Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 114 of 150
Found at i:35255561 original size:25 final size:25
Alignment explanation
Indices: 35255519--35255703 Score: 142
Period size: 25 Copynumber: 7.4 Consensus size: 25
35255509 AGTTGTATAA
* * * *
35255519 CGGGAAACTTATACGAGCCAATTAT
1 CGGGAAGCTCATAAGAGCCAAATAT
* * **
35255544 CTGGAAGCTCAAAAGAGCC-GTTAAT
1 CGGGAAGCTCATAAGAGCCAAAT-AT
* *
35255569 CGGGAAGCTCATGAGAGACAAATAT
1 CGGGAAGCTCATAAGAGCCAAATAT
35255594 CGGGAAGCTCATGAA-AGCCAAATAT
1 CGGGAAGCTCAT-AAGAGCCAAATAT
* * *
35255619 CAGGATGCTCATAAGAGCTAAATAAT
1 CGGGAAGCTCATAAGAGCCAAAT-AT
* *
35255645 -GGGAAGCTCGTGAGAGCCAAATAT
1 CGGGAAGCTCATAAGAGCCAAATAT
* * * *
35255669 CGGGATGCTCATAAGCGCTAAATAA
1 CGGGAAGCTCATAAGAGCCAAATAT
*
35255694 CGGAAAGCTC
1 CGGGAAGCTC
35255704 GTGAGAGCTA
Statistics
Matches: 124, Mismatches: 30, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
24 6 0.05
25 114 0.92
26 4 0.03
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (25 bp):
CGGGAAGCTCATAAGAGCCAAATAT
Found at i:35255598 original size:75 final size:75
Alignment explanation
Indices: 35255534--35255673 Score: 174
Period size: 75 Copynumber: 1.9 Consensus size: 75
35255524 AACTTATACG
* * ***
35255534 AGCCAATTATCTGGAAGCTCAAAAGAGC-CGTTAATCGGGAAGCTCATGAGAGACAAATATCGGG
1 AGCCAAATATCAGGAAGCTCAAAAGAGCTAAATAAT-GGGAAGCTCATGAGAGACAAATATCGGG
*
35255598 AAGCTCATGAA
65 AAACTCATGAA
* * * *
35255609 AGCCAAATATCAGGATGCTCATAAGAGCTAAATAATGGGAAGCTCGTGAGAGCCAAATATCGGGA
1 AGCCAAATATCAGGAAGCTCAAAAGAGCTAAATAATGGGAAGCTCATGAGAGACAAATATCGGGA
35255674 TGCTCATAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
75 51 0.93
76 4 0.07
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.19
Consensus pattern (75 bp):
AGCCAAATATCAGGAAGCTCAAAAGAGCTAAATAATGGGAAGCTCATGAGAGACAAATATCGGGA
AACTCATGAA
Found at i:35255704 original size:50 final size:50
Alignment explanation
Indices: 35255575--35255711 Score: 186
Period size: 50 Copynumber: 2.7 Consensus size: 50
35255565 TAATCGGGAA
* * * *
35255575 GCTCATGAGAGAC-AAATATCGGGAAGCTCATGAAAGCCAAATATCAGGAT
1 GCTCATAAGAG-CTAAATAACGGGAAGCTCGTGAGAGCCAAATATCAGGAT
* *
35255625 GCTCATAAGAGCTAAATAATGGGAAGCTCGTGAGAGCCAAATATCGGGAT
1 GCTCATAAGAGCTAAATAACGGGAAGCTCGTGAGAGCCAAATATCAGGAT
* *
35255675 GCTCATAAGCGCTAAATAACGGAAAGCTCGTGAGAGC
1 GCTCATAAGAGCTAAATAACGGGAAGCTCGTGAGAGC
35255712 TATGGTATGT
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
49 1 0.01
50 76 0.99
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.18
Consensus pattern (50 bp):
GCTCATAAGAGCTAAATAACGGGAAGCTCGTGAGAGCCAAATATCAGGAT
Found at i:35255711 original size:75 final size:75
Alignment explanation
Indices: 35255565--35255713 Score: 178
Period size: 75 Copynumber: 2.0 Consensus size: 75
35255555 AAAGAGCCGT
* *
35255565 TAATCGGGAAGCTCATGAGAGACAAATATCGGGAAGCTCATGAAAGCCAAATATCAGGATGCTCA
1 TAATCGGGAAGCTCATGAGAGACAAATATCGGGAAGCTCAT-AAAGCCAAATAACAGGAAGCTCA
35255630 TAAGAGCTAAA
65 TAAGAGCTAAA
* * *
35255641 TAAT-GGGAAGCTCGTGAGAGCCAAATATCGGGATGCTCAT-AAGCGCTAAATAAC-GGAAAGCT
1 TAATCGGGAAGCTCATGAGAGACAAATATCGGGAAGCTCATAAAGC-C-AAATAACAGG-AAGCT
* *
35255703 CGTGAGAGCTA
63 CATAAGAGCTA
35255714 TGGTATGTCC
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
73 4 0.06
74 3 0.05
75 52 0.83
76 4 0.06
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (75 bp):
TAATCGGGAAGCTCATGAGAGACAAATATCGGGAAGCTCATAAAGCCAAATAACAGGAAGCTCAT
AAGAGCTAAA
Found at i:35261758 original size:75 final size:75
Alignment explanation
Indices: 35261694--35261840 Score: 181
Period size: 75 Copynumber: 2.0 Consensus size: 75
35261684 AGCTTATATG
* *** *
35261694 AGCCAATTATCTAGAA-GCTCAAAAGAGC-CGTTAATCGGGAAGCTCATGAGAGCCAAATATCGG
1 AGCCAAATATC-AGAATGCTCAAAAGAGCTAAATAAT-GGAAAGCTCATGAGAGCCAAATATCGG
35261757 GAAGCTCATGAA
64 GAAGCTCATGAA
* * *
35261769 AGCCAAATATCGGAATGCTCATAAGAGCTAAATAATGGAAAGCTCGTGAGAGCCAAATATCGGGA
1 AGCCAAATATCAGAATGCTCAAAAGAGCTAAATAATGGAAAGCTCATGAGAGCCAAATATCGGGA
*
35261834 TGCTCAT
66 AGCTCAT
35261841 AAGAGCTAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
74 3 0.05
75 54 0.89
76 4 0.07
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (75 bp):
AGCCAAATATCAGAATGCTCAAAAGAGCTAAATAATGGAAAGCTCATGAGAGCCAAATATCGGGA
AGCTCATGAA
Found at i:35261852 original size:75 final size:75
Alignment explanation
Indices: 35261732--35261896 Score: 210
Period size: 75 Copynumber: 2.2 Consensus size: 75
35261722 CGTTAATCGG
* *
35261732 GAAGCTCATGAGAGCCAAATATCGGGAAGCTCATGAAAGCCAAATATC-GGAATGCTCATAAGAG
1 GAAGCTCGTGAGAGCCAAATATCGGGAAGCTCATGAAAGCCAAATAACGGGAA-GCTCATAAGAG
**
35261796 CTAAATAATGGA
65 CTAAAT-ATCAA
* * * *
35261808 -AAGCTCGTGAGAGCCAAATATCGGGATGCTCAT-AAGAGCTAAATAACGGGAAGCTCGTGAGAG
1 GAAGCTCGTGAGAGCCAAATATCGGGAAGCTCATGAA-AGCCAAATAACGGGAAGCTCATAAGAG
35261871 CTAAATATCAA
65 CTAAATATCAA
35261882 GAAGCTCGTGAGAGC
1 GAAGCTCGTGAGAGC
35261897 TATAGTGTGT
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
74 5 0.06
75 69 0.88
76 4 0.05
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (75 bp):
GAAGCTCGTGAGAGCCAAATATCGGGAAGCTCATGAAAGCCAAATAACGGGAAGCTCATAAGAGC
TAAATATCAA
Found at i:35261897 original size:25 final size:25
Alignment explanation
Indices: 35261727--35261898 Score: 186
Period size: 25 Copynumber: 6.9 Consensus size: 25
35261717 AGAGCCGTTA
*
35261727 ATCGGGAAGCTCATGAGAGCCAAAT
1 ATCGGGAAGCTCATGAGAGCTAAAT
* *
35261752 ATCGGGAAGCTCATGAAAGCCAAAT
1 ATCGGGAAGCTCATGAGAGCTAAAT
*
35261777 ATC-GGAATGCTCATAAGAGCTAAAT
1 ATCGGGAA-GCTCATGAGAGCTAAAT
* * *
35261802 AAT-GGAAAGCTCGTGAGAGCCAAAT
1 -ATCGGGAAGCTCATGAGAGCTAAAT
* *
35261827 ATCGGGATGCTCATAAGAGCTAAAT
1 ATCGGGAAGCTCATGAGAGCTAAAT
* *
35261852 AACGGGAAGCTCGTGAGAGCTAAAT
1 ATCGGGAAGCTCATGAGAGCTAAAT
** *
35261877 ATCAAGAAGCTCGTGAGAGCTA
1 ATCGGGAAGCTCATGAGAGCTA
35261899 TAGTGTGTTC
Statistics
Matches: 123, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
24 6 0.05
25 112 0.91
26 5 0.04
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (25 bp):
ATCGGGAAGCTCATGAGAGCTAAAT
Found at i:35270595 original size:3 final size:3
Alignment explanation
Indices: 35270587--35270638 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
35270577 AGAATAACAT
35270587 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35270635 TAA T
1 TAA T
35270639 CTAAGGTTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:35272950 original size:5 final size:5
Alignment explanation
Indices: 35272940--35272976 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
35272930 AAAAATCTTG
35272940 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA
35272977 TATGATGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:35296764 original size:23 final size:23
Alignment explanation
Indices: 35296729--35296773 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
35296719 TCTTATTTAA
**
35296729 TTCAAATTGATTAT-AATATTATT
1 TTCAAATAAATTATCAA-ATTATT
35296752 TTCAAATAAATTATCAAATTAT
1 TTCAAATAAATTATCAAATTAT
35296774 AAAATGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (23 bp):
TTCAAATAAATTATCAAATTATT
Found at i:35298392 original size:92 final size:91
Alignment explanation
Indices: 35298235--35298443 Score: 269
Period size: 92 Copynumber: 2.3 Consensus size: 91
35298225 TTGATTTTAG
* * *
35298235 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
35298300 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
* *
35298327 TAAATTCATATAAGAAAATTTATTATCAAGAGTTTTATGAAAATTA-ATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATG-AAATTATATA-TAACTATTAAATTA
35298391 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
35298419 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
35298444 GTTATAATTA
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
91 23 0.22
92 77 0.75
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:35298406 original size:24 final size:25
Alignment explanation
Indices: 35298371--35298418 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
35298361 TTATGAAAAT
35298371 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
35298395 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
35298419 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:35298573 original size:66 final size:63
Alignment explanation
Indices: 35298489--35298707 Score: 190
Period size: 66 Copynumber: 3.5 Consensus size: 63
35298479 TTTAATTAAA
*
35298489 ATATATGATATATTAATTATTTCAAATTTTCATTTATAGTATCATATATTATGATTTGAGTAAAT
1 ATATAAGA-ATATTAATTATTT-AAATTTT-ATTTA-AGTATCATATATTATGATTTGAGTAAAT
35298554 TC
62 TC
* * * *
35298556 ATATAAGAATATTAATTATTAAGAATTTTA-TTAA--ATTATATATT-TTAATT-A-T-AA-T-
1 ATATAAGAATATTAATTATTTA-AATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTC
** *
35298611 ATAT-TTAATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATAAGAATATTAATTAT-TTAAATTT-TA-TTTA-AGTATCATATATTATGATTTGAGTAAAT
35298674 TC
62 TC
*
35298676 ATATAAGAATATTAATTATTAAGAATTTTATT
1 ATATAAGAATATTAATTATTTA-AATTTTATT
35298708 AAATTATATA
Statistics
Matches: 119, Mismatches: 16, Indels: 36
0.70 0.09 0.21
Matches are distributed among these distances:
53 5 0.04
54 13 0.11
55 5 0.04
56 4 0.03
57 3 0.03
58 1 0.01
59 10 0.08
60 8 0.07
61 10 0.08
62 1 0.01
63 3 0.03
64 4 0.03
65 9 0.08
66 31 0.26
67 12 0.10
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (63 bp):
ATATAAGAATATTAATTATTTAAATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTC
Found at i:35298583 original size:120 final size:120
Alignment explanation
Indices: 35298459--35298751 Score: 468
Period size: 120 Copynumber: 2.4 Consensus size: 120
35298449 AATTATTTTA
* * *
35298459 AATTTTATTAAATCATATATTTTAATTAAAATATATGAT-ATATTAATTAT-TTCAAATTT-TCA
1 AATTTTATTAAATTATATATTTTAATTATAATATAT-ATAATAATAATTATGTT--AATTTAT-A
*
35298521 -TTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
62 TTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
35298579 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATATAATAATAATTATGTTAATTTATATTTT
35298644 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
35298699 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATATAATAATAATTATGTT
35298752 TAAATATGAT
Statistics
Matches: 164, Mismatches: 5, Indels: 8
0.93 0.03 0.05
Matches are distributed among these distances:
119 7 0.04
120 155 0.95
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATATAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:35298619 original size:15 final size:15
Alignment explanation
Indices: 35298584--35298635 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
35298574 TTAAGAATTT
*
35298584 TATTAAATTAT-ATA
1 TATTTAATTATAATA
35298598 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
35298612 TATTTAATAATAAT-
1 TATTTAATTATAATA
35298626 TATGTTAATT
1 TAT-TTAATT
35298636 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:35298734 original size:16 final size:16
Alignment explanation
Indices: 35298713--35298754 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
35298703 TTATTAAATT
*
35298713 ATATATTTTAATTATA
1 ATATATTTTAATAATA
35298729 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
35298744 AT-TATGTTTAA
1 ATATAT-TTTAA
35298755 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:35298739 original size:15 final size:15
Alignment explanation
Indices: 35298704--35298745 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
35298694 TTAAGAATTT
*
35298704 TATTAAATTAT-ATA
1 TATTTAATTATAATA
35298718 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
35298732 TATTTAATAATAAT
1 TATTTAATTATAAT
35298746 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:35298866 original size:157 final size:157
Alignment explanation
Indices: 35298688--35299004 Score: 580
Period size: 157 Copynumber: 2.0 Consensus size: 157
35298678 ATAAGAATAT
* *
35298688 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATATTT
* *
35298753 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
35298818 TAATAATTTACCAAAACAAATTTTTGC
131 TAATAATTTACCAAAACAAATTTATGC
35298845 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATATTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATATTT
35298910 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
35298975 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
35299002 TAA
1 TAA
35299005 GGGTATTCTA
Statistics
Matches: 154, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 154 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATATTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:35298885 original size:18 final size:18
Alignment explanation
Indices: 35298857--35298907 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
35298847 ATTATTAAGA
35298857 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
35298874 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
*
35298890 A-TTTAATAATAATTATAT
1 ATTTTAATTA-AATTATAT
35298908 TTAAATATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 7 0.24
16 7 0.24
17 5 0.17
18 10 0.34
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:35299152 original size:16 final size:16
Alignment explanation
Indices: 35299127--35299162 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
35299117 GATTTGCTAT
*
35299127 TACACTTCTAATCCAA
1 TACACCTCTAATCCAA
35299143 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
35299159 TACA
1 TACA
35299163 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:35300757 original size:26 final size:26
Alignment explanation
Indices: 35300728--35300779 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
35300718 AAAATGTACG
35300728 TGGATGAGTACAAGAGAGAGTTTATT
1 TGGATGAGTACAAGAGAGAGTTTATT
35300754 TGGATGAGTACAAGAGAGAGTTTATT
1 TGGATGAGTACAAGAGAGAGTTTATT
35300780 AGACTTAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.31, T:0.31
Consensus pattern (26 bp):
TGGATGAGTACAAGAGAGAGTTTATT
Found at i:35302702 original size:46 final size:46
Alignment explanation
Indices: 35302635--35302819 Score: 325
Period size: 46 Copynumber: 4.0 Consensus size: 46
35302625 ACATTGCTAT
* *
35302635 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
* * *
35302681 AACTCAGTATGGTTTTCTTCACTGAAACACCATACATACTTTTCAT
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
35302727 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
35302773 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
35302819 A
1 A
35302820 CTTTGCCATG
Statistics
Matches: 132, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 132 1.00
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
Found at i:35304091 original size:16 final size:16
Alignment explanation
Indices: 35304051--35304092 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
35304041 TTTTAAATCG
*
35304051 CAAAAATCCACTAAAT
1 CAAAAATTCACTAAAT
*
35304067 CACAAAATTCACTAATT
1 CA-AAAATTCACTAAAT
35304084 CAAAAATTC
1 CAAAAATTC
35304093 TTCTAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (16 bp):
CAAAAATTCACTAAAT
Found at i:35308646 original size:19 final size:19
Alignment explanation
Indices: 35308622--35308663 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
35308612 CGAAATTTGG
35308622 AATAAATAAATAATAAA-AT
1 AATAAA-AAATAATAAATAT
*
35308641 AATAAAACATAATAAATAT
1 AATAAAAAATAATAAATAT
35308660 AATA
1 AATA
35308664 TTGGACTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AATAAAAAATAATAAATAT
Found at i:35309039 original size:24 final size:24
Alignment explanation
Indices: 35309007--35309054 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
35308997 ATCAAAATAG
35309007 AATGATTTTCATTCTCATCTTCTT
1 AATGATTTTCATTCTCATCTTCTT
35309031 AATGATTTTCATTCTCATCTTCTT
1 AATGATTTTCATTCTCATCTTCTT
35309055 CTCTGAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.04, T:0.54
Consensus pattern (24 bp):
AATGATTTTCATTCTCATCTTCTT
Found at i:35310192 original size:19 final size:19
Alignment explanation
Indices: 35310170--35310211 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
35310160 AATTCATGAA
35310170 CATTTAACTAA-TATCATAT
1 CATTTAACTAATTATCA-AT
* *
35310189 CATTTCAGTAATTATCAAT
1 CATTTAACTAATTATCAAT
35310208 CATT
1 CATT
35310212 CATATTCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43
Consensus pattern (19 bp):
CATTTAACTAATTATCAAT
Found at i:35310843 original size:15 final size:16
Alignment explanation
Indices: 35310823--35310854 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
35310813 TACTTTAACA
35310823 CCCATTT-CCCCATTT
1 CCCATTTCCCCCATTT
35310838 CCCATTTCCCCCATTT
1 CCCATTTCCCCCATTT
35310854 C
1 C
35310855 TCGTTTACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.12, C:0.50, G:0.00, T:0.38
Consensus pattern (16 bp):
CCCATTTCCCCCATTT
Found at i:35310952 original size:17 final size:17
Alignment explanation
Indices: 35310930--35310969 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 17
35310920 CCTTCACCTT
35310930 CACCTCCGGCACCAATC
1 CACCTCCGGCACCAATC
*
35310947 CACCT-C--CACCGATC
1 CACCTCCGGCACCAATC
35310961 CACCTCCGG
1 CACCTCCGG
35310970 TCCTCCACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 6
0.73 0.04 0.23
Matches are distributed among these distances:
14 12 0.63
15 1 0.05
16 1 0.05
17 5 0.26
ACGTcount: A:0.20, C:0.55, G:0.12, T:0.12
Consensus pattern (17 bp):
CACCTCCGGCACCAATC
Found at i:35313024 original size:24 final size:24
Alignment explanation
Indices: 35312997--35313044 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
35312987 GGAATTTTAA
*
35312997 GTTTTAAATTGTTTAAACTGAATT
1 GTTTTAAATTGTTTAAACTCAATT
35313021 GTTTTAAATTGTTTAAACTCAATT
1 GTTTTAAATTGTTTAAACTCAATT
35313045 TTTAAGTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.50
Consensus pattern (24 bp):
GTTTTAAATTGTTTAAACTCAATT
Found at i:35321934 original size:16 final size:17
Alignment explanation
Indices: 35321913--35321948 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
35321903 ATAAAAATAG
35321913 AAATATCTT-TACATTT
1 AAATATCTTATACATTT
*
35321929 AAATATTTTATACATTT
1 AAATATCTTATACATTT
35321946 AAA
1 AAA
35321949 AAAAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATATCTTATACATTT
Found at i:35326489 original size:15 final size:14
Alignment explanation
Indices: 35326460--35326523 Score: 58
Period size: 15 Copynumber: 4.5 Consensus size: 14
35326450 ATATAAAATA
*
35326460 GGTTCACAC-GAAG
1 GGTTCACACATAAG
35326473 GGTTCACACATACAG
1 GGTTCACACATA-AG
* *
35326488 GGTTCTCACATATG
1 GGTTCACACATAAG
* *
35326502 GGTTCTCACATGTAG
1 GGTTCACACAT-AAG
35326517 GGTTCAC
1 GGTTCAC
35326524 TGTAACACTC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
13 9 0.21
14 13 0.31
15 20 0.48
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (14 bp):
GGTTCACACATAAG
Found at i:35326506 original size:14 final size:15
Alignment explanation
Indices: 35326471--35326512 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
35326461 GTTCACACGA
*
35326471 AGGGTTCACACATAC
1 AGGGTTCTCACATAC
35326486 AGGGTTCTCACATA-
1 AGGGTTCTCACATAC
*
35326500 TGGGTTCTCACAT
1 AGGGTTCTCACAT
35326513 GTAGGGTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (15 bp):
AGGGTTCTCACATAC
Found at i:35328452 original size:15 final size:15
Alignment explanation
Indices: 35328432--35328470 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
35328422 CATTGACACT
*
35328432 TATAGGGTT-TGCACG
1 TATAGGGTTAT-CACA
35328447 TATAGGGTTATCACA
1 TATAGGGTTATCACA
35328462 TATAGGGTT
1 TATAGGGTT
35328471 CGAATATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 21 0.95
16 1 0.05
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.36
Consensus pattern (15 bp):
TATAGGGTTATCACA
Found at i:35328557 original size:16 final size:16
Alignment explanation
Indices: 35328538--35328620 Score: 64
Period size: 16 Copynumber: 5.4 Consensus size: 16
35328528 TCGCATTCAT
*
35328538 GGGTTCGCATGTAAGG
1 GGGTTCGCATGCAAGG
* *
35328554 GGGTTCACAT--ATGG
1 GGGTTCGCATGCAAGG
* *
35328568 GGGTCCGCATGCAAGA
1 GGGTTCGCATGCAAGG
* *
35328584 GGGTTCACTTGCAAGG
1 GGGTTCGCATGCAAGG
* *
35328600 GGGTTCGC-TACAAGA
1 GGGTTCGCATGCAAGG
35328615 GGGTTC
1 GGGTTC
35328621 ACATATGGGA
Statistics
Matches: 52, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
14 11 0.21
15 11 0.21
16 30 0.58
ACGTcount: A:0.20, C:0.18, G:0.39, T:0.23
Consensus pattern (16 bp):
GGGTTCGCATGCAAGG
Found at i:35328618 original size:15 final size:16
Alignment explanation
Indices: 35328579--35328622 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
35328569 GGTCCGCATG
*
35328579 CAAGAGGGTTCACTTG
1 CAAGAGGGTTCACTTA
* *
35328595 CAAGGGGGTTCGC-TA
1 CAAGAGGGTTCACTTA
35328610 CAAGAGGGTTCAC
1 CAAGAGGGTTCAC
35328623 ATATGGGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.20
Consensus pattern (16 bp):
CAAGAGGGTTCACTTA
Found at i:35330144 original size:16 final size:17
Alignment explanation
Indices: 35330114--35330146 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
35330104 TAGAAAATAT
35330114 TTTTATTATACTAATTA
1 TTTTATTATACTAATTA
*
35330131 TTTT-TTATAGTAATTA
1 TTTTATTATACTAATTA
35330147 ATATTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (17 bp):
TTTTATTATACTAATTA
Found at i:35331149 original size:30 final size:29
Alignment explanation
Indices: 35331088--35331150 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
35331078 TATATATATA
* * *
35331088 TATTTTTAATTTTTAAAACTTTTAATCAT
1 TATTTGTAATTTTTAAAACTCTTAATAAT
*
35331117 TATTTGTAATTTCTTATAACTCTTAATAAT
1 TATTTGTAATTT-TTAAAACTCTTAATAAT
35331147 TATT
1 TATT
35331151 AAATAATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (29 bp):
TATTTGTAATTTTTAAAACTCTTAATAAT
Found at i:35331157 original size:11 final size:10
Alignment explanation
Indices: 35331139--35331229 Score: 55
Period size: 10 Copynumber: 9.0 Consensus size: 10
35331129 CTTATAACTC
*
35331139 TTAATAATTA
1 TTAAAAATTA
35331149 TTAAATAATTA
1 TTAAA-AATTA
35331160 -TATAAAATTA
1 TTA-AAAATTA
35331170 TTTAAAAATTA
1 -TTAAAAATTA
* *
35331181 TTAAGAGTTA
1 TTAAAAATTA
35331191 -TAAGAAATTA
1 TTAA-AAATTA
* *
35331201 -CAAATAATGA
1 TTAAA-AATTA
*
35331211 TTAAAAGTT-
1 TTAAAAATTA
35331220 TTAAAAATTA
1 TTAAAAATTA
35331230 AAAAAAAATA
Statistics
Matches: 62, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
9 12 0.19
10 31 0.50
11 17 0.27
12 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:35335354 original size:79 final size:77
Alignment explanation
Indices: 35335216--35335371 Score: 240
Period size: 79 Copynumber: 2.0 Consensus size: 77
35335206 ATGGAAATTA
* *
35335216 ATATTATTTTGGAAAGAATATATTTCATTTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAA
1 ATATTATTTTGGAAAAAATATATTCCATTTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAA
35335281 GGGAATAATCCT
66 GGGAATAATCCT
* * * *
35335293 ATATTCTTTTGGAAAAAATATAATTCCTTTTTTTTTCTAGCTTTTCATTTGCCTTCTCTATTAAT
1 ATATTATTTTGGAAAAAATAT-ATTCC-ATTTTTTTCTAACTTTCCATTTGCCTTCTCTATTAAT
35335358 AAGGGAATAATCCT
64 AAGGGAATAATCCT
35335372 GATTTTCCCT
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
77 19 0.27
78 4 0.06
79 48 0.68
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (77 bp):
ATATTATTTTGGAAAAAATATATTCCATTTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAA
GGGAATAATCCT
Found at i:35347028 original size:52 final size:52
Alignment explanation
Indices: 35346966--35347069 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
35346956 TGAGATTTCA
35346966 CTACGAACGTAATATAATACCATAGAAATTAAATAAATATTAAAATAATAAT
1 CTACGAACGTAATATAATACCATAGAAATTAAATAAATATTAAAATAATAAT
35347018 CTACGAACGTAATATAATACCATAGAAATTAAATAAATATTAAAATAATAAT
1 CTACGAACGTAATATAATACCATAGAAATTAAATAAATATTAAAATAATAAT
35347070 TTACTCATCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.56, C:0.10, G:0.06, T:0.29
Consensus pattern (52 bp):
CTACGAACGTAATATAATACCATAGAAATTAAATAAATATTAAAATAATAAT
Found at i:35348431 original size:10 final size:11
Alignment explanation
Indices: 35348411--35348436 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35348401 CTAAATAAAA
35348411 TTTTTCTTTTT
1 TTTTTCTTTTT
35348422 TTTTTCTTTTT
1 TTTTTCTTTTT
35348433 TTTT
1 TTTT
35348437 AACCTTAAAG
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:35354037 original size:43 final size:43
Alignment explanation
Indices: 35353971--35354125 Score: 167
Period size: 43 Copynumber: 3.7 Consensus size: 43
35353961 AACTCGTACA
35353971 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCATATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCATATATCG
* ** * *
35354014 ATGCCACTGTCCCAGACAG-GGTCTTACA-CAAATGAAATA-CG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACATGTAATCATATATCG
* * *
35354055 ATGCCAATGTCCCAGACATGGTCTTTCATGTCCA-CATA-AGTCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGT-AATCATATA-TCG
*
35354098 ATGCCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAATGTCCCAGACGTGGTCTTACA
35354126 CGAAAACACA
Statistics
Matches: 90, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
41 27 0.30
42 9 0.10
43 53 0.59
44 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCATATATCG
Found at i:35354069 original size:41 final size:43
Alignment explanation
Indices: 35353971--35354079 Score: 134
Period size: 41 Copynumber: 2.6 Consensus size: 43
35353961 AACTCGTACA
** *
35353971 ATGCCAATGTCCCAGAC-GTGGTCTTACATGTAATCATATATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACATCAAATCAAATATCG
* *
35354014 ATGCCACTGTCCCAGACAGGGTCTTACA-CAAATGAAATA-CG
1 ATGCCAATGTCCCAGACAGGGTCTTACATCAAATCAAATATCG
*
35354055 ATGCCAATGTCCCAGACATGGTCTT
1 ATGCCAATGTCCCAGACAGGGTCTT
35354080 TCATGTCCAC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
41 25 0.43
42 7 0.12
43 25 0.43
44 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACATCAAATCAAATATCG
Found at i:35354112 original size:84 final size:84
Alignment explanation
Indices: 35353971--35354126 Score: 221
Period size: 84 Copynumber: 1.9 Consensus size: 84
35353961 AACTCGTACA
*
35353971 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCATATATCGATGCCACTGTCCCAGACAG-GG
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCATATATCGATGCCACTGTCCCAGAC-GTGG
35354035 TCTTACACAAATGAAATACG
65 TCTTACACAAATGAAATACG
* *
35354055 ATGCCAATGTCCCAGACATGGTCTTTCATGTCCA-CATA-AGTCGATGCCAAC-GTCCCAGACGT
1 ATGCCAATGTCCCAGACATGGTCTTACATGT-AATCATATA-TCGATGCC-ACTGTCCCAGACGT
35354117 GGTCTTACAC
63 GGTCTTACAC
35354127 GAAAACACAG
Statistics
Matches: 65, Mismatches: 3, Indels: 8
0.86 0.04 0.11
Matches are distributed among these distances:
83 2 0.03
84 60 0.92
85 3 0.05
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (84 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGTAATCATATATCGATGCCACTGTCCCAGACGTGGT
CTTACACAAATGAAATACG
Found at i:35355298 original size:14 final size:15
Alignment explanation
Indices: 35355279--35355307 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
35355269 TCATGAAACT
35355279 TTCACACAT-ATAAA
1 TTCACACATAATAAA
35355293 TTCACACATAATAAA
1 TTCACACATAATAAA
35355308 CACAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:35361510 original size:27 final size:26
Alignment explanation
Indices: 35361467--35361541 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
35361457 TCATCCCAAA
*
35361467 TTTA-CCCCAGTAAAATTTTTGACGAT
1 TTTACCCCCAATAAAA-TTTTGACGAT
* *
35361493 TTTACCCCCAATATAATTTTGATGAT
1 TTTACCCCCAATAAAATTTTGACGAT
* *
35361519 TTTACCCCTCGATAAAGTTTTGA
1 TTTACCCC-CAATAAAATTTTGA
35361542 GAAAATTCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 21 0.51
27 20 0.49
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (26 bp):
TTTACCCCCAATAAAATTTTGACGAT
Found at i:35372848 original size:32 final size:32
Alignment explanation
Indices: 35372812--35372872 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
35372802 AATGAAATGT
35372812 ATGGGCTGCTATGAACATATATGATATTCAGA
1 ATGGGCTGCTATGAACATATATGATATTCAGA
35372844 ATGGGCTGCTATGAACATATATGATATTC
1 ATGGGCTGCTATGAACATATATGATATTC
35372873 GGATAGGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (32 bp):
ATGGGCTGCTATGAACATATATGATATTCAGA
Found at i:35376108 original size:38 final size:37
Alignment explanation
Indices: 35376066--35376167 Score: 123
Period size: 37 Copynumber: 2.7 Consensus size: 37
35376056 ACAATCTACT
* ** *
35376066 TTAAGATTTCTACCTAAGATTTTAAGATCGTAACTCCC
1 TTAAGGTTTCTACCTAA-ACCTTAAGATCGCAACTCCC
* * *
35376104 TTAAGGTTTCTACCCAAACCTTAAGATTGCAACTTCC
1 TTAAGGTTTCTACCTAAACCTTAAGATCGCAACTCCC
*
35376141 TTATGGTTTCTACCTAAACCTTAAGAT
1 TTAAGGTTTCTACCTAAACCTTAAGAT
35376168 ACAACCCTCT
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
37 40 0.73
38 15 0.27
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (37 bp):
TTAAGGTTTCTACCTAAACCTTAAGATCGCAACTCCC
Found at i:35377196 original size:11 final size:11
Alignment explanation
Indices: 35377180--35377206 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
35377170 TAGAATTTTC
35377180 AAAAATTATAA
1 AAAAATTATAA
35377191 AAAAATTATAA
1 AAAAATTATAA
35377202 AAAAA
1 AAAAA
35377207 ACAACAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:35377485 original size:19 final size:18
Alignment explanation
Indices: 35377445--35377515 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
35377435 AATTTTATAA
*
35377445 AATTTTTA-ATAATTTTC
1 AATTTTTATATTATTTTC
* *
35377462 TATTTTTAATATTATTTGC
1 AATTTTT-ATATTATTTTC
*
35377481 AATTTTTATACTTTTTTTC
1 AATTTTTATA-TTATTTTC
35377500 AA-TTTTATATTATTTT
1 AATTTTTATATTATTTT
35377516 AAATAAGTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
17 12 0.27
18 11 0.25
19 21 0.48
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (18 bp):
AATTTTTATATTATTTTC
Found at i:35377515 original size:18 final size:19
Alignment explanation
Indices: 35377445--35377515 Score: 62
Period size: 18 Copynumber: 3.9 Consensus size: 19
35377435 AATTTTATAA
*
35377445 AATTTTTA-ATAATTTT-C
1 AATTTTTATATTATTTTGC
*
35377462 TATTTTTAATATTA-TTTGC
1 AATTTTT-ATATTATTTTGC
*
35377481 AATTTTTATACTT-TTTTTC
1 AATTTTTATA-TTATTTTGC
35377500 AA-TTTTATATTATTTT
1 AATTTTTATATTATTTT
35377516 AAATAAGTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
17 8 0.18
18 18 0.41
19 18 0.41
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (19 bp):
AATTTTTATATTATTTTGC
Found at i:35377576 original size:18 final size:18
Alignment explanation
Indices: 35377555--35377618 Score: 67
Period size: 18 Copynumber: 3.5 Consensus size: 18
35377545 TTCCTTTTTA
35377555 TAATTTTTTTGAAAATTC
1 TAATTTTTTTGAAAATTC
* * *
35377573 TAATTCTTTT-ACAATTTT
1 TAATTTTTTTGA-AAATTC
*
35377591 TATAATTTTTTGAAAATTC
1 TA-ATTTTTTTGAAAATTC
35377610 TAATTTTTT
1 TAATTTTTT
35377619 AAATAATTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
17 1 0.03
18 21 0.60
19 12 0.34
20 1 0.03
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.59
Consensus pattern (18 bp):
TAATTTTTTTGAAAATTC
Found at i:35377609 original size:37 final size:35
Alignment explanation
Indices: 35377549--35377701 Score: 139
Period size: 37 Copynumber: 4.1 Consensus size: 35
35377539 TATTTTTTCC
35377549 TTTTTATAATTTTTTTGAAAATTCTAATTCTTTTACAA
1 TTTTTATAA-TTTTTTGAAAATTCTAATT-TTTTA-AA
35377587 TTTTTATAATTTTTTGAAAATTCTAATTTTTTAAATAA
1 TTTTTATAATTTTTTGAAAATTCTAATTTTTT--A-AA
* *
35377625 TTTTCTATTATTTTTTAGATAAATTTCCATATATTTTTAAA
1 TTTT-TATAATTTTTT-GA-AAA-TTCTA-AT-TTTTTAAA
* *
35377666 TTTTTATAA--TTTTAAAAATTCTATTTTTTTGAAA
1 TTTTTATAATTTTTTGAAAATTCTAATTTTTT-AAA
35377700 TT
1 TT
35377702 CTAATTATTT
Statistics
Matches: 99, Mismatches: 7, Indels: 22
0.77 0.05 0.17
Matches are distributed among these distances:
33 5 0.05
34 6 0.06
35 4 0.04
36 7 0.07
37 20 0.20
38 20 0.20
39 10 0.10
40 6 0.06
41 9 0.09
42 5 0.05
43 2 0.02
44 5 0.05
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (35 bp):
TTTTTATAATTTTTTGAAAATTCTAATTTTTTAAA
Found at i:35377613 original size:17 final size:17
Alignment explanation
Indices: 35377559--35377618 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
35377549 TTTTTATAAT
35377559 TTTTTTGAAAATTCTAA
1 TTTTTTGAAAATTCTAA
* *
35377576 TTCTTTT-ACAATTTTTATAA
1 TT-TTTTGA-AA--ATTCTAA
35377596 TTTTTTGAAAATTCTAA
1 TTTTTTGAAAATTCTAA
35377613 TTTTTT
1 TTTTTT
35377619 AAATAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 14 0.41
18 6 0.18
19 6 0.18
20 8 0.24
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (17 bp):
TTTTTTGAAAATTCTAA
Found at i:35377638 original size:77 final size:77
Alignment explanation
Indices: 35377549--35377700 Score: 179
Period size: 77 Copynumber: 2.0 Consensus size: 77
35377539 TATTTTTTCC
* * *
35377549 TTTTTATAATTTTTTTGA-AAA-TTCTA-AT-TCTTTTACAATTTTTATAATTTTTTGAAAATTC
1 TTTTTATAATTTTTTAGATAAATTTCCATATAT-TTTTA-AATTTTTATAA--TTTTAAAAATTC
35377610 TAATTTTTT-AAATAA
62 TAATTTTTTGAAATAA
* *
35377625 TTTTCTATTATTTTTTAGATAAATTTCCATATATTTTTAAATTTTTATAATTTTAAAAATTCTAT
1 TTTT-TATAATTTTTTAGATAAATTTCCATATATTTTTAAATTTTTATAATTTTAAAAATTCTAA
35377690 TTTTTTGAAAT
65 TTTTTTGAAAT
35377701 TCTAATTATT
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
76 4 0.06
77 31 0.48
78 7 0.11
79 15 0.23
80 7 0.11
81 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.59
Consensus pattern (77 bp):
TTTTTATAATTTTTTAGATAAATTTCCATATATTTTTAAATTTTTATAATTTTAAAAATTCTAAT
TTTTTGAAATAA
Found at i:35377659 original size:23 final size:22
Alignment explanation
Indices: 35377612--35377666 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
35377602 GAAAATTCTA
* *
35377612 ATTTTTTAAATAATTTTCTATT
1 ATTTTTTAAATAAATTTCCATT
*
35377634 ATTTTTTAGATAAATTTCCA-T
1 ATTTTTTAAATAAATTTCCATT
35377655 ATATTTTTAAAT
1 AT-TTTTTAAAT
35377667 TTTTATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (22 bp):
ATTTTTTAAATAAATTTCCATT
Found at i:35377951 original size:2 final size:2
Alignment explanation
Indices: 35377944--35377990 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
35377934 CATAGGCTTT
35377944 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35377986 TA TA T
1 TA TA T
35377991 TAANNNNNNN
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35378678 original size:10 final size:10
Alignment explanation
Indices: 35378660--35378711 Score: 59
Period size: 10 Copynumber: 4.9 Consensus size: 10
35378650 CCAAAAATTT
35378660 ATTTTAAAAA
1 ATTTTAAAAA
*
35378670 ATTTAAAAAA
1 ATTTTAAAAA
35378680 ATTTTAAAAA
1 ATTTTAAAAA
*
35378690 GTATTTTAAAAGT
1 --ATTTTAAAA-A
35378703 ATTTTAAAA
1 ATTTTAAAA
35378712 TTAAAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
10 18 0.50
11 9 0.25
12 9 0.25
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (10 bp):
ATTTTAAAAA
Found at i:35378685 original size:11 final size:11
Alignment explanation
Indices: 35378660--35378711 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
35378650 CCAAAAATTT
35378660 ATTTT-AAAAA
1 ATTTTAAAAAA
35378670 A-TTTAAAAAA
1 ATTTTAAAAAA
*
35378680 ATTTTAAAAAGT
1 ATTTTAAAAA-A
**
35378692 ATTTTAAAAGT
1 ATTTTAAAAAA
35378703 ATTTTAAAA
1 ATTTTAAAA
35378712 TTAAAAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
9 3 0.08
10 7 0.19
11 18 0.49
12 9 0.24
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (11 bp):
ATTTTAAAAAA
Found at i:35378777 original size:41 final size:40
Alignment explanation
Indices: 35378667--35378778 Score: 147
Period size: 41 Copynumber: 2.8 Consensus size: 40
35378657 TTTATTTTAA
** *
35378667 AAAATTTAAAAAAATTTTAAAAAGTATTTTAAAAGTATTTT
1 AAAA-TTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTT
35378708 AAAATTAAAAATTAA-TAAAAAAAGTATTTTAAAAATATTTT
1 AAAATTAAAAA--AATTAAAAAAAGTATTTTAAAAATATTTT
35378749 AAAATTAAAAAAATTAAAAAAA-TATATTTA
1 AAAATTAAAAAAATTAAAAAAAGTAT-TTTA
35378779 TTATATCGGC
Statistics
Matches: 64, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
39 5 0.08
40 19 0.30
41 38 0.59
42 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (40 bp):
AAAATTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTT
Found at i:35379014 original size:30 final size:31
Alignment explanation
Indices: 35378969--35379028 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
35378959 AGAGGTGGGA
*
35378969 TGGGAAGGGAATAAAAGTTTTAGG-GGAAAAG
1 TGGGAAGGGAATAAAAATTTT-GGAGGAAAAG
*
35379000 TGGG-AGGGAGTAAAAATTTTGGAGGAAAA
1 TGGGAAGGGAATAAAAATTTTGGAGGAAAA
35379029 TAAAATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 2 0.08
30 20 0.77
31 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGGAGGAAAAG
Found at i:35385323 original size:22 final size:22
Alignment explanation
Indices: 35385298--35385343 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
35385288 GTTGTTTCTT
35385298 TTAGTCCTATGTTCAAGCTTTG
1 TTAGTCCTATGTTCAAGCTTTG
*
35385320 TTAGTCCTATGTTCGAGCTTTG
1 TTAGTCCTATGTTCAAGCTTTG
35385342 TT
1 TT
35385344 GTACGTAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.48
Consensus pattern (22 bp):
TTAGTCCTATGTTCAAGCTTTG
Found at i:35391523 original size:20 final size:19
Alignment explanation
Indices: 35391479--35391522 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
35391469 GTAACAATCG
35391479 TTTTTTATTATTTTTTTAA
1 TTTTTTATTATTTTTTTAA
*
35391498 ATTTTTATTTATTTTTTT-A
1 TTTTTTA-TTATTTTTTTAA
35391517 TTTTTT
1 TTTTTT
35391523 TTCCAAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTATTATTTTTTTAA
Found at i:35403165 original size:114 final size:114
Alignment explanation
Indices: 35402953--35403182 Score: 415
Period size: 114 Copynumber: 2.0 Consensus size: 114
35402943 CTATAATTAG
35402953 TCATTTCTACAATTTAGCCAAGTAAGTTCATAGTGATTTGTTATTTAATATAATTCACTTGTGAT
1 TCATTTCTACAATTTAGCCAAGTAAGTTCATAGTGATTTGTTATTTAATATAATTCACTTGTGAT
*
35403018 TATTATTTTTTCTCTAATTATTTGATTTATATATATGTGAAATTACTTC
66 TATTATTTTTTCTCTAATTAATTGATTTATATATATGTGAAATTACTTC
* *
35403067 TCATTTCTACAATTTAGCTAGGTAAGTTCATAGTGATTTGTTATTTAATATAATTCACTTGTGAT
1 TCATTTCTACAATTTAGCCAAGTAAGTTCATAGTGATTTGTTATTTAATATAATTCACTTGTGAT
35403132 TATTATTTTTGTTCTCTAATTAATTGATTTATATATATGTGAAATTACTTC
66 TATTA-TTTT-TTCTCTAATTAATTGATTTATATATATGTGAAATTACTTC
35403183 GGTTATTTAT
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
114 68 0.61
115 4 0.04
116 39 0.35
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (114 bp):
TCATTTCTACAATTTAGCCAAGTAAGTTCATAGTGATTTGTTATTTAATATAATTCACTTGTGAT
TATTATTTTTTCTCTAATTAATTGATTTATATATATGTGAAATTACTTC
Found at i:35403399 original size:20 final size:20
Alignment explanation
Indices: 35403348--35403452 Score: 60
Period size: 20 Copynumber: 5.2 Consensus size: 20
35403338 TACTTCGGTA
*
35403348 CCCCTGAATGCACATTTG-TG
1 CCCCTGAATGCAC-TTCGATG
* **
35403368 CCCTTGTTTGCACTTCGATG
1 CCCCTGAATGCACTTCGATG
35403388 CCCCTGAATGCACATAT-G-TG
1 CCCCTGAATGCAC-T-TCGATG
*
35403408 CCCCT-AATTGCA-TTTGAATG
1 CCCCTGAA-TGCACTTCG-ATG
*
35403428 CCCCTGATTGCACTTC-AGTG
1 CCCCTGAATGCACTTCGA-TG
35403448 CCCCT
1 CCCCT
35403453 ATTATACATC
Statistics
Matches: 66, Mismatches: 9, Indels: 20
0.69 0.09 0.21
Matches are distributed among these distances:
17 1 0.02
18 2 0.03
19 6 0.09
20 51 0.77
21 5 0.08
22 1 0.02
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.31
Consensus pattern (20 bp):
CCCCTGAATGCACTTCGATG
Found at i:35403419 original size:40 final size:40
Alignment explanation
Indices: 35403325--35403455 Score: 131
Period size: 40 Copynumber: 3.3 Consensus size: 40
35403315 AAATGAAGAA
* * * * *
35403325 GTGCCCCTGTTTGTACTTCGGTACCCCTGAATGCACATTT
1 GTGCCCCTATTTGCACTTCGATGCCCCTGAATGCACATAT
* *
35403365 GTGCCCTTGTTTGCACTTCGATGCCCCTGAATGCACATAT
1 GTGCCCCTATTTGCACTTCGATGCCCCTGAATGCACATAT
* * * *
35403405 GTGCCCCTAATTGCA-TTTGAATGCCCCTGATTGCACTTCA-
1 GTGCCCCTATTTGCACTTCG-ATGCCCCTGAATGCACAT-AT
35403445 GTGCCCCTATT
1 GTGCCCCTATT
35403456 ATACATCTAT
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 3 0.04
40 73 0.95
41 1 0.01
ACGTcount: A:0.17, C:0.31, G:0.19, T:0.34
Consensus pattern (40 bp):
GTGCCCCTATTTGCACTTCGATGCCCCTGAATGCACATAT
Found at i:35404342 original size:33 final size:33
Alignment explanation
Indices: 35404302--35404376 Score: 150
Period size: 33 Copynumber: 2.3 Consensus size: 33
35404292 TGATGCCTTG
35404302 ATGGTTGGTATGCTTTTGGCACTTTGATACTTA
1 ATGGTTGGTATGCTTTTGGCACTTTGATACTTA
35404335 ATGGTTGGTATGCTTTTGGCACTTTGATACTTA
1 ATGGTTGGTATGCTTTTGGCACTTTGATACTTA
35404368 ATGGTTGGT
1 ATGGTTGGT
35404377 GTTGTATGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.17, C:0.11, G:0.27, T:0.45
Consensus pattern (33 bp):
ATGGTTGGTATGCTTTTGGCACTTTGATACTTA
Found at i:35408367 original size:67 final size:65
Alignment explanation
Indices: 35408241--35408533 Score: 253
Period size: 67 Copynumber: 4.4 Consensus size: 65
35408231 ATAGGCTGTA
** * * * *****
35408241 ATGGGGTATAATGTGTAAGACCATAGCTCAGCTATGGTAGCAGAGAGAGTTTGTTAGAACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTC-GCTATGACAACATAG-GAATCCACCAGAACATTAA
35408306 AC
64 AC
* * *
35408308 ATGGGGTATAATGTGTAAGACCATAGCTATGCTACGATAACATAGCGAATCCACCAGAACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCT-CGCTATGACAACATAG-GAATCCACCAGAACATTAA
35408373 AC
64 AC
* * * * * *
35408375 ATGGGGTATAATGCGTAAGACCATAGCTCGGCTATGGCAACATAGAAAGTCCGCTAGGACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTC-GCTATGACAACATAGGAA-TCCACCAGAACATTAA
*
35408440 AT
64 AC
* * * ** *
35408442 ATCGGGTATAAAGTGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCTTCCAGGACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCG-CTATGACAACATAG-GAATCCACCAGAACATTAA
35408507 AC
64 AC
* * *
35408509 ATGGGGTATGATGAGTAAAACCATA
1 ATGGGGTATAATGTGTAAGACCATA
35408534 ACTTAGTGAT
Statistics
Matches: 184, Mismatches: 37, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
66 3 0.02
67 180 0.98
68 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (65 bp):
ATGGGGTATAATGTGTAAGACCATAGCTCGCTATGACAACATAGGAATCCACCAGAACATTAAAC
Found at i:35408484 original size:134 final size:134
Alignment explanation
Indices: 35408241--35408533 Score: 354
Period size: 134 Copynumber: 2.2 Consensus size: 134
35408231 ATAGGCTGTA
* * * * ** *
35408241 ATGGGGTATAATGTGTAAGACCATAGCTCAGCTATGGTAGCAGAGAGAGTTTGTTAGAACATTAA
1 ATGGGGTATAATGAGTAAGACCATAGCTCAGCTATGGCAACAGAGAAAGTCCGCTAGAACATTAA
* * * * *
35408306 ACATGGGGTATAATGTGTAAGACCATAGCTATGCTACGATAACATAGCGAATCCACCAGAACATT
66 ACATCGGGTATAAAGTGTAAGACCATAGCTACGCTACGACAACATAGAGAATCCACCAGAACATT
35408371 AAAC
131 AAAC
* * * *
35408375 ATGGGGTATAATGCGTAAGACCATAGCTCGGCTATGGCAACATAGAAAGTCCGCTAGGACATTAA
1 ATGGGGTATAATGAGTAAGACCATAGCTCAGCTATGGCAACAGAGAAAGTCCGCTAGAACATTAA
* * * ** *
35408440 ATATCGGGTATAAAGTGTAAGACCATAGCT-CGACTATGACAACATAGAGAGTCTTCCAGGACAT
66 ACATCGGGTATAAAGTGTAAGACCATAGCTACG-CTACGACAACATAGAGAATCCACCAGAACAT
35408504 TAAAC
130 TAAAC
* *
35408509 ATGGGGTATGATGAGTAAAACCATA
1 ATGGGGTATAATGAGTAAGACCATA
35408534 ACTTAGTGAT
Statistics
Matches: 134, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
133 1 0.01
134 133 0.99
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (134 bp):
ATGGGGTATAATGAGTAAGACCATAGCTCAGCTATGGCAACAGAGAAAGTCCGCTAGAACATTAA
ACATCGGGTATAAAGTGTAAGACCATAGCTACGCTACGACAACATAGAGAATCCACCAGAACATT
AAAC
Found at i:35408560 original size:134 final size:134
Alignment explanation
Indices: 35408241--35408574 Score: 321
Period size: 134 Copynumber: 2.5 Consensus size: 134
35408231 ATAGGCTGTA
* * * * * * * **** *
35408241 ATGGGGTATAATGTGTAAGACCATAGCTCAGCTATGGTAGCAGAGAGAGTTTGTTAGAACATTAA
1 ATGGGGTATAATGAGTAAAACCATAACTCAGCTATGGCAACATAGAAAGTCCACTAGGACATTAA
* * * * *
35408306 ACATGGGGTATAATGTGTAAGACCATAGCTATGCTACGATAACATAGCGAATCCACCAGAACATT
66 ACATCGGGTATAAAGTGTAAGACCATAGCTACGCTACGACAACATAGAGAATCCACCAGAACATT
35408371 AAAC
131 AAAC
* * * * *
35408375 ATGGGGTATAATGCGTAAGACCATAGCTCGGCTATGGCAACATAGAAAGTCCGCTAGGACATTAA
1 ATGGGGTATAATGAGTAAAACCATAACTCAGCTATGGCAACATAGAAAGTCCACTAGGACATTAA
* * * ** *
35408440 ATATCGGGTATAAAGTGTAAGACCATAGCT-CGACTATGACAACATAGAGAGTCTTCCAGGACAT
66 ACATCGGGTATAAAGTGTAAGACCATAGCTACG-CTACGACAACATAGAGAATCCACCAGAACAT
35408504 TAAAC
130 TAAAC
* * * * * *
35408509 ATGGGGTATGATGAGTAAAACCATAACTTAG-TGATGGCAGCATATAGAGTCCACTGGGACAATT
1 ATGGGGTATAATGAGTAAAACCATAACTCAGCT-ATGGCAACATAGAAAGTCCACTAGGAC-ATT
35408573 AA
64 AA
35408575 CGCAGGGTAG
Statistics
Matches: 165, Mismatches: 32, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
133 2 0.01
134 158 0.96
135 5 0.03
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (134 bp):
ATGGGGTATAATGAGTAAAACCATAACTCAGCTATGGCAACATAGAAAGTCCACTAGGACATTAA
ACATCGGGTATAAAGTGTAAGACCATAGCTACGCTACGACAACATAGAGAATCCACCAGAACATT
AAAC
Found at i:35412263 original size:62 final size:60
Alignment explanation
Indices: 35412157--35412274 Score: 166
Period size: 62 Copynumber: 1.9 Consensus size: 60
35412147 ATCACTTTAA
* * * *
35412157 TATTAAATTTAATCTAATATTTATGAAGATAAATATTTAATTTAATTTAATATTAAATCT
1 TATTAAATTTAATATAATATTTATCAAGATAAACATTAAATTTAATTTAATATTAAATCT
35412217 TATTAAA-TTAATATAATATTTATCTACAAGATAAACATTAAATTTAATTTAATATTAA
1 TATTAAATTTAATATAATATTTA--T-CAAGATAAACATTAAATTTAATTTAATATTAA
35412275 GATAATCACT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
59 14 0.27
60 7 0.14
61 1 0.02
62 29 0.57
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (60 bp):
TATTAAATTTAATATAATATTTATCAAGATAAACATTAAATTTAATTTAATATTAAATCT
Found at i:35418546 original size:24 final size:23
Alignment explanation
Indices: 35418502--35418546 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
35418492 GGGCCGAGAG
* *
35418502 CAGGTTATAAAAACAATGCGTAT
1 CAGGTTAAAAAAACAAAGCGTAT
*
35418525 CAGGTTAAATAAAATAAAGCGT
1 CAGGTTAAA-AAAACAAAGCGT
35418547 TTCATAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (23 bp):
CAGGTTAAAAAAACAAAGCGTAT
Found at i:35425789 original size:21 final size:21
Alignment explanation
Indices: 35425756--35425799 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
35425746 CACTCATTTC
* * *
35425756 TTTTTTCAGAATTAATTTTAT
1 TTTTTTAAAAATTAATTTCAT
*
35425777 TTTTTTAAAAATTGATTTCAT
1 TTTTTTAAAAATTAATTTCAT
35425798 TT
1 TT
35425800 ACGAAAAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (21 bp):
TTTTTTAAAAATTAATTTCAT
Found at i:35426040 original size:22 final size:22
Alignment explanation
Indices: 35426006--35426047 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
35425996 AATTTTTCTA
35426006 TAAAAATCTAAATAATTCCATG
1 TAAAAATCTAAATAATTCCATG
*
35426028 TAAAACATC-AAATTATTCCA
1 TAAAA-ATCTAAATAATTCCA
35426048 CAAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAAATCTAAATAATTCCATG
Found at i:35438930 original size:2 final size:2
Alignment explanation
Indices: 35438923--35438966 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
35438913 CGTCGTGGAG
35438923 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
35438965 AT
1 AT
35438967 GATTGTTGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35439748 original size:28 final size:28
Alignment explanation
Indices: 35439693--35439748 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
35439683 TTCATAGGTA
* *
35439693 AAGAGGGAAGTCCATCAAGGAATCTCTT
1 AAGAAGGAAGTCCATCAAGGAATATCTT
* * *
35439721 AAGAAGGAAGTCCGTCGAGGACTATCTT
1 AAGAAGGAAGTCCATCAAGGAATATCTT
35439749 GGGTAGAAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.21
Consensus pattern (28 bp):
AAGAAGGAAGTCCATCAAGGAATATCTT
Found at i:35441595 original size:18 final size:19
Alignment explanation
Indices: 35441569--35441605 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
35441559 ATTGAAATAG
*
35441569 TTATTATTATTTT-GATTC
1 TTATAATTATTTTAGATTC
35441587 TTATAATTATTTTAGATTC
1 TTATAATTATTTTAGATTC
35441606 ACATGTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (19 bp):
TTATAATTATTTTAGATTC
Found at i:35443095 original size:43 final size:43
Alignment explanation
Indices: 35443043--35443269 Score: 226
Period size: 43 Copynumber: 5.3 Consensus size: 43
35443033 CTTTAGAAAT
*
35443043 AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCATCACCTTTAGCGGCGCTTTTCCCAC
* ** *
35443086 AAATGCCGCTATGGGTCATCACTTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCATCACCTTTAGCGGCGCTTTTCCCAC
* * * *
35443129 AAACGCCGCTATAGGTCATCACTTTTAGCAGCGTTTTTCCCAC
1 AAACGCCGCTAAAGGTCATCACCTTTAGCGGCGCTTTTCCCAC
** * * * **
35443172 AAACGCCGCTATAA-AACA-GATCTTTAGCGACGCTTTTTCGTAC
1 AAACGCCGCTA-AAGGTCATCACCTTTAGCGGCGC-TTTTCCCAC
* * * * *
35443215 AAACGCCGCTATAGGACA-AACCTTTAGCTGCGCTTTTCACAC
1 AAACGCCGCTAAAGGTCATCACCTTTAGCGGCGCTTTTCCCAC
35443257 AAACGCCGCTAAA
1 AAACGCCGCTAAA
35443270 AGCATATCTT
Statistics
Matches: 152, Mismatches: 29, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
42 29 0.19
43 122 0.80
44 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATCACCTTTAGCGGCGCTTTTCCCAC
Found at i:35443133 original size:86 final size:86
Alignment explanation
Indices: 35443043--35443281 Score: 252
Period size: 86 Copynumber: 2.8 Consensus size: 86
35443033 CTTTAGAAAT
* * * * ****
35443043 AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCACAAATGCCGCTATGGGTCATCA-
1 AAACGCCGCTATAGGTCATAACCTTTAGCAGCGCTTTTCCCACAAACGCCGCTATAAAACA-CAT
*
35443107 CTTTTAGCGGCGC-TTTTCCCAC
65 C-TTTAGCGACGCTTTTTCCCAC
* * * *
35443129 AAACGCCGCTATAGGTCATCACTTTTAGCAGCGTTTTTCCCACAAACGCCGCTATAAAACAGATC
1 AAACGCCGCTATAGGTCATAACCTTTAGCAGCGCTTTTCCCACAAACGCCGCTATAAAACACATC
**
35443194 TTTAGCGACGCTTTTTCGTAC
66 TTTAGCGACGCTTTTTCCCAC
* * * * *
35443215 AAACGCCGCTATAGGACA-AACCTTTAGCTGCGCTTTTCACACAAACGCCGCTA-AAAGCATATC
1 AAACGCCGCTATAGGTCATAACCTTTAGCAGCGCTTTTCCCACAAACGCCGCTATAAAACACATC
35443278 TTTA
66 TTTA
35443282 AAAAAATAAT
Statistics
Matches: 129, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
84 12 0.09
85 41 0.32
86 76 0.59
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (86 bp):
AAACGCCGCTATAGGTCATAACCTTTAGCAGCGCTTTTCCCACAAACGCCGCTATAAAACACATC
TTTAGCGACGCTTTTTCCCAC
Found at i:35443259 original size:85 final size:84
Alignment explanation
Indices: 35443109--35443281 Score: 222
Period size: 85 Copynumber: 2.0 Consensus size: 84
35443099 GGTCATCACT
* * * * * *
35443109 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGGTCATCACTTTTAGCAGCGTTTTTCCCACAA
1 TTTAGCGACGCTTTTCCCACAAACGCCGCTATAGGACATAACCTTTAGCAGCGCTTTTCACACAA
35443174 ACGCCGCTATAAAACAGATC
66 ACGCCGCTA-AAAACAGATC
** *
35443194 TTTAGCGACGCTTTTTCGTACAAACGCCGCTATAGGACA-AACCTTTAGCTGCGCTTTTCACACA
1 TTTAGCGACGC-TTTTCCCACAAACGCCGCTATAGGACATAACCTTTAGCAGCGCTTTTCACACA
* *
35443258 AACGCCGCTAAAAGCATATC
65 AACGCCGCTAAAAACAGATC
35443278 TTTA
1 TTTA
35443282 AAAAAATAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
84 12 0.16
85 40 0.53
86 24 0.32
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (84 bp):
TTTAGCGACGCTTTTCCCACAAACGCCGCTATAGGACATAACCTTTAGCAGCGCTTTTCACACAA
ACGCCGCTAAAAACAGATC
Found at i:35443614 original size:43 final size:43
Alignment explanation
Indices: 35443537--35443620 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
35443527 ACATATGCAA
* * ** *
35443537 GGTAATAAAACATACAATGCATTTTCTTGGTCAAGTAAATCTT
1 GGTAATAAAACATACAATACATTTACTTAATCAAGGAAATCTT
* *
35443580 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATC
1 GGTAATAAAACATACAATACATTTACTTAATCAAGGAAATC
35443621 GTGTAATGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (43 bp):
GGTAATAAAACATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:35446094 original size:3 final size:3
Alignment explanation
Indices: 35446086--35446123 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
35446076 AAAGTATCGC
35446086 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
35446124 TTAGTGTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:35446868 original size:20 final size:21
Alignment explanation
Indices: 35446820--35446872 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
35446810 GGGGGTTTCA
*
35446820 AGGGGGAAAATTAGGGATTTT
1 AGGGGGAAAATTAGGGATATT
* *
35446841 AGGGGGAAAGTTGGGGATATT
1 AGGGGGAAAATTAGGGATATT
35446862 A-GGGGAAAATT
1 AGGGGGAAAATT
35446873 TATAAAATGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.34, C:0.00, G:0.42, T:0.25
Consensus pattern (21 bp):
AGGGGGAAAATTAGGGATATT
Found at i:35447886 original size:20 final size:21
Alignment explanation
Indices: 35447848--35447888 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
35447838 CCTAACCCCT
*
35447848 AACCCCTAAACCTTAAATCTC
1 AACCCCTAAACCATAAATCTC
*
35447869 AACCCTTAAACCAT-AATCTC
1 AACCCCTAAACCATAAATCTC
35447889 TAGTCCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.37, G:0.00, T:0.24
Consensus pattern (21 bp):
AACCCCTAAACCATAAATCTC
Found at i:35448049 original size:297 final size:302
Alignment explanation
Indices: 35447699--35448305 Score: 931
Period size: 311 Copynumber: 2.0 Consensus size: 302
35447689 CAATATATTT
*
35447699 AATTTATTATTATCTCTTTTACAATTATATAAGAACATGTTTAAAATATAAATTAAAAAAATAAT
1 AATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAAT
* *
35447764 TAATTTAAACCCAAAACCCTAACCCGACCCCTGAATCCCTAAACCTTAAATCCCTAGCTCTTAAC
66 TAATCTAAACCCAAAACCCTAACCCGACCCCTGAATCCCTAAACCCTAAATCCCTAGCTCTTAAC
* *
35447829 CCCTAA-C-A-T-C-CTAACCCCTAACCCCTAAACCTTAAATCTCAACCCTTAAACCATAAT-CT
131 CCCTAACCAACTACACTAACCCCTAACCCCTAAACCTTAAAACCCAACCCTTAAACCATAATCCT
* *
35447888 CTAGTCCATAATCCCTAAATCCATACCCCCTAAACCTTAAAATA-TGAACTCCTAAACCGGCCTT
196 -TAATCCATAATCCCTAAATCCATACCCCCTAAACCTTAAAATAGT-AACTCCTAAACCGACCTT
*
35447952 AAATCTTAAATTAATCATATAACCTAAACTAAAAACCCTAAACA
259 AAATCTTAAATAAATCATATAACCTAAACTAAAAACCCTAAACA
*
35447996 AATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTGAAATATAAATTAAAAAAATAAT
1 AATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAAT
**
35448061 TAATCTAAACCCAAAACCCTAACTTGACCCCTGAATCCCTAAACCCTAAATCCCTAGCTCTTAAC
66 TAATCTAAACCCAAAACCCTAACCCGACCCCTGAATCCCTAAACCCTAAATCCCTAGCTCTTAAC
*
35448126 CCCTAACGTCTAACCCCTAAACCACTAACCCCTAACCCCTAAACCTTAAAACCCAGCCCTTAAAC
131 CCCTAAC--C-AA---CT--A-CACTAACCCCTAACCCCTAAACCTTAAAACCCAACCCTTAAAC
* *
35448191 CATAATCCTTAATCCATAATCCCTAAATCCATACTCCCTAAACCTTAAACTAGTAACTCCTAAAC
187 CATAATCCTTAATCCATAATCCCTAAATCCATACCCCCTAAACCTTAAAATAGTAACTCCTAAAC
*
35448256 CGACCTTAAATCTTAAATAAATCATATACCCTAAACTAAAAACCCTAAAC
252 CGACCTTAAATCTTAAATAAATCATATAACCTAAACTAAAAACCCTAAAC
35448306 TATAGTGATA
Statistics
Matches: 279, Mismatches: 15, Indels: 18
0.89 0.05 0.06
Matches are distributed among these distances:
297 130 0.47
300 1 0.00
302 1 0.00
306 1 0.00
310 1 0.00
311 142 0.51
312 3 0.01
ACGTcount: A:0.41, C:0.29, G:0.03, T:0.27
Consensus pattern (302 bp):
AATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAAT
TAATCTAAACCCAAAACCCTAACCCGACCCCTGAATCCCTAAACCCTAAATCCCTAGCTCTTAAC
CCCTAACCAACTACACTAACCCCTAACCCCTAAACCTTAAAACCCAACCCTTAAACCATAATCCT
TAATCCATAATCCCTAAATCCATACCCCCTAAACCTTAAAATAGTAACTCCTAAACCGACCTTAA
ATCTTAAATAAATCATATAACCTAAACTAAAAACCCTAAACA
Found at i:35448145 original size:7 final size:7
Alignment explanation
Indices: 35448122--35448167 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
35448112 CCCTAGCTCT
35448122 TAACCCC
1 TAACCCC
**
35448129 TAACGTC
1 TAACCCC
35448136 TAACCCC
1 TAACCCC
*
35448143 TAAACCAC
1 T-AACCCC
35448151 TAACCCC
1 TAACCCC
35448158 TAACCCC
1 TAACCCC
35448165 TAA
1 TAA
35448168 ACCTTAAAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
7 26 0.81
8 6 0.19
ACGTcount: A:0.35, C:0.46, G:0.02, T:0.17
Consensus pattern (7 bp):
TAACCCC
Found at i:35448155 original size:15 final size:15
Alignment explanation
Indices: 35448122--35448160 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
35448112 CCCTAGCTCT
**
35448122 TAACCCCT-AACGTC
1 TAACCCCTAAACCAC
35448136 TAACCCCTAAACCAC
1 TAACCCCTAAACCAC
35448151 TAACCCCTAA
1 TAACCCCTAA
35448161 CCCCTAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.36, C:0.44, G:0.03, T:0.18
Consensus pattern (15 bp):
TAACCCCTAAACCAC
Found at i:35448200 original size:14 final size:14
Alignment explanation
Indices: 35448186--35448234 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
35448176 ACCCAGCCCT
*
35448186 TAAACCATAATCCT
1 TAAACCATAATCCC
*
35448200 TAATCCATAATCCC
1 TAAACCATAATCCC
*
35448214 TAAATCCATACTCCC
1 TAAA-CCATAATCCC
35448229 TAAACC
1 TAAACC
35448235 TTAAACTAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 17 0.57
15 13 0.43
ACGTcount: A:0.39, C:0.35, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAACCATAATCCC
Found at i:35448221 original size:15 final size:15
Alignment explanation
Indices: 35448186--35448232 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
35448176 ACCCAGCCCT
35448186 TAAA-CCATAAT-CC
1 TAAATCCATAATCCC
*
35448199 TTAATCCATAATCCC
1 TAAATCCATAATCCC
*
35448214 TAAATCCATACTCCC
1 TAAATCCATAATCCC
35448229 TAAA
1 TAAA
35448233 CCTTAAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 3 0.10
14 7 0.24
15 19 0.66
ACGTcount: A:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:35448466 original size:23 final size:25
Alignment explanation
Indices: 35448439--35448493 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
35448429 TAAATAATAG
*
35448439 TATTTTAATT-TTTCCATGTGTT-T
1 TATTTTAATTATTTCCACGTGTTAT
* *
35448462 TATTTCAAATTATTTCTACGTGTTAT
1 TATTT-TAATTATTTCCACGTGTTAT
35448488 TATTTT
1 TATTTT
35448494 TTCTGAAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 5 0.20
24 4 0.16
25 10 0.40
26 6 0.24
ACGTcount: A:0.22, C:0.09, G:0.07, T:0.62
Consensus pattern (25 bp):
TATTTTAATTATTTCCACGTGTTAT
Found at i:35448622 original size:41 final size:41
Alignment explanation
Indices: 35448577--35448895 Score: 350
Period size: 41 Copynumber: 7.8 Consensus size: 41
35448567 TAAAATGTTT
* *
35448577 TTAGCGGCTCTTTTTCAAAAACGCTGCTAAAACCCCGAGCA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* ** *
35448618 TTAGCGGCACTTTTTTAAAAAATACCGCTAAAATCCCGAGCA
1 TTAGCGGCAC-TTTTTCAAAAACGCCGCTAAAACCCCGAGCA
** * *
35448660 TTAGCGGTGCTTTTTAAAAAACGCCGCTAAAACACCGAGCA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* * * *
35448701 TTAGCGACACTTTTTCAAAAACGCCGCTAAAGCCCCCAACA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* *
35448742 TTAGCGGCACCTTTTCAAAAACGCCGCTAAAACCCCAAGCA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* * * ** * *
35448783 CTAGCGGCGCTTTTTAAAAAATACCGCTAAAACACCGAACA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* ** * *
35448824 TTAGTGGTGCTTTTTCAAAAGCGCCGCTAAAACCCCAAGCA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* * *
35448865 TTAGCGGCGCATTTTCAAAAACGTCGCTAAA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAA
35448896 GCCCTGAAAG
Statistics
Matches: 228, Mismatches: 49, Indels: 2
0.82 0.18 0.01
Matches are distributed among these distances:
41 194 0.85
42 34 0.15
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (41 bp):
TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
Found at i:35448826 original size:123 final size:122
Alignment explanation
Indices: 35448577--35448895 Score: 386
Period size: 123 Copynumber: 2.6 Consensus size: 122
35448567 TAAAATGTTT
* * * * * * **
35448577 TTAGCGGCTCTTTTTCAAAAACGCTGCTAAAACCCCGAGCATTAGCGGCACTTTTTTAAAAAATA
1 TTAGCGGCACTTTTTCAAAAACGCCGCT-AAACCCCCAACATTAGCGGCAC-ATTTTCAAAAACG
* * * * * *
35448642 CCGCTAAAATCCCGAGCATTAGCGGTGCTTTTTAAAAAACGCCGCTAAAACACCGAGCA
64 CCGCTAAAACCCCAAGCACTAGCGGCGCTTTTTAAAAAACACCGCTAAAACACCGAACA
* *
35448701 TTAGCGACACTTTTTCAAAAACGCCGCTAAAGCCCCCAACATTAGCGGCACCTTTTCAAAAACGC
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAA-CCCCCAACATTAGCGGCACATTTTCAAAAACGC
*
35448766 CGCTAAAACCCCAAGCACTAGCGGCGCTTTTTAAAAAATACCGCTAAAACACCGAACA
65 CGCTAAAACCCCAAGCACTAGCGGCGCTTTTTAAAAAACACCGCTAAAACACCGAACA
* ** * * * *
35448824 TTAGTGGTGCTTTTTCAAAAGCGCCGCTAAAACCCCAAGCATTAGCGGCGCATTTTCAAAAACGT
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAACCCCCAA-CATTAGCGGCACATTTTCAAAAACGC
35448889 CGCTAAA
65 CGCTAAA
35448896 GCCCTGAAAG
Statistics
Matches: 168, Mismatches: 25, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
122 6 0.04
123 120 0.71
124 42 0.25
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (122 bp):
TTAGCGGCACTTTTTCAAAAACGCCGCTAAACCCCCAACATTAGCGGCACATTTTCAAAAACGCC
GCTAAAACCCCAAGCACTAGCGGCGCTTTTTAAAAAACACCGCTAAAACACCGAACA
Found at i:35448997 original size:39 final size:40
Alignment explanation
Indices: 35448934--35449012 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 40
35448924 TGGGCTTTGG
* *
35448934 TTTTTTGCGGCGTTTTTCTGAAAAACGCCGCGAATGCTCA
1 TTTTTAGCGGCGTTTTTCTAAAAAACGCCGCGAATGCTCA
* *
35448974 TTTTTAGCGGTGTTTTTC-AAAAAACGCCGCTAATGCTCA
1 TTTTTAGCGGCGTTTTTCTAAAAAACGCCGCGAATGCTCA
35449013 ATCTTTACTG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
39 19 0.54
40 16 0.46
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTCTAAAAAACGCCGCGAATGCTCA
Found at i:35452404 original size:36 final size:35
Alignment explanation
Indices: 35452324--35452443 Score: 134
Period size: 36 Copynumber: 3.4 Consensus size: 35
35452314 ACTCTCTATT
* * *
35452324 TGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCATC
1 TGGTGTGTTTTGGATGGATTAGCTCTT-TGAGCATC
* *
35452360 -AGTGTGTTTTGGATGGATTGGCTCGTTTGAGCATC
1 TGGTGTGTTTTGGATGGATTAGCTC-TTTGAGCATC
* * *
35452395 TGGTGTGTTTTGGAGGGATTAGCTCATGTGATCATC
1 TGGTGTGTTTTGGATGGATTAGCTC-TTTGAGCATC
35452431 TGGTGTGTTTTGG
1 TGGTGTGTTTTGG
35452444 TTGATCTGAC
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
35 27 0.38
36 44 0.62
ACGTcount: A:0.13, C:0.12, G:0.34, T:0.41
Consensus pattern (35 bp):
TGGTGTGTTTTGGATGGATTAGCTCTTTGAGCATC
Found at i:35453090 original size:22 final size:22
Alignment explanation
Indices: 35453030--35453087 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
35453020 AATCTTCAAG
35453030 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
35453049 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
35453071 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
35453088 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:35453335 original size:23 final size:23
Alignment explanation
Indices: 35453291--35453335 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
35453281 TCTTATTTTG
* *
35453291 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
35453314 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
35453336 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:35453693 original size:38 final size:38
Alignment explanation
Indices: 35453616--35453693 Score: 88
Period size: 38 Copynumber: 2.0 Consensus size: 38
35453606 CATACATACG
*
35453616 TTTTATAATATATACATATACGTACACATTTTTTAATTT
1 TTTTATAATATATACATATACG-ACACATTTTATAATTT
* *
35453655 TTTTATAA-ATATATATATAC-ACATACTTTTATATATTT
1 TTTTATAATATATACATATACGACACA-TTTTATA-ATTT
35453693 T
1 T
35453694 CTATGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
36 4 0.12
37 6 0.18
38 16 0.47
39 8 0.24
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.53
Consensus pattern (38 bp):
TTTTATAATATATACATATACGACACATTTTATAATTT
Found at i:35453822 original size:23 final size:22
Alignment explanation
Indices: 35453795--35453837 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
35453785 TAATTCACAC
*
35453795 ACATATATATTTTTCTTATATGT
1 ACATATATATATTT-TTATATGT
35453818 ACATATATATATTTTTATAT
1 ACATATATATATTTTTATAT
35453838 TTTATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (22 bp):
ACATATATATATTTTTATATGT
Found at i:35462078 original size:19 final size:18
Alignment explanation
Indices: 35462032--35462080 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
35462022 GATAGAATTT
*
35462032 TTGTCATAAAATAATTAAT
1 TTGT-ATAAAATAATTAAA
*
35462051 TTTTATAAAATAATTAAA
1 TTGTATAAAATAATTAAA
35462069 TTGTATTAAAAT
1 TTGTA-TAAAAT
35462081 TTTGAACATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (18 bp):
TTGTATAAAATAATTAAA
Found at i:35466100 original size:35 final size:36
Alignment explanation
Indices: 35466060--35466212 Score: 146
Period size: 36 Copynumber: 4.3 Consensus size: 36
35466050 ACTTTATGTT
** *
35466060 TGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCATC
1 TGGTGTGTTTCGGAGGGACTAGCTCGTATGAGCATC
* * * *
35466096 -GGTGTGTTTTGGAGGGATTGGCTCGTGTGAGCATC
1 TGGTGTGTTTCGGAGGGACTAGCTCGTATGAGCATC
** * * *
35466131 TGGTGTGTTTTAGAGGGATTGGCTCGTGTGAGCATC
1 TGGTGTGTTTCGGAGGGACTAGCTCGTATGAGCATC
* * * * *
35466167 TGGTGTGTTTTGGAGGGATTGGCTCGTGTGATCATC
1 TGGTGTGTTTCGGAGGGACTAGCTCGTATGAGCATC
35466203 TGGTGTGTTT
1 TGGTGTGTTT
35466213 TGGTTGATTT
Statistics
Matches: 106, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
35 28 0.26
36 78 0.74
ACGTcount: A:0.12, C:0.12, G:0.38, T:0.39
Consensus pattern (36 bp):
TGGTGTGTTTCGGAGGGACTAGCTCGTATGAGCATC
Found at i:35466139 original size:36 final size:36
Alignment explanation
Indices: 35466088--35466215 Score: 231
Period size: 36 Copynumber: 3.6 Consensus size: 36
35466078 CTAGCTCTTA
35466088 TGAGCATC-GGTGTGTTTTGGAGGGATTGGCTCGTG
1 TGAGCATCTGGTGTGTTTTGGAGGGATTGGCTCGTG
*
35466123 TGAGCATCTGGTGTGTTTTAGAGGGATTGGCTCGTG
1 TGAGCATCTGGTGTGTTTTGGAGGGATTGGCTCGTG
35466159 TGAGCATCTGGTGTGTTTTGGAGGGATTGGCTCGTG
1 TGAGCATCTGGTGTGTTTTGGAGGGATTGGCTCGTG
*
35466195 TGATCATCTGGTGTGTTTTGG
1 TGAGCATCTGGTGTGTTTTGG
35466216 TTGATTTGAC
Statistics
Matches: 89, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 8 0.09
36 81 0.91
ACGTcount: A:0.12, C:0.11, G:0.40, T:0.38
Consensus pattern (36 bp):
TGAGCATCTGGTGTGTTTTGGAGGGATTGGCTCGTG
Found at i:35481099 original size:30 final size:31
Alignment explanation
Indices: 35481065--35481132 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 31
35481055 TTTGAGGGGA
*
35481065 TGAAAATCAAATTATATAT-TTTTATTATAG
1 TGAAAATCAAATTATATATATTTCATTATAG
*
35481095 TGAAAATTAAATTATATATATTTCATTATAG
1 TGAAAATCAAATTATATATATTTCATTATAG
*
35481126 TAAAAAT
1 TGAAAAT
35481133 ATAGTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 18 0.53
31 16 0.47
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (31 bp):
TGAAAATCAAATTATATATATTTCATTATAG
Found at i:35495723 original size:44 final size:43
Alignment explanation
Indices: 35495675--35496224 Score: 217
Period size: 44 Copynumber: 12.3 Consensus size: 43
35495665 AATAGATCAG
*
35495675 TGAAGCTACAAATTC-TATACCCTTGAAGTTGCAGTGGGTTAGAT
1 TGAAGCTACAAATTCTTAT-CCCCTGAAGTTGCAGTGGG-TAGAT
* * *
35495719 TGAAG-TCACCATAACGAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGAT
1 TGAAGCT-A-C--AA--ATTCTTATC-CCCTGAAGTTGCAGTGG-GTAGAT
* * *
35495769 CGAAGCTACAAA-TCTTATCCCCTAAAGTTGCAGTAGAGTAGAT
1 TGAAGCTACAAATTCTTATCCCCTGAAGTTGCAGT-GGGTAGAT
* * * * *
35495812 TGAAGCTAC-AAGTCCTACACCCCTGAAGTTGCAGTGGGATGGAC
1 TGAAGCTACAAATTCTTA-TCCCCTGAAGTTGCAGTGGG-TAGAT
* * * *
35495856 TGAATCTACCATAGCGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGAT
1 TGAAGCTA-CA-A---ATTCTTATC-CCCTGAAGTTGCAGTGG-GTAGAT
* ** * * **
35495906 CGAAGCTATGAA-TCTTATCTCCCTAAAGTTGTAGTGGACCAGAT
1 TGAAGCTACAAATTCTTATC-CCCTGAAGTTGCAGTGG-GTAGAT
* * * **
35495950 TGAAACTACAAA-TCTTATGTCCCTGAAGTTACAGTGAAATAGAT
1 TGAAGCTACAAATTCTTAT-CCCCTGAAGTTGCAGTG-GGTAGAT
* * *
35495994 TAAAGCTACAAA-TCTTATCTCCTTGAAGTTGCAGTGGAGCAGAT
1 TGAAGCTACAAATTCTTATC-CCCTGAAGTTGCAGTGG-GTAGAT
* * * * *
35496038 TGAAGCTACAAA-TCGTATCTCTCTAAAGTTGTAGTGGAGCAGAT
1 TGAAGCTACAAATTCTTATC-CCCTGAAGTTGCAGTGG-GTAGAT
* * *
35496082 TGAAG-TA-ATAAATCTTATCTCCTTGAAGTTGTAGTGGAGTAAGA-
1 TGAAGCTACA-AATTCTTATC-CCCTGAAGTTGCAGTGG-GT-AGAT
* * * *
35496126 TGAAGCTACAACTCCTATAT-CCCTAAAGTTGCAGTGGATCAGAT
1 TGAAGCTACAAATTCT-TATCCCCTGAAGTTGCAGTGGGT-AGAT
* * * * * * * * *
35496170 TAAAACTA-TAATTCCTATACCCCTGAGGTTACAATGGGTTAAAA
1 TGAAGCTACAAATTCTTAT-CCCCTGAAGTTGCAGTGGG-TAGAT
35496214 TGAAGCTACAA
1 TGAAGCTACAA
35496225 CAATAAATTT
Statistics
Matches: 385, Mismatches: 84, Indels: 73
0.71 0.15 0.13
Matches are distributed among these distances:
42 6 0.02
43 44 0.11
44 246 0.64
45 14 0.04
46 4 0.01
47 5 0.01
48 1 0.00
49 6 0.02
50 56 0.15
51 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (43 bp):
TGAAGCTACAAATTCTTATCCCCTGAAGTTGCAGTGGGTAGAT
Found at i:35495921 original size:137 final size:135
Alignment explanation
Indices: 35495675--35496086 Score: 490
Period size: 137 Copynumber: 3.0 Consensus size: 135
35495665 AATAGATCAG
* * *
35495675 TGAAGCTACAAATTCTATACCCTTGAAGTTGCAGTGGGTTAGATTGAAGTCACCATAACGAATCT
1 TGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGATAGA-TGAA-TCACCAT-ACGAATCT
* * *
35495740 TATCTCCCTGAAGTTGTAGTGGAGCAGATCGAAGCTACAAATCTTATC-CCCTAAAGTTGCAGTA
63 TATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTGTAGTG
*
35495804 GAGTAGAT
128 GAGCAGAT
* * *
35495812 TGAAGCTACAAGTCCTACACCCCTGAAGTTGCAGTGGGATGGACTGAATCTACCATAGCGAATCT
1 TGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGATAGA-TGAATC-ACCATA-CGAATCT
* **
35495877 TATCTCCCTAAAGTTGCAGTGGAGCAGATCGAAGCTATGAATCTTATCTCCCTAAAGTTGTAGTG
63 TATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTGTAGTG
*
35495942 GACCAGAT
128 GAGCAGAT
* * ** * ** * * *
35495950 TGAAACTACAAATCTTATGTCCCTGAAGTTACAGTGAAATAGATTAA--AGC-TACAAATCTTAT
1 TGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGATAGATGAATCACCATACGAATCTTAT
* * * *
35496012 CTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCGTATCTCTCTAAAGTTGTAGTGGAG
66 CTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTGTAGTGGAG
35496077 CAGAT
131 CAGAT
35496082 TGAAG
1 TGAAG
35496087 TAATAAATCT
Statistics
Matches: 235, Mismatches: 37, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
132 75 0.32
133 2 0.01
134 2 0.01
136 3 0.01
137 100 0.43
138 53 0.23
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (135 bp):
TGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGATAGATGAATCACCATACGAATCTTAT
CTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTGTAGTGGAG
CAGAT
Found at i:35496000 original size:88 final size:88
Alignment explanation
Indices: 35495735--35496180 Score: 380
Period size: 88 Copynumber: 5.0 Consensus size: 88
35495725 CACCATAACG
* * * *
35495735 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATCGAAGCTACAAATCTTATC-CCCTAAAGTTG
1 AATCTTATCTCCTTGAAGTTGTAGTGGACCAGATTGAAACTACAAATCTTATCTCCCTAAAGTTG
* * *
35495799 CAGTAGAGTAGATTGAAGCTACA
66 CAGTGGAGCAGATTGAAGCTATA
* * * * * ** * *
35495822 AGTCCTA-CACCCCTGAAGTTGCAGTGGGA-TGGACTGAATCTACCATAGCGAATCTTATCTCCC
1 AATCTTATC-TCCTTGAAGTTGTAGT-GGACCAGATTGAA---A-C-TA-CAAATCTTATCTCCC
* *
35495885 TAAAGTTGCAGTGGAGCAGATCGAAGCTATG
58 TAAAGTTGCAGTGGAGCAGATTGAAGCTATA
* * * * *
35495916 AATCTTATCTCCCTAAAGTTGTAGTGGACCAGATTGAAACTACAAATCTTATGTCCCTGAAGTTA
1 AATCTTATCTCCTTGAAGTTGTAGTGGACCAGATTGAAACTACAAATCTTATCTCCCTAAAGTTG
* ** * *
35495981 CAGTGAAATAGATTAAAGCTACA
66 CAGTGGAGCAGATTGAAGCTATA
* * * * *
35496004 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCGTATCTCTCTAAAGTTG
1 AATCTTATCTCCTTGAAGTTGTAGTGGACCAGATTGAAACTACAAATCTTATCTCCCTAAAGTTG
*
35496069 TAGTGGAGCAGATTGAAG-TAATA
66 CAGTGGAGCAGATTGAAGCT-ATA
** * * * *
35496092 AATCTTATCTCCTTGAAGTTGTAGTGGAGTAAGA-TGAAGCTACAACTCCTATATCCCTAAAGTT
1 AATCTTATCTCCTTGAAGTTGTAGTGGA-CCAGATTGAAACTACAAATCTTATCTCCCTAAAGTT
* * *
35496156 GCAGTGGATCAGATTAAAACTATA
65 GCAGTGGAGCAGATTGAAGCTATA
35496180 A
1 A
35496181 TTCCTATACC
Statistics
Matches: 284, Mismatches: 61, Indels: 27
0.76 0.16 0.07
Matches are distributed among these distances:
86 1 0.00
87 25 0.09
88 180 0.63
89 6 0.02
90 1 0.00
91 2 0.01
92 2 0.01
93 13 0.05
94 53 0.19
95 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (88 bp):
AATCTTATCTCCTTGAAGTTGTAGTGGACCAGATTGAAACTACAAATCTTATCTCCCTAAAGTTG
CAGTGGAGCAGATTGAAGCTATA
Found at i:35496057 original size:132 final size:132
Alignment explanation
Indices: 35495735--35496169 Score: 444
Period size: 132 Copynumber: 3.3 Consensus size: 132
35495725 CACCATAACG
* *
35495735 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATCGAAGCTACAAATCTTATC-CCCTAAAGTTG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTG
* * * * * * * * * * *
35495799 CAGTAGAGTAGATTGAAGCTACAAGTCCTACACCCCTGAAGTTGCAGTGGGATGGACTGAATCTA
66 TAGTGGAGCAGATTGAAACTACAAATCTTATATCCCTGAAGTTGCAGTGGAATAGA-TTAA---A
* *
35495864 CCATAGCG
127 GC-TA-CA
**
35495872 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATCGAAGCTATGAATCTTATCTCCCTAAAGTTG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTG
* * * *
35495937 TAGTGGACCAGATTGAAACTACAAATCTTATGTCCCTGAAGTTACAGTGAAATAGATTAAAGCTA
66 TAGTGGAGCAGATTGAAACTACAAATCTTATATCCCTGAAGTTGCAGTGGAATAGATTAAAGCTA
35496002 CA
131 CA
* * * * *
35496004 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCGTATCTCTCTAAAGTTG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTG
* * * * * * *
35496069 TAGTGGAGCAGATTG-AAGTAATAAATCTTATCTCCTTGAAGTTGTAGTGGAGTAAGA-TGAAGC
66 TAGTGGAGCAGATTGAAACT-ACAAATCTTATATCCCTGAAGTTGCAGTGGAAT-AGATTAAAGC
35496132 TACA
129 TACA
* * * *
35496136 ACTCCTATATCCCTAAAGTTGCAGTGGATCAGAT
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGAT
35496170 TAAAACTATA
Statistics
Matches: 251, Mismatches: 44, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
131 3 0.01
132 136 0.54
133 5 0.02
134 2 0.01
137 52 0.21
138 53 0.21
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (132 bp):
AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTG
TAGTGGAGCAGATTGAAACTACAAATCTTATATCCCTGAAGTTGCAGTGGAATAGATTAAAGCTA
CA
Found at i:35501296 original size:21 final size:20
Alignment explanation
Indices: 35501258--35501296 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35501248 TTGAAATGGA
*
35501258 AAATTGGACTCTATAATAAT
1 AAATTGGACTCTAAAATAAT
*
35501278 AAATTGGATTTCTAAAATA
1 AAATTGGA-CTCTAAAATA
35501297 TTTCCAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (20 bp):
AAATTGGACTCTAAAATAAT
Found at i:35510077 original size:16 final size:18
Alignment explanation
Indices: 35510051--35510083 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35510041 TAGAATTGAG
35510051 TTGAGAAAATTA-TTTAA
1 TTGAGAAAATTAGTTTAA
35510068 TTGA-AAAATTAGTTTA
1 TTGAGAAAATTAGTTTA
35510084 TCTAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAGTTTAA
Found at i:35511702 original size:62 final size:62
Alignment explanation
Indices: 35511605--35511731 Score: 236
Period size: 62 Copynumber: 2.0 Consensus size: 62
35511595 ATAGGGTCAA
*
35511605 TTTCACGACACAGGAAATTGGGGGTCCAACACTGACTGATGTCACGACATTGAGCTTCTGAT
1 TTTCACGACACAGGAAATTGGGGGTCCAACACTGACTGATGTCACGACATTGAGCTTCTAAT
*
35511667 TTTCATGACACAGGAAATTGGGGGTCCAACACTGACTGATGTCACGACATTGAGCTTCTAAT
1 TTTCACGACACAGGAAATTGGGGGTCCAACACTGACTGATGTCACGACATTGAGCTTCTAAT
35511729 TTT
1 TTT
35511732 GTGACGCCAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (62 bp):
TTTCACGACACAGGAAATTGGGGGTCCAACACTGACTGATGTCACGACATTGAGCTTCTAAT
Found at i:35513551 original size:39 final size:40
Alignment explanation
Indices: 35513489--35513574 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 40
35513479 CACTTAATAA
*
35513489 TTATAAAAAATTTGGAATAAAAAAATAAAATAAAAAGAGC
1 TTATAAAAAATTTGCAATAAAAAAATAAAATAAAAAGAGC
35513529 TTATAAAAAATTTGCAAT-AAAAAATAAAATAAAAAGAGC
1 TTATAAAAAATTTGCAATAAAAAAATAAAATAAAAAGAGC
35513568 TTATAAA
1 TTATAAA
35513575 TACAATATTG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 28 0.62
40 17 0.38
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.24
Consensus pattern (40 bp):
TTATAAAAAATTTGCAATAAAAAAATAAAATAAAAAGAGC
Found at i:35515449 original size:15 final size:15
Alignment explanation
Indices: 35515431--35515464 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
35515421 AGAAATGTCG
35515431 CAATAACAAATACAA
1 CAATAACAAATACAA
*
35515446 CAATAATAAATACAA
1 CAATAACAAATACAA
35515461 CAAT
1 CAAT
35515465 GGCATAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.65, C:0.18, G:0.00, T:0.18
Consensus pattern (15 bp):
CAATAACAAATACAA
Found at i:35515490 original size:13 final size:14
Alignment explanation
Indices: 35515471--35515508 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
35515461 CAATGGCATA
35515471 GAAATAATATAAAC
1 GAAATAATATAAAC
35515485 -AAATAA-ATAAAC
1 GAAATAATATAAAC
35515497 GAAACTAATATA
1 GAAA-TAATATA
35515509 CATAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 3 0.14
15 3 0.14
ACGTcount: A:0.66, C:0.08, G:0.05, T:0.21
Consensus pattern (14 bp):
GAAATAATATAAAC
Found at i:35517544 original size:63 final size:63
Alignment explanation
Indices: 35517455--35517580 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
35517445 GAAAACAAAG
*
35517455 AAAACAAATCACTACCTTTAATCTCTATTTTGTTTTTCTCTGCTTGATATTGTGAAAATACTC
1 AAAACAAATAACTACCTTTAATCTCTATTTTGTTTTTCTCTGCTTGATATTGTGAAAATACTC
35517518 AAAACAAATAACTACCTTTAATCTCTATTTTGTTTTTCTCTGCTTGATATTGTGAAAATACTC
1 AAAACAAATAACTACCTTTAATCTCTATTTTGTTTTTCTCTGCTTGATATTGTGAAAATACTC
35517581 GTTTTTTTAT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.43
Consensus pattern (63 bp):
AAAACAAATAACTACCTTTAATCTCTATTTTGTTTTTCTCTGCTTGATATTGTGAAAATACTC
Found at i:35520164 original size:195 final size:197
Alignment explanation
Indices: 35519824--35520221 Score: 674
Period size: 195 Copynumber: 2.0 Consensus size: 197
35519814 ATAATGTAAC
* *
35519824 AATTTATCTAATCATCATTTTGTTTAATTCACATCTCGTCAATTCAATTCATTGTTCAAATCATC
1 AATTTATCCAATCATCATTTTGTTTAATTCACATCTCATCAATTCAATTCATTG-----AT-ATC
*
35519889 AAATCATCACATAGCAAATTTTATTTCAACCCAATTCAAAGTTAATTCCATAATTTCATCGAATT
60 AAATCATCACATAGCAAATTTTATTTCAACCCAATTCAAAGTCAATTCCATAATTTCATCGAATT
*
35519954 TCACTATTTTCAATTCTATTTAATTTACTCCTCCATCTCAAAAATTAAACATTTAGATACTAATT
125 TCACTATTTTCAATTCTATTTAATTTACTCCTCCATCTCAAAAATTAAACATTTAGATACCAATT
35520019 CAATTCAA
190 CAATTCAA
35520027 AATTTATCCAATCATCATTTTGTTTAATTCACATCTCATCAATTCAATTCATTG-T-TCAAATCA
1 AATTTATCCAATCATCATTTTGTTTAATTCACATCTCATCAATTCAATTCATTGATATCAAATCA
35520090 TCACATAGCAAATTTTATTTCAACCCAATTCAAAGTCAATTCCATAATTTCATCGAATTTCACTA
66 TCACATAGCAAATTTTATTTCAACCCAATTCAAAGTCAATTCCATAATTTCATCGAATTTCACTA
* *
35520155 TTTTCAATTCTATTTAATTTAGTTCTCCATCTCAAAAATTAAACATTTAGATACCAATTCAATTC
131 TTTTCAATTCTATTTAATTTACTCCTCCATCTCAAAAATTAAACATTTAGATACCAATTCAATTC
35520220 AA
196 AA
35520222 CTAATCAATC
Statistics
Matches: 189, Mismatches: 6, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
195 136 0.72
197 1 0.01
203 52 0.28
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (197 bp):
AATTTATCCAATCATCATTTTGTTTAATTCACATCTCATCAATTCAATTCATTGATATCAAATCA
TCACATAGCAAATTTTATTTCAACCCAATTCAAAGTCAATTCCATAATTTCATCGAATTTCACTA
TTTTCAATTCTATTTAATTTACTCCTCCATCTCAAAAATTAAACATTTAGATACCAATTCAATTC
AA
Found at i:35524202 original size:2 final size:2
Alignment explanation
Indices: 35524190--35524221 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
35524180 AGTATGAATG
*
35524190 AT AT GT 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 AT AT AT
35524222 GTATGTATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35524484 original size:76 final size:78
Alignment explanation
Indices: 35524355--35524497 Score: 209
Period size: 76 Copynumber: 1.9 Consensus size: 78
35524345 TTGGACTTGG
* *
35524355 TTAAAGGTATGAATGTTATATATATGTATATGTGAGTTGGAACATATATGTATATACATGAATAA
1 TTAAAGGTATGAATGTTATATATATGTATATGTAAGTTCGAACATATATGTATATACATGAATAA
35524420 GTCTTGAATATAT
66 GTCTTGAATATAT
* * * * *
35524433 TTAAAGGTATGAATG-T-TATGTATGTATATGTAATTTCGAATATGTATGTATATACATGTATAA
1 TTAAAGGTATGAATGTTATATATATGTATATGTAAGTTCGAACATATATGTATATACATGAATAA
35524496 GT
66 GT
35524498 TTTTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
76 42 0.72
77 1 0.02
78 15 0.26
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.41
Consensus pattern (78 bp):
TTAAAGGTATGAATGTTATATATATGTATATGTAAGTTCGAACATATATGTATATACATGAATAA
GTCTTGAATATAT
Found at i:35528989 original size:28 final size:30
Alignment explanation
Indices: 35528957--35529017 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 30
35528947 TGATATTGAT
35528957 TTAGTTA-TTGATTAATATG-TTATGTT-TG
1 TTAGTTAGTTG-TTAATATGATTATGTTATG
* *
35528985 TTAGTTAGTTGTTTATATGATTTTGTTATG
1 TTAGTTAGTTGTTAATATGATTATGTTATG
35529015 TTA
1 TTA
35529018 TATTTGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 14 0.50
29 9 0.32
30 5 0.18
ACGTcount: A:0.23, C:0.00, G:0.18, T:0.59
Consensus pattern (30 bp):
TTAGTTAGTTGTTAATATGATTATGTTATG
Found at i:35529984 original size:45 final size:44
Alignment explanation
Indices: 35529916--35530088 Score: 147
Period size: 45 Copynumber: 3.9 Consensus size: 44
35529906 ATTGATTTGA
* *
35529916 GAAAAGGGAAAGACCATGATTGAAAGATA-TCATGGCATTATAATT
1 GAAAAGGAAAAGACCATGATTGAAAGATACT-ATGGCATTA-AATC
* *
35529961 GAAAAGGAAAAGAGCATGGTTGAAAGATACTATGGCATTAAATC
1 GAAAAGGAAAAGACCATGATTGAAAGATACTATGGCATTAAATC
* ** * * * *
35530005 GAAACGGGTAAGACCCT-AGTTGAAAGATACTACGGCACTATATC
1 GAAAAGGAAAAGACCATGA-TTGAAAGATACTATGGCATTAAATC
*
35530049 GAAAAACGATCAAA-ACCAT-AGTTGAAAGATACTATGGCAT
1 G-AAAAGGA--AAAGACCATGA-TTGAAAGATACTATGGCAT
35530089 CACTTTGGGA
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
44 38 0.37
45 39 0.38
46 24 0.23
47 2 0.02
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.21
Consensus pattern (44 bp):
GAAAAGGAAAAGACCATGATTGAAAGATACTATGGCATTAAATC
Found at i:35530034 original size:44 final size:44
Alignment explanation
Indices: 35529925--35530088 Score: 154
Period size: 44 Copynumber: 3.7 Consensus size: 44
35529915 AGAAAAGGGA
* * *
35529925 AAGACCAT-GATTGAAAGATA-TCATGGCATTATAATTGAAAAGGAA
1 AAGACCATAG-TTGAAAGATACT-ATGGCATTA-AATCGAAACGGAT
* * *
35529970 AAGAGCATGGTTGAAAGATACTATGGCATTAAATCGAAACGGGT
1 AAGACCATAGTTGAAAGATACTATGGCATTAAATCGAAACGGAT
* * * *
35530014 AAGACCCTAGTTGAAAGATACTACGGCACTATATCGAAAAAC-GAT
1 AAGACCATAGTTGAAAGATACTATGGCATTAAATCG--AAACGGAT
*
35530059 CAAAACCATAGTTGAAAGATACTATGGCAT
1 -AAGACCATAGTTGAAAGATACTATGGCAT
35530089 CACTTTGGGA
Statistics
Matches: 98, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
44 39 0.40
45 28 0.29
46 31 0.32
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.23
Consensus pattern (44 bp):
AAGACCATAGTTGAAAGATACTATGGCATTAAATCGAAACGGAT
Found at i:35534776 original size:14 final size:13
Alignment explanation
Indices: 35534759--35534788 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
35534749 TTAGTCTTTT
35534759 CTTCCAAAATTTCA
1 CTTCCAAAATTT-A
35534773 CTTCCAAAATTTA
1 CTTCCAAAATTTA
35534786 CTT
1 CTT
35534789 TATTGATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (13 bp):
CTTCCAAAATTTA
Done.