAGGCTT
*
43206461 GTCGG
65 ATCGG
* * * * * * * * *
43206466 TTTATGATCGCAACCTCCAACACAGCTAGCGGACCTATGCTCCAAACTAAT-GTCATGAAGGTTT
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAACTGATACTC-TAAAGGCTT
* **
43206530 GTTAG
65 ATCGG
* * * * * * * *
43206535 TTTAAGATCGTAACCTCTGAAACA-A-CTA-CCAGACTTACATTCCCAGCTGATACTTTAAA-GC
1 TTTATGATCGCAACCTC--CAACATAGCTAGCGA-ACCTACGTTCCCAACTGATACTCTAAAGGC
* *
43206596 TTGTCGA
63 TTATCGG
* * * ** * * * ** * * * *
43206603 TTTATAATCGCAGCCTCTAACACGGCTAGCGAAACTACGCTCCTAGTTAAT-GTCATAAAAGTTT
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAACTGATACTC-TAAAGGCTT
* *
43206667 TTCGA
65 ATCGG
* * * * * * * * * * *
43206672 TTTAAGATTGTAACCTCTAAAATAACTAGCGGACCTACATTCCCAGCTGATTA-TCTAAGGGCTC
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAACTGA-TACTCTAAAGGCTT
*
43206736 ACCGG
65 ATCGG
** * * ** * * * * *
43206741 TTTATGATCATAGCCTCCAACATAACTAGAAAACCTACGCTCTCAATTGAT-GTCATAAAGGTTT
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAACTGATACTC-TAAAGGCTT
* *
43206805 ACCAG
65 ATCGG
** * * * * * * **
43206810 TTTAAAATCGCAACCTCCAAAATAACTAGTGGACCTATGTTCCCAGCTGATACTCTAAAGGCTCG
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAACTGATACTCTAAAGGCTTA
* *
43206875 CCAG
66 TCGG
* * * ** * * * *
43206879 TTTATTATCGCAACCTCCAACATAGCTAACAGACCTCTACACTCCTAGCTGA-AATCATAAATG-
1 TTTATGATCGCAACCTCCAACATAGCTAGC-GAAC-CTACGTTCCCAACTGATACTC-TAAAGGC
* *
43206942 TTTTCTAG
63 TTATC-GG
* * * * * * * *
43206950 TTTAAGATCGTAACCTCCAAAACAACTAGCGATCCTACGTTCCCAACTGATACTCAAAAGGCTTG
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAACTGATACTCTAAAGGCTTA
* *
43207015 CCGA
66 TCGG
** * * * * * * *** * *
43207019 TTTATGATTACAACCTCTAACACAACTTGTGTACCTATACTCCCAACTGAT-GTCATAAAGGTTT
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAACTGATACTC-TAAAGGCTT
* *
43207083 TTCGA
65 ATCGG
* * * * * * * * *
43207088 TTTAAGATCGTAAACTCTAAAACAACTAGCGAACCTACGTTCCCAACTAATACTCTAAAGGCTCA
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAACTGATACTCTAAAGGCTTA
* *
43207153 CCGA
66 TCGG
* * * * * * * * * *
43207157 TTTATGATCACAACCTTCAACACAGCTAGTGGACCTACGCTCCTAACTGAT-GTCATAAACGTTT
1 TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAACTGATACTC-TAAAGGCTT
*
43207221 AGCGG
65 ATCGG
*
43207226 TTTAAGATCGCAACCTCCAA
1 TTTATGATCGCAACCTCCAA
43207246 AACAACTAGT
Statistics
Matches: 1323, Mismatches: 478, Indels: 164
0.67 0.24 0.08
Matches are distributed among these distances:
66 4 0.00
67 5 0.00
68 126 0.10
69 1081 0.82
70 58 0.04
71 49 0.04
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (69 bp):
TTTATGATCGCAACCTCCAACATAGCTAGCGAACCTACGTTCCCAACTGATACTCTAAAGGCTTA
TCGG
Found at i:43205536 original size:138 final size:138
Alignment explanation
Indices: 43205291--43207266 Score: 1316
Period size: 138 Copynumber: 14.3 Consensus size: 138
43205281 AAAGGTATGT
* * *
43205291 CGATTTAAGATCGCAACCTCCAAAACAACTAG-AGAACCTACATTCCCAGCTGATACTCTAAAGG
1 CGATTTAAGATCGCAACCTCCAAAATAGCTAGCAG-ACCTACATTTCCAGCTGATACTCTAAAGG
* * * ** * * * **
43205355 CTTATCGGTTTATGATCTCAACCTCTGACATAGCTAGCAAACCTATGCTCCCAGTTGATGTCATA
65 CTCATCGGTTTATGATCGCAGCCTCCAACACAGCTAGCGAACCTACGCTCCCAACTGATGTCATA
*
43205420 AAAGTTTTC
130 AAGGTTTTC
* ** * * * *
43205429 CGATTTGAGATCGCAACCTCCGGAATAGCTACCAAACATACATTTCCAACTGATACTCTAAAGGC
1 CGATTTAAGATCGCAACCTCCAAAATAGCTAGCAGACCTACATTTCCAGCTGATACTCTAAAGGC
* * * * * *
43205494 TCGTCGATTTATAATCCCAGCCTCCAACACAACTAGTGAACCTACGCTCCCAACTGATGTCATAA
66 TCATCGGTTTATGATCGCAGCCTCCAACACAGCTAGCGAACCTACGCTCCCAACTGATGTCATAA
*
43205559 AGGTTTGC
131 AGGTTTTC
* * * * * * *
43205567 C-AATTAAGATAGCAAACTCCAAAATAGCTAGC-GAACCAACATTCCCAGCCGATACTCCAAAGG
1 CGATTTAAGATCGCAACCTCCAAAATAGCTAGCAG-ACCTACATTTCCAGCTGATACTCTAAAGG
* * * *
43205630 CTCATCGGTTTATGATCGCAGCCTCCAATACAGCTAGCGAACCTATGCTTCCAACTGATGTCAAA
65 CTCATCGGTTTATGATCGCAGCCTCCAACACAGCTAGCGAACCTACGCTCCCAACTGATGTCATA
**
43205695 AAGGTAGGT-
130 AAGGT-TTTC
* * *** * * **
43205704 CGGTTTAAGATTGCAACCTTTGAAATAGCTAGCAGACCTATATTCCCAATTGATACTCTAAAGGC
1 CGATTTAAGATCGCAACCTCCAAAATAGCTAGCAGACCTACATTTCCAGCTGATACTCTAAAGGC
* * * * * * * * * *
43205769 TCGTCGGTTTATAATCACAACCTCTAACATAGCTAGTGGACCTATGGTCCCAACTGATGTCATAA
66 TCATCGGTTTATGATCGCAGCCTCCAACACAGCTAGCGAACCTACGCTCCCAACTGATGTCATAA
*
43205834 AGGTTTGC
131 AGGTTTTC
* * * *
43205842 C-AGTTTAAGATCACAACCTCCAAAATAGTTAGCAGACCTAC-GTTCCTAGCTAATACTCTAAAG
1 CGA-TTTAAGATCGCAACCTCCAAAATAGCTAGCAGACCTACATTTCC-AGCTGATACTCTAAAG
* * * * * * *
43205905 GCTCACCGATTTATGATC-CTAGCCTCTAACATAGCTAGCGAACCTACACTTCCAA-TCGATGTT
64 GCTCATCGGTTTATGATCGC-AGCCTCCAACACAGCTAGCGAACCTACGCTCCCAACT-GATGTC
*
43205968 ATAAAGGTTTAC
127 ATAAAGGTTTTC
* * * * ** ** * *
43205980 TGGTTTAAGATCGCAACCTCTAAAATAGCTAAC-GAACCTATGTTTTAAGTTGATACTTTAAAGG
1 CGATTTAAGATCGCAACCTCCAAAATAGCTAGCAG-ACCTACATTTCCAGCTGATACTCTAAAGG
* * * ** ** * *
43206044 CTCACCGGTTTATGATTGCAACCTCCGGCACAGCTAATGGACCTACGCTCCCAGCTGATGTCATA
65 CTCATCGGTTTATGATCGCAGCCTCCAACACAGCTAGCGAACCTACGCTCCCAACTGATGTCATA
* **
43206109 AAAGTTTGG
130 AAGGTTTTC
* * ** * * *
43206118 CGGTTTAAGATCACAACCTCCAAAATAGCTAGTGGTCCTAC-GTTCCGAACTGATA-TGCTAAAG
1 CGATTTAAGATCGCAACCTCCAAAATAGCTAGCAGACCTACATTTCC-AGCTGATACT-CTAAAG
* * * * * * * * * * * *
43206181 GCTCACCGATTTATGATCACAACCTTCAACACAACTAACAAACCTATGCTCCTAGCTGACGTCAT
64 GCTCATCGGTTTATGATCGCAGCCTCCAACACAGCTAGCGAACCTACGCTCCCAACTGATGTCAT
* *
43206246 AAAGCTTTGC
129 AAAGGTTTTC
* * * *
43206256 TGATTTAAGATCGCAACCTCTAAAATAGCTAGCAGTCCT--ATGTTCCGAGCCGATACTCTAAAG
1 CGATTTAAGATCGCAACCTCCAAAATAGCTAGCAGACCTACAT-TTCC-AGCTGATACTCTAAAG
* * * * * *
43206319 GCTCACCAGTTTATGATCGGAGCCTCTAACACAACTAGCGGAA-CTACGCTCCCAAATGATGTCA
64 GCTCATCGGTTTATGATCGCAGCCTCCAACACAGCTAGC-GAACCTACGCTCCCAACTGATGTCA
43206383 TAAAGGTTTGTC
128 TAAAGGTTT-TC
* * * * * * * * *
43206395 AG-TTTAAGATTGCAACCTTCAAAACAGTTAGCAGACCCAC-TTTCCTTGTTGATAATCTAAAGG
1 CGATTTAAGATCGCAACCTCCAAAATAGCTAGCAGACCTACATTTCC-AGCTGATACTCTAAAGG
* * * * * * *
43206458 CTCGTCGGTTTATGATCGCAACCTCCAACACAGCTAGCGGACCTATGCTCCAAACTAATGTCATG
65 CTCATCGGTTTATGATCGCAGCCTCCAACACAGCTAGCGAACCTACGCTCCCAACTGATGTCATA
*
43206523 AAGGTTTGTT
130 AAGGTTT-TC
* * ** * * * * * *
43206533 AG-TTTAAGATCGTAACCTCTGAAACAACTACCAGACTTACATTCCCAGCTGATACTTTAAA-GC
1 CGATTTAAGATCGCAACCTCCAAAATAGCTAGCAGACCTACATTTCCAGCTGATACTCTAAAGGC
** * * * * * * ** *
43206596 TTGTCGATTTATAATCGCAGCCTCTAACACGGCTAGCGAAACTACGCTCCTAGTTAATGTCATAA
66 TCATCGGTTTATGATCGCAGCCTCCAACACAGCTAGCGAACCTACGCTCCCAACTGATGTCATAA
* *
43206661 AAGTTTTT
131 AGGTTTTC
* * * * * * *
43206669 CGATTTAAGATTGTAACCTCTAAAATAACTAGCGGACCTACATTCCCAGCTGATTA-TCTAAGGG
1 CGATTTAAGATCGCAACCTCCAAAATAGCTAGCAGACCTACATTTCCAGCTGA-TACTCTAAAGG
* ** * * ** * *
43206733 CTCACCGGTTTATGATCATAGCCTCCAACATAACTAGAAAACCTACGCTCTCAATTGATGTCATA
65 CTCATCGGTTTATGATCGCAGCCTCCAACACAGCTAGCGAACCTACGCTCCCAACTGATGTCATA
*
43206798 AAGGTTTAC
130 AAGGTTTTC
* * ** ** *
43206807 C-AGTTTAAAATCGCAACCTCCAAAATAACTAGTGGACCTATGTTCCCAGCTGATACTCTAAAGG
1 CGA-TTTAAGATCGCAACCTCCAAAATAGCTAGCAGACCTACATTTCCAGCTGATACTCTAAAGG
** * * * * * * * * * **
43206871 CTCGCCAGTTTATTATCGCAACCTCCAACATAGCTAACAGACCTCTACACTCCTAGCTGAAATCA
65 CTCATCGGTTTATGATCGCAGCCTCCAACACAGCTAGC-GAAC-CTACGCTCCCAACTGATGTCA
*
43206936 TAAATGTTTT-
128 TAAAGGTTTTC
* * * * * * * *
43206946 CTAGTTTAAGATCGTAACCTCCAAAACAACTAGC-GATCCTACGTTCCCAACTGATACTCAAAAG
1 CGA-TTTAAGATCGCAACCTCCAAAATAGCTAGCAGA-CCTACATTTCCAGCTGATACTCTAAAG
*** * ** * * * * * * **
43207010 GCTTGCCGATTTATGATTACAACCTCTAACACAACTTGTGTACCTATACTCCCAACTGATGTCAT
64 GCTCATCGGTTTATGATCGCAGCCTCCAACACAGCTAGCGAACCTACGCTCCCAACTGATGTCAT
*
43207075 AAAGGTTTTT
129 AAAGGTTTTC
* * * * * * * * *
43207085 CGATTTAAGATCGTAAACTCTAAAACAACTAGC-GAACCTACGTTCCCAACTAATACTCTAAAGG
1 CGATTTAAGATCGCAACCTCCAAAATAGCTAGCAG-ACCTACATTTCCAGCTGATACTCTAAAGG
* * * * * * * *
43207149 CTCACCGATTTATGATCACAACCTTCAACACAGCTAGTGGACCTACGCTCCTAACTGATGTCATA
65 CTCATCGGTTTATGATCGCAGCCTCCAACACAGCTAGCGAACCTACGCTCCCAACTGATGTCATA
* **
43207214 AACGTTTAG
130 AAGGTTTTC
* * * **
43207223 CGGTTTAAGATCGCAACCTCCAAAACAACTAGTGGACCTACATT
1 CGATTTAAGATCGCAACCTCCAAAATAGCTAGCAGACCTACATT
43207267 CACAATTAAC
Statistics
Matches: 1441, Mismatches: 358, Indels: 78
0.77 0.19 0.04
Matches are distributed among these distances:
136 3 0.00
137 229 0.16
138 1080 0.75
139 28 0.02
140 101 0.07
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (138 bp):
CGATTTAAGATCGCAACCTCCAAAATAGCTAGCAGACCTACATTTCCAGCTGATACTCTAAAGGC
TCATCGGTTTATGATCGCAGCCTCCAACACAGCTAGCGAACCTACGCTCCCAACTGATGTCATAA
AGGTTTTC
Found at i:43205998 original size:276 final size:276
Alignment explanation
Indices: 43205294--43207267 Score: 1507
Period size: 276 Copynumber: 7.2 Consensus size: 276
43205284 GGTATGTCGA
* * *
43205294 TTTAAGATCGCAACCTCCAAAACAACTAG-AGAACCTACATTCCCAGCTGATACTCTAAAGGCTT
1 TTTAAGATCGCAACCTCCAAAATAGCTAGCAG-ACCTACATTCCCAGCTGATACTCTAAAGGCTC
* * * * * *
43205358 ATCGGTTTATGATCTCAACCTCTGACATAGCTAGCAAACCTATGCTCCCAGT-TGATGTCATAAA
65 ACCGGTTTATGATC-CAACCTCTAACACAGCTAGCGAACCTATGCTTCCAATCTGATGTCATAAA
* * * * * *** * * * ** *
43205422 AGTTTTCCGATTTGAGATCGCAACCTCCGGAATAGCTACCAAACATACATTTCCAACTGATACTC
129 GGTTTACTGGTTTAAGATCGCAACCTCTAAAATAGCTAGCAGACCTATGTTCCCAACTGATACTC
* * * * * * *
43205487 TAAAGGCTCGTCGATTTATAATCCCAGCCTCCAACACAACTAGTGAACCTACGCTCCCAACTGAT
194 TAAAGGCTCGCCGGTTTATAATCGCAACCTCTAACACAGCTAGTGGACCTACGCTCCCAACTGAT
43205552 GTCATAAAGGTTTGCCA-
259 GTCATAAAGGTTTGCCAG
* * * * * *
43205569 ATTAAGATAGCAAACTCCAAAATAGCTAGC-GAACCAACATTCCCAGCCGATACTCCAAAGGCTC
1 TTTAAGATCGCAACCTCCAAAATAGCTAGCAG-ACCTACATTCCCAGCTGATACTCTAAAGGCTC
* * * * *
43205633 ATCGGTTTATGATCGCAGCCTCCAATACAGCTAGCGAACCTATGCTTCCAA-CTGATGTCAAAAA
65 ACCGGTTTATGATC-CAACCTCTAACACAGCTAGCGAACCTATGCTTCCAATCTGATGTCATAAA
* * * * * *
43205697 GG--TAGGTCGGTTTAAGATTGCAACCTTTGAAATAGCTAGCAGACCTATATTCCCAATTGATAC
129 GGTTTA-CT-GGTTTAAGATCGCAACCTCTAAAATAGCTAGCAGACCTATGTTCCCAACTGATAC
* * * * *
43205760 TCTAAAGGCTCGTCGGTTTATAATCACAACCTCTAACATAGCTAGTGGACCTATGGTCCCAACTG
192 TCTAAAGGCTCGCCGGTTTATAATCGCAACCTCTAACACAGCTAGTGGACCTACGCTCCCAACTG
43205825 ATGTCATAAAGGTTTGCCAG
257 ATGTCATAAAGGTTTGCCAG
* * * * *
43205845 TTTAAGATCACAACCTCCAAAATAGTTAGCAGACCTACGTTCCTAGCTAATACTCTAAAGGCTCA
1 TTTAAGATCGCAACCTCCAAAATAGCTAGCAGACCTACATTCCCAGCTGATACTCTAAAGGCTCA
* * * ** *
43205910 CCGATTTATGATCCTAGCCTCTAACATAGCTAGCGAACCTACACTTCCAATC-GATGTTATAAAG
66 CCGGTTTATGATCC-AACCTCTAACACAGCTAGCGAACCTATGCTTCCAATCTGATGTCATAAAG
* ** *
43205974 GTTTACTGGTTTAAGATCGCAACCTCTAAAATAGCTAAC-GAACCTATGTT-TTAAGTTGATACT
130 GTTTACTGGTTTAAGATCGCAACCTCTAAAATAGCTAGCAG-ACCTATGTTCCCAA-CTGATACT
* * * * *** * *
43206037 TTAAAGGCTCACCGGTTTATGATTGCAACCTCCGGCACAGCTAATGGACCTACGCTCCCAGCTGA
193 CTAAAGGCTCGCCGGTTTATAATCGCAACCTCTAACACAGCTAGTGGACCTACGCTCCCAACTGA
* * *
43206102 TGTCATAAAAGTTTGGCGG
258 TGTCATAAAGGTTTGCCAG
* ** * * * *
43206121 TTTAAGATCACAACCTCCAAAATAGCTAGTGGTCCTACGTTCCGAACTGATA-TGCTAAAGGCTC
1 TTTAAGATCGCAACCTCCAAAATAGCTAGCAGACCTACATTCCCAGCTGATACT-CTAAAGGCTC
* * * * * * *
43206185 ACCGATTTATGATCACAACCT-TCAACACAACTAACAAACCTATGC-TCCTAGCTGACGTCATAA
65 ACCGGTTTATGATC-CAACCTCT-AACACAGCTAGCGAACCTATGCTTCCAATCTGATGTCATAA
* * * * * * *
43206248 AGCTTTGCTGATTTAAGATCGCAACCTCTAAAATAGCTAGCAGTCCTATGTTCCGAGCCGATACT
128 AGGTTTACTGGTTTAAGATCGCAACCTCTAAAATAGCTAGCAGACCTATGTTCCCAACTGATACT
* * * * * * * * *
43206313 CTAAAGGCTCACCAGTTTATGATCGGAGCCTCTAACACAACTAGCGGAACTACGCTCCCAAATGA
193 CTAAAGGCTCGCCGGTTTATAATCGCAACCTCTAACACAGCTAGTGGACCTACGCTCCCAACTGA
*
43206378 TGTCATAAAGGTTTGTCAG
258 TGTCATAAAGGTTTGCCAG
* * * * * * ** * * *
43206397 TTTAAGATTGCAACCTTCAAAACAGTTAGCAGACCCACTTTCCTTGTTGATAATCTAAAGGCTCG
1 TTTAAGATCGCAACCTCCAAAATAGCTAGCAGACCTACATTCCCAGCTGATACTCTAAAGGCTCA
* * * * * *
43206462 TCGGTTTATGATCGCAACCTCCAACACAGCTAGCGGACCTATGC-TCCAAACTAATGTCATGAAG
66 CCGGTTTATGATC-CAACCTCTAACACAGCTAGCGAACCTATGCTTCCAATCTGATGTCATAAAG
** * * * * * * * ** * *
43206526 GTTTGTTAGTTTAAGATCGTAACCTCTGAAACAACTACCAGACTTACATTCCCAGCTGATACTTT
130 GTTTACTGGTTTAAGATCGCAACCTCTAAAATAGCTAGCAGACCTATGTTCCCAACTGATACTCT
* * * * * * * * * ** *
43206591 AAA-GCTTGTCGATTTATAATCGCAGCCTCTAACACGGCTAGCGAAACTACGCTCCTAGTTAATG
195 AAAGGCTCGCCGGTTTATAATCGCAACCTCTAACACAGCTAGTGGACCTACGCTCCCAACTGATG
* **
43206655 TCATAAAAGTTTTTC-G
260 TCATAAAGGTTTGCCAG
* * * * * *
43206671 ATTTAAGATTGTAACCTCTAAAATAACTAGCGGACCTACATTCCCAGCTGATTA-TCTAAGGGCT
1 -TTTAAGATCGCAACCTCCAAAATAGCTAGCAGACCTACATTCCCAGCTGA-TACTCTAAAGGCT
* * * ** *
43206735 CACCGGTTTATGAT-CATAGCCTCCAACATAACTAGAAAACCTACGC-TCTCAAT-TGATGTCAT
64 CACCGGTTTATGATCCA-A-CCTCTAACACAGCTAGCGAACCTATGCTTC-CAATCTGATGTCAT
** * * * ** *
43206797 AAAGGTTTACCAGTTTAAAATCGCAACCTCCAAAATAACTAGTGGACCTATGTTCCCAGCTGATA
126 AAAGGTTTACTGGTTTAAGATCGCAACCTCTAAAATAGCTAGCAGACCTATGTTCCCAACTGATA
* * * * *** * * *
43206862 CTCTAAAGGCTCGCCAGTTTATTATCGCAACCTCCAACATAGCTAACAGACCTCTACACTCCTAG
191 CTCTAAAGGCTCGCCGGTTTATAATCGCAACCTCTAACACAGCTAGTGGA-C-CTACGCTCCCAA
** * * *
43206927 CTGAAATCATAAATGTTTTCTAG
254 CTGATGTCATAAAGGTTTGCCAG
* * * * * * *
43206950 TTTAAGATCGTAACCTCCAAAACAACTAGC-GATCCTACGTTCCCAACTGATACTCAAAAGGCTT
1 TTTAAGATCGCAACCTCCAAAATAGCTAGCAGA-CCTACATTCCCAGCTGATACTCTAAAGGCTC
* * * * * * * * *
43207014 GCCGATTTATGATTACAACCTCTAACACAACTTGTGTACCTATACTCCCAA-CTGATGTCATAAA
65 ACCGGTTTATGA-TCCAACCTCTAACACAGCTAGCGAACCTATGCTTCCAATCTGATGTCATAAA
* * * * * * * *
43207078 GGTTT-TTCGATTTAAGATCGTAAACTCTAAAACAACTAGC-GAACCTACGTTCCCAACTAATAC
129 GGTTTACT-GGTTTAAGATCGCAACCTCTAAAATAGCTAGCAG-ACCTATGTTCCCAACTGATAC
* * * * *
43207141 TCTAAAGGCTCACCGATTTATGATCACAACCT-TCAACACAGCTAGTGGACCTACGCTCCTAACT
192 TCTAAAGGCTCGCCGGTTTATAATCGCAACCTCT-AACACAGCTAGTGGACCTACGCTCCCAACT
* *
43207205 GATGTCATAAACGTTTAG-CGG
256 GATGTCATAAAGGTTT-GCCAG
* * **
43207226 TTTAAGATCGCAACCTCCAAAACAACTAGTGGACCTACATTC
1 TTTAAGATCGCAACCTCCAAAATAGCTAGCAGACCTACATTC
43207268 ACAATTAACA
Statistics
Matches: 1352, Mismatches: 307, Indels: 79
0.78 0.18 0.05
Matches are distributed among these distances:
273 3 0.00
274 2 0.00
275 443 0.33
276 677 0.50
277 15 0.01
278 206 0.15
279 4 0.00
280 2 0.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (276 bp):
TTTAAGATCGCAACCTCCAAAATAGCTAGCAGACCTACATTCCCAGCTGATACTCTAAAGGCTCA
CCGGTTTATGATCCAACCTCTAACACAGCTAGCGAACCTATGCTTCCAATCTGATGTCATAAAGG
TTTACTGGTTTAAGATCGCAACCTCTAAAATAGCTAGCAGACCTATGTTCCCAACTGATACTCTA
AAGGCTCGCCGGTTTATAATCGCAACCTCTAACACAGCTAGTGGACCTACGCTCCCAACTGATGT
CATAAAGGTTTGCCAG
Found at i:43210718 original size:21 final size:21
Alignment explanation
Indices: 43210688--43210742 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
43210678 AAAACTGAAA
* *
43210688 ACACGACCGTGTGGCTACCCC
1 ACACGCCCGTGTGACTACCCC
*
43210709 ACACGCCCGTGTGACTACTCC
1 ACACGCCCGTGTGACTACCCC
*
43210730 ACACACCCGTGTG
1 ACACGCCCGTGTG
43210743 CTCAGACTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.42, G:0.22, T:0.16
Consensus pattern (21 bp):
ACACGCCCGTGTGACTACCCC
Found at i:43211867 original size:13 final size:13
Alignment explanation
Indices: 43211829--43211871 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
43211819 ATATCTATAC
*
43211829 TCATAAAAACATT
1 TCATATAAACATT
* *
43211842 TCGTATAACCATT
1 TCATATAAACATT
*
43211855 TCATCTAAACATT
1 TCATATAAACATT
43211868 TCAT
1 TCAT
43211872 TCTACCATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.37
Consensus pattern (13 bp):
TCATATAAACATT
Found at i:43211870 original size:53 final size:52
Alignment explanation
Indices: 43211764--43211871 Score: 128
Period size: 53 Copynumber: 2.1 Consensus size: 52
43211754 CCCTTTTTTA
* * * * *
43211764 CATATTCTATATTCCTAAAAATATTTCGTATAAACACTTCATCTATCTGTTT
1 CATATTCTATACTCATAAAAACATTTCGTATAAACACTTCATCTAACTATTT
* *
43211816 CATATATCTATACTCATAAAAACATTTCGTATAACCATTTCATCTAAAC-ATTT
1 CATAT-TCTATACTCATAAAAACATTTCGTATAAACACTTCATCT-AACTATTT
43211869 CAT
1 CAT
43211872 TCTACCATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
52 5 0.11
53 40 0.85
54 2 0.04
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.41
Consensus pattern (52 bp):
CATATTCTATACTCATAAAAACATTTCGTATAAACACTTCATCTAACTATTT
Found at i:43220192 original size:17 final size:17
Alignment explanation
Indices: 43220171--43220216 Score: 76
Period size: 17 Copynumber: 2.7 Consensus size: 17
43220161 GAGCTCACAC
43220171 CTTTGGTGAGCTTGCA-
1 CTTTGGTGAGCTTGCAG
43220187 CATTTGGTGAGCTTGCAG
1 C-TTTGGTGAGCTTGCAG
43220205 CTTTGGTGAGCT
1 CTTTGGTGAGCT
43220217 CACACATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 1 0.04
17 26 0.93
18 1 0.04
ACGTcount: A:0.13, C:0.17, G:0.33, T:0.37
Consensus pattern (17 bp):
CTTTGGTGAGCTTGCAG
Found at i:43220327 original size:18 final size:18
Alignment explanation
Indices: 43220269--43220329 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
43220259 TTTTAGGCTT
*
43220269 GTATCTTTGGTTG-GCTC
1 GTATCTTTGGATGAGCTC
*
43220286 GTATATTTGGATGAGCTC
1 GTATCTTTGGATGAGCTC
** *
43220304 ACATCTTTGGGTGAGCTC
1 GTATCTTTGGATGAGCTC
43220322 GTATCTTT
1 GTATCTTT
43220330 ACAATTGATG
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 11 0.31
18 24 0.69
ACGTcount: A:0.15, C:0.16, G:0.26, T:0.43
Consensus pattern (18 bp):
GTATCTTTGGATGAGCTC
Found at i:43241562 original size:12 final size:12
Alignment explanation
Indices: 43241545--43241569 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43241535 TTAAGATTAC
43241545 TAAACCTAAAAT
1 TAAACCTAAAAT
43241557 TAAACCTAAAAT
1 TAAACCTAAAAT
43241569 T
1 T
43241570 CACTTCTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (12 bp):
TAAACCTAAAAT
Found at i:43243227 original size:41 final size:43
Alignment explanation
Indices: 43243167--43243280 Score: 133
Period size: 41 Copynumber: 2.7 Consensus size: 43
43243157 TAACACATAT
* * * *
43243167 CGATGCCACTATCCCAGACAGGGTCTTATACGAATCAT-AC-A
1 CGATGCCAATGTCCCAGACATGGTCTTACACGAATCATCACTA
* ** * *
43243208 CGATGCCAATGTCCTAGACATGGTCTTACACGTTTCCTCACTT
1 CGATGCCAATGTCCCAGACATGGTCTTACACGAATCATCACTA
43243251 CGATGCCAATGTCCCAGACATGGTCTTACA
1 CGATGCCAATGTCCCAGACATGGTCTTACA
43243281 TGAAATTACA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
41 30 0.49
42 2 0.03
43 29 0.48
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (43 bp):
CGATGCCAATGTCCCAGACATGGTCTTACACGAATCATCACTA
Found at i:43243510 original size:64 final size:64
Alignment explanation
Indices: 43243433--43243871 Score: 614
Period size: 64 Copynumber: 6.9 Consensus size: 64
43243423 ATAAATACAA
** *
43243433 ATACAAATT-AATTCGGCAATAGGTGTATACCTATACAATTCAATTCGGTGATATAAGTATACAT
1 ATAC-AATTCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGGCAATATAAGTATATAT
* *
43243497 ATAAAATTCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGGCAATATAAATATATAT
1 ATACAATTCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGGCAATATAAGTATATAT
* *
43243561 ATACAATTCAATTCGGCAATAGGTGTATACCTATACAATTCCATTCGGTAATATAAGTATATAT
1 ATACAATTCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGGCAATATAAGTATATAT
* ** * *
43243625 ACACAATTCAATTCGATAATAGGTGTATACCTATACAATTCCATTCGGAAATATAAGTATATAT
1 ATACAATTCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGGCAATATAAGTATATAT
* * *
43243689 ATACAATTCAATTCGACAATAGGTGTATAGCTATGCAATTCAATTCGGCAATATAAGTATATAT
1 ATACAATTCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGGCAATATAAGTATATAT
* * *
43243753 ATACAATTCAATTCTGCAATAGGTGTATACTTATACAATTCAATTCGGCAATATAAATATATAT
1 ATACAATTCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGGCAATATAAGTATATAT
* * * ** *
43243817 ATAAAATTCAATTCGACAAAATA-AT-TATATATATACAATTCAATTCAGCAATATA
1 ATACAATTCAATTCGGC--AATAGGTGTATACCTATACAATTCAATTCGGCAATATA
43243872 TAAAACATAT
Statistics
Matches: 340, Mismatches: 32, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
63 4 0.01
64 331 0.97
65 1 0.00
66 4 0.01
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33
Consensus pattern (64 bp):
ATACAATTCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGGCAATATAAGTATATAT
Found at i:43243825 original size:32 final size:32
Alignment explanation
Indices: 43243433--43243871 Score: 405
Period size: 32 Copynumber: 13.7 Consensus size: 32
43243423 ATAAATACAA
*** **
43243433 ATACAAATT-AATTCGGCAATAGGTGTATACCT
1 ATAC-AATTCAATTCGGCAATATAAGTATATAT
** *
43243465 ATACAATTCAATTCGGTGATATAAGTATACAT
1 ATACAATTCAATTCGGCAATATAAGTATATAT
* *** **
43243497 ATAAAATTCAATTCGGCAATAGGTGTATACCT
1 ATACAATTCAATTCGGCAATATAAGTATATAT
*
43243529 ATACAATTCAATTCGGCAATATAAATATATAT
1 ATACAATTCAATTCGGCAATATAAGTATATAT
*** **
43243561 ATACAATTCAATTCGGCAATAGGTGTATACCT
1 ATACAATTCAATTCGGCAATATAAGTATATAT
* *
43243593 ATACAATTCCATTCGGTAATATAAGTATATAT
1 ATACAATTCAATTCGGCAATATAAGTATATAT
* ** *** **
43243625 ACACAATTCAATTCGATAATAGGTGTATACCT
1 ATACAATTCAATTCGGCAATATAAGTATATAT
* *
43243657 ATACAATTCCATTCGGAAATATAAGTATATAT
1 ATACAATTCAATTCGGCAATATAAGTATATAT
* *** **
43243689 ATACAATTCAATTCGACAATAGGTGTATAGCT
1 ATACAATTCAATTCGGCAATATAAGTATATAT
*
43243721 ATGCAATTCAATTCGGCAATATAAGTATATAT
1 ATACAATTCAATTCGGCAATATAAGTATATAT
* ***
43243753 ATACAATTCAATTCTGCAATAGGTGTATACT-T
1 ATACAATTCAATTCGGCAATATAAGTATA-TAT
*
43243785 ATACAATTCAATTCGGCAATATAAATATATAT
1 ATACAATTCAATTCGGCAATATAAGTATATAT
* * * *
43243817 ATAAAATTCAATTCGACAAAATAATTATATAT
1 ATACAATTCAATTCGGCAATATAAGTATATAT
*
43243849 ATACAATTCAATTCAGCAATATA
1 ATACAATTCAATTCGGCAATATA
43243872 TAAAACATAT
Statistics
Matches: 321, Mismatches: 83, Indels: 6
0.78 0.20 0.01
Matches are distributed among these distances:
31 5 0.02
32 315 0.98
33 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33
Consensus pattern (32 bp):
ATACAATTCAATTCGGCAATATAAGTATATAT
Found at i:43246993 original size:18 final size:19
Alignment explanation
Indices: 43246970--43247007 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
43246960 ATTTTAAAAA
43246970 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAATTTT
*
43246988 TATAAATATTTTGAATTTT
1 TATAAATATTTAGAATTTT
43247007 T
1 T
43247008 GAATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:43247023 original size:19 final size:17
Alignment explanation
Indices: 43246992--43247027 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
43246982 AATTTTTATA
43246992 AATATTTTGAATTTTTG
1 AATATTTTGAATTTTTG
43247009 AATATTTTTGTAATTTTTG
1 AATA-TTTTG-AATTTTTG
43247028 TTGAGAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 5 0.29
19 8 0.47
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (17 bp):
AATATTTTGAATTTTTG
Found at i:43261945 original size:43 final size:43
Alignment explanation
Indices: 43261887--43261970 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
43261877 CGCAAAATAT
* *
43261887 ATCATGTTCTTTAGCGGCGTTTGTAGTAAAAGTGCCGCTAAAA
1 ATCATGTTCTATAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAA
*
43261930 ATCATGTTCTATAGCGGCGTTTGTGGTAAAAGCGCCGCTAA
1 ATCATGTTCTATAGCGGCGTTTGTAGTAAAAGCGCCGCTAA
43261971 CATTAACAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (43 bp):
ATCATGTTCTATAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAA
Found at i:43262303 original size:21 final size:21
Alignment explanation
Indices: 43262264--43262308 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
43262254 TCATATTTTC
*
43262264 TTGTTGCCTCTGTTGCCCTTG
1 TTGTTGCCTCTGTTGCCCTCG
*
43262285 TTGTTGCCTTTGCTT-CCCTCG
1 TTGTTGCCTCTG-TTGCCCTCG
43262306 TTG
1 TTG
43262309 CTACCTCTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.00, C:0.29, G:0.22, T:0.49
Consensus pattern (21 bp):
TTGTTGCCTCTGTTGCCCTCG
Found at i:43263319 original size:34 final size:34
Alignment explanation
Indices: 43263280--43263348 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
43263270 TTCTTTAAAG
43263280 TACTTTTATGGTCTCTCAATTTCTTTGCTAATGC
1 TACTTTTATGGTCTCTCAATTTCTTTGCTAATGC
43263314 TACTTTTATGGTCTCTCAATTTCTTTGCTAATGC
1 TACTTTTATGGTCTCTCAATTTCTTTGCTAATGC
43263348 T
1 T
43263349 TTCTTCACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.17, C:0.20, G:0.12, T:0.51
Consensus pattern (34 bp):
TACTTTTATGGTCTCTCAATTTCTTTGCTAATGC
Found at i:43268087 original size:3 final size:3
Alignment explanation
Indices: 43268073--43268112 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
43268063 GTCTAATATA
*
43268073 AAT AAG AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
43268113 TATGAAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:43268148 original size:33 final size:33
Alignment explanation
Indices: 43268110--43268178 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
43268100 AATAATAATA
*
43268110 ATATATGAAACATTTTAAAGA-ATATAT-ATATAT
1 ATATATGAAA-ATTTGAAAGACATAT-TCATATAT
43268143 ATATATGAAAATTTGAAAGACATATTCATATAT
1 ATATATGAAAATTTGAAAGACATATTCATATAT
43268176 ATA
1 ATA
43268179 ATAGTTTACA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 10 0.30
33 23 0.70
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (33 bp):
ATATATGAAAATTTGAAAGACATATTCATATAT
Found at i:43272505 original size:14 final size:14
Alignment explanation
Indices: 43272486--43272515 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
43272476 GCTACCATTT
43272486 TACTATTATGTTGC
1 TACTATTATGTTGC
*
43272500 TACTATTTTGTTGC
1 TACTATTATGTTGC
43272514 TA
1 TA
43272516 TTGTTTGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.53
Consensus pattern (14 bp):
TACTATTATGTTGC
Found at i:43272580 original size:30 final size:30
Alignment explanation
Indices: 43272546--43272604 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
43272536 ACTTATTTTA
43272546 TTGTTAATTTTGTTATTATTTTAAAGGCAC
1 TTGTTAATTTTGTTATTATTTTAAAGGCAC
*
43272576 TTGTTAATTTTGTTATTATTTTAGAGGCA
1 TTGTTAATTTTGTTATTATTTTAAAGGCA
43272605 TTTGCTTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.05, G:0.15, T:0.54
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAC
Found at i:43272759 original size:12 final size:12
Alignment explanation
Indices: 43272730--43272763 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
43272720 TATATATATT
43272730 TAAAAATT-ATA
1 TAAAAATTAATA
43272741 T-AAAATTAATA
1 TAAAAATTAATA
43272752 TAAAAATTAATA
1 TAAAAATTAATA
43272764 CGAGTGGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.29
11 5 0.24
12 10 0.48
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TAAAAATTAATA
Found at i:43276460 original size:3 final size:3
Alignment explanation
Indices: 43276452--43276496 Score: 63
Period size: 3 Copynumber: 14.3 Consensus size: 3
43276442 ACAAATTTTA
*
43276452 TAT TAT TAT TGT TAT TGCAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T--AT TAT TAT TAT TAT TAT TAT TAT TAT T
43276497 GCTTTTATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 35 0.92
5 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:43276668 original size:24 final size:24
Alignment explanation
Indices: 43276641--43276695 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
43276631 ATTTCTAACC
43276641 TTTATAAATATATATATACATATT
1 TTTATAAATATATATATACATATT
* * *
43276665 TTTACATATATATATGTACATATT
1 TTTATAAATATATATATACATATT
43276689 TTATATA
1 TT-TATA
43276696 TTTTATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (24 bp):
TTTATAAATATATATATACATATT
Found at i:43283398 original size:21 final size:22
Alignment explanation
Indices: 43283372--43283417 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
43283362 AGGAATTAAA
43283372 GGTGAGAA-GTAAAAG-TTTGGG
1 GGTGAGAATG-AAAAGTTTTGGG
43283393 GGTGAGAATGAAAAGTTTTGGG
1 GGTGAGAATGAAAAGTTTTGGG
43283415 GGT
1 GGT
43283418 TGAGGGAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.30, C:0.00, G:0.43, T:0.26
Consensus pattern (22 bp):
GGTGAGAATGAAAAGTTTTGGG
Found at i:43283539 original size:30 final size:29
Alignment explanation
Indices: 43283500--43283558 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
43283490 GAGTGGGATG
* *
43283500 GGAAGGGAGTAAAAGTTTTGGGGAGAAAGT
1 GGAAAGGAGTAAAAGTTTTGAGG-GAAAGT
43283530 GGAAAGGAGTAAAAGTTTTGAGGGAAAGT
1 GGAAAGGAGTAAAAGTTTTGAGGGAAAGT
43283559 AAAGAGGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.39, C:0.00, G:0.41, T:0.20
Consensus pattern (29 bp):
GGAAAGGAGTAAAAGTTTTGAGGGAAAGT
Found at i:43286090 original size:29 final size:30
Alignment explanation
Indices: 43286053--43286109 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
43286043 ATTAATGTCA
43286053 TTAATATTTT-TTCCTCATTGATAATATTGC
1 TTAATATTTTGTT-CTCATTGATAATATTGC
*
43286083 TTAA-ATTTTGTTCTCATTGTTAATATT
1 TTAATATTTTGTTCTCATTGATAATATT
43286110 ACTATATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.56
Consensus pattern (30 bp):
TTAATATTTTGTTCTCATTGATAATATTGC
Found at i:43288400 original size:47 final size:47
Alignment explanation
Indices: 43288340--43288435 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
43288330 TAATTGTATT
*
43288340 CATAAGAGATATAAAGAGTTTCTAATAACAATACAAAGGTATTAATC
1 CATAAGAGATATAAAGAGTTTCTAACAACAATACAAAGGTATTAATC
* *
43288387 CATAAGAGATATAAGGAGTTTCTAACAACAATACGAAGGTATTAATC
1 CATAAGAGATATAAAGAGTTTCTAACAACAATACAAAGGTATTAATC
43288434 CA
1 CA
43288436 CCCGTACCCG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (47 bp):
CATAAGAGATATAAAGAGTTTCTAACAACAATACAAAGGTATTAATC
Found at i:43296960 original size:6 final size:6
Alignment explanation
Indices: 43296949--43296983 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
43296939 CTGTCGTTTA
*
43296949 ATCTTC ATCTTC ATCTTC ATCTTC GTCTTC ATCTT
1 ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCTT
43296984 TGTCTTGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.14, C:0.31, G:0.03, T:0.51
Consensus pattern (6 bp):
ATCTTC
Found at i:43296988 original size:12 final size:12
Alignment explanation
Indices: 43296950--43296989 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
43296940 TGTCGTTTAA
*
43296950 TCTTCATCTTCA
1 TCTTCATCTTCG
43296962 TCTTCATCTTCG
1 TCTTCATCTTCG
*
43296974 TCTTCATCTTTG
1 TCTTCATCTTCG
43296986 TCTT
1 TCTT
43296990 GGGTTGTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.10, C:0.30, G:0.05, T:0.55
Consensus pattern (12 bp):
TCTTCATCTTCG
Found at i:43309908 original size:39 final size:39
Alignment explanation
Indices: 43309864--43309991 Score: 150
Period size: 39 Copynumber: 3.2 Consensus size: 39
43309854 CTATAACTAT
*
43309864 TACTCAAATTTCTCGTGAAAATACAATTTTATAACCAAA
1 TACTCAAATTTCTCGTGAAAATACAATTTTGTAACCAAA
** ** * *
43309903 TACTCAAA-TTCTTATTGAAAACCCAACTTTGTATCCAAA
1 TACTCAAATTTC-TCGTGAAAATACAATTTTGTAACCAAA
43309942 TACTCAAATTTCTCGTGAAAAAAATACAATTTTGTAACCAAA
1 TACTCAAATTTCTCGTG---AAAATACAATTTTGTAACCAAA
43309984 TACTCAAA
1 TACTCAAA
43309992 GTCCTTGGAA
Statistics
Matches: 71, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
38 3 0.04
39 39 0.55
40 3 0.04
42 26 0.37
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (39 bp):
TACTCAAATTTCTCGTGAAAATACAATTTTGTAACCAAA
Found at i:43312908 original size:21 final size:21
Alignment explanation
Indices: 43312884--43312927 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
43312874 TGGTTAGTAT
43312884 ATCTTAGTCCTTTTTATATAA
1 ATCTTAGTCCTTTTTATATAA
43312905 ATCTTAGTCCTTTTTATATAA
1 ATCTTAGTCCTTTTTATATAA
43312926 AT
1 AT
43312928 TTTATGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.52
Consensus pattern (21 bp):
ATCTTAGTCCTTTTTATATAA
Found at i:43316376 original size:102 final size:102
Alignment explanation
Indices: 43316200--43316567 Score: 585
Period size: 102 Copynumber: 3.6 Consensus size: 102
43316190 ATTGCATATA
* * *
43316200 AAGGGGTTGTTGTATGCTGATTCCCCGATTTATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
*
43316265 TGAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCTCC
66 TGAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
* *
43316302 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
*
43316367 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TGAAATGTG-AAGGGGGTTGCTAAGTGCTGATTCCCCC
* ** *
43316405 GA-GGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
43316469 TGAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TGAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
* * *
43316506 AAGGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAATGCGGAATCCACCG
1 AA-GGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
43316568 ATAACGGTTA
Statistics
Matches: 242, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
101 29 0.12
102 133 0.55
103 80 0.33
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.32
Consensus pattern (102 bp):
AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
TGAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:43316510 original size:28 final size:28
Alignment explanation
Indices: 43316478--43316532 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
43316468 CTGAAATGTG
43316478 AAGGGGGTTGCTAAGTGCTGATTCCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCCC
**
43316506 AAGGGGGTTGCTGTGTGCTGATTCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCC
43316533 GATTCATTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.15, C:0.24, G:0.35, T:0.27
Consensus pattern (28 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:43320480 original size:11 final size:11
Alignment explanation
Indices: 43320464--43320489 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
43320454 TTATTTTTTA
43320464 TTTTAAAATAC
1 TTTTAAAATAC
43320475 TTTTAAAATAC
1 TTTTAAAATAC
43320486 TTTT
1 TTTT
43320490 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:43320501 original size:10 final size:10
Alignment explanation
Indices: 43320486--43320547 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 10
43320476 TTTAAAATAC
43320486 TTTTTTTAAA
1 TTTTTTTAAA
43320496 -TTTTTTAAA
1 TTTTTTTAAA
43320505 ---TTTTAAA
1 TTTTTTTAAA
43320512 TTTTTTTAAAA
1 TTTTTTT-AAA
43320523 TACTTTTTT-AA
1 T--TTTTTTAAA
*
43320534 TTTTTTTTAA
1 TTTTTTTAAA
43320544 TTTT
1 TTTT
43320548 AAAATATTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
7 7 0.16
9 15 0.33
10 10 0.22
11 7 0.16
13 6 0.13
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:43320519 original size:40 final size:41
Alignment explanation
Indices: 43320456--43320579 Score: 177
Period size: 40 Copynumber: 3.1 Consensus size: 41
43320446 AAATATTTTT
*
43320456 ATTTTTT--ATTTTAAAATACTTTTAAAATACTTTTTTTAA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAA
*
43320495 ATTTTTTAAATTTT-AAATTTTTTTAAAATAC-TTTTTTAA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAA
* *
43320534 TTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT-A
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAA
43320574 ATTTTT
1 ATTTTT
43320580 GTTTTAATTT
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
39 27 0.36
40 37 0.49
41 11 0.15
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (41 bp):
ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAA
Found at i:43320837 original size:30 final size:30
Alignment explanation
Indices: 43320803--43320874 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 30
43320793 CTTCATTGGA
43320803 AATTATTTTAAAATAATAATTTATAATTAT
1 AATTATTTTAAAATAATAATTTATAATTAT
** *** *
43320833 AATTATTCCATGCTATTAATTTATAATTAT
1 AATTATTTTAAAATAATAATTTATAATTAT
43320863 --TTATTTTAAAAT
1 AATTATTTTAAAAT
43320875 TATTGATATA
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
28 7 0.23
30 24 0.77
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (30 bp):
AATTATTTTAAAATAATAATTTATAATTAT
Found at i:43321513 original size:35 final size:36
Alignment explanation
Indices: 43321461--43321541 Score: 137
Period size: 35 Copynumber: 2.3 Consensus size: 36
43321451 GGGGTCATGT
* *
43321461 CCAAAACGACGCTGTTATGGGGCTTCTGAAGTCAGC
1 CCAAAACGACGCCGTTATGGGGCTTCTGAAGCCAGC
43321497 CC-AAACGACGCCGTTATGGGGCTTCTGAAGCCAGC
1 CCAAAACGACGCCGTTATGGGGCTTCTGAAGCCAGC
43321532 CCAAAACGAC
1 CCAAAACGAC
43321542 AATGTTTCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 33 0.79
36 9 0.21
ACGTcount: A:0.27, C:0.30, G:0.26, T:0.17
Consensus pattern (36 bp):
CCAAAACGACGCCGTTATGGGGCTTCTGAAGCCAGC
Found at i:43322485 original size:25 final size:25
Alignment explanation
Indices: 43322431--43322485 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
43322421 GGCATCTACA
** *
43322431 TTATTTATTATTAAGTTTATATATG
1 TTATTTATTATTAAGAATATATATC
*
43322456 ATATTTATTATTATAGAATAT-TATC
1 TTATTTATTATTA-AGAATATATATC
43322481 TTATT
1 TTATT
43322486 ATAAAATAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (25 bp):
TTATTTATTATTAAGAATATATATC
Found at i:43322879 original size:29 final size:29
Alignment explanation
Indices: 43322843--43322898 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
43322833 TAGAATTTCT
*
43322843 TTTAATAATATGAAG-ATTAGTTTGACCTG
1 TTTAATAATAT-AAGAATTAATTTGACCTG
43322872 TTTAATAATATAAGAATTAATTTGACC
1 TTTAATAATATAAGAATTAATTTGACC
43322899 CGATTCTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (29 bp):
TTTAATAATATAAGAATTAATTTGACCTG
Found at i:43349471 original size:28 final size:28
Alignment explanation
Indices: 43349439--43349502 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
43349429 ATACAATGAT
*
43349439 TTCATACATGATGATTCATAGACACAAA
1 TTCATACATGATGAATCATAGACACAAA
* * ** *
43349467 TTCATATATGCTGAATCATAGTTACAGA
1 TTCATACATGATGAATCATAGACACAAA
43349495 TTCATACA
1 TTCATACA
43349503 GGCGGATTTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (28 bp):
TTCATACATGATGAATCATAGACACAAA
Found at i:43354837 original size:37 final size:37
Alignment explanation
Indices: 43354786--43354944 Score: 174
Period size: 37 Copynumber: 4.3 Consensus size: 37
43354776 TCCACAGATC
* *
43354786 ATCATATCTTGAAACATGAGGACAAGTCTAGCGGACT
1 ATCATAACTTGAAACATGAGGACAAGTCCAGCGGACT
* * *
43354823 ATCTTAACTTGAAACATGAAGACAAGTCCAGTGGACT
1 ATCATAACTTGAAACATGAGGACAAGTCCAGCGGACT
** * * **
43354860 ATCATAACTTGAAATGTGAGGACGAGTCCAACAAACT
1 ATCATAACTTGAAACATGAGGACAAGTCCAGCGGACT
* * * *
43354897 GTCATAACTTGAAACATGAGGACGATTCCAGTGGACT
1 ATCATAACTTGAAACATGAGGACAAGTCCAGCGGACT
*
43354934 GTCATAACTTG
1 ATCATAACTTG
43354945 CGTATGCCCA
Statistics
Matches: 100, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 100 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.25
Consensus pattern (37 bp):
ATCATAACTTGAAACATGAGGACAAGTCCAGCGGACT
Found at i:43354872 original size:74 final size:74
Alignment explanation
Indices: 43354786--43354944 Score: 192
Period size: 74 Copynumber: 2.1 Consensus size: 74
43354776 TCCACAGATC
* * * ** *
43354786 ATCATATCTTGAAACATGAGGACAAGTCTAGCGGACTATCTTAACTTGAAACATGAAGACAAGTC
1 ATCATAACTTGAAACATGAGGACAAGTCCAACAAACTATCATAACTTGAAACATGAAGACAAGTC
43354851 CAGTGGACT
66 CAGTGGACT
** * * * * *
43354860 ATCATAACTTGAAATGTGAGGACGAGTCCAACAAACTGTCATAACTTGAAACATGAGGACGATTC
1 ATCATAACTTGAAACATGAGGACAAGTCCAACAAACTATCATAACTTGAAACATGAAGACAAGTC
43354925 CAGTGGACT
66 CAGTGGACT
*
43354934 GTCATAACTTG
1 ATCATAACTTG
43354945 CGTATGCCCA
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.25
Consensus pattern (74 bp):
ATCATAACTTGAAACATGAGGACAAGTCCAACAAACTATCATAACTTGAAACATGAAGACAAGTC
CAGTGGACT
Found at i:43358776 original size:9 final size:9
Alignment explanation
Indices: 43358762--43358800 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
43358752 TTTTTAAAAT
43358762 AATTTTAAA
1 AATTTTAAA
*
43358771 AATTTT-GA
1 AATTTTAAA
*
43358779 ATTTTTAAA
1 AATTTTAAA
43358788 AATTTTAAA
1 AATTTTAAA
43358797 AATT
1 AATT
43358801 AATTAAATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
8 6 0.24
9 19 0.76
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (9 bp):
AATTTTAAA
Done.