Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 155 of 163
Found at i:43259792 original size:2 final size:2
Alignment explanation
Indices: 43259785--43259814 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43259775 TGCGAAGAAG
43259785 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
43259815 ATTGTTCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:43261091 original size:23 final size:23
Alignment explanation
Indices: 43261058--43261104 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
43261048 AAATTACAAT
43261058 TAATCCATCCATTTGTT-ATAATA
1 TAATCCATCCATTT-TTAATAATA
*
43261081 TAATCCTTCCATTTTTAATAATA
1 TAATCCATCCATTTTTAATAATA
43261104 T
1 T
43261105 CTAAAAGTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.34, C:0.17, G:0.02, T:0.47
Consensus pattern (23 bp):
TAATCCATCCATTTTTAATAATA
Found at i:43263603 original size:20 final size:20
Alignment explanation
Indices: 43263584--43263620 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
43263574 TATATATAAT
43263584 TGTACAAAATTA-AAATTAA
1 TGTACAAAATTACAAATTAA
*
43263603 TGTATAAAATTACAAATT
1 TGTACAAAATTACAAATT
43263621 GAATCAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (20 bp):
TGTACAAAATTACAAATTAA
Found at i:43264276 original size:19 final size:21
Alignment explanation
Indices: 43264238--43264276 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
43264228 GGGTGATATT
*
43264238 TTTTTATATATTGTTCTAAAG
1 TTTTTATATATTCTTCTAAAG
43264259 TTTTTATAT-TTCTT-TAAA
1 TTTTTATATATTCTTCTAAA
43264277 TTTGCATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTTTATATATTCTTCTAAAG
Found at i:43270074 original size:21 final size:22
Alignment explanation
Indices: 43270050--43270092 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
43270040 AAAATTATTT
*
43270050 AATAATTTT-ATTATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
43270071 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
43270093 TCATTTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:43286338 original size:28 final size:29
Alignment explanation
Indices: 43286272--43286341 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
43286262 TTCTTTTTTT
*
43286272 GTCACTCAACTATAAAAAGTTACAAAATG
1 GTCACTCAACTATAAAAACTTACAAAATG
* *
43286301 GTCACCCAACTATGAAAACTTAC-AAATG
1 GTCACTCAACTATAAAAACTTACAAAATG
43286329 GTCACTCAACTAT
1 GTCACTCAACTAT
43286342 TCAATTGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 17 0.46
29 20 0.54
ACGTcount: A:0.43, C:0.23, G:0.10, T:0.24
Consensus pattern (29 bp):
GTCACTCAACTATAAAAACTTACAAAATG
Found at i:43298858 original size:4 final size:4
Alignment explanation
Indices: 43298843--43298871 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
43298833 TGAAGTGGAC
43298843 TTCT TT-T TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
43298872 TTCATTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTCT
Found at i:43302578 original size:82 final size:82
Alignment explanation
Indices: 43302440--43302597 Score: 271
Period size: 82 Copynumber: 1.9 Consensus size: 82
43302430 TGGAGCATAG
* *
43302440 TCAAGGTGTTTAAGTTCAAGGCACCTAGGGCAGAAGGCCAAACCTCTATAAATTGCTCATGTTTA
1 TCAAGGTGTTTAAGTTCAAGACACCTAGGGAAGAAGGCCAAACCTCTATAAATTGCTCATGTTTA
43302505 ACCTTCTTTACTTTAAA
66 ACCTTCTTTACTTTAAA
* * *
43302522 TCAAGGTGTTTCAGTTCAAGACACCTAGGGAAGAAGGCCAAGCCTCTATAAGTTGCTCATGTTTA
1 TCAAGGTGTTTAAGTTCAAGACACCTAGGGAAGAAGGCCAAACCTCTATAAATTGCTCATGTTTA
43302587 ACCTTCTTTAC
66 ACCTTCTTTAC
43302598 CTACTCTCTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 71 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (82 bp):
TCAAGGTGTTTAAGTTCAAGACACCTAGGGAAGAAGGCCAAACCTCTATAAATTGCTCATGTTTA
ACCTTCTTTACTTTAAA
Found at i:43308398 original size:5 final size:5
Alignment explanation
Indices: 43308384--43308441 Score: 71
Period size: 5 Copynumber: 11.0 Consensus size: 5
43308374 CATGGATTAT
* *
43308384 TTTTA TTTTTA TTTTA TTTCTA TTTTA TATTGA TTTTA TTTTA CTTTA
1 TTTTA -TTTTA TTTTA TTT-TA TTTTA T-TTTA TTTTA TTTTA TTTTA
43308432 TTTTA TTTTA
1 TTTTA TTTTA
43308442 AAAATGTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
5 32 0.70
6 14 0.30
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:43308400 original size:11 final size:11
Alignment explanation
Indices: 43308384--43308441 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
43308374 CATGGATTAT
43308384 TTTTATTTTTA
1 TTTTATTTTTA
*
43308395 TTTTATTTCTA
1 TTTTATTTTTA
* *
43308406 TTTTATATTGA
1 TTTTATTTTTA
43308417 TTTTA-TTTTA
1 TTTTATTTTTA
*
43308427 CTTTA-TTTTA
1 TTTTATTTTTA
43308437 TTTTA
1 TTTTA
43308442 AAAATGTTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
10 16 0.41
11 23 0.59
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:43309200 original size:92 final size:91
Alignment explanation
Indices: 43309019--43309193 Score: 233
Period size: 92 Copynumber: 1.9 Consensus size: 91
43309009 TTAGATTCAA
* * * * *
43309019 TTAGTTAACTTTATTAAATATGATTGATTGGATTTAGTATTTTTATGGTAAATATTTTTTTAAAT
1 TTAGATAACTTCATTAAATATGATTAATTGAATTTAGTATTTTTATGATAAATATTTTTTTAAAT
43309084 GATTAATTGAATAAACAATAAATTAAT
66 GATTAATTGAAT-AACAATAAATTAAT
* *
43309111 TTAGATAACTTCATTAAATGTGATTAATTGAATTTAGTATTTTTATTATAAATATATATTTTTTT
1 TTAGATAACTTCATTAAATATGATTAATTGAATTTAGTATTTTTATGAT--A-A-ATATTTTTTT
*
43309176 AAATGATTGATTGAATAA
62 AAATGATTAATTGAATAA
43309194 AAAATTATAA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
92 42 0.59
94 1 0.01
95 3 0.04
96 25 0.35
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (91 bp):
TTAGATAACTTCATTAAATATGATTAATTGAATTTAGTATTTTTATGATAAATATTTTTTTAAAT
GATTAATTGAATAACAATAAATTAAT
Found at i:43309848 original size:22 final size:23
Alignment explanation
Indices: 43309798--43309840 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
43309788 CCATCTATAT
*
43309798 TATTT-TTTTATTTTTTTAAAAG
1 TATTTATTTTATTTTATTAAAAG
43309820 TATTTATTTTA-TTTATTAAAA
1 TATTTATTTTATTTTATTAAAA
43309841 TTTTTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
TATTTATTTTATTTTATTAAAAG
Found at i:43309959 original size:18 final size:17
Alignment explanation
Indices: 43309936--43309969 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
43309926 ATTGTAAATT
43309936 ACATAATATATAAATATA
1 ACATAATATA-AAATATA
43309954 ACATAATATAAAATAT
1 ACATAATATAAAATAT
43309970 TATAAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (17 bp):
ACATAATATAAAATATA
Found at i:43314867 original size:106 final size:106
Alignment explanation
Indices: 43314682--43314895 Score: 392
Period size: 106 Copynumber: 2.0 Consensus size: 106
43314672 TACGATGCAA
43314682 AATTTGATGCAACAACCGTACCTCAACCAACCCACTATCAGCCCCTCCACCTGATGAAAAAAGAT
1 AATTTGATGCAACAACCGTACCTCAACCAACCCACTATCAGCCCCTCCACCTGATGAAAAAAGAT
43314747 CAACTAATAAAGAGTTATCACATTCCGCAATAACCTTCCTG
66 CAACTAATAAAGAGTTATCACATTCCGCAATAACCTTCCTG
* *
43314788 AATTTGATGCAACAACCGTACCTCAACCAACCTACTATCAGCCCCTCCACCTGATGAAAGAAGAT
1 AATTTGATGCAACAACCGTACCTCAACCAACCCACTATCAGCCCCTCCACCTGATGAAAAAAGAT
* *
43314853 CAATTAATAAAGAGTTATCACATTCCGCAATAATCTTCCTG
66 CAACTAATAAAGAGTTATCACATTCCGCAATAACCTTCCTG
43314894 AA
1 AA
43314896 CCCCTTATCC
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.23
Consensus pattern (106 bp):
AATTTGATGCAACAACCGTACCTCAACCAACCCACTATCAGCCCCTCCACCTGATGAAAAAAGAT
CAACTAATAAAGAGTTATCACATTCCGCAATAACCTTCCTG
Found at i:43319040 original size:3 final size:3
Alignment explanation
Indices: 43319032--43319073 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
43319022 CAATCCCCAA
43319032 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
43319074 ATTTTGTCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:43320383 original size:2 final size:2
Alignment explanation
Indices: 43320376--43320412 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
43320366 TTATGGAACA
43320376 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
43320413 AGGGGGGGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:43321701 original size:33 final size:33
Alignment explanation
Indices: 43321663--43321740 Score: 147
Period size: 33 Copynumber: 2.4 Consensus size: 33
43321653 GAATATTATT
43321663 ATGGGATATTATCTCTTAGTAATTTGATTTTTA
1 ATGGGATATTATCTCTTAGTAATTTGATTTTTA
*
43321696 ATGGGATATTATCTCTTAGTAATTTGGTTTTTA
1 ATGGGATATTATCTCTTAGTAATTTGATTTTTA
43321729 ATGGGATATTAT
1 ATGGGATATTAT
43321741 AAGATATTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (33 bp):
ATGGGATATTATCTCTTAGTAATTTGATTTTTA
Found at i:43325073 original size:5 final size:5
Alignment explanation
Indices: 43325065--43325105 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
43325055 TTAATTGCTC
43325065 CTCTA CTCTA CTCTA CTCTA CTCTA CTCTA CTCTA CTCTA C
1 CTCTA CTCTA CTCTA CTCTA CTCTA CTCTA CTCTA CTCTA C
43325106 CCTTCCAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.20, C:0.41, G:0.00, T:0.39
Consensus pattern (5 bp):
CTCTA
Found at i:43326837 original size:21 final size:21
Alignment explanation
Indices: 43326812--43326860 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
43326802 TAACGGTCAA
43326812 CGGTCAAAGGTCAATCAACAC
1 CGGTCAAAGGTCAATCAACAC
* ** *
43326833 CGGTCAACGGTCGGTCAACAT
1 CGGTCAAAGGTCAATCAACAC
43326854 CGGTCAA
1 CGGTCAA
43326861 TGCCAGTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CGGTCAAAGGTCAATCAACAC
Found at i:43326957 original size:21 final size:22
Alignment explanation
Indices: 43326931--43326976 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
43326921 TGGTTCAAAA
43326931 GGGTTTGGTTTAAAT-GAATTT
1 GGGTTTGGTTTAAATAGAATTT
*
43326952 GGGTTTGGTTTAAATAGGATTT
1 GGGTTTGGTTTAAATAGAATTT
43326974 GGG
1 GGG
43326977 CTTAATGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (22 bp):
GGGTTTGGTTTAAATAGAATTT
Found at i:43331684 original size:20 final size:20
Alignment explanation
Indices: 43331659--43331715 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
43331649 GCCCAAATCT
43331659 CATTTAAACCAAACCAAACC
1 CATTTAAACCAAACCAAACC
*
43331679 CATTTAAACCTAACCAAACC
1 CATTTAAACCAAACCAAACC
43331699 CATTTAAACCAAACCAA
1 CATTTAAACCAAACCAA
43331716 TTGAACCAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (20 bp):
CATTTAAACCAAACCAAACC
Found at i:43331781 original size:21 final size:22
Alignment explanation
Indices: 43331757--43331808 Score: 88
Period size: 21 Copynumber: 2.4 Consensus size: 22
43331747 TAATTGACCG
43331757 ACCGTTGACCGACTGTTGA-TC
1 ACCGTTGACCGACTGTTGACTC
*
43331778 ACCGTTGACCGACTGTTGACTG
1 ACCGTTGACCGACTGTTGACTC
43331800 ACCGTTGAC
1 ACCGTTGAC
43331809 TTTGATTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.19, C:0.29, G:0.25, T:0.27
Consensus pattern (22 bp):
ACCGTTGACCGACTGTTGACTC
Found at i:43331809 original size:11 final size:11
Alignment explanation
Indices: 43331750--43331808 Score: 75
Period size: 11 Copynumber: 5.5 Consensus size: 11
43331740 AGTCAAATAA
43331750 TTGACCGACCG
1 TTGACCGACCG
*
43331761 TTGACCGACTG
1 TTGACCGACCG
*
43331772 TTGATC-ACCG
1 TTGACCGACCG
*
43331782 TTGACCGACTG
1 TTGACCGACCG
*
43331793 TTGACTGACCG
1 TTGACCGACCG
43331804 TTGAC
1 TTGAC
43331809 TTTGATTGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
10 8 0.20
11 32 0.80
ACGTcount: A:0.19, C:0.29, G:0.25, T:0.27
Consensus pattern (11 bp):
TTGACCGACCG
Found at i:43331823 original size:20 final size:20
Alignment explanation
Indices: 43331798--43331862 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
43331788 GACTGTTGAC
*
43331798 TGACCGTTGACTTTGATTGT
1 TGACCGTTGACTTTGACTGT
*
43331818 TGACCGTTGACTTTGACAGT
1 TGACCGTTGACTTTGACTGT
*
43331838 TGACCGTTAACTTTGACTGT
1 TGACCGTTGACTTTGACTGT
43331858 TGACC
1 TGACC
43331863 ACTGACCGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.38
Consensus pattern (20 bp):
TGACCGTTGACTTTGACTGT
Found at i:43331887 original size:7 final size:7
Alignment explanation
Indices: 43331798--43331895 Score: 51
Period size: 7 Copynumber: 14.6 Consensus size: 7
43331788 GACTGTTGAC
43331798 TGACCGT
1 TGACCGT
*
43331805 TGA-CTT
1 TGACCGT
**
43331811 TGATTGT
1 TGACCGT
43331818 TGACCGT
1 TGACCGT
*
43331825 TGA-CTT
1 TGACCGT
*
43331831 TGACAGT
1 TGACCGT
43331838 TGACCGT
1 TGACCGT
* *
43331845 T-AACTT
1 TGACCGT
*
43331851 TGACTGT
1 TGACCGT
**
43331858 TGACCAC
1 TGACCGT
*
43331865 TGACCGG
1 TGACCGT
*
43331872 TG-CCTT
1 TGACCGT
43331878 TGACCGT
1 TGACCGT
*
43331885 TGACTGT
1 TGACCGT
43331892 TGAC
1 TGAC
43331896 TTTTTTTCGA
Statistics
Matches: 64, Mismatches: 23, Indels: 8
0.67 0.24 0.08
Matches are distributed among these distances:
6 18 0.28
7 46 0.72
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.36
Consensus pattern (7 bp):
TGACCGT
Found at i:43331898 original size:20 final size:19
Alignment explanation
Indices: 43331798--43331898 Score: 85
Period size: 20 Copynumber: 5.1 Consensus size: 19
43331788 GACTGTTGAC
*
43331798 TGACCGTTGACTTTGATTGT
1 TGACCGTTGACTTTGACT-T
*
43331818 TGACCGTTGACTTTGACAGT
1 TGACCGTTGACTTTGAC-TT
*
43331838 TGACCGTTAACTTTGACTGT
1 TGACCGTTGACTTTGACT-T
** ** *
43331858 TGACCACTGACCGGTGCCTT
1 TGACCGTTGA-CTTTGACTT
43331878 TGACCGTTGACTGTTGACTT
1 TGACCGTTGACT-TTGACTT
43331898 T
1 T
43331899 TTTTCGAAAA
Statistics
Matches: 62, Mismatches: 15, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
19 1 0.02
20 56 0.90
21 5 0.08
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.38
Consensus pattern (19 bp):
TGACCGTTGACTTTGACTT
Found at i:43335695 original size:3 final size:3
Alignment explanation
Indices: 43335687--43335728 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
43335677 TACATCCCAA
43335687 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
43335729 GAATAGAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:43336800 original size:14 final size:14
Alignment explanation
Indices: 43336777--43336816 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
43336767 TTTCGAAAAA
*
43336777 GTCAACGGTCAACG
1 GTCAAAGGTCAACG
43336791 GTCAAAGGTCAACG
1 GTCAAAGGTCAACG
43336805 GTCAAAGGTCAA
1 GTCAAAGGTCAA
43336817 TCAACATCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.35, C:0.23, G:0.28, T:0.15
Consensus pattern (14 bp):
GTCAAAGGTCAACG
Found at i:43336801 original size:21 final size:21
Alignment explanation
Indices: 43336777--43336816 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
43336767 TTTCGAAAAA
*
43336777 GTCAACGGTCAACGGTCAAAG
1 GTCAACGGTCAAAGGTCAAAG
43336798 GTCAACGGTCAAAGGTCAA
1 GTCAACGGTCAAAGGTCAA
43336817 TCAACATCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.23, G:0.28, T:0.15
Consensus pattern (21 bp):
GTCAACGGTCAAAGGTCAAAG
Found at i:43336827 original size:21 final size:21
Alignment explanation
Indices: 43336803--43336850 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
43336793 CAAAGGTCAA
43336803 CGGTCAAAGGTCAA-TCAACAT
1 CGGTCAAAGGT-AAGTCAACAT
*
43336824 CGGTCAACGGTAAGTCAACAT
1 CGGTCAAAGGTAAGTCAACAT
43336845 CGGTCA
1 CGGTCA
43336851 TCGCCAGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (21 bp):
CGGTCAAAGGTAAGTCAACAT
Found at i:43336834 original size:7 final size:7
Alignment explanation
Indices: 43336777--43336816 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
43336767 TTTCGAAAAA
43336777 GTCAACG
1 GTCAACG
43336784 GTCAACG
1 GTCAACG
*
43336791 GTCAAAG
1 GTCAACG
43336798 GTCAACG
1 GTCAACG
*
43336805 GTCAAAG
1 GTCAACG
43336812 GTCAA
1 GTCAA
43336817 TCAACATCGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.35, C:0.23, G:0.28, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:43336949 original size:21 final size:22
Alignment explanation
Indices: 43336923--43336967 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
43336913 GGTTTAAAAC
43336923 GGTTTGGTTTAAAT-GAATTTG
1 GGTTTGGTTTAAATAGAATTTG
*
43336944 GGTTTGGTTTAAATAGGATTTG
1 GGTTTGGTTTAAATAGAATTTG
43336966 GG
1 GG
43336968 CTTAATGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (22 bp):
GGTTTGGTTTAAATAGAATTTG
Found at i:43346816 original size:16 final size:17
Alignment explanation
Indices: 43346795--43346835 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
43346785 AACTCTTTAA
43346795 AAATTATAAAAATAAT-
1 AAATTATAAAAATAATG
* *
43346811 AAATTATTAAAATGATG
1 AAATTATAAAAATAATG
43346828 AAATTATA
1 AAATTATA
43346836 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (17 bp):
AAATTATAAAAATAATG
Found at i:43347763 original size:29 final size:32
Alignment explanation
Indices: 43347723--43347789 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 32
43347713 AATAGCTTAT
*
43347723 ATTTTATAATTTTTA-AAGGA-TTAAA-TAAA
1 ATTTTATAATTTTTAGAAGGAGCTAAAGTAAA
* *
43347752 ATTTTATTATTTTTAGGAGGAGCTAAAGTAAA
1 ATTTTATAATTTTTAGAAGGAGCTAAAGTAAA
43347784 ATTTTA
1 ATTTTA
43347790 CCTTATCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 14 0.44
30 4 0.12
31 4 0.12
32 10 0.31
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.45
Consensus pattern (32 bp):
ATTTTATAATTTTTAGAAGGAGCTAAAGTAAA
Found at i:43363411 original size:80 final size:79
Alignment explanation
Indices: 43363267--43363415 Score: 208
Period size: 80 Copynumber: 1.9 Consensus size: 79
43363257 TTTAGCATTG
* * *
43363267 TTTTAATCTCAAAAGTTGCACCAAAATCAATACTAACTGGGACACAAGTAGTTGGAGGCCGTGAT
1 TTTTAATCTAAAAAGTTGCACCAAAATCAATACTAACTGGGACACAAGTAGTAGAAGGCCGTGAT
43363332 CAAATTAACACAAC
66 CAAATTAACACAAC
* * * * * *
43363346 TTTTAATCTAAAAAAGTTGTATCAATATCAATGCTAACTGGGACCCAAGTAGTAGAAGGCTGTGA
1 TTTTAATCT-AAAAAGTTGCACCAAAATCAATACTAACTGGGACACAAGTAGTAGAAGGCCGTGA
43363411 TCAAA
65 TCAAA
43363416 ATCAATTTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
79 9 0.15
80 51 0.85
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.26
Consensus pattern (79 bp):
TTTTAATCTAAAAAGTTGCACCAAAATCAATACTAACTGGGACACAAGTAGTAGAAGGCCGTGAT
CAAATTAACACAAC
Found at i:43375395 original size:63 final size:65
Alignment explanation
Indices: 43375324--43375468 Score: 224
Period size: 67 Copynumber: 2.2 Consensus size: 65
43375314 GAAACCCAAT
43375324 TTTATTTATTATTATTTTTATGAACATAAATAAAT-A-TAAAATAATATTAATTTTATTTTATTA
1 TTTATTTATTATTATTTTTATGAACATAAATAAATAAGTAAAATAATATTAATTTTATTTTATTA
* *
43375387 TTTATTTATTTATTA-TTTTATGAATATAAATAAATAAATGTAAAATAATATTAATTTTGTTTTA
1 TTTATTTA-TTATTATTTTTATGAACATAAATAAAT-AA-GTAAAATAATATTAATTTTATTTTA
43375451 TTA
63 TTA
43375454 TTTATTTATTATTAT
1 TTTATTTATTATTAT
43375469 AAATAAATAA
Statistics
Matches: 74, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
63 27 0.36
64 6 0.08
65 1 0.01
66 6 0.08
67 34 0.46
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (65 bp):
TTTATTTATTATTATTTTTATGAACATAAATAAATAAGTAAAATAATATTAATTTTATTTTATTA
Found at i:43375479 original size:63 final size:67
Alignment explanation
Indices: 43375349--43375482 Score: 204
Period size: 67 Copynumber: 2.1 Consensus size: 67
43375339 TTTTATGAAC
**
43375349 ATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTTATTTATTATTTTATGAATAT
1 ATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTTATTTATTATTAAATGAATAT
43375414 AA
66 AA
* *
43375416 ATAAATAAATGTAAAATAATATTAATTTTGTTTTATTATTTATTTA-TTATTA-TAAAT-AA-AT
1 ATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTTATTTATTATTAAATGAATAT
43375477 AA
66 AA
43375479 ATAA
1 ATAA
43375483 CAAACCAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
63 8 0.13
64 2 0.03
65 3 0.05
66 6 0.10
67 44 0.70
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (67 bp):
ATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTTATTTATTATTAAATGAATAT
AA
Found at i:43379511 original size:13 final size:13
Alignment explanation
Indices: 43379493--43379518 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43379483 TGACTTGTTA
43379493 TAAAAAAAAGAGG
1 TAAAAAAAAGAGG
43379506 TAAAAAAAAGAGG
1 TAAAAAAAAGAGG
43379519 GTCGAGATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (13 bp):
TAAAAAAAAGAGG
Found at i:43380488 original size:6 final size:6
Alignment explanation
Indices: 43380479--43380537 Score: 55
Period size: 6 Copynumber: 9.0 Consensus size: 6
43380469 AAAAAATTAA
* *
43380479 AAAAAG AAAAAAG AAAAAAAG ACAAAG AAAAGG AAAAAG AAGAAAAG AAAAAG
1 AAAAAG -AAAAAG --AAAAAG AAAAAG AAAAAG AAAAAG -A-AAAAG AAAAAG
43380532 AAAAAG
1 AAAAAG
43380538 GAGAGGTCGA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
6 25 0.56
7 8 0.18
8 12 0.27
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:43380488 original size:8 final size:8
Alignment explanation
Indices: 43380459--43380530 Score: 58
Period size: 8 Copynumber: 8.6 Consensus size: 8
43380449 GAAATTTCAA
43380459 AAAAAAAG
1 AAAAAAAG
*
43380467 ATAAAAAATT
1 A-AAAAAA-G
43380477 AAAAAAAG
1 AAAAAAAG
43380485 -AAAAAAG
1 AAAAAAAG
43380492 AAAAAAAG
1 AAAAAAAG
43380500 ACAAAGAAA-
1 A-AAA-AAAG
*
43380509 AGGAAAAAG
1 A-AAAAAAG
*
43380518 AAGAAAAG
1 AAAAAAAG
43380526 AAAAA
1 AAAAA
43380531 GAAAAAGGAG
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
7 7 0.14
8 21 0.41
9 19 0.37
10 4 0.08
ACGTcount: A:0.81, C:0.01, G:0.14, T:0.04
Consensus pattern (8 bp):
AAAAAAAG
Found at i:43380488 original size:15 final size:15
Alignment explanation
Indices: 43380477--43380536 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 15
43380467 ATAAAAAATT
43380477 AAAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
*
43380492 AAAAAAAG-ACAAAG
1 AAAAAAAGAAAAAAG
*
43380506 ---AAAAGGAAAAAG
1 AAAAAAAGAAAAAAG
*
43380518 AAGAAAAG-AAAAAG
1 AAAAAAAGAAAAAAG
43380532 AAAAA
1 AAAAA
43380537 GGAGAGGTCG
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 5 0.13
12 5 0.13
14 15 0.39
15 13 0.34
ACGTcount: A:0.82, C:0.02, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:43380537 original size:20 final size:20
Alignment explanation
Indices: 43380480--43380537 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
43380470 AAAAATTAAA
43380480 AAAAGAAAAAAGAAAAA-AAG
1 AAAAG-AAAAAGAAAAAGAAG
*
43380500 ACAAAGAAAAGGAAAAAGAAG
1 A-AAAGAAAAAGAAAAAGAAG
43380521 AAAAGAAAAAGAAAAAG
1 AAAAGAAAAAGAAAAAG
43380538 GAGAGGTCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAGAAAAAGAAG
Found at i:43381524 original size:50 final size:50
Alignment explanation
Indices: 43381462--43381619 Score: 192
Period size: 50 Copynumber: 3.2 Consensus size: 50
43381452 TCTTTTACCC
*
43381462 CTAAAGCGGTGGAGGTGCAGATTGAAACTGCAATGGTAAATCTCAGACAT
1 CTAAAGCTGTGGAGGTGCAGATTGAAACTGCAATGGTAAATCTCAGACAT
* * *
43381512 CTAAAGCTGTGGAGGTGCAGATTGAAACCGCAAT-GTCAAATCTCATACAC
1 CTAAAGCTGTGGAGGTGCAGATTGAAACTGCAATGGT-AAATCTCAGACAT
* * * * * * *
43381562 CTAAAGCTGTAGAGGGGCAGAATGAAGCTGTAATGGCAAATCTCAGTCAT
1 CTAAAGCTGTGGAGGTGCAGATTGAAACTGCAATGGTAAATCTCAGACAT
*
43381612 TTAAAGCT
1 CTAAAGCT
43381620 ATAGAGGAGA
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
49 2 0.02
50 88 0.97
51 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (50 bp):
CTAAAGCTGTGGAGGTGCAGATTGAAACTGCAATGGTAAATCTCAGACAT
Found at i:43381638 original size:50 final size:50
Alignment explanation
Indices: 43381482--43381637 Score: 145
Period size: 50 Copynumber: 3.1 Consensus size: 50
43381472 GGAGGTGCAG
* * * * * *
43381482 ATTGAAACTGCAATGGTAAATCTCAGACATCTAAAGCTGTGGAGGTGCAG
1 ATTGAAACTGCAATGGCAAATCTCAGTCATCTAAAGCTGTAGAGGAGAAA
* * * * *
43381532 ATTGAAACCGCAATGTCAAATCTCA-TACACCTAAAGCTGTAGAGGGGCAGA
1 ATTGAAACTGCAATGGCAAATCTCAGT-CATCTAAAGCTGTAGAGGAG-AAA
* * * *
43381583 A-TGAAGCTGTAATGGCAAATCTCAGTCATTTAAAGCTATAGAGGAGAAA
1 ATTGAAACTGCAATGGCAAATCTCAGTCATCTAAAGCTGTAGAGGAGAAA
43381632 ATTGAA
1 ATTGAA
43381638 GTCATAAGGA
Statistics
Matches: 83, Mismatches: 19, Indels: 8
0.75 0.17 0.07
Matches are distributed among these distances:
49 3 0.04
50 78 0.94
51 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (50 bp):
ATTGAAACTGCAATGGCAAATCTCAGTCATCTAAAGCTGTAGAGGAGAAA
Found at i:43381825 original size:80 final size:80
Alignment explanation
Indices: 43381692--43382349 Score: 1088
Period size: 80 Copynumber: 8.2 Consensus size: 80
43381682 AATTACAACC
43381692 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
43381757 GGCAGATTAAAGAAA
66 GGCAGATTGAAGAAA
*
43381772 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGAACTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
43381837 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* * *
43381852 TTCAATCTTTTACCCTAACCAGAGGGCAATATTGAAGAGCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
43381917 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* * *
43381932 TCAAATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATAG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
43381997 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* * *
43382012 TCCAATCTTTTACCCTAACTAAAGGGCAATATTGAAGACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
43382077 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
*
43382092 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTCTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
43382157 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* *
43382172 TCCAATCTTTTACCCTAACCAAAGGGCAAGATTGAAAACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
43382237 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* * * * *
43382252 TCCAATCTTTTACCCTAACCAAAGGGC-AGATTGAAGACCATCAGATCTCTTACCTCGACCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
43382316 GGCA-AGTTGAA-ACAA
66 GGCAGA-TTGAAGA-AA
*
43382331 TCTAATCTTTTACACCTAA
1 TCCAATCTTTTAC-CCTAA
43382350 GGTTATAGAG
Statistics
Matches: 546, Mismatches: 29, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
78 2 0.00
79 55 0.10
80 489 0.90
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (80 bp):
TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
GGCAGATTGAAGAAA
Found at i:43382974 original size:63 final size:64
Alignment explanation
Indices: 43382870--43383026 Score: 228
Period size: 67 Copynumber: 2.4 Consensus size: 64
43382860 TCCATTTTTC
*
43382870 TTATTATTTTTATTTATTTATTATTATTTTTATGAACATAAATAAAT-A-TAAAATAATATTAAT
1 TTATT-TTATTATTTATTTATTATTA-TTTTATGAACATAAATAAATAAGTAAAATAATATTAAT
43382933 T
64 T
*
43382934 TTATTTTATTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATGTAAAATAATATTAA
1 TTATTTTATTATTTATTTA-TTATTATTTTATGAACATAAATAAAT-AA-GTAAAATAATATTAA
43382999 TT
63 TT
*
43383001 TTGTTTTATTATTTATTTATTATTAT
1 TTATTTTATTATTTATTTATTATTAT
43383027 AAATAAATAA
Statistics
Matches: 85, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
63 32 0.38
64 11 0.13
65 1 0.01
66 7 0.08
67 34 0.40
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (64 bp):
TTATTTTATTATTTATTTATTATTATTTTATGAACATAAATAAATAAGTAAAATAATATTAATT
Found at i:43387153 original size:39 final size:39
Alignment explanation
Indices: 43387096--43387264 Score: 196
Period size: 39 Copynumber: 4.3 Consensus size: 39
43387086 CTACTGAAGG
* ** *
43387096 GCAATATAATACCGAATTGGCAGTAACATTGTAAATACT
1 GCAATACAATACTAAATTGGCAGTAACACTGTAAATACT
* * *
43387135 GCAATACAAAACTAAATTGGCAGTAACACAGTAAATATT
1 GCAATACAATACTAAATTGGCAGTAACACTGTAAATACT
* *
43387174 GCAATACAATACTAGATTGGCGGTAACACTGTAAATACT
1 GCAATACAATACTAAATTGGCAGTAACACTGTAAATACT
* * * *
43387213 GCAATACAATACTAAACTGACGGTAACACTATATAA-ACT
1 GCAATACAATACTAAATTGGCAGTAACACTGTA-AATACT
*
43387252 GCAATGCAATACT
1 GCAATACAATACT
43387265 GAACTGATGG
Statistics
Matches: 112, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 110 0.98
40 2 0.02
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (39 bp):
GCAATACAATACTAAATTGGCAGTAACACTGTAAATACT
Found at i:43387270 original size:39 final size:39
Alignment explanation
Indices: 43387118--43387286 Score: 162
Period size: 39 Copynumber: 4.3 Consensus size: 39
43387108 CGAATTGGCA
* * * * * *
43387118 GTAACATTGTAAATACTGCAATACAAAACTAAATTGGCA
1 GTAACACTATAAATACTGCAATACAATACTAAACTGACG
* * * *
43387157 GTAACAC-AGTAAATATTGCAATACAATACTAGATTGGCG
1 GTAACACTA-TAAATACTGCAATACAATACTAAACTGACG
*
43387196 GTAACACTGTAAATACTGCAATACAATACTAAACTGACG
1 GTAACACTATAAATACTGCAATACAATACTAAACTGACG
* * *
43387235 GTAACACTATATAA-ACTGCAATGCAATACTGAACTGATG
1 GTAACACTATA-AATACTGCAATACAATACTAAACTGACG
* *
43387274 GTGACACTGTAAA
1 GTAACACTATAAA
43387287 CATCGTAATG
Statistics
Matches: 110, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
38 2 0.02
39 106 0.96
40 2 0.02
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (39 bp):
GTAACACTATAAATACTGCAATACAATACTAAACTGACG
Found at i:43387281 original size:78 final size:78
Alignment explanation
Indices: 43387118--43387286 Score: 191
Period size: 78 Copynumber: 2.2 Consensus size: 78
43387108 CGAATTGGCA
* * * *
43387118 GTAACATTGTAAATACTGCAATACAAAACTAAATTGGCAGTAACACAGTAAATATTGCAATACAA
1 GTAACACTGTAAATACTGCAATACAAAACTAAACTGACAGTAACACAGTAAATACTGCAATACAA
* *
43387183 TACTAGATTGGCG
66 TACTAGACTGACG
* * *
43387196 GTAACACTGTAAATACTGCAATACAATACTAAACTGACGGTAACACTA-TATAA-ACTGCAATGC
1 GTAACACTGTAAATACTGCAATACAAAACTAAACTGACAGTAACAC-AGTA-AATACTGCAATAC
*
43387259 AATACT-GAACTGATG
64 AATACTAG-ACTGACG
*
43387274 GTGACACTGTAAA
1 GTAACACTGTAAA
43387287 CATCGTAATG
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
77 1 0.01
78 73 0.95
79 3 0.04
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (78 bp):
GTAACACTGTAAATACTGCAATACAAAACTAAACTGACAGTAACACAGTAAATACTGCAATACAA
TACTAGACTGACG
Found at i:43391568 original size:20 final size:20
Alignment explanation
Indices: 43391512--43391569 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
43391502 TGTTTCATAT
43391512 TTTTTAAAAATTAAGTCT-A-A
1 TTTTTAAAAATT-AGT-TAATA
*
43391532 TTATT-AAAATT-GTTAATA
1 TTTTTAAAAATTAGTTAATA
43391550 TTTTTAAAAATTAGTTAATA
1 TTTTTAAAAATTAGTTAATA
43391570 GTTAAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 1 0.03
17 3 0.09
18 5 0.16
19 12 0.38
20 11 0.34
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (20 bp):
TTTTTAAAAATTAGTTAATA
Found at i:43400337 original size:30 final size:30
Alignment explanation
Indices: 43400303--43400359 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
43400293 TTGTGTGTAA
* *
43400303 AAAATTAAAATAAAAAAATAGTTTAAATTG
1 AAAATTAAAAGAAAAAAATAATTTAAATTG
*
43400333 AAAATTAAAAGGAAAAAATAATTTAAA
1 AAAATTAAAAGAAAAAAATAATTTAAA
43400360 CTAAAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (30 bp):
AAAATTAAAAGAAAAAAATAATTTAAATTG
Found at i:43404527 original size:26 final size:26
Alignment explanation
Indices: 43404492--43404551 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 26
43404482 ATATATTTTC
*
43404492 TTCTAAAAAAATCTATGCAATATATA
1 TTCTAAAAAAATCTATGCAATACATA
*
43404518 TTCT-AAAAAATCTATGCGATACATA
1 TTCTAAAAAAATCTATGCAATACATA
43404543 TCTCTAAAA
1 T-TCTAAAA
43404552 TCTTCAATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 20 0.67
26 7 0.23
27 3 0.10
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (26 bp):
TTCTAAAAAAATCTATGCAATACATA
Found at i:43411580 original size:34 final size:35
Alignment explanation
Indices: 43411516--43411592 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
43411506 CATAAACTAA
* * *
43411516 ACCCAAATATTTTTAATTTTTTTACATTTTATTTT
1 ACCCAAATATTTCTAATTTTTATACATTTTATCTT
43411551 ACCCAAATATTTCTAATATTTTAT-C-TTTTATCTT
1 ACCCAAATATTTCTAAT-TTTTATACATTTTATCTT
*
43411585 ACCAAAAT
1 ACCCAAAT
43411593 GTTGTTTACT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 15 0.41
35 17 0.46
36 5 0.14
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (35 bp):
ACCCAAATATTTCTAATTTTTATACATTTTATCTT
Found at i:43418647 original size:28 final size:25
Alignment explanation
Indices: 43418593--43418641 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
43418583 CAATCACATC
*
43418593 AATTTTTAACAATAAAAATTGATTA
1 AATTTTTAACAATAAAAATCGATTA
43418618 AATTTTTAACAA-AAATAATCGATT
1 AATTTTTAACAATAAA-AATCGATT
43418642 TATAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (25 bp):
AATTTTTAACAATAAAAATCGATTA
Found at i:43418808 original size:2 final size:2
Alignment explanation
Indices: 43418801--43418830 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43418791 TAGCTGGCAT
43418801 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
43418831 AAAACACACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:43423555 original size:18 final size:20
Alignment explanation
Indices: 43423516--43423561 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
43423506 TTTAAAAAAA
43423516 TTAAAAAAATTTCATTTATT
1 TTAAAAAAATTTCATTTATT
43423536 TTAAAAAGAATTT-A-TT-TT
1 TTAAAAA-AATTTCATTTATT
43423554 TTAAAAAA
1 TTAAAAAA
43423562 GTTATTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.04
18 9 0.36
19 2 0.08
20 8 0.32
21 5 0.20
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (20 bp):
TTAAAAAAATTTCATTTATT
Found at i:43442365 original size:15 final size:17
Alignment explanation
Indices: 43442330--43442370 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
43442320 ATTTTTGAAT
*
43442330 TTTTTAAAATATTAACA
1 TTTTTAAAATATCAACA
*
43442347 -TTTTAAAAT-TCATCA
1 TTTTTAAAATATCAACA
43442362 TTTTTAAAA
1 TTTTTAAAA
43442371 ATTTGAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTTAAAATATCAACA
Found at i:43455228 original size:34 final size:34
Alignment explanation
Indices: 43455185--43455251 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
43455175 GTTCAACCTT
** *
43455185 TAACCTCCCTTGATTTTTAACCTTTCATCTTCCA
1 TAACCTCCCTTGACCTTTAACATTTCATCTTCCA
*
43455219 TAACCTCCCTTGACCTTTAACATTTTATCTTCC
1 TAACCTCCCTTGACCTTTAACATTTCATCTTCC
43455252 TTAATCTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.21, C:0.33, G:0.03, T:0.43
Consensus pattern (34 bp):
TAACCTCCCTTGACCTTTAACATTTCATCTTCCA
Found at i:43456512 original size:24 final size:22
Alignment explanation
Indices: 43456468--43456513 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
43456458 ACATTAAATT
*
43456468 GAAAAAAATATCTTAATTTAAA
1 GAAAAAAATATATTAATTTAAA
*
43456490 GAAAATAAATATATTTATCTTAAA
1 GAAAA-AAATATATTAAT-TTAAA
43456514 AAATAATCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 10 0.50
24 5 0.25
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (22 bp):
GAAAAAAATATATTAATTTAAA
Found at i:43460303 original size:6 final size:6
Alignment explanation
Indices: 43460292--43460317 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
43460282 AAAGAACTCG
43460292 GTGAAA GTGAAA GTGAAA GTGAAA GT
1 GTGAAA GTGAAA GTGAAA GTGAAA GT
43460318 AAAACCATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.35, T:0.19
Consensus pattern (6 bp):
GTGAAA
Found at i:43470128 original size:4 final size:4
Alignment explanation
Indices: 43470119--43470168 Score: 91
Period size: 4 Copynumber: 12.5 Consensus size: 4
43470109 GAAAATAGAT
*
43470119 TACA TACA TACA TAAA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
43470167 TA
1 TA
43470169 ACATGGATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:43471278 original size:20 final size:21
Alignment explanation
Indices: 43471255--43471296 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
43471245 AGAATCAAAC
43471255 TAAAATTAAATACAT-AATAA
1 TAAAATTAAATACATAAATAA
* *
43471275 TAAATTTAAATATATAAATAA
1 TAAAATTAAATACATAAATAA
43471296 T
1 T
43471297 CGATTCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAAATTAAATACATAAATAA
Found at i:43473013 original size:22 final size:21
Alignment explanation
Indices: 43472986--43473035 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
43472976 TTTAAAACAA
*
43472986 ATTTTATAT-TTTATTAATTTT
1 ATTTTATATATTTA-AAATTTT
43473007 ATATTTATATATTTAAAATTTT
1 AT-TTTATATATTTAAAATTTT
43473029 ATTTTAT
1 ATTTTAT
43473036 TTAATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 7 0.27
22 15 0.58
23 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTTATATATTTAAAATTTT
Found at i:43473043 original size:20 final size:22
Alignment explanation
Indices: 43473001--43473044 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
43472991 ATATTTTATT
*
43473001 AATTTTATATTTATATATTTAA
1 AATTTTATATTTATATATATAA
*
43473023 AATTTTAT-TTTATTTA-ATAA
1 AATTTTATATTTATATATATAA
43473043 AA
1 AA
43473045 ATGGCTAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 7 0.35
22 8 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTTTATATTTATATATATAA
Found at i:43473045 original size:21 final size:22
Alignment explanation
Indices: 43473001--43473046 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
43472991 ATATTTTATT
* *
43473001 AATTTTATATTTATATATTTAA
1 AATTTTATATTTATATAATAAA
*
43473023 AATTTTAT-TTTATTTAATAAA
1 AATTTTATATTTATATAATAAA
43473044 AAT
1 AAT
43473047 GGCTAAACTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTTTATATTTATATAATAAA
Found at i:43473353 original size:22 final size:23
Alignment explanation
Indices: 43473305--43473361 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
43473295 ATTTTTATTA
43473305 AATAAAATA-AAATTATAAAAAG
1 AATAAAATATAAATTATAAAAAG
* **
43473327 GATAAAATATAAA-TATAAAATT
1 AATAAAATATAAATTATAAAAAG
43473349 AATAAAATATAAA
1 AATAAAATATAAA
43473362 AATTATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 27 0.90
23 3 0.10
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (23 bp):
AATAAAATATAAATTATAAAAAG
Found at i:43473372 original size:22 final size:21
Alignment explanation
Indices: 43473328--43473383 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
43473318 TATAAAAAGG
*
43473328 ATAAAATATAAATATAAAATT
1 ATAAAATATAAAAATAAAATT
* **
43473349 AATAAAATATAAAAATTATTTT
1 -ATAAAATATAAAAATAAAATT
43473371 A-AAAATATAAAAA
1 ATAAAATATAAAAA
43473384 AAATAACAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 12 0.40
21 1 0.03
22 17 0.57
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAAAATATAAAAATAAAATT
Found at i:43474702 original size:17 final size:16
Alignment explanation
Indices: 43474671--43474705 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
43474661 TTGAACTAAA
43474671 TTATTTTTAATAATTT
1 TTATTTTTAATAATTT
*
43474687 TTATTTTTAATAAATT
1 TTATTTTTAATAATTT
43474703 TTA
1 TTA
43474706 ATCAAACCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTTTAATAATTT
Found at i:43490911 original size:14 final size:14
Alignment explanation
Indices: 43490892--43490918 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43490882 AAAGATACTT
43490892 TGGAGTTTGGAGTG
1 TGGAGTTTGGAGTG
43490906 TGGAGTTTGGAGT
1 TGGAGTTTGGAGT
43490919 AGAGGTGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.48, T:0.37
Consensus pattern (14 bp):
TGGAGTTTGGAGTG
Found at i:43496109 original size:16 final size:17
Alignment explanation
Indices: 43496084--43496116 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
43496074 TAATTTTTTG
*
43496084 AAATTTTAAAA-ATTCA
1 AAATTATAAAATATTCA
43496100 AAATTATAAAATATTCA
1 AAATTATAAAATATTCA
43496117 TTAAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTATAAAATATTCA
Found at i:43513019 original size:32 final size:32
Alignment explanation
Indices: 43512973--43513040 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
43512963 GTTAAATTTC
* *
43512973 TAATCAATCGTAATTTCTTCAAGGGTTTGAAT
1 TAATCAATCCTAATTTCTTCAAGGATTTGAAT
* * *
43513005 TAATCAATCCTAATTTTTTTAAGGATTTGTAT
1 TAATCAATCCTAATTTCTTCAAGGATTTGAAT
43513037 TAAT
1 TAAT
43513041 GAACATCTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (32 bp):
TAATCAATCCTAATTTCTTCAAGGATTTGAAT
Found at i:43516587 original size:18 final size:18
Alignment explanation
Indices: 43516543--43516587 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
43516533 CAATATTTAA
* *
43516543 AAATAAAATTTTAAATTT
1 AAATAAAATTTAAAAATT
* *
43516561 ACATTAAATTTAAAAATT
1 AAATAAAATTTAAAAATT
43516579 AAATAAAAT
1 AAATAAAAT
43516588 AATTATTTGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATAAAATTTAAAAATT
Found at i:43517088 original size:15 final size:15
Alignment explanation
Indices: 43517068--43517097 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
43517058 GATATGCCTT
43517068 CTACAAAGTATAAAG
1 CTACAAAGTATAAAG
43517083 CTACAAAGTATAAAG
1 CTACAAAGTATAAAG
43517098 TAAAATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (15 bp):
CTACAAAGTATAAAG
Found at i:43518694 original size:23 final size:24
Alignment explanation
Indices: 43518664--43518724 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
43518654 GTTCACGAAC
*
43518664 AAGCTCGTTTATTAGCTAGTATA-
1 AAGCTCGTTTATTAGCCAGTATAT
* * *
43518687 AAGCTCGTTTA-AAGCCCGTTTAT
1 AAGCTCGTTTATTAGCCAGTATAT
43518710 AAGCTCGTTTATTAG
1 AAGCTCGTTTATTAG
43518725 ACCCATCAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 7 0.23
23 22 0.71
24 2 0.06
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (24 bp):
AAGCTCGTTTATTAGCCAGTATAT
Found at i:43518718 original size:12 final size:12
Alignment explanation
Indices: 43518664--43518721 Score: 66
Period size: 12 Copynumber: 5.0 Consensus size: 12
43518654 GTTCACGAAC
43518664 AAGCTCGTTTAT
1 AAGCTCGTTTAT
* * *
43518676 TAGCTAGTATA-
1 AAGCTCGTTTAT
43518687 AAGCTCGTTTA-
1 AAGCTCGTTTAT
*
43518698 AAGCCCGTTTAT
1 AAGCTCGTTTAT
43518710 AAGCTCGTTTAT
1 AAGCTCGTTTAT
43518722 TAGACCCATC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
11 18 0.49
12 19 0.51
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (12 bp):
AAGCTCGTTTAT
Found at i:43531423 original size:30 final size:34
Alignment explanation
Indices: 43531389--43531468 Score: 96
Period size: 34 Copynumber: 2.5 Consensus size: 34
43531379 AAAATTACAT
*
43531389 AAAATTATAAAAGAAAG-G-ATAAAAATA-T-AG
1 AAAATTATAAAAAAAAGTGTATAAAAATATTGAG
* * *
43531419 AAAATTGTAAAAAAAAGTGTATTAAAATATTGAT
1 AAAATTATAAAAAAAAGTGTATAAAAATATTGAG
43531453 AAAATTATAAAAAAAA
1 AAAATTATAAAAAAAA
43531469 AAATTATGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 15 0.37
31 1 0.02
32 8 0.20
33 1 0.02
34 16 0.39
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (34 bp):
AAAATTATAAAAAAAAGTGTATAAAAATATTGAG
Found at i:43531457 original size:34 final size:30
Alignment explanation
Indices: 43531378--43531468 Score: 92
Period size: 30 Copynumber: 2.9 Consensus size: 30
43531368 ATTTACTCTT
* * *
43531378 TAAAATTACATAAAATTATAAAAGAAAGGA
1 TAAAAATATATAAAATTATAAAAAAAAGGA
* *
43531408 TAAAAATATAGAAAATTGTAAAAAAAAGTGTA
1 TAAAAATATATAAAATTATAAAAAAAAG-G-A
*
43531440 TTAAAATATTGATAAAATTATAAAAAAAA
1 TAAAAATA-T-ATAAAATTATAAAAAAAA
43531469 AAATTATGAG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 23 0.47
31 1 0.02
32 8 0.16
33 1 0.02
34 16 0.33
ACGTcount: A:0.64, C:0.01, G:0.09, T:0.26
Consensus pattern (30 bp):
TAAAAATATATAAAATTATAAAAAAAAGGA
Found at i:43531465 original size:32 final size:30
Alignment explanation
Indices: 43531379--43531466 Score: 72
Period size: 32 Copynumber: 2.8 Consensus size: 30
43531369 TTTACTCTTT
*
43531379 AAAAT-TACATAAAATTATAAAAGAAAGGATA
1 AAAATATAGATAAAATTAT-AAA-AAAGGATA
* * *
43531410 AAAATATAGA-AAATTGTAAAAAAAAGTGTATT
1 AAAATATAGATAAAAT-TATAAAAAAG-G-ATA
*
43531442 AAAATATTGATAAAATTATAAAAAA
1 AAAATATAGATAAAATTATAAAAAA
43531467 AAAAATTATG
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
30 4 0.09
31 13 0.29
32 24 0.53
33 4 0.09
ACGTcount: A:0.64, C:0.01, G:0.09, T:0.26
Consensus pattern (30 bp):
AAAATATAGATAAAATTATAAAAAAGGATA
Found at i:43537571 original size:25 final size:23
Alignment explanation
Indices: 43537440--43537600 Score: 157
Period size: 23 Copynumber: 6.9 Consensus size: 23
43537430 CAAAGTACTT
43537440 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
*
43537466 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * * * *
43537488 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACAAAGTGCGA
* *
43537510 AATCAGTAGGCACACGAAGTGCGA
1 AA-CAGTAAGCACACAAAGTGCGA
* *
43537534 AACAGTAGGCACACAAAGTGTGA
1 AACAGTAAGCACACAAAGTGCGA
43537557 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
43537580 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACAAAGTGC
43537601 TGAACGGTAA
Statistics
Matches: 116, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
22 19 0.16
23 75 0.65
24 3 0.03
26 14 0.12
27 5 0.04
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.11
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:43542408 original size:2 final size:2
Alignment explanation
Indices: 43542401--43542426 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43542391 CCGCCACCAA
43542401 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
43542427 GCCTCAGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43542971 original size:77 final size:77
Alignment explanation
Indices: 43542878--43543044 Score: 316
Period size: 77 Copynumber: 2.2 Consensus size: 77
43542868 TTTTTTTTTA
43542878 CTTTTTGACCTAATGGGAGTAATCCCATTGGGGTTTTAAAAGGAACATATGAGCAAAAGTTTACG
1 CTTTTTGACCTAATGGGAGTAATCCCATTGGGGTTTTAAAAGGAACATATGAGCAAAAGTTTACG
43542943 GCTGCACTCTTG
66 GCTGCACTCTTG
*
43542955 CTTTTTGACCTAATGGGAGTAATCCCATTGGGGTTTTAAAAGGAACATATGAGCAAAAGTTTATG
1 CTTTTTGACCTAATGGGAGTAATCCCATTGGGGTTTTAAAAGGAACATATGAGCAAAAGTTTACG
43543020 GCTGCACTCTTG
66 GCTGCACTCTTG
*
43543032 CTTTTTCACCTAA
1 CTTTTTGACCTAA
43543045 GCTGACGTTA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
77 88 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (77 bp):
CTTTTTGACCTAATGGGAGTAATCCCATTGGGGTTTTAAAAGGAACATATGAGCAAAAGTTTACG
GCTGCACTCTTG
Found at i:43544295 original size:2 final size:2
Alignment explanation
Indices: 43544288--43544312 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43544278 ACTCACTTTG
43544288 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
43544313 CCAGATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43555856 original size:28 final size:31
Alignment explanation
Indices: 43555811--43555879 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 31
43555801 CAATTTATTT
*
43555811 TTTTTTATTTTTTGTTCT-TT-TAATTT-TCCC
1 TTTTTT-TTTTCTGTTCTCTTCT-ATTTCTCCC
43555841 TTTTTTTTTTCT-TTCTCTTCTATTTCTCCC
1 TTTTTTTTTTCTGTTCTCTTCTATTTCTCCC
*
43555871 TTTTGTTTT
1 TTTTTTTTT
43555880 CCTCCCTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 4 0.12
29 11 0.32
30 19 0.56
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.74
Consensus pattern (31 bp):
TTTTTTTTTTCTGTTCTCTTCTATTTCTCCC
Found at i:43558173 original size:22 final size:24
Alignment explanation
Indices: 43558147--43558194 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
43558137 TTTAAAAAAG
*
43558147 TTTTTTGTTT-TATAATTTAATAA
1 TTTTATGTTTCTATAATTTAATAA
*
43558170 TTTTGATTTTTCTATAATTTAATAA
1 TTTT-ATGTTTCTATAATTTAATAA
43558195 ATGGTTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 4 0.19
25 13 0.62
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (24 bp):
TTTTATGTTTCTATAATTTAATAA
Found at i:43560699 original size:2 final size:2
Alignment explanation
Indices: 43560692--43560720 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43560682 GGATGGGTTT
43560692 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43560721 CCCAAAAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43560915 original size:22 final size:22
Alignment explanation
Indices: 43560890--43560936 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
43560880 TTTGCCTAAG
43560890 TTAGCAATGGCGTGAAAACAAC
1 TTAGCAATGGCGTGAAAACAAC
43560912 TTAGCAATGGCGTGAAAACAAC
1 TTAGCAATGGCGTGAAAACAAC
43560934 TTA
1 TTA
43560937 CATCACCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (22 bp):
TTAGCAATGGCGTGAAAACAAC
Found at i:43561661 original size:26 final size:26
Alignment explanation
Indices: 43561621--43561688 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
43561611 TAGAAAATTC
* * **
43561621 TTAACTTCAAATTAATTCAAATTAAA-
1 TTAAATTCAATTTAATT-AAAAAAAAT
* *
43561647 TTAAATTCGATTTAAGTAAAAAAAAT
1 TTAAATTCAATTTAATTAAAAAAAAT
43561673 TTAAATTCAATTTAAT
1 TTAAATTCAATTTAAT
43561689 GTGTTTTTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
25 6 0.18
26 27 0.82
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (26 bp):
TTAAATTCAATTTAATTAAAAAAAAT
Found at i:43563312 original size:18 final size:18
Alignment explanation
Indices: 43563286--43563328 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
43563276 AGGTTACCCT
43563286 ACGCAGGTCGAGTTGTCC
1 ACGCAGGTCGAGTTGTCC
*
43563304 ACGCGGGTCGAGTTGTCC
1 ACGCAGGTCGAGTTGTCC
43563322 ACTGCAG
1 AC-GCAG
43563329 TAACTAGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.16, C:0.28, G:0.35, T:0.21
Consensus pattern (18 bp):
ACGCAGGTCGAGTTGTCC
Found at i:43569576 original size:3 final size:3
Alignment explanation
Indices: 43569570--43569639 Score: 122
Period size: 3 Copynumber: 23.3 Consensus size: 3
43569560 TGTTGTTGTT
* *
43569570 GTG GTG GTG GTG GTG TTG GTG GTG GTG GTG GTG GTG GTG GTG ATG GTG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
43569618 GTG GTG GTG GTG GTG GTG GTG G
1 GTG GTG GTG GTG GTG GTG GTG G
43569640 AGTGGAAGGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.01, C:0.00, G:0.64, T:0.34
Consensus pattern (3 bp):
GTG
Found at i:43579900 original size:26 final size:27
Alignment explanation
Indices: 43579858--43579918 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
43579848 TTAAAATAAT
43579858 TATATAAAAAATCAATA-A-ATTAAAAA
1 TATATAAAAAATCAATATATATT-AAAA
*
43579884 TATATAAAATTAT-AATATATATTAAAA
1 TATATAAAA-AATCAATATATATTAAAA
43579911 TAGTATAA
1 TA-TATAA
43579919 TATAAATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 13 0.43
27 9 0.30
28 8 0.27
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (27 bp):
TATATAAAAAATCAATATATATTAAAA
Found at i:43579919 original size:20 final size:17
Alignment explanation
Indices: 43579874--43579922 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
43579864 AAAAATCAAT
*
43579874 AAATTA-AAAATATATA
1 AAATTATAATATATATA
43579890 AAATTATAATATATATTA
1 AAATTATAATATATA-TA
43579908 AAATAGTATAATATA
1 AAAT--TATAATATA
43579923 AATATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 6 0.21
17 7 0.25
18 6 0.21
20 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
AAATTATAATATATATA
Found at i:43580644 original size:113 final size:113
Alignment explanation
Indices: 43580446--43580672 Score: 400
Period size: 113 Copynumber: 2.0 Consensus size: 113
43580436 ATCTTCTTCC
* *
43580446 CTTTTGATTCCAATATCTTTAGTTATAAATCTGTCTCAAAGCTTGAATCTTTAAAACCCATTAAC
1 CTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAACTTGAATCTTTAAAACCCATTAAC
* * *
43580511 CAAAATATTCAATATCTTTGGTTTCAATATCTTCTTCCCTTTAAGTTT
66 CAAAAGATTCAATATCTTTGGTTCCAATATCTTCTTCCCGTTAAGTTT
*
43580559 CTTTTGATTCCAATATTTTTAGTTACAAATCTGTCTCAAAACTTGAATCTTTAAAACCCATTAAC
1 CTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAACTTGAATCTTTAAAACCCATTAAC
43580624 CAAAAGATTCAATATCTTTGGTTCCAATATCTTCTTCCCGTTAAGTTT
66 CAAAAGATTCAATATCTTTGGTTCCAATATCTTCTTCCCGTTAAGTTT
43580672 C
1 C
43580673 CTTGTGTCAA
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 108 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.42
Consensus pattern (113 bp):
CTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAACTTGAATCTTTAAAACCCATTAAC
CAAAAGATTCAATATCTTTGGTTCCAATATCTTCTTCCCGTTAAGTTT
Found at i:43583411 original size:6 final size:6
Alignment explanation
Indices: 43583400--43583434 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
43583390 TATATCGAAG
43583400 CTCCCT CTCCCTCT CTCCCT CTCCCT CTCCCT CTC
1 CTCCCT CT-CC-CT CTCCCT CTCCCT CTCCCT CTC
43583435 TACCACATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.70
7 4 0.15
8 4 0.15
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCCCT
Found at i:43583435 original size:14 final size:14
Alignment explanation
Indices: 43583400--43583428 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
43583390 TATATCGAAG
43583400 CTCCCTCTCCCTCT
1 CTCCCTCTCCCTCT
43583414 CTCCCTCTCCCTCT
1 CTCCCTCTCCCTCT
43583428 C
1 C
43583429 CCTCTCTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (14 bp):
CTCCCTCTCCCTCT
Found at i:43592165 original size:32 final size:30
Alignment explanation
Indices: 43592108--43592167 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 30
43592098 AAGAGTGAGT
43592108 AAAATTTAATTCGAATTAAAAAATTTAATA
1 AAAATTTAATTCGAATTAAAAAATTTAATA
* *
43592138 AAAATTTAAATTTTGAATTAAATAATTTAA
1 AAAATTT-AA-TTCGAATTAAAAAATTTAA
43592168 GTTATTCGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 7 0.27
31 2 0.08
32 17 0.65
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (30 bp):
AAAATTTAATTCGAATTAAAAAATTTAATA
Found at i:43592733 original size:17 final size:17
Alignment explanation
Indices: 43592711--43592744 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43592701 ATATACTAAC
*
43592711 TTAAAATTTTAAAAATT
1 TTAAAATATTAAAAATT
43592728 TTAAAATATTAAAAATT
1 TTAAAATATTAAAAATT
43592745 AAATTTACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAAATATTAAAAATT
Found at i:43593897 original size:30 final size:30
Alignment explanation
Indices: 43593838--43593906 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 30
43593828 TTTTATTTTT
*
43593838 TAAATATTAATATTTAATATTATTAAACATA
1 TAAAT-TTAATATTTAATATTAATAAACATA
43593869 TAAATTTAATTATTT-ATATTTAAT-AACATA
1 TAAATTTAA-TATTTAATA-TTAATAAACATA
43593899 -ATAATTTA
1 TA-AATTTA
43593907 TGGGCTAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
29 1 0.03
30 19 0.56
31 14 0.41
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAATTTAATATTTAATATTAATAAACATA
Found at i:43594184 original size:37 final size:36
Alignment explanation
Indices: 43594134--43594220 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 36
43594124 CTAACCTAAT
*
43594134 ATCTCATTCTCTTAGCGTGGTGAA-TCACCTGTCCTC
1 ATCTCATTCTCTTAGCGTGATGAACT-ACCTGTCCTC
*
43594170 ATCTCATTTCTCTTAGCGTGATGAACTATCTGTCCTC
1 ATCTCA-TTCTCTTAGCGTGATGAACTACCTGTCCTC
*
43594207 ATCTTATTCTCTTA
1 ATCTCATTCTCTTA
43594221 TCGATCACAT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
36 14 0.30
37 31 0.67
38 1 0.02
ACGTcount: A:0.18, C:0.28, G:0.13, T:0.41
Consensus pattern (36 bp):
ATCTCATTCTCTTAGCGTGATGAACTACCTGTCCTC
Found at i:43594533 original size:36 final size:30
Alignment explanation
Indices: 43594506--43594576 Score: 99
Period size: 29 Copynumber: 2.3 Consensus size: 30
43594496 TAAATTAGTA
43594506 AATATAAAATTATATTTTAATTATTTTAAAAAT
1 AATA-AAAATTA-A-TTTAATTATTTTAAAAAT
43594539 AATAAAAATTAATTTAATT-TTTTAAAAAT
1 AATAAAAATTAATTTAATTATTTTAAAAAT
*
43594568 TATAAAAAT
1 AATAAAAAT
43594577 ATAAATTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 18 0.49
30 7 0.19
31 1 0.03
32 7 0.19
33 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
AATAAAAATTAATTTAATTATTTTAAAAAT
Found at i:43594572 original size:29 final size:32
Alignment explanation
Indices: 43594506--43594621 Score: 105
Period size: 33 Copynumber: 3.7 Consensus size: 32
43594496 TAAATTAGTA
43594506 AATATAAAATTATATTTTAATTATTTTAAAAAT
1 AATA-AAAATTATATTTTAATTATTTTAAAAAT
43594539 AATAAAAATTA-A-TTTAATT-TTTTAAAAAT
1 AATAAAAATTATATTTTAATTATTTTAAAAAT
* * * ** *
43594568 TATAAAAATATAAATTATT-ATAATAATGAAAAT
1 AATAAAAAT-TATATT-TTAATTATTTTAAAAAT
* *
43594601 AATAAAATTTATAATTTAATT
1 AATAAAAATTATATTTTAATT
43594622 TCGATCAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 13
0.74 0.11 0.14
Matches are distributed among these distances:
29 18 0.27
30 9 0.13
31 4 0.06
32 16 0.24
33 20 0.30
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (32 bp):
AATAAAAATTATATTTTAATTATTTTAAAAAT
Found at i:43597374 original size:32 final size:32
Alignment explanation
Indices: 43597335--43597425 Score: 110
Period size: 32 Copynumber: 2.8 Consensus size: 32
43597325 CTGAATTTGA
*
43597335 TTTTTTTAACTTAGTACTTGAATTTAAATATT
1 TTTTTTTAATTTAGTACTTGAATTTAAATATT
* * * *
43597367 TTTTTTTAGTTTAATACTTGAACTTAGATATT
1 TTTTTTTAATTTAGTACTTGAATTTAAATATT
* *
43597399 TTTTTCTTAATTTAGTACCTAAATTTA
1 TTTTT-TTAATTTAGTACTTGAATTTA
43597426 TTAAATGTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 32 0.67
33 16 0.33
ACGTcount: A:0.30, C:0.08, G:0.07, T:0.56
Consensus pattern (32 bp):
TTTTTTTAATTTAGTACTTGAATTTAAATATT
Found at i:43597841 original size:13 final size:13
Alignment explanation
Indices: 43597823--43597848 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43597813 CAACCTCAAA
43597823 AAATATCAAATTT
1 AAATATCAAATTT
43597836 AAATATCAAATTT
1 AAATATCAAATTT
43597849 GGAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATATCAAATTT
Found at i:43601817 original size:1 final size:1
Alignment explanation
Indices: 43601811--43601835 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
43601801 ATGACTCCCT
43601811 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
43601836 TCCACACTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:43602194 original size:17 final size:19
Alignment explanation
Indices: 43602174--43602214 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
43602164 GTTTAGAATC
*
43602174 TATTTTTTAA-AA-TTTTT
1 TATTTTCTAATAATTTTTT
43602191 TA-TTTCTAATAATTTTTT
1 TATTTTCTAATAATTTTTT
43602209 TATTTT
1 TATTTT
43602215 ACAAGGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 6 0.30
17 4 0.20
18 7 0.35
19 3 0.15
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTTCTAATAATTTTTT
Found at i:43607745 original size:17 final size:17
Alignment explanation
Indices: 43607723--43607756 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43607713 ACAAAATGAT
* *
43607723 AATATAATTGATTAAAA
1 AATATAAGTGACTAAAA
43607740 AATATAAGTGACTAAAA
1 AATATAAGTGACTAAAA
43607757 TGTAATATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.03, G:0.09, T:0.29
Consensus pattern (17 bp):
AATATAAGTGACTAAAA
Found at i:43608803 original size:2 final size:2
Alignment explanation
Indices: 43608796--43608826 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43608786 CATAAAATAT
43608796 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
43608827 GGAATCAAAA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:43615885 original size:12 final size:12
Alignment explanation
Indices: 43615868--43615903 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
43615858 CTTTTAGATT
*
43615868 ATTGACGTTGGC
1 ATTGACGTTGAC
43615880 ATTGACGTTGAC
1 ATTGACGTTGAC
*
43615892 ATTGACCTTGAC
1 ATTGACGTTGAC
43615904 GAAGTAGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (12 bp):
ATTGACGTTGAC
Found at i:43616157 original size:14 final size:15
Alignment explanation
Indices: 43616133--43616178 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 15
43616123 TAAAATAAAC
* *
43616133 TATAATTTAATTATT
1 TATATTTTAATAATT
43616148 T-TATTTTAATAATT
1 TATATTTTAATAATT
43616162 TATATTTT-ATAATT
1 TATATTTTAATAATT
43616176 TAT
1 TAT
43616179 TATTATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 21 0.75
15 7 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATATTTTAATAATT
Found at i:43616182 original size:15 final size:16
Alignment explanation
Indices: 43616148--43616182 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
43616138 TTTAATTATT
43616148 TTATTTTAATAATTTA
1 TTATTTTAATAATTTA
43616164 -TATTTT-ATAATTTA
1 TTATTTTAATAATTTA
43616178 TTATT
1 TTATT
43616183 ATTTTTAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTTAATAATTTA
Found at i:43616232 original size:8 final size:8
Alignment explanation
Indices: 43616219--43616243 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
43616209 TATTTTTATT
43616219 AATTTTAA
1 AATTTTAA
43616227 AATTTTAA
1 AATTTTAA
43616235 AATTTTAA
1 AATTTTAA
43616243 A
1 A
43616244 GAATTCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:43617050 original size:17 final size:19
Alignment explanation
Indices: 43617028--43617065 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
43617018 TTTGAAAAAT
43617028 AATTTAAA-TGAA-TTGAA
1 AATTTAAATTGAACTTGAA
43617045 AATTTAAATTGAACTTGAA
1 AATTTAAATTGAACTTGAA
43617064 AA
1 AA
43617066 AATTTATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 4 0.21
19 7 0.37
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.34
Consensus pattern (19 bp):
AATTTAAATTGAACTTGAA
Found at i:43617753 original size:16 final size:17
Alignment explanation
Indices: 43617734--43617773 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
43617724 CATAAATTTA
*
43617734 TTTATAAATTT-ATAAT
1 TTTATAAATTTAAAAAT
*
43617750 TTTATAATTTTAAAAAT
1 TTTATAAATTTAAAAAT
43617767 TTTATAA
1 TTTATAA
43617774 CTTTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTATAAATTTAAAAAT
Found at i:43617769 original size:17 final size:16
Alignment explanation
Indices: 43617734--43617778 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
43617724 CATAAATTTA
* *
43617734 TTTATAAATTTATAAT
1 TTTATAATTTTAAAAT
43617750 TTTATAATTTTAAAAAT
1 TTTATAATTTT-AAAAT
43617767 TTTATAACTTTT
1 TTTATAA-TTTT
43617779 TTTATATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.40
17 11 0.44
18 4 0.16
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTATAATTTTAAAAT
Found at i:43617778 original size:9 final size:8
Alignment explanation
Indices: 43617734--43617778 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
43617724 CATAAATTTA
*
43617734 TTTATAAA
1 TTTATAAT
43617742 TTTATAAT
1 TTTATAAT
43617750 TTTATAAT
1 TTTATAAT
*
43617758 TTTAAAAAT
1 TTT-ATAAT
43617767 TTTATAACT
1 TTTATAA-T
43617776 TTT
1 TTT
43617779 TTTATATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
8 21 0.66
9 11 0.34
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (8 bp):
TTTATAAT
Found at i:43624693 original size:6 final size:6
Alignment explanation
Indices: 43624682--43624714 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
43624672 AGGGAGGGAA
43624682 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGA
1 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGA
43624715 AAGAGAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GGAGAG
Found at i:43625746 original size:12 final size:12
Alignment explanation
Indices: 43625729--43625755 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
43625719 AATTCTTATA
43625729 AATTATTAATAT
1 AATTATTAATAT
43625741 AATTATTAATAT
1 AATTATTAATAT
43625753 AAT
1 AAT
43625756 ATCATTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTATTAATAT
Found at i:43627855 original size:21 final size:21
Alignment explanation
Indices: 43627825--43627868 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
43627815 TATAAACAAT
*
43627825 TTAATAATTTTGTCTTTTAAC
1 TTAATAATTTTGACTTTTAAC
*
43627846 TTAATGATTTTGACTTTTAAC
1 TTAATAATTTTGACTTTTAAC
43627867 TT
1 TT
43627869 TAGAAAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.09, G:0.07, T:0.57
Consensus pattern (21 bp):
TTAATAATTTTGACTTTTAAC
Found at i:43628343 original size:31 final size:30
Alignment explanation
Indices: 43628289--43628354 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
43628279 CATATGCAAG
43628289 TTTT-AAAAAATTAAATCGAAATTTTATAAT
1 TTTTAAAAAAATTAAATCGAAATTTTAT-AT
* *
43628319 TTTTAAAAAAATTAAAAT-GTAATTTTATTT
1 TTTTAAAAAAATT-AAATCGAAATTTTATAT
43628349 TTTTAA
1 TTTTAA
43628355 TTTAAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 11 0.34
31 17 0.53
32 4 0.12
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (30 bp):
TTTTAAAAAAATTAAATCGAAATTTTATAT
Found at i:43628457 original size:29 final size:29
Alignment explanation
Indices: 43628416--43628473 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
43628406 CTACCTCACT
43628416 TTTTATAACCACTTATAAATATAAATTTC
1 TTTTATAACCACTTATAAATATAAATTTC
43628445 TTTTATAACCACTTATAAATATAAATTTC
1 TTTTATAACCACTTATAAATATAAATTTC
43628474 GTAAATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (29 bp):
TTTTATAACCACTTATAAATATAAATTTC
Found at i:43663164 original size:2 final size:2
Alignment explanation
Indices: 43663157--43663183 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43663147 TTTCCTATGC
43663157 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 A
43663184 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.