Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397270.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_55.0, whole genome shotgun sequence
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: 4719911
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 90628 characters in sequence are not A, C, G, or T
File 10 of 10
Found at i:4195973 original size:16 final size:16
Alignment explanation
Indices: 4195930--4195983 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
4195920 TATAATTTTA
*
4195930 TAATAA-TAATATAAT
1 TAATAATTAAAATAAT
4195945 TAATTATATTAAAA-AAT
1 TAA-TA-ATTAAAATAAT
4195962 ATAATAATTAAAATAAT
1 -TAATAATTAAAATAAT
4195979 TAATA
1 TAATA
4195984 TAATGTCTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
15 3 0.09
16 14 0.42
17 9 0.27
18 7 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATAATTAAAATAAT
Found at i:4224774 original size:29 final size:28
Alignment explanation
Indices: 4224708--4224774 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
4224698 ATTATACCCG
4224708 ATTAATTTTTATTTTATCCAATTGAATT
1 ATTAATTTTTATTTTATCCAATTGAATT
* * *
4224736 CTTATTTTTTTATTTTATTCAATTGAGATT
1 ATTA-ATTTTTATTTTATCCAATTGA-ATT
*
4224766 ATTACTTTT
1 ATTAATTTT
4224775 ACTGGTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
28 3 0.09
29 23 0.72
30 6 0.19
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.61
Consensus pattern (28 bp):
ATTAATTTTTATTTTATCCAATTGAATT
Found at i:4231797 original size:17 final size:16
Alignment explanation
Indices: 4231766--4231796 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4231756 TTAACCTCTA
4231766 AAAAATAACTGTTTTC
1 AAAAATAACTGTTTTC
*
4231782 AAAAATAACTATTTT
1 AAAAATAACTGTTTT
4231797 TTTAATTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (16 bp):
AAAAATAACTGTTTTC
Found at i:4232694 original size:19 final size:19
Alignment explanation
Indices: 4232670--4232730 Score: 122
Period size: 19 Copynumber: 3.2 Consensus size: 19
4232660 TGCAAGCATA
4232670 AGCAAATGTTACACGCTTT
1 AGCAAATGTTACACGCTTT
4232689 AGCAAATGTTACACGCTTT
1 AGCAAATGTTACACGCTTT
4232708 AGCAAATGTTACACGCTTT
1 AGCAAATGTTACACGCTTT
4232727 AGCA
1 AGCA
4232731 GAAGATGTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (19 bp):
AGCAAATGTTACACGCTTT
Found at i:4232801 original size:34 final size:33
Alignment explanation
Indices: 4232745--4232853 Score: 103
Period size: 34 Copynumber: 3.2 Consensus size: 33
4232735 ATGTTACATA
* *
4232745 CCAAAACTTCAGCAAC-AAATGTTACATGCCAATG
1 CCAAAGCTTCAGC-ACTAGATGTTACATGCCAA-G
* *
4232779 TCAAAGCTTCAGCACTAGATGTTACATGCTAAG
1 CCAAAGCTTCAGCACTAGATGTTACATGCCAAG
* * * *
4232812 ACCAAACCTTTATCACTAGATGTTACTTGCCAAGG
1 -CCAAAGCTTCAGCACTAGATGTTACATGCCAA-G
4232847 CCAAAGC
1 CCAAAGC
4232854 AGAAAATGTT
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
33 3 0.05
34 57 0.93
35 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.24
Consensus pattern (33 bp):
CCAAAGCTTCAGCACTAGATGTTACATGCCAAG
Found at i:4233055 original size:132 final size:132
Alignment explanation
Indices: 4232765--4233192 Score: 385
Period size: 132 Copynumber: 3.3 Consensus size: 132
4232755 AGCAACAAAT
* * * * * * * *
4232765 GTTACATGCCAATGTCAAAGCTTCAGCACTAGATGTTACATG-CTAAGACCAAACCTTTATCACT
1 GTTACATGCCAAGGTCAAAGCTTCAGCACCAAATGTTACACGTC-AAGGCCAAAACTTCAACACT
* * * * * * * *
4232829 AGATGTTACTTGC-C-AAGGCCAAAGCAGAAAATGTTATATA-CC--A---AAA-CTTCAGTAGC
65 AAATGTTACATGCACTAAAGCAAAAGCAAAAAATATTATA-AGCCAAAGTCAAAGCTTCAATACC
4232885 A-AA
129 AGAA
* * * * * * *
4232888 TGTTATATGCGAAGGTCAAAGCTTCAACACCAAATGTTATACTTTAAGGCCAAAACTTCAGCACT
1 -GTTACATGCCAAGGTCAAAGCTTCAGCACCAAATGTTACACGTCAAGGCCAAAACTTCAACACT
* * * * * *
4232953 ACATGTTACATGCACTAAAGCCAAAGCAAAAGATGTTATAGGCC-AAGATCAAAGCTTTAATACC
65 AAATGTTACATGCACTAAAGCAAAAGCAAAAAATATTATAAGCCAAAG-TCAAAGCTTCAATACC
4233017 AGAA
129 AGAA
* * * * *
4233021 GTTACATGCCAAGGTCAAAGTTTCAGTATCAAATGTTGCACGTCAAGGTCAAAACTTCAACACTA
1 GTTACATGCCAAGGTCAAAGCTTCAGCACCAAATGTTACACGTCAAGGCCAAAACTTCAACACTA
** *
4233086 AATGTTACATGCACTAAAGCAAAAGCAAAAAATATTATAAGCCAAAGTCAAAGCTTCGGTATCAG
66 AATGTTACATGCACTAAAGCAAAAGCAAAAAATATTATAAGCCAAAGTCAAAGCTTCAATACCAG
*
4233151 AT
131 AA
*
4233153 GTTACATGCCAAGGTCCAAGCTTCAGCACCAAATGTTACA
1 GTTACATGCCAAGGTCAAAGCTTCAGCACCAAATGTTACA
4233193 AGCCAAAGCT
Statistics
Matches: 242, Mismatches: 50, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
124 60 0.25
125 1 0.00
126 23 0.10
127 1 0.00
131 3 0.01
132 149 0.62
133 5 0.02
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (132 bp):
GTTACATGCCAAGGTCAAAGCTTCAGCACCAAATGTTACACGTCAAGGCCAAAACTTCAACACTA
AATGTTACATGCACTAAAGCAAAAGCAAAAAATATTATAAGCCAAAGTCAAAGCTTCAATACCAG
AA
Found at i:4233164 original size:34 final size:34
Alignment explanation
Indices: 4233115--4233200 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 34
4233105 CAAAAGCAAA
* * * * *
4233115 AAATATTATAAGCCAAAGTCAAAGCTTCGGTATC
1 AAATGTTACAAGCCAAAGTCAAAGCTTCAGCACC
* * * *
4233149 AGATGTTACATGCCAAGGTCCAAGCTTCAGCACC
1 AAATGTTACAAGCCAAAGTCAAAGCTTCAGCACC
4233183 AAATGTTACAAGCCAAAG
1 AAATGTTACAAGCCAAAG
4233201 CTTCCTTCTT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (34 bp):
AAATGTTACAAGCCAAAGTCAAAGCTTCAGCACC
Found at i:4235108 original size:162 final size:161
Alignment explanation
Indices: 4234782--4235109 Score: 521
Period size: 162 Copynumber: 2.0 Consensus size: 161
4234772 GTGTATTTTT
* *
4234782 ATTTACATTGGAACCCATATTGGCATAAGGTAGTGGATTTTCTTTGTTCGATCAACATGCTGAAT
1 ATTTACATTGGAACCCATATTGGCATAAGGTAATGGATTTTCTTTGTTCGATCAACATGCTGAAG
* * *
4234847 GAGTTTGATCAAGCAAATCTCTCACATTATCATTGTCTATGCTTAAGGTAAATTACTTATAAAAT
66 GAGTTTCATCAAGCAAATCTCTCACATTATCACTGTCTACGCTTAAGGTAAATTACTTATAAAAT
* *
4234912 ATGGTGATTGATCTTGTTCTTAAAATCTTTG
131 ATGGTGATTAATCTTGTTCTTAAAATCATTG
* * ** *
4234943 ATTTGCATTGGAACCCATATTGGTATAAGGTAATGGATTTTCTTTGTTTTATCAACATGCTTAAG
1 ATTTACATTGGAACCCATATTGGCATAAGGTAATGGATTTTCTTTGTTCGATCAACATGCTGAAG
* *
4235008 GAGTTTCATCAAGCAAAATCTTTCACATTATCACTGTCTACGGTTAAGGTAAATTACTTATAAAA
66 GAGTTTCATCAAGC-AAATCTCTCACATTATCACTGTCTACGCTTAAGGTAAATTACTTATAAAA
4235073 TATGGTGATTAATCTTGTTCTTAAAATCATTG
130 TATGGTGATTAATCTTGTTCTTAAAATCATTG
4235105 ATTTA
1 ATTTA
4235110 AGTGTTAACT
Statistics
Matches: 151, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
161 71 0.47
162 80 0.53
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.40
Consensus pattern (161 bp):
ATTTACATTGGAACCCATATTGGCATAAGGTAATGGATTTTCTTTGTTCGATCAACATGCTGAAG
GAGTTTCATCAAGCAAATCTCTCACATTATCACTGTCTACGCTTAAGGTAAATTACTTATAAAAT
ATGGTGATTAATCTTGTTCTTAAAATCATTG
Found at i:4235615 original size:31 final size:31
Alignment explanation
Indices: 4235580--4235659 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
4235570 GCAGATATAT
*
4235580 GGCGTGACACGCTAAGTGGTACTAGATAAAG
1 GGCGTGACACGCTGAGTGGTACTAGATAAAG
4235611 GGCGTGACACGCTGAGTGGTACTAGATAAAG
1 GGCGTGACACGCTGAGTGGTACTAGATAAAG
*
4235642 GGCGTGACATGCTGAGTG
1 GGCGTGACACGCTGAGTG
4235660 AAAGCAGATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.28, C:0.16, G:0.36, T:0.20
Consensus pattern (31 bp):
GGCGTGACACGCTGAGTGGTACTAGATAAAG
Found at i:4235657 original size:96 final size:95
Alignment explanation
Indices: 4235569--4235885 Score: 289
Period size: 96 Copynumber: 3.3 Consensus size: 95
4235559 GAGTAGTAGT
* * *
4235569 AGCAGATATATGGCGTGACACGCTAAGTGGTACT-A-GATAAAGGGCGTGACACGCTGAGTGGTA
1 AGCAGATATATGGCGTCACACGCTAAGTAGTACTAACGATAAAGGGCGTGACACACTGAGTGGTA
*
4235632 CTAGATAAAGGGCGTGACATGCTGAGTGAA
66 CCAGATAAAGGGCGTGACATGCTGAGTGAA
* * * * * *
4235662 AGCAGATTTATGGCGTCACACGTTGAGTAGTAGTAACGGATATATGGCGTGACACACTGAGTGGT
1 AGCAGATATATGGCGTCACACGCTAAGTAGTACTAAC-GATAAAGGGCGTGACACACTGAGTGGT
* * ***
4235727 ACCAGATAGAGTGCGTGACACATTGAGTGAA
65 ACCAGATAAAGGGCGTGACATGCTGAGTGAA
* * * * * * * * *
4235758 AGCAGATTTATGGCGTCACAAGCTAAGTAGTAGTAGCGGATATATGACTTGACATGA-TGAGTGG
1 AGCAGATATATGGCGTCACACGCTAAGTAGTACTAAC-GATAAAGGGCGTGACA-CACTGAGTGG
* * * *
4235822 TACCAGATTAAGGGCATGACATACTGAGTAAA
64 TACCAGATAAAGGGCGTGACATGCTGAGTGAA
* * * * *
4235854 AGTAGATTTATGGCATCACACGTTGAGTAGTA
1 AGCAGATATATGGCGTCACACGCTAAGTAGTA
4235886 GTAGCTATAT
Statistics
Matches: 186, Mismatches: 34, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
93 28 0.15
94 1 0.01
96 156 0.84
97 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.24
Consensus pattern (95 bp):
AGCAGATATATGGCGTCACACGCTAAGTAGTACTAACGATAAAGGGCGTGACACACTGAGTGGTA
CCAGATAAAGGGCGTGACATGCTGAGTGAA
Found at i:4235689 original size:31 final size:31
Alignment explanation
Indices: 4235654--4235777 Score: 90
Period size: 31 Copynumber: 3.9 Consensus size: 31
4235644 CGTGACATGC
* *
4235654 TGAGTGAAAGCAGATTTATGGCGTCACACGT
1 TGAGTGAAAGCAGATATATGGCGTCACACAT
* * *
4235685 TGAGTAGTAGTAA-CGGATATATGGCGTGACACAC
1 TGAGT-G-A--AAGCAGATATATGGCGTCACACAT
** * * *
4235719 TGAGTGGTACCAGATAGA-GTGCGTGACACAT
1 TGAGTGAAAGCAGATATATG-GCGTCACACAT
*
4235750 TGAGTGAAAGCAGATTTATGGCGTCACA
1 TGAGTGAAAGCAGATATATGGCGTCACA
4235778 AGCTAAGTAG
Statistics
Matches: 70, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
30 2 0.03
31 41 0.59
32 2 0.03
33 2 0.03
34 21 0.30
35 2 0.03
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (31 bp):
TGAGTGAAAGCAGATATATGGCGTCACACAT
Found at i:4235754 original size:127 final size:127
Alignment explanation
Indices: 4235488--4235755 Score: 356
Period size: 127 Copynumber: 2.1 Consensus size: 127
4235478 GTATATGGCA
* * *
4235488 TGACACATTGAGTGGTACCAGATAGAGGATGTGACACACTTAGTAAAAGCAGATTTATGGCATCA
1 TGACACATTGAGTGGTACCAGATAAAGGACGTGACACACTGAGTAAAAGCAGATTTATGGCATCA
* * *
4235553 CACACTGAGTAGTAGTAGCAGATATATGGCGTGACACGCTAAGTGGTACTAGATAAAGGGCG
66 CACACTGAGTAGTAGTAACAGATATATGGCGTGACACACTAAGTGGTACCAGATAAAGGGCG
** * * ** * *
4235615 TGACACGCTGAGTGGTACTAGATAAAGGGCGTGACATGCTGAGTGAAAGCAGATTTATGGCGTCA
1 TGACACATTGAGTGGTACCAGATAAAGGACGTGACACACTGAGTAAAAGCAGATTTATGGCATCA
** * * * *
4235680 CACGTTGAGTAGTAGTAACGGATATATGGCGTGACACACTGAGTGGTACCAGATAGAGTGCG
66 CACACTGAGTAGTAGTAACAGATATATGGCGTGACACACTAAGTGGTACCAGATAAAGGGCG
4235742 TGACACATTGAGTG
1 TGACACATTGAGTG
4235756 AAAGCAGATT
Statistics
Matches: 119, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
127 119 1.00
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (127 bp):
TGACACATTGAGTGGTACCAGATAAAGGACGTGACACACTGAGTAAAAGCAGATTTATGGCATCA
CACACTGAGTAGTAGTAACAGATATATGGCGTGACACACTAAGTGGTACCAGATAAAGGGCG
Found at i:4235881 original size:31 final size:31
Alignment explanation
Indices: 4235846--4235912 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
4235836 CATGACATAC
* *
4235846 TGAGTAAAAGTAGATTTATGGCATCACACGT
1 TGAGTAAAAGTAGATATATGGCATAACACGT
** * *
4235877 TGAGTAGTAGTAGCTATATGGCGTAACACGT
1 TGAGTAAAAGTAGATATATGGCATAACACGT
4235908 TGAGT
1 TGAGT
4235913 GATACCAGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (31 bp):
TGAGTAAAAGTAGATATATGGCATAACACGT
Found at i:4235886 original size:96 final size:96
Alignment explanation
Indices: 4235613--4235955 Score: 365
Period size: 96 Copynumber: 3.6 Consensus size: 96
4235603 AGATAAAGGG
* * * *
4235613 CGTGACACGCTGAGTGGTACTAGATAAAGGGCGTGACATGCTGAGTGAAAGCAGATTTATGGCGT
1 CGTGACACACTGAGTGGTACCAGATTAAGGGCGTGACATACTGAGTGAAAGCAGATTTATGGCGT
* *
4235678 CACACGTTGAGTAGTAGTAACGGATATATGG
66 CACACGTTGAGTAGTAGTAGCGGATATATGA
* * *
4235709 CGTGACACACTGAGTGGTACCAGA-TAGAGTGCGTGACACATTGAGTGAAAGCAGATTTATGGCG
1 CGTGACACACTGAGTGGTACCAGATTA-AGGGCGTGACATACTGAGTGAAAGCAGATTTATGGCG
* * *
4235773 TCACAAGCTAAGTAGTAGTAGCGGATATATGA
65 TCACACGTTGAGTAGTAGTAGCGGATATATGA
* * * * * *
4235805 CTTGACATGA-TGAGTGGTACCAGATTAAGGGCATGACATACTGAGTAAAAGTAGATTTATGGCA
1 CGTGACA-CACTGAGTGGTACCAGATTAAGGGCGTGACATACTGAGTGAAAGCAGATTTATGGCG
*
4235869 TCACACGTTGAGTAGTAGTAGC---TATATGG
65 TCACACGTTGAGTAGTAGTAGCGGATATATGA
* ** * * * ** *
4235898 CGTAACACGTTGAGTGATACCAGATTTAA-GGCATAACATGTTGAGTGCAAGCAGATTT
1 CGTGACACACTGAGTGGTACCAGA-TTAAGGGCGTGACATACTGAGTGAAAGCAGATTT
4235956 CTAAGGTGAC
Statistics
Matches: 206, Mismatches: 36, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
93 47 0.23
94 4 0.02
95 1 0.00
96 151 0.73
97 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (96 bp):
CGTGACACACTGAGTGGTACCAGATTAAGGGCGTGACATACTGAGTGAAAGCAGATTTATGGCGT
CACACGTTGAGTAGTAGTAGCGGATATATGA
Found at i:4236100 original size:31 final size:31
Alignment explanation
Indices: 4236065--4236132 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
4236055 GTGTGACATG
**
4236065 CTGAGTGAAAACAAATTTATCAGGTCACACA
1 CTGAGTGAAAACAAATTTATCACATCACACA
** * *
4236096 CTGAGTGGTAACAGATTTATGACATCACACA
1 CTGAGTGAAAACAAATTTATCACATCACACA
4236127 CTGAGT
1 CTGAGT
4236133 AATAGCAGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (31 bp):
CTGAGTGAAAACAAATTTATCACATCACACA
Found at i:4265196 original size:30 final size:30
Alignment explanation
Indices: 4265137--4265197 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
4265127 TATAAGGCTT
**
4265137 TTGTTGTTAGCATGAAAGAGGGGTTTGGCC
1 TTGTTGTTAGCATGAAAGAGGGGCCTGGCC
4265167 TTGTTGTTAGCATGAAAGAGGGGCCTGGCC
1 TTGTTGTTAGCATGAAAGAGGGGCCTGGCC
4265197 T
1 T
4265198 GGCTGGACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.20, C:0.13, G:0.36, T:0.31
Consensus pattern (30 bp):
TTGTTGTTAGCATGAAAGAGGGGCCTGGCC
Found at i:4275236 original size:19 final size:19
Alignment explanation
Indices: 4275212--4275249 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4275202 TCTTTCCCTG
4275212 TGCCTGCTTATACTCTTCC
1 TGCCTGCTTATACTCTTCC
4275231 TGCCTGCTTATACTCTTCC
1 TGCCTGCTTATACTCTTCC
4275250 ATGTAACTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.37, G:0.11, T:0.42
Consensus pattern (19 bp):
TGCCTGCTTATACTCTTCC
Found at i:4300216 original size:12 final size:12
Alignment explanation
Indices: 4300201--4300250 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
4300191 AGGCGCCGGT
4300201 GACGGCGACGGA
1 GACGGCGACGGA
* *
4300213 GACGGCGATGGT
1 GACGGCGACGGA
*
4300225 GACTGCGACGGA
1 GACGGCGACGGA
4300237 GACGGCGACGGA
1 GACGGCGACGGA
4300249 GA
1 GA
4300251 AGACTTTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.24, C:0.22, G:0.48, T:0.06
Consensus pattern (12 bp):
GACGGCGACGGA
Found at i:4300219 original size:24 final size:24
Alignment explanation
Indices: 4300192--4300247 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
4300182 ACTTGGCCCA
*
4300192 GGCGCCGGTGACGGCGACGGAGAC
1 GGCGACGGTGACGGCGACGGAGAC
* *
4300216 GGCGATGGTGACTGCGACGGAGAC
1 GGCGACGGTGACGGCGACGGAGAC
4300240 GGCGACGG
1 GGCGACGG
4300248 AGAAGACTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.18, C:0.25, G:0.50, T:0.07
Consensus pattern (24 bp):
GGCGACGGTGACGGCGACGGAGAC
Found at i:4320547 original size:8 final size:8
Alignment explanation
Indices: 4320536--4320578 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
4320526 ACATATATAC
4320536 ATATATGT
1 ATATATGT
4320544 ATATATGT
1 ATATATGT
* *
4320552 ATAGATAT
1 ATATATGT
**
4320560 ATGCATGT
1 ATATATGT
4320568 ATATATGT
1 ATATATGT
4320576 ATA
1 ATA
4320579 CGTATCTGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.44
Consensus pattern (8 bp):
ATATATGT
Found at i:4322980 original size:49 final size:48
Alignment explanation
Indices: 4322913--4323092 Score: 206
Period size: 49 Copynumber: 3.8 Consensus size: 48
4322903 TCGCTTTCAT
* *
4322913 TTCATGAATAATATCTTTCAATGTTAGCCACATATAACTAAGTTTTGAC
1 TTCATGGATAATAGCTTTCAATGTTAGCCACATATAA-TAAGTTTTGAC
* * * * *
4322962 TGCATGGATAATAGCTTTCAATGTTAGCCACATATGATTGAGTTTTCAT
1 TTCATGGATAATAGCTTTCAATGTTAGCCACATAT-AATAAGTTTTGAC
* *
4323011 TTCATGGATAATATG-GTTCAATGTTAGCCAC--AT-ATAGGTTTTGAC
1 TTCATGGATAATA-GCTTTCAATGTTAGCCACATATAATAAGTTTTGAC
* *
4323056 TTCATGGATAATATCTTTCAATGTTAGCCGCATATAA
1 TTCATGGATAATAGCTTTCAATGTTAGCCACATATAA
4323093 GATTTCATGT
Statistics
Matches: 108, Mismatches: 17, Indels: 13
0.78 0.12 0.09
Matches are distributed among these distances:
45 34 0.31
47 4 0.04
48 1 0.01
49 67 0.62
50 2 0.02
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (48 bp):
TTCATGGATAATAGCTTTCAATGTTAGCCACATATAATAAGTTTTGAC
Found at i:4323090 original size:94 final size:97
Alignment explanation
Indices: 4322907--4323090 Score: 275
Period size: 94 Copynumber: 1.9 Consensus size: 97
4322897 CTCATCTCGC
*
4322907 TTTCATTTCATGAATAATATCTTTCAATGTTAGCCACATATAACTAAGTTTTGACTGCATGGATA
1 TTTCATTTCATGAATAATATCGTTCAATGTTAGCCACA-ATAACTAAGTTTTGACTGCATGGATA
4322972 ATAGCTTTCAATGTTAGCCACATATGATTGAGT
65 ATAGCTTTCAATGTTAGCCACATATGATTGAGT
* * * *
4323005 TTTCATTTCATGGATAATATGGTTCAATGTTAGCCAC-AT-A-TAGGTTTTGACTTCATGGATAA
1 TTTCATTTCATGAATAATATCGTTCAATGTTAGCCACAATAACTAAGTTTTGACTGCATGGATAA
* *
4323067 TATCTTTCAATGTTAGCCGCATAT
66 TAGCTTTCAATGTTAGCCACATAT
4323091 AAGATTTCAT
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
94 42 0.53
95 1 0.01
96 2 0.03
98 34 0.43
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (97 bp):
TTTCATTTCATGAATAATATCGTTCAATGTTAGCCACAATAACTAAGTTTTGACTGCATGGATAA
TAGCTTTCAATGTTAGCCACATATGATTGAGT
Found at i:4336312 original size:53 final size:54
Alignment explanation
Indices: 4336184--4336315 Score: 158
Period size: 54 Copynumber: 2.5 Consensus size: 54
4336174 TTGATATTCA
* * **
4336184 CTTCAAAGGTCTTGATGACTTAATCTTAATCAAGAACTAGACTTGATATCTTTG
1 CTTCAAAGGTCTTGACGACTTGATCTTAATCAAGAACTAGACTCAATATCTTTG
* * * * * *
4336238 TTTCAAAGGTCTTGACAACTTGATCTTGATTATGAATTAGACTCAATATC-TTG
1 CTTCAAAGGTCTTGACGACTTGATCTTAATCAAGAACTAGACTCAATATCTTTG
*
4336291 CTTCAAAAGTCTTGACGACTTGATC
1 CTTCAAAGGTCTTGACGACTTGATC
4336316 ACAAACTTTG
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
53 25 0.38
54 40 0.62
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37
Consensus pattern (54 bp):
CTTCAAAGGTCTTGACGACTTGATCTTAATCAAGAACTAGACTCAATATCTTTG
Found at i:4336329 original size:25 final size:25
Alignment explanation
Indices: 4336301--4336374 Score: 94
Period size: 25 Copynumber: 3.0 Consensus size: 25
4336291 CTTCAAAAGT
*
4336301 CTTGACGACTTGATCACAAACTTTG
1 CTTGAAGACTTGATCACAAACTTTG
* * *
4336326 CTTGATGGCTTAATCACAAACTTTG
1 CTTGAAGACTTGATCACAAACTTTG
* *
4336351 CTTGAAGACTTGATTACGAACTTT
1 CTTGAAGACTTGATCACAAACTTT
4336375 ACTATTTGAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35
Consensus pattern (25 bp):
CTTGAAGACTTGATCACAAACTTTG
Found at i:4347947 original size:20 final size:19
Alignment explanation
Indices: 4347918--4347971 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 19
4347908 GCAAATCAAT
*
4347918 TAGTTATTAAGTTACATTA
1 TAGTTTTTAAGTTACATTA
4347937 CTAGTTTTTAAGTATTACATTA
1 -TAGTTTTTAAG--TTACATTA
*
4347959 TTGATTTTTAAGT
1 TAG-TTTTTAAGT
4347972 ATTGCAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 11 0.38
21 2 0.07
22 16 0.55
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.52
Consensus pattern (19 bp):
TAGTTTTTAAGTTACATTA
Found at i:4347957 original size:22 final size:22
Alignment explanation
Indices: 4347929--4347974 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
4347919 AGTTATTAAG
4347929 TTACATTACTAG-TTTTTAAGTA
1 TTACATTA-TAGATTTTTAAGTA
*
4347951 TTACATTATTGATTTTTAAGTA
1 TTACATTATAGATTTTTAAGTA
4347973 TT
1 TT
4347975 GCAAAACTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.54
Consensus pattern (22 bp):
TTACATTATAGATTTTTAAGTA
Found at i:4347985 original size:22 final size:22
Alignment explanation
Indices: 4347941--4347988 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
4347931 ACATTACTAG
** *
4347941 TTTTTAAGTATTACATTATTGA
1 TTTTTAAGTATTACAAAACTGA
*
4347963 TTTTTAAGTATTGCAAAACTGA
1 TTTTTAAGTATTACAAAACTGA
4347985 TTTT
1 TTTT
4347989 AGATATTACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.52
Consensus pattern (22 bp):
TTTTTAAGTATTACAAAACTGA
Found at i:4348221 original size:22 final size:22
Alignment explanation
Indices: 4348170--4348234 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
4348160 AAAAATCAAG
*
4348170 AACATAATATTTAAAAATTAGT
1 AACATAATATTTAAAAACTAGT
* *
4348192 AACGTAATACTTAAAAACTAGT
1 AACATAATATTTAAAAACTAGT
* * *
4348214 GATATAATGTTTAAAAACTAG
1 AACATAATATTTAAAAACTAG
4348235 CTATGCAACG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.51, C:0.08, G:0.09, T:0.32
Consensus pattern (22 bp):
AACATAATATTTAAAAACTAGT
Found at i:4348594 original size:15 final size:16
Alignment explanation
Indices: 4348574--4348610 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
4348564 CATATGTATC
4348574 AATTTTATT-AAAAAT
1 AATTTTATTCAAAAAT
*
4348589 AATTTTATTCAAAATT
1 AATTTTATTCAAAAAT
4348605 AATTTT
1 AATTTT
4348611 TTTTAGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTTTATTCAAAAAT
Found at i:4369778 original size:550 final size:545
Alignment explanation
Indices: 4368649--4370571 Score: 1803
Period size: 550 Copynumber: 3.5 Consensus size: 545
4368639 AATGTAGTGC
* * * * * * *
4368649 TTCAGTTGACTTTTTTCACCCTTTGATGAATGGAATTTTTTGTATTTTATGGACTTCATTGAAGA
1 TTCAGTTGAC-TTTTTCACCCCTTGATAAATGGAGTTTTTGGTATTTTAAGAATTTCATTGAAGA
* * ** * * * * *
4368714 AGGTTTTAAACGTATGTGTTATGATGCATCCAAGCATTTTGCTCGTTCATTGGTGCATGATCTTC
65 AGTTTTTAAAAGTATGCATTATGATGCA-CC-AGCATTTGGCTCATTAATTAGTACATGATC-TC
*** * * * *
4368779 C-CGCTCAAAGAGTAGGG-TCGAA-TCCCCTTTTCTCC-AAATAAAAATAAAGTATGTATTTTTA
127 CTTATTC-AAGAGCAGGGCTTGAATTCCCC--TTCCCCTAAATAAAAAAAAAGTATGTATTTTTA
* * * * * **
4368840 TAAATTAAATTCATGTGAATTTTGACGTGTTTTCTATTTATGCGTG-C--TTT-T---CCATGTT
189 TGAATTAAATTCATGTGAATTATGAGGTGTCTTCTATTTATGTGTGCCTTTTTATGGGTTATGTT
* * * * *
4368898 TTTATTG-TTTCTTTTCTCGTTTTCAGTTGACTTTTTTCACCTTTGA-TGAATGATAATTTTGTT
254 TTTA-TGCCTTCTTTTCTTGTTTTCAGTTGACTTTTTTCACCCTTGATTGGA-G-T--TTTTGGT
* * * * * * * *
4368961 ATTTTACGAACTTCATTGAAGAAGTATTTTAGAAGTATGTATTACGACGCAATT-AAGCATTTGA
314 ATTTTAGGAATTTCATTGAAGAAGT-TTTTAAAAGTATGAATTATGATGCACTTGAA-CATTTGG
* * * * * *
4369025 CTCATTAATTGGTGCATCATCTCCCTACGCAAAGGATAGGGTTCAAATCCCCTTTCCCCAAATAA
377 CTCATTGATTGGTGTATGATCTCCTTACTCAAA-GATAGGGTTCGAATCCCCTTTCCCCAAAT--
*
4369090 AAAGAAAGTATGTAT-T-TTTTTATGAATTAAATTCATGTGAATTATGACGTGTTTTCTATTTAT
439 AAAGAAA-TAT-TATGTATTTTTATGAATTAAATTCATGTGAATTATGACGTGTCTTCTATTTAT
*
4369153 GTGTGCTTTTTTATGGGTTATGTTTTCATGGCTTCTTTTCTTGTT
502 GTGTGC-TTTTTATGGGTTATGTTTTTATGGCTTCTTTTCTTGTT
* *
4369198 TTCAGTTGACTTTTTTTACCCCTTGATAAATGGAGTTTTTGGTATTTT-TGAAGTTTCATTGAAG
1 TTCAGTTGAC-TTTTTCACCCCTTGATAAATGGAGTTTTTGGTATTTTAAGAA-TTTCATTGAAG
*
4369262 AAG-TTTTAAAAGTATACATTATGATGCAGCCGAGCATTTGGCTCATTAATTAGTACATGATCTC
64 AAGTTTTTAAAAGTATGCATTATGATGCA-CC-AGCATTTGGCTCATTAATTAGTACATGATCTC
* * * * *
4369326 CTTATTCAAGGAACAGGGCTTGAATTCGCCTTCCCCTTAATAAAAATAAAGTATGTATTTTAATG
127 CTTATTCAA-GAGCAGGGCTTGAATTCCCCTTCCCCTAAATAAAAAAAAAGTATGTATTTTTATG
* * *
4369391 AATTAAATTCATGTGAATTATGAGGTGTCTTCTA-TTAT-TGGTGCCTTTTTATAGTTTATGCTT
191 AATTAAATTCATGTGAATTATGAGGTGTCTTCTATTTATGT-GTGCCTTTTTATGGGTTATGTTT
*
4369454 TTATGCCTTCTTTTCTTGTTTTCAGTTGAATTTTTTCACCCCTTGATTGGAGTTTTTGGTATTTT
255 TTATGCCTTCTTTTCTTGTTTTCAGTTGACTTTTTTCA-CCCTTGATTGGAGTTTTTGGTATTTT
* *
4369519 AGGAATTTCATTGATGAAGTTTTTAAAACTATGAATTATGATGCACTTGAACATTTGGCTCATTG
319 AGGAATTTCATTGAAGAAGTTTTTAAAAGTATGAATTATGATGCACTTGAACATTTGGCTCATTG
* * *
4369584 ATCGGTGTATGATCTCCTTACTCAAAGACCAGGGTTCGAA-CCCTCTTTCCCCGAATAAAGAAAT
384 ATTGGTGTATGATCTCCTTACTCAAAGA-TAGGGTTCGAATCCC-CTTTCCCCAAATAAAGAAAT
* * * * **
4369648 ATTATGTATTTTTATGAATTAAATTCAAGTGAATTATGATGTATCTTCTACTTATGTGCCCATTT
447 ATTATGTATTTTTATGAATTAAATTCATGTGAATTATGACGTGTCTTCTATTTATGTGTGC-TTT
*
4369713 TTATGGGTCATGTTTTTATGGCTTCTTTTCTTGTT
511 TTATGGGTTATGTTTTTATGGCTTCTTTTCTTGTT
* * * *
4369748 TTCGGTTGACGTCTTGCACCCCTCGATAAATGGAGTTTTTGGTATTTTAAGAATTTCATTGAAGA
1 TTCAGTTGAC-TTTTTCACCCCTTGATAAATGGAGTTTTTGGTATTTTAAGAATTTCATTGAAGA
* * * * *
4369813 AGTTTTTAGAAGTATGCATTATGATGCTACTCAGCATTT-GCTTCATTGATTTAG-GCATCATCA
65 AGTTTTTAAAAGTATGCATTATGATGC-AC-CAGCATTTGGC-TCATT-AATTAGTACATGATCT
* * * * * ** *
4369876 CCCTACTCAAAGAGTAGGGCTCGAA-TCCTCTTTTTCCTAAATAAAAAAAAATTATGTATTTTTA
126 CCTTATTC-AAGAGCAGGGCTTGAATTCC-CCTTCCCCTAAATAAAAAAAAAGTATGTATTTTTA
* * * * * *
4369940 TGAATTAGATTCACGTGAATTATGAGGTGTCGTT-TATTTCTGTGTGCGTGTTTATGGGATATGT
189 TGAATTAAATTCATGTGAATTATGAGGTGTC-TTCTATTTATGTGTGCCTTTTTATGGGTTATGT
*
4370004 TTTTAT-CGCTTC-TTTCTTGTTTTCAGTT--CTTTTTTCAGTCCTTGATAAATGGAGTTTTTGG
253 TTTTATGC-CTTCTTTTCTTGTTTTCAGTTGACTTTTTTCA-CCCTTGAT---TGGAGTTTTTGG
* * * * * * * *
4370065 TATTTTTGGAATTTCATTTAAGAAGTTTTTGAAAGTATGCATAATGATGC-CTCCGAGCATTTAG
313 TATTTTAGGAATTTCATTGAAGAAGTTTTTAAAAGTATGAATTATGATGCACT-TGAACATTTGG
* * ** ** ** * * *
4370129 CTCATTGGTTAGCATATGATCTTTTTGTTTAAAGAGTATGGTTCGAATCCCCCTTCCCCAAATAA
377 CTCATTGATTGGTGTATGATCTCCTTACTCAAAGA-TAGGGTTCGAATCCCCTTTCCCCAAATAA
*** * * * * * *
4370194 A-TTTTTTTTTGTATTTTTATGAATTAAATTCATGTGAATTATGAGGTGCCCTCTATTTATATGT
441 AGAAATATTATGTATTTTTATGAATTAAATTCATGTGAATTATGACGTGTCTTCTATTTATGTGT
* * **
4370258 GCTTCTTTATGGCTTGTGTTTTTATGGCTTCTTTTCTCATT
506 GCTT-TTTATGGGTTATGTTTTTATGGCTTCTTTTCTTGTT
* * *
4370299 TTCAGTTGACTTTTTCACCCCTTGATAAATGGAG-TTTT-GTATTTTAGGAATGTCATTAAAGAA
1 TTCAGTTGACTTTTTCACCCCTTGATAAATGGAGTTTTTGGTATTTTAAGAATTTCATTGAAGAA
* * * * *
4370362 GTTTTTAAAAGTATGCATTATTAATACATCCAAGCATTTGGCTCATTGATTGGTACATGGTCTCC
66 GTTTTTAAAAGTATGCATTA-TGATGCA-CC-AGCATTTGGCTCATTAATTAGTACATGATCTCC
* *
4370427 TTGTTCCAAGAGCAGGG-TTCGAATTCCCCTTTCCCC-AAATAAAAGAAAAAATTATGTA-TTTT
128 TTATT-CAAGAGCAGGGCTT-GAATTCCCC-TTCCCCTAAAT-AAA-AAAAAAGTATGTATTTTT
* * *
4370489 ATGAATTAAATTCATGTGAATTATGAGGTGTCTTCTATTTATGTGTGCTTTTTTGTGGGCTATGT
188 ATGAATTAAATTCATGTGAATTATGAGGTGTCTTCTATTTATGTGTGCCTTTTTATGGGTTATGT
*
4370554 TTTTATGGCTTCTTTTCT
253 TTTTATGCCTTCTTTTCT
4370572 CATTTCCTTA
Statistics
Matches: 1134, Mismatches: 186, Indels: 106
0.80 0.13 0.07
Matches are distributed among these distances:
547 5 0.00
548 121 0.11
549 185 0.16
550 258 0.23
551 256 0.23
552 225 0.20
553 34 0.03
554 2 0.00
555 38 0.03
556 7 0.01
557 3 0.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.43
Consensus pattern (545 bp):
TTCAGTTGACTTTTTCACCCCTTGATAAATGGAGTTTTTGGTATTTTAAGAATTTCATTGAAGAA
GTTTTTAAAAGTATGCATTATGATGCACCAGCATTTGGCTCATTAATTAGTACATGATCTCCTTA
TTCAAGAGCAGGGCTTGAATTCCCCTTCCCCTAAATAAAAAAAAAGTATGTATTTTTATGAATTA
AATTCATGTGAATTATGAGGTGTCTTCTATTTATGTGTGCCTTTTTATGGGTTATGTTTTTATGC
CTTCTTTTCTTGTTTTCAGTTGACTTTTTTCACCCTTGATTGGAGTTTTTGGTATTTTAGGAATT
TCATTGAAGAAGTTTTTAAAAGTATGAATTATGATGCACTTGAACATTTGGCTCATTGATTGGTG
TATGATCTCCTTACTCAAAGATAGGGTTCGAATCCCCTTTCCCCAAATAAAGAAATATTATGTAT
TTTTATGAATTAAATTCATGTGAATTATGACGTGTCTTCTATTTATGTGTGCTTTTTATGGGTTA
TGTTTTTATGGCTTCTTTTCTTGTT
Found at i:4370576 original size:277 final size:277
Alignment explanation
Indices: 4368893--4370571 Score: 1694
Period size: 277 Copynumber: 6.1 Consensus size: 277
4368883 GTGCTTTTCC
* * * * *
4368893 ATGTTTTTATTGTTTCTTTTCTCGTTTTCAGTTGACTTTTTTCA-CCTTTGATGAAT-GA-TAAT
1 ATGTTTTTATGGCTTCTTTTCTTGTTTTCAGTTGACTTTTTTCACCCCTTGATAAATGGAGT--T
* * * * * * * *
4368955 TTTGTTATTTTACGAACTTCATTGAAGAAGTATTTTAGAAGTATGTATTACGACGCAAT-TAAGC
64 TTTGGTATTTTAGGAATTTCATTGAAGAAGT-TTTTAAAAGTATGCATTATGATGC-ATCCAAGC
* * * * * * *
4369019 ATTTGACTCATTAATTGGTGCATCATCTCCCTACGCAAAG-GATAGGGTTCAAATCCCCTTTCCC
127 ATTTGGCTCATTGATTGGTACATGATCTCCTTACTCAAAGAG-TAGGGTTCGAATCCCCTTTCCC
* * * *
4369083 CAAATAAAAAGAAAGTATGTATTTTTTTATGAATTAAATTCATGTGAATTATGACGTGTTTTCTA
191 CAAATAAAAAAAAATTATGTA--TTTTTATGAATTAAATTCATGTGAATTATGAGGTGTCTTCTA
*
4369148 TTTATGTGTGCTTTTTTATGGGTT
254 TTTATGTGTGCTTTTTTATGGGCT
* *
4369172 ATGTTTTCATGGCTTCTTTTCTTGTTTTCAGTTGACTTTTTTTACCCCTTGATAAATGGAGTTTT
1 ATGTTTTTATGGCTTCTTTTCTTGTTTTCAGTTGACTTTTTTCACCCCTTGATAAATGGAGTTTT
* * * *
4369237 TGGTATTTT-TGAAGTTTCATTGAAGAAG-TTTTAAAAGTATACATTATGATGCAGCCGAGCATT
66 TGGTATTTTAGGAA-TTTCATTGAAGAAGTTTTTAAAAGTATGCATTATGATGCATCCAAGCATT
* * * * ** *
4369300 TGGCTCATTAATTAGTACATGATCTCCTTATTCAAGGAACAGGGCTT-GAATTCGCC-TTCCCCT
130 TGGCTCATTGATTGGTACATGATCTCCTTACTCAAAGAGTAGGG-TTCGAA-TCCCCTTTCCCC-
* * * *
4369363 TAATAAAAATAAAGTATGTATTTTAATGAATTAAATTCATGTGAATTATGAGGTGTCTTCTA-TT
192 AAATAAAAAAAAATTATGTATTTTTATGAATTAAATTCATGTGAATTATGAGGTGTCTTCTATTT
* * **
4369427 AT-TGGTGCCTTTTTATAGTTT
257 ATGT-GTGCTTTTTTATGGGCT
* * *
4369448 ATGCTTTTATGCCTTCTTTTCTTGTTTTCAGTTGAATTTTTTCACCCCTTGAT---TGGAGTTTT
1 ATGTTTTTATGGCTTCTTTTCTTGTTTTCAGTTGACTTTTTTCACCCCTTGATAAATGGAGTTTT
* * * **
4369510 TGGTATTTTAGGAATTTCATTGATGAAGTTTTTAAAACTATGAATTATGATGCACTTGAA-CATT
66 TGGTATTTTAGGAATTTCATTGAAGAAGTTTTTAAAAGTATGCATTATGATGCA-TCCAAGCATT
* ** ** *
4369574 TGGCTCATTGATCGGTGTATGATCTCCTTACTCAAAGACCAGGGTTCGAA-CCCTCTTTCCCCGA
130 TGGCTCATTGATTGGTACATGATCTCCTTACTCAAAGAGTAGGGTTCGAATCCC-CTTTCCCCAA
* * * * * *
4369638 ATAAAGAAATATTATGTATTTTTATGAATTAAATTCAAGTGAATTATGATGTATCTTCTACTTAT
194 ATAAAAAAAAATTATGTATTTTTATGAATTAAATTCATGTGAATTATGAGGTGTCTTCTATTTAT
** *
4369703 GTGCCCATTTTTATGGG-T
259 GTGTGCTTTTTTATGGGCT
* * * * *
4369721 CATGTTTTTATGGCTTCTTTTCTTGTTTTCGGTTGACGTCTTGCACCCCTCGATAAATGGAGTTT
1 -ATGTTTTTATGGCTTCTTTTCTTGTTTTCAGTTGACTTTTTTCACCCCTTGATAAATGGAGTTT
* *
4369786 TTGGTATTTTAAGAATTTCATTGAAGAAGTTTTTAGAAGTATGCATTATGATGC-TACTC-AGCA
65 TTGGTATTTTAGGAATTTCATTGAAGAAGTTTTTAAAAGTATGCATTATGATGCAT-C-CAAGCA
* * * * * *
4369849 TTT-GCTTCATTGATT--TAGGCATCATCACCCTACTCAAAGAGTAGGGCTCGAATCCTCTTTTT
128 TTTGGC-TCATTGATTGGTA--CATGATCTCCTTACTCAAAGAGTAGGGTTCGAATCC-CCTTTC
* * *
4369911 CCTAAATAAAAAAAAATTATGTATTTTTATGAATTAGATTCACGTGAATTATGAGGTGTCGTT-T
189 CCCAAATAAAAAAAAATTATGTATTTTTATGAATTAAATTCATGTGAATTATGAGGTGTC-TTCT
* * * *
4369975 ATTTCTGTGTGCGTGTTTATGGGAT
253 ATTTATGTGTGCTTTTTTATGGGCT
* **
4370000 ATGTTTTTATCGCTTC-TTTCTTGTTTTCAGTT--CTTTTTTCAGTCCTTGATAAATGGAGTTTT
1 ATGTTTTTATGGCTTCTTTTCTTGTTTTCAGTTGACTTTTTTCACCCCTTGATAAATGGAGTTTT
* * * * * *
4370062 TGGTATTTTTGGAATTTCATTTAAGAAGTTTTTGAAAGTATGCATAATGATGCCTCCGAGCATTT
66 TGGTATTTTAGGAATTTCATTGAAGAAGTTTTTAAAAGTATGCATTATGATGCATCCAAGCATTT
* * * * * ** ** * * *
4370127 AGCTCATTGGTTAGCATATGATCTTTTTGTTTAAAGAGTATGGTTCGAATCCCCCTTCCCCAAAT
131 GGCTCATTGATTGGTACATGATCTCCTTACTCAAAGAGTAGGGTTCGAATCCCCTTTCCCCAAAT
***** * * * *
4370192 -AAATTTTTTTTTGTATTTTTATGAATTAAATTCATGTGAATTATGAGGTGCCCTCTATTTATAT
196 AAAAAAAAATTATGTATTTTTATGAATTAAATTCATGTGAATTATGAGGTGTCTTCTATTTATGT
*
4370256 GTGCTTCTTTAT-GGCTT
261 GTGCTTTTTTATGGGC-T
* **
4370273 GTGTTTTTATGGCTTCTTTTCTCATTTTCAGTTGAC-TTTTTCACCCCTTGATAAATGGAG-TTT
1 ATGTTTTTATGGCTTCTTTTCTTGTTTTCAGTTGACTTTTTTCACCCCTTGATAAATGGAGTTTT
* * * *
4370336 T-GTATTTTAGGAATGTCATTAAAGAAGTTTTTAAAAGTATGCATTATTAATACATCCAAGCATT
66 TGGTATTTTAGGAATTTCATTGAAGAAGTTTTTAAAAGTATGCATTA-TGATGCATCCAAGCATT
* ** * *
4370400 TGGCTCATTGATTGGTACATGGTCTCCTTGTTCCAAGAGCAGGGTTCGAATTCCCCTTTCCCCAA
130 TGGCTCATTGATTGGTACATGATCTCCTTACTCAAAGAGTAGGGTTCGAA-TCCCCTTTCCCCAA
4370465 ATAAAAGAAAAAATTATGTA-TTTTATGAATTAAATTCATGTGAATTATGAGGTGTCTTCTATTT
194 AT-AAA-AAAAAATTATGTATTTTTATGAATTAAATTCATGTGAATTATGAGGTGTCTTCTATTT
*
4370529 ATGTGTGCTTTTTTGTGGGCT
257 ATGTGTGCTTTTTTATGGGCT
4370550 ATGTTTTTATGGCTTCTTTTCT
1 ATGTTTTTATGGCTTCTTTTCT
4370572 CATTTCCTTA
Statistics
Matches: 1151, Mismatches: 201, Indels: 98
0.79 0.14 0.07
Matches are distributed among these distances:
272 5 0.00
273 203 0.18
274 212 0.18
275 154 0.13
276 73 0.06
277 231 0.20
278 166 0.14
279 70 0.06
280 34 0.03
281 2 0.00
282 1 0.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (277 bp):
ATGTTTTTATGGCTTCTTTTCTTGTTTTCAGTTGACTTTTTTCACCCCTTGATAAATGGAGTTTT
TGGTATTTTAGGAATTTCATTGAAGAAGTTTTTAAAAGTATGCATTATGATGCATCCAAGCATTT
GGCTCATTGATTGGTACATGATCTCCTTACTCAAAGAGTAGGGTTCGAATCCCCTTTCCCCAAAT
AAAAAAAAATTATGTATTTTTATGAATTAAATTCATGTGAATTATGAGGTGTCTTCTATTTATGT
GTGCTTTTTTATGGGCT
Found at i:4371242 original size:468 final size:468
Alignment explanation
Indices: 4370304--4371194 Score: 1692
Period size: 468 Copynumber: 1.9 Consensus size: 468
4370294 TCATTTTCAG
*
4370304 TTGACTTTTTCACCCCTTGATAAATGGAGTTTTGTATTTTAGGAATGTCATTAAAGAAGTTTTTA
1 TTGACTTTTTCACCCCTTGATAAATGGAGTTTGGTATTTTAGGAATGTCATTAAAGAAGTTTTTA
*
4370369 AAAGTATGCATTATTAATACATCCAAGCATTTGGCTCATTGATTGGTACATGGTCTCCTTGTTCC
66 AAAGTATGCATTATTAATACATCCAAGCATTTGGCTCATTGATTGGTACATGGTCTCCTTGTTCA
*
4370434 AAGAGCAGGGTTCGAATTCCCCTTTCCCCAAATAAAAGAAAAAATTATGTATTTTATGAATTAAA
131 AAGAGCAGGGTTCGAATCCCCCTTTCCCCAAATAAAAGAAAAAATTATGTATTTTATGAATTAAA
*
4370499 TTCATGTGAATTATGAGGTGTCTTCTATTTATGTGTGCTTTTTTGTGGGCTATGTTTTTATGGCT
196 TTCATGTGAATTATGAGGTGTCTTCTATTTATGTGTGCTTTTTTATGGGCTATGTTTTTATGGCT
4370564 TCTTTTCTCATTTCCTTAATGAGGAAAATGCAATGTTATATATTTTTCTGAATTTTGATGACTTG
261 TCTTTTCTCATTTCCTTAATGAGGAAAATGCAATGTTATATATTTTTCTGAATTTTGATGACTTG
* * * *
4370629 TTTTCCTGTTATGATTAGGAGATGGCATAAATGCTTCGCGAAATATTGAAGTAACTATAAGTACT
326 TTTTCCTATTATGATTAGGAGATGGCATAAATGCTTCCCGAAATATCGAAGTAACTATAAATACT
4370694 TAATTGCAATATTGTATTAGTAAATCAGATCAGAGTATGAGATTGTATAATCTGAATCTCCAATT
391 TAATTGCAATATTGTATTAGTAAATCAGATCAGAGTATGAGATTGTATAATCTGAATCTCCAATT
4370759 GCTAAGTACATTT
456 GCTAAGTACATTT
*
4370772 TTGACTTTTTCACCCGTTGATAAATGGAGTTTGGTATTTTAGGAATGTCATTAAAGAAGTTTTTA
1 TTGACTTTTTCACCCCTTGATAAATGGAGTTTGGTATTTTAGGAATGTCATTAAAGAAGTTTTTA
*
4370837 AAAGTATGCATTATTAATACATCCGAGCATTTGGCTCATTGATTGGTACATGGTCTCCTTGTTCA
66 AAAGTATGCATTATTAATACATCCAAGCATTTGGCTCATTGATTGGTACATGGTCTCCTTGTTCA
4370902 AAGAGCAGGGTTCGAATCCCCCTTTCCCCAAATAAAAGAAAAAATTATGTATTTTATGAATTAAA
131 AAGAGCAGGGTTCGAATCCCCCTTTCCCCAAATAAAAGAAAAAATTATGTATTTTATGAATTAAA
4370967 TTCATGTGAATTATGAGGTGTCTTCTATTTATGTGTGCTTTTTTATGGGCTATGTTTTTATGGCT
196 TTCATGTGAATTATGAGGTGTCTTCTATTTATGTGTGCTTTTTTATGGGCTATGTTTTTATGGCT
4371032 TCTTTTCTCATTTCCTTAATGAGGAAAATGCAATGTTATATATTTTTCTGAATTTTGATGACTTG
261 TCTTTTCTCATTTCCTTAATGAGGAAAATGCAATGTTATATATTTTTCTGAATTTTGATGACTTG
4371097 TTTTCCTATTATGATTAGGAGATGGCATAAATGCTTCCCGAAATATCGAAGTAACTATAAATACT
326 TTTTCCTATTATGATTAGGAGATGGCATAAATGCTTCCCGAAATATCGAAGTAACTATAAATACT
4371162 TAATTGCAATATTGTATTAGTAAATCAGATCAG
391 TAATTGCAATATTGTATTAGTAAATCAGATCAG
4371195 NNNNNNNNNN
Statistics
Matches: 413, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
468 413 1.00
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (468 bp):
TTGACTTTTTCACCCCTTGATAAATGGAGTTTGGTATTTTAGGAATGTCATTAAAGAAGTTTTTA
AAAGTATGCATTATTAATACATCCAAGCATTTGGCTCATTGATTGGTACATGGTCTCCTTGTTCA
AAGAGCAGGGTTCGAATCCCCCTTTCCCCAAATAAAAGAAAAAATTATGTATTTTATGAATTAAA
TTCATGTGAATTATGAGGTGTCTTCTATTTATGTGTGCTTTTTTATGGGCTATGTTTTTATGGCT
TCTTTTCTCATTTCCTTAATGAGGAAAATGCAATGTTATATATTTTTCTGAATTTTGATGACTTG
TTTTCCTATTATGATTAGGAGATGGCATAAATGCTTCCCGAAATATCGAAGTAACTATAAATACT
TAATTGCAATATTGTATTAGTAAATCAGATCAGAGTATGAGATTGTATAATCTGAATCTCCAATT
GCTAAGTACATTT
Found at i:4381304 original size:22 final size:22
Alignment explanation
Indices: 4381274--4381323 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
4381264 TTTAGGGATC
*
4381274 ACGTTATTAATTTTTAGATATT
1 ACGTAATTAATTTTTAGATATT
*
4381296 ATGTAATTAATTTTTAGATATT
1 ACGTAATTAATTTTTAGATATT
4381318 ACGTAA
1 ACGTAA
4381324 CTGGTTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.10, T:0.50
Consensus pattern (22 bp):
ACGTAATTAATTTTTAGATATT
Found at i:4381363 original size:23 final size:23
Alignment explanation
Indices: 4381315--4381394 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 23
4381305 ATTTTTAGAT
* * * *
4381315 ATTACGTAACTGGTTAATATGAC
1 ATTACGTGACTGATTAATAAGGC
4381338 ATTACGTGACTGATTAATAAGGC
1 ATTACGTGACTGATTAATAAGGC
* * * * *
4381361 ATTGCATGAGCAGA-TAGTAAGGT
1 ATTACGTGA-CTGATTAATAAGGC
4381384 ATTACGTGACT
1 ATTACGTGACT
4381395 AGTTTTTACG
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
22 1 0.02
23 40 0.91
24 3 0.07
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (23 bp):
ATTACGTGACTGATTAATAAGGC
Found at i:4412084 original size:4 final size:4
Alignment explanation
Indices: 4412077--4412103 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4412067 CACGCGCACG
4412077 CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CAT
4412104 TTTGCTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:4414420 original size:6 final size:6
Alignment explanation
Indices: 4414409--4414442 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
4414399 TGAAGCAGAA
*
4414409 ATCACC ATCACC ATCACC ATCACC ATCATC ATCA
1 ATCACC ATCACC ATCACC ATCACC ATCACC ATCA
4414443 GCAGCAGCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.35, C:0.44, G:0.00, T:0.21
Consensus pattern (6 bp):
ATCACC
Found at i:4417206 original size:28 final size:28
Alignment explanation
Indices: 4417174--4417228 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
4417164 ATTCCTCCAT
4417174 TTCACTTGTTTAAA-CCCTAATTTTTACA
1 TTCACTTGTTTAAATCCC-AATTTTTACA
4417202 TTCACTTGTTTAAATCCCAATTTTTAC
1 TTCACTTGTTTAAATCCCAATTTTTAC
4417229 GTTATTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.27, C:0.22, G:0.04, T:0.47
Consensus pattern (28 bp):
TTCACTTGTTTAAATCCCAATTTTTACA
Found at i:4425148 original size:100 final size:101
Alignment explanation
Indices: 4424963--4425165 Score: 255
Period size: 100 Copynumber: 2.0 Consensus size: 101
4424953 GTTTTAAGAA
* *
4424963 AATACCGAAGCATGCACTGTGAATTCAATAGGAGTATCTACATTAAGGAGAGGTATTGAAGAATT
1 AATACCGAAGCATGCACTGTGAATTCAATAGGAGTATATACATTAAGGAGAGGTATTGAAGAATG
* **
4425028 AGACGGTGCACAACCTTTATTTGTTAAATGACTAAC
66 AGAAGAAGCACAACCTTTATTTGTTAAATGACTAAC
** * * * * *
4425064 AATACCGAAGCATGTGCTGTGAATTTAAT-GGCGTATATAGATTATGGAGAGGTATTGAAGGATG
1 AATACCGAAGCATGCACTGTGAATTCAATAGGAGTATATACATTAAGGAGAGGTATTGAAGAATG
** * *
4425128 AGAAGAAGCACCTCCTTTATTTGTTAAGTGAGTAAC
66 AGAAGAAGCACAACCTTTATTTGTTAAATGACTAAC
4425164 AA
1 AA
4425166 ATATGCGGTC
Statistics
Matches: 86, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
100 60 0.70
101 26 0.30
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (101 bp):
AATACCGAAGCATGCACTGTGAATTCAATAGGAGTATATACATTAAGGAGAGGTATTGAAGAATG
AGAAGAAGCACAACCTTTATTTGTTAAATGACTAAC
Found at i:4427287 original size:2 final size:2
Alignment explanation
Indices: 4427280--4427312 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4427270 CACGAGATCA
4427280 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4427313 GTATTTACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4434373 original size:28 final size:29
Alignment explanation
Indices: 4434306--4434373 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
4434296 TAAAGAAAAA
* * *
4434306 AAATTTAAAATGAAAAAGTTTAAAATTTT
1 AAATTTTAAATTAAAAAGATTAAAATTTT
* *
4434335 -AATTATAAATTAAAAA-ATTAATATTTT
1 AAATTTTAAATTAAAAAGATTAAAATTTT
4434362 AAATTTTAAATT
1 AAATTTTAAATT
4434374 TATTAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 9 0.28
28 23 0.72
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (29 bp):
AAATTTTAAATTAAAAAGATTAAAATTTT
Found at i:4434448 original size:42 final size:40
Alignment explanation
Indices: 4434359--4434466 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 40
4434349 AAATTAATAT
* * *
4434359 TTTAAATT-TTAAATTTATTAATATTTTAATGATAATAATG
1 TTTAAATTATTAAA-ATATTATTATTTTAATAATAATAATG
*
4434399 TTTAAATTATAACTAAAATATTATTATTTTAA-AATATTAATG
1 TTTAAATTAT---TAAAATATTATTATTTTAATAATAATAATG
*
4434441 TTTAAATTATTAAATTATTATTATTT
1 TTTAAATTATTAAAATATTATTATTT
4434467 CAAATTTTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
39 15 0.25
40 8 0.14
41 1 0.02
42 18 0.31
43 13 0.22
44 4 0.07
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (40 bp):
TTTAAATTATTAAAATATTATTATTTTAATAATAATAATG
Found at i:4434476 original size:23 final size:22
Alignment explanation
Indices: 4434424--4434476 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
4434414 AAATATTATT
*
4434424 ATTTTAAAATATTAATGTTTAA
1 ATTTTAAAATATTAATATTTAA
* *
4434446 ATTATTAAATTATTATTATTTCAA
1 ATT-TTAAAATATTAATATTT-AA
4434470 ATTTTAA
1 ATTTTAA
4434477 TGAAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 3 0.12
23 18 0.69
24 5 0.19
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTTAAAATATTAATATTTAA
Found at i:4443907 original size:156 final size:152
Alignment explanation
Indices: 4443707--4443991 Score: 373
Period size: 156 Copynumber: 1.8 Consensus size: 152
4443697 ATCTATGTCT
* * * * *
4443707 TTTACATCCTTTCATTGTCTCTGCCGTCTACCCCCAACTCCAAAATGCCATTACGTTTTC-TTTC
1 TTTAAATCCTTTAATTGTCTCTGCCATCTACCCCCAACTCCAAAATGACATTACATTTTCATTT-
4443771 CTTTTT-TTCTT-TAATTCTTATAATTTCTCATTGCAAAGGATTTCCT-GAC-TTTCGAACTTGT
65 -TTTTTATTCTTCT--TTC-T-T-ATTTCTCATTGCAAAGGATTT-CTAGACATTT-GAACTTGT
4443832 TGACGGAGAATTAAATTGATGAAGTTTATCC
122 TGACGGAGAATTAAATTGATGAAGTTTATCC
*
4443863 TTTAAATCCTTTAATTGTCTCTGCCATCTACCCCCAACTTCAAAATGACATTACATTTTCATTTT
1 TTTAAATCCTTTAATTGTCTCTGCCATCTACCCCCAACTCCAAAATGACATTACATTTTCATTTT
* * *
4443928 TTTTATTCTTCTTTCTTGTTTCTTATTGCAAAGGATTTCTAGACATTTGAACTTGTTGATGGAG
66 TTTTATTCTTCTTTCTTATTTCTCATTGCAAAGGATTTCTAGACATTTGAACTTGTTGACGGAG
4443992 CATTGACTTG
Statistics
Matches: 115, Mismatches: 9, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
151 2 0.02
152 37 0.32
153 4 0.03
154 1 0.01
155 8 0.07
156 59 0.51
157 4 0.03
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.44
Consensus pattern (152 bp):
TTTAAATCCTTTAATTGTCTCTGCCATCTACCCCCAACTCCAAAATGACATTACATTTTCATTTT
TTTTATTCTTCTTTCTTATTTCTCATTGCAAAGGATTTCTAGACATTTGAACTTGTTGACGGAGA
ATTAAATTGATGAAGTTTATCC
Found at i:4450413 original size:112 final size:112
Alignment explanation
Indices: 4450272--4450834 Score: 885
Period size: 112 Copynumber: 5.0 Consensus size: 112
4450262 TTAAACTGAA
* * * * *
4450272 ACTAAGATGATTGAGCATTTTTGGCTAAAATGATAATGTTTTGTTTATGCAGGCCCATCAGTCTT
1 ACTAAGATGGTTGAGCATTTTTTGCTAAAATGATAATGTTTTATTCATGCAGACCCATCAGTCTT
* * * *
4450337 ACAGAGATATGCAATCATGGGTAAGTGCAAGAAATCCTAAGTCTGCT
66 ACAGAGATACGCAATCATGGGTAAGTACAAGAAGTCCCAAGTCTGCT
4450384 ACTAAGATGGTTGAGCATTTTTTGCTAAAATGATAATGTTTTATTCATGCAGACCCATCAGTCTT
1 ACTAAGATGGTTGAGCATTTTTTGCTAAAATGATAATGTTTTATTCATGCAGACCCATCAGTCTT
* * * * *
4450449 ATAGAGATGCGAAATCATGGGTAAGTACAAGAAATCCCAAGTCCGCT
66 ACAGAGATACGCAATCATGGGTAAGTACAAGAAGTCCCAAGTCTGCT
*
4450496 ACTAAGATGGTTGAGCATTTTTTGCTGAAATGATAATGTTTTATTCATGCAGACCCATCAGTCTT
1 ACTAAGATGGTTGAGCATTTTTTGCTAAAATGATAATGTTTTATTCATGCAGACCCATCAGTCTT
*
4450561 ACAGAGATACGCAATCATGGGTAAGTACAAGAAGTCCCAAGTCTGCA
66 ACAGAGATACGCAATCATGGGTAAGTACAAGAAGTCCCAAGTCTGCT
4450608 ACTAAGATGGTTGAGCATTTTTTGCTAAAATGATAATGTTTTATTCATGCAGACCCATCAGTCTT
1 ACTAAGATGGTTGAGCATTTTTTGCTAAAATGATAATGTTTTATTCATGCAGACCCATCAGTCTT
* * * *
4450673 ACAGAAATACGCAATCATGGGTAAGGAAAAGAAGTCTCAAGTCTGCT
66 ACAGAGATACGCAATCATGGGTAAGTACAAGAAGTCCCAAGTCTGCT
* *
4450720 ACTAAGA-GCGTTGAGCATTTTTTGCTAAACTGATAATGTTTTATACATGCAGACCCATCAGTCT
1 ACTAAGATG-GTTGAGCATTTTTTGCTAAAATGATAATGTTTTATTCATGCAGACCCATCAGTCT
** *
4450784 CGCAGAGATACGCAATCATGGGTAAGTACAAGAAGTCCCGAGTCTGCT
65 TACAGAGATACGCAATCATGGGTAAGTACAAGAAGTCCCAAGTCTGCT
4450832 ACT
1 ACT
4450835 CCTGGTCTGT
Statistics
Matches: 416, Mismatches: 34, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
111 1 0.00
112 415 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (112 bp):
ACTAAGATGGTTGAGCATTTTTTGCTAAAATGATAATGTTTTATTCATGCAGACCCATCAGTCTT
ACAGAGATACGCAATCATGGGTAAGTACAAGAAGTCCCAAGTCTGCT
Found at i:4471634 original size:4 final size:4
Alignment explanation
Indices: 4471625--4471666 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
4471615 TTAATGGGGT
* *
4471625 TCTA TCTA TCTA TCTA TCTA TCTA TCTA CCTA CCTA TCTA TC
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TC
4471667 CATCCACCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.24, C:0.31, G:0.00, T:0.45
Consensus pattern (4 bp):
TCTA
Found at i:4489638 original size:19 final size:20
Alignment explanation
Indices: 4489605--4489643 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
4489595 AATAAAAAAG
4489605 CAACAATAACTTAA-CTGTC
1 CAACAATAACTTAACCTGTC
4489624 CAACAATAA-TATAACCTGTC
1 CAACAATAACT-TAACCTGTC
4489644 AGGATCAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.06
19 12 0.67
20 5 0.28
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.26
Consensus pattern (20 bp):
CAACAATAACTTAACCTGTC
Found at i:4499013 original size:15 final size:15
Alignment explanation
Indices: 4498993--4499021 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4498983 TGTTTAAAAG
4498993 TCTATGTATTAGAAT
1 TCTATGTATTAGAAT
4499008 TCTATGTATTAGAA
1 TCTATGTATTAGAA
4499022 CCGTTAGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (15 bp):
TCTATGTATTAGAAT
Found at i:4503234 original size:4 final size:4
Alignment explanation
Indices: 4503225--4503250 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4503215 CACCAGAAAT
4503225 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
4503251 TCCAAGCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:4535373 original size:21 final size:20
Alignment explanation
Indices: 4535349--4535395 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
4535339 AACAATGCAA
*
4535349 AAAAGCTAGAGAAA-AGAATAT
1 AAAAGCT-GAGAAAGAGAA-AC
*
4535370 AAAACCTGAGAAAGAGAAAC
1 AAAAGCTGAGAAAGAGAAAC
4535390 AAAAGC
1 AAAAGC
4535396 AATACCTGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.62, C:0.11, G:0.19, T:0.09
Consensus pattern (20 bp):
AAAAGCTGAGAAAGAGAAAC
Found at i:4546020 original size:123 final size:123
Alignment explanation
Indices: 4545796--4546048 Score: 373
Period size: 123 Copynumber: 2.1 Consensus size: 123
4545786 TTATCATGAT
* *
4545796 CACTATCACTATCACCAGATATATTTTGATCCTCGTCATAGTGATCACTATGTTGCCCCTCAATT
1 CACTTTCACTATCACCAGATATATTTTGATCCTCGTCATAGTGATCACTATGTTGCCCCTCAACT
* * *
4545861 GATAAGTTCTCATCATGCTTCTCACTGTAAGAGTCTCTAGATATGTTCTGATTCCCCC
66 GATAAGTTCTCACCATGCTTCTCACTATAAGAGTCTCTAGAAATGTTCTGATTCCCCC
* * * * *
4545919 CACTTTCACTATCA-CAGGATGTATTTTGATCCTTGTCATAGTGATCATTATGTTGCCCTTCGAC
1 CACTTTCACTATCACCA-GATATATTTTGATCCTCGTCATAGTGATCACTATGTTGCCCCTCAAC
* * *
4545983 TGATAAGTTCTCACCATGTTTTTCACTATGAGAGTCTCTAGAAATGTTCTGATTCCCCC
65 TGATAAGTTCTCACCATGCTTCTCACTATAAGAGTCTCTAGAAATGTTCTGATTCCCCC
4546042 CACTTTC
1 CACTTTC
4546049 TTGACTTAAG
Statistics
Matches: 116, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
122 2 0.02
123 114 0.98
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (123 bp):
CACTTTCACTATCACCAGATATATTTTGATCCTCGTCATAGTGATCACTATGTTGCCCCTCAACT
GATAAGTTCTCACCATGCTTCTCACTATAAGAGTCTCTAGAAATGTTCTGATTCCCCC
Found at i:4548107 original size:15 final size:16
Alignment explanation
Indices: 4548087--4548119 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4548077 TCTGTGTTCC
4548087 CTCTTTTT-TACTTTT
1 CTCTTTTTCTACTTTT
*
4548102 CTCTTTTTCTTCTTTT
1 CTCTTTTTCTACTTTT
4548118 CT
1 CT
4548120 TTGCCTCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (16 bp):
CTCTTTTTCTACTTTT
Found at i:4557868 original size:6 final size:6
Alignment explanation
Indices: 4557857--4557882 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4557847 ACTACTCATG
4557857 TGCTGA TGCTGA TGCTGA TGCTGA TG
1 TGCTGA TGCTGA TGCTGA TGCTGA TG
4557883 AAGAAAGTAA
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:0.15, C:0.15, G:0.35, T:0.35
Consensus pattern (6 bp):
TGCTGA
Found at i:4564015 original size:2 final size:2
Alignment explanation
Indices: 4564008--4564033 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4563998 GAAAATTAAG
4564008 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
4564034 TTATGCCTAG
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:4588000 original size:17 final size:17
Alignment explanation
Indices: 4587980--4588045 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 17
4587970 TATTATAATT
4587980 AAAATA-AAAATATTAAA
1 AAAATATAAAATA-TAAA
*
4587997 AAAATATATAATAT--A
1 AAAATATAAAATATAAA
4588012 AAAAT-TAAAAT-TAAA
1 AAAATATAAAATATAAA
4588027 AATAA-AT-AAATATAAA
1 AA-AATATAAAATATAAA
4588043 AAA
1 AAA
4588046 TTAATTTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
13 1 0.02
14 5 0.12
15 14 0.34
16 9 0.22
17 7 0.17
18 5 0.12
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATATAAAATATAAA
Found at i:4588018 original size:38 final size:40
Alignment explanation
Indices: 4587951--4588030 Score: 110
Period size: 38 Copynumber: 2.0 Consensus size: 40
4587941 TTTAATACTT
* * * *
4587951 TATTAAAAATATTTTATAATATTATAATTAAAA-TAAAAA
1 TATTAAAAATAATATATAATATAAAAATTAAAATTAAAAA
4587990 TATTAAAAA-AATATATAATATAAAAATTAAAATTAAAAA
1 TATTAAAAATAATATATAATATAAAAATTAAAATTAAAAA
4588029 TA
1 TA
4588031 AATAAATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
38 19 0.53
39 17 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (40 bp):
TATTAAAAATAATATATAATATAAAAATTAAAATTAAAAA
Found at i:4588025 original size:30 final size:30
Alignment explanation
Indices: 4587991--4588049 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
4587981 AAATAAAAAT
4587991 ATTAAAAA-AATATATAATAT-AAAAATTAAA
1 ATTAAAAATAA-ATA-AATATAAAAAATTAAA
4588021 ATTAAAAATAAATAAATATAAAAAATTAA
1 ATTAAAAATAAATAAATATAAAAAATTAA
4588050 TTTATATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 5 0.19
30 20 0.74
31 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (30 bp):
ATTAAAAATAAATAAATATAAAAAATTAAA
Found at i:4588155 original size:29 final size:29
Alignment explanation
Indices: 4588117--4588342 Score: 104
Period size: 29 Copynumber: 7.8 Consensus size: 29
4588107 TAAAGAAATG
4588117 AAAATAAAAATATATAAATTATAATAATAA
1 AAAAT-AAAATATATAAATTATAATAATAA
* *
4588147 AAAATAAAATATATGACATTA-AAAAAT-A
1 AAAATAAAATATAT-AAATTATAATAATAA
* **
4588175 TATTTAAAATATGAT--ATTAT-ATAA-AA
1 AAAATAAAATAT-ATAAATTATAATAATAA
*
4588201 ATTAATAATAA-ATATAAA-TAT-AT--TAA
1 A-AAATAA-AATATATAAATTATAATAATAA
4588227 AAAA-AAAATATA-AAATATAATAATAATAA
1 AAAATAAAATATATAAAT-T-ATAATAATAA
* * *
4588256 AAAA-AAAATATATGATATTAAAATATATTTA
1 AAAATAAAATATAT-AAATTATAATA-A-TAA
*
4588287 AAAATAATATATTATATAAAAT-TAATAATAAA
1 AAAATAA-A-A-TATATAAATTATAATAAT-AA
*
4588319 AAAATATAATATATTAAACTTATA
1 AAAATAAAATATA-TAAA-TTATA
4588343 TTTTAATAAT
Statistics
Matches: 148, Mismatches: 20, Indels: 54
0.67 0.09 0.24
Matches are distributed among these distances:
23 5 0.03
24 5 0.03
25 3 0.02
26 15 0.10
27 12 0.08
28 13 0.09
29 40 0.27
30 17 0.11
31 12 0.08
32 12 0.08
33 5 0.03
34 4 0.03
35 5 0.03
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (29 bp):
AAAATAAAATATATAAATTATAATAATAA
Found at i:4588211 original size:58 final size:57
Alignment explanation
Indices: 4588123--4588319 Score: 175
Period size: 58 Copynumber: 3.6 Consensus size: 57
4588113 AATGAAAATA
* * * * *
4588123 AAAATATATA-AATTATAATAATAAAAAATAAAATATATGACATTAAAAAATATATTT
1 AAAATATATATTA-TATAAAAATTAATAATAAAATATATGATATTAAAAAATATATTT
* * * *
4588180 AAAATATGATATTATATAAAAATTAATAATAAATATAAAT-ATATTAAAAAAAAAATAT
1 AAAATAT-ATATTATATAAAAATTAATAATAAA-ATATATGATATTAAAAAATATATTT
*
4588238 AAAATATA-A-TA-ATAATAA--AA-AA-AAAATATATGATATT--AAAATATATTT
1 AAAATATATATTATATAAAAATTAATAATAAAATATATGATATTAAAAAATATATTT
4588286 AAAAATAATATATTATAT-AAAATTAATAATAAAA
1 -AAAAT-ATATATTATATAAAAATTAATAATAAAA
4588320 AAATATAATA
Statistics
Matches: 112, Mismatches: 15, Indels: 27
0.73 0.10 0.18
Matches are distributed among these distances:
48 8 0.07
49 10 0.09
50 11 0.10
51 3 0.03
52 7 0.06
53 2 0.02
54 8 0.07
55 4 0.04
56 5 0.04
57 8 0.07
58 40 0.36
59 6 0.05
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.33
Consensus pattern (57 bp):
AAAATATATATTATATAAAAATTAATAATAAAATATATGATATTAAAAAATATATTT
Found at i:4588238 original size:22 final size:24
Alignment explanation
Indices: 4588203--4588268 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 24
4588193 ATATAAAAAT
*
4588203 TAATAATAAATATAAATATATTAA
1 TAATAAAAAATATAAATATATTAA
*
4588227 -AA-AAAAAATATAAAATATAATAA
1 TAATAAAAAATAT-AAATATATTAA
4588250 TAATAAAAAA-A-AAATATAT
1 TAATAAAAAATATAAATATAT
4588269 GATATTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
22 15 0.42
23 12 0.33
24 3 0.08
25 6 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (24 bp):
TAATAAAAAATATAAATATATTAA
Found at i:4588304 original size:59 final size:59
Alignment explanation
Indices: 4588216--4588345 Score: 156
Period size: 59 Copynumber: 2.2 Consensus size: 59
4588206 TAATAAATAT
*
4588216 AAATATATTAAAAAAAAAATATAAAATATAATAA-TAATAAAAAAAAAATAT-ATGATATTA
1 AAATATATT-TAAAAAAAATATAAAATATAA-AATTAATAAAAAAAAAATATAAT-ATATTA
* ** *
4588276 AAATATATTTAAAAATAATATATTATATAAAATTAATAATAAAAAAATATAATATATTA
1 AAATATATTTAAAAAAAATATAAAATATAAAATTAATAAAAAAAAAATATAATATATTA
*
4588335 AACTTATATTT
1 AA-ATATATTT
4588346 TAATAATTAG
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
58 2 0.03
59 41 0.67
60 18 0.30
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.35
Consensus pattern (59 bp):
AAATATATTTAAAAAAAATATAAAATATAAAATTAATAAAAAAAAAATATAATATATTA
Found at i:4596175 original size:30 final size:30
Alignment explanation
Indices: 4596141--4596219 Score: 133
Period size: 30 Copynumber: 2.6 Consensus size: 30
4596131 GACAAAAGCC
4596141 CTTGGATTTAGCCCAAGTGGTTTTAGTGTT
1 CTTGGATTTAGCCCAAGTGGTTTTAGTGTT
*
4596171 CTTGGGTTTAGCCCAAGTGGTTTTAGTGTT
1 CTTGGATTTAGCCCAAGTGGTTTTAGTGTT
4596201 CTT-GAGTTTAGCCCAAGTG
1 CTTGGA-TTTAGCCCAAGTG
4596220 ATTAACCTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 1 0.02
30 45 0.98
ACGTcount: A:0.16, C:0.15, G:0.28, T:0.41
Consensus pattern (30 bp):
CTTGGATTTAGCCCAAGTGGTTTTAGTGTT
Found at i:4612188 original size:2 final size:2
Alignment explanation
Indices: 4612163--4612204 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
4612153 TGAGATTAAA
* *
4612163 AT AT -T AT AT AT -T AT AC AT AC 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
4612203 AT
1 AT
4612205 GTAAATGCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4612510 original size:3 final size:3
Alignment explanation
Indices: 4612502--4612527 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4612492 TACATGACAA
4612502 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
4612528 CCGTCTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:4621583 original size:105 final size:105
Alignment explanation
Indices: 4621401--4621611 Score: 379
Period size: 105 Copynumber: 2.0 Consensus size: 105
4621391 AGCTGTCAAA
* * *
4621401 CGTATGCTTCCTCCAATTCCCATTCCAAACGCAGGTGTCCAACTCTTGCCACAACTATCACGCAT
1 CGTATGCTTCCTCCAATTCCCATTCCAAACGCAGGTGTCCAACTCTGGCAACAACTATCACCCAT
4621466 GCCTTTTCTCTCTCCGGCTCCGGCTCC-GACGCCGAATATC
66 GCCTTTTCTCTCTCCGGCTCCGGCTCCAG-CGCCGAATATC
4621506 CGTATGCTTCCTCCAATTCCCATTCCAAACGCAGGTGTCCAACTCTGGCAACAACTATCACCCAT
1 CGTATGCTTCCTCCAATTCCCATTCCAAACGCAGGTGTCCAACTCTGGCAACAACTATCACCCAT
4621571 GCCTTTTCTCTCTCCGGCTCCGGCTCCAGCGCCGAATATC
66 GCCTTTTCTCTCTCCGGCTCCGGCTCCAGCGCCGAATATC
4621611 C
1 C
4621612 TGCAGGTGCG
Statistics
Matches: 102, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
105 101 0.99
106 1 0.01
ACGTcount: A:0.19, C:0.39, G:0.15, T:0.26
Consensus pattern (105 bp):
CGTATGCTTCCTCCAATTCCCATTCCAAACGCAGGTGTCCAACTCTGGCAACAACTATCACCCAT
GCCTTTTCTCTCTCCGGCTCCGGCTCCAGCGCCGAATATC
Found at i:4631422 original size:222 final size:222
Alignment explanation
Indices: 4631117--4631573 Score: 734
Period size: 222 Copynumber: 2.1 Consensus size: 222
4631107 AAGAAGATGC
* * * * *
4631117 AAAGACGGAGCAAACCCCAAACTCGCGGACTGAGTCATTTTTCCTCGGAAGTCACCGAGACTTTC
1 AAAGATGGAGCAAACCCCAAACTCGCGGACTGAGTCATGTTCCCTCGGAAGTCACCAAGACTTCC
4631182 CAGTCTGCTGCCAGGTTGACTAACTCCTCTGTTCAAAGCATCATTTATGTTCAATGTATTACACG
66 CAGTCTGCTGCCAGGTTGACTAACTCCTCTGTTCAAAGCATCATTTATGTTCAATGTATTACACG
* *
4631247 TTGATGCCTGCCCTCCATTTAAGAAACCACTCTGAATGTGCATTTTATCACCTGACATGTTTTGG
131 ATGATGCCTGCCCTCCATTTAAGAAACCACTCTGAATGTCCATTTTATCACCTGACATGTTTTGG
* * *
4631312 TATCTAGGTGTATTTGAAGGGACCCTA
196 AATCCAGGTGTACTTGAAGGGACCCTA
* *
4631339 AATGATGGAGCAAACCCCAAACTCGCGGACTGAGTCATGTTCCCTCGGAAGTCACTAAGACTTCC
1 AAAGATGGAGCAAACCCCAAACTCGCGGACTGAGTCATGTTCCCTCGGAAGTCACCAAGACTTCC
* * * *
4631404 CAGTCTGCTTCCAGGTTGACTTACTCCTCTGTTTAAAGCATCATTTATGTTCAATGTATTACCCG
66 CAGTCTGCTGCCAGGTTGACTAACTCCTCTGTTCAAAGCATCATTTATGTTCAATGTATTACACG
* * * *
4631469 ATGATGCCTGTCCTCCATTTGAGAAACCAGTCTGAATGTCCATTTTATCACGTGACATGTTTTGG
131 ATGATGCCTGCCCTCCATTTAAGAAACCACTCTGAATGTCCATTTTATCACCTGACATGTTTTGG
4631534 AATCCAGGTGTACTTGAAGGGACCCTA
196 AATCCAGGTGTACTTGAAGGGACCCTA
4631561 AAAGATGGAGCAA
1 AAAGATGGAGCAA
4631574 CCTTGATATT
Statistics
Matches: 214, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
222 214 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (222 bp):
AAAGATGGAGCAAACCCCAAACTCGCGGACTGAGTCATGTTCCCTCGGAAGTCACCAAGACTTCC
CAGTCTGCTGCCAGGTTGACTAACTCCTCTGTTCAAAGCATCATTTATGTTCAATGTATTACACG
ATGATGCCTGCCCTCCATTTAAGAAACCACTCTGAATGTCCATTTTATCACCTGACATGTTTTGG
AATCCAGGTGTACTTGAAGGGACCCTA
Found at i:4642879 original size:40 final size:40
Alignment explanation
Indices: 4642835--4642938 Score: 172
Period size: 40 Copynumber: 2.6 Consensus size: 40
4642825 TCGTGACGAG
4642835 GTTAGGAAACCCACTAAGGTGAACCACCAATCTTGGCAAA
1 GTTAGGAAACCCACTAAGGTGAACCACCAATCTTGGCAAA
* *
4642875 GTTAGGAAACCCATTAAGGTGAACCACCAATCTTGGCAAG
1 GTTAGGAAACCCACTAAGGTGAACCACCAATCTTGGCAAA
*
4642915 GTTAGAAAACCCTACTAAGGTGAA
1 GTTAGGAAACCC-ACTAAGGTGAA
4642939 GAATAACCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 49 0.83
41 10 0.17
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (40 bp):
GTTAGGAAACCCACTAAGGTGAACCACCAATCTTGGCAAA
Found at i:4653496 original size:2 final size:2
Alignment explanation
Indices: 4653489--4653513 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4653479 CTAACACAAC
4653489 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 A
4653514 CACACACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4660706 original size:30 final size:30
Alignment explanation
Indices: 4660670--4660728 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
4660660 CATTACATCA
4660670 TGGTAATTATACGAGTACCAGTATTATTAT
1 TGGTAATTATACGAGTACCAGTATTATTAT
* *
4660700 TGGTAATTATACGAGTGCTAGTATTATTA
1 TGGTAATTATACGAGTACCAGTATTATTA
4660729 ATTAATATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (30 bp):
TGGTAATTATACGAGTACCAGTATTATTAT
Found at i:4661102 original size:5 final size:5
Alignment explanation
Indices: 4661094--4661123 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
4661084 AGGGGAAGAA
4661094 AGGAG AGGAG AGGAG AGGAG AGGAG AGGAG
1 AGGAG AGGAG AGGAG AGGAG AGGAG AGGAG
4661124 TCGCCATCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (5 bp):
AGGAG
Found at i:4668690 original size:33 final size:33
Alignment explanation
Indices: 4668646--4668724 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
4668636 CCAAATGGCT
4668646 GCTGTCCTGCCATTTGTGAAGGCCCAGGATATG
1 GCTGTCCTGCCATTTGTGAAGGCCCAGGATATG
* * *
4668679 GCTGTCGTGCCATTTGTGAAGGTCCAGGATATT
1 GCTGTCCTGCCATTTGTGAAGGCCCAGGATATG
4668712 GCTGTCCTGCCAT
1 GCTGTCCTGCCAT
4668725 CGGAGGAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.30
Consensus pattern (33 bp):
GCTGTCCTGCCATTTGTGAAGGCCCAGGATATG
Found at i:4684716 original size:6 final size:6
Alignment explanation
Indices: 4684708--4684792 Score: 143
Period size: 6 Copynumber: 14.2 Consensus size: 6
4684698 ACGAGGCTGA
*
4684708 GATTGA GATTGC GATTGC GATTGC GATTGC GATTGC GATTGC GATTGC
1 GATTGC GATTGC GATTGC GATTGC GATTGC GATTGC GATTGC GATTGC
* *
4684756 GATTGC GATTGC GATTGC GATTGC GACTGC GACTGC G
1 GATTGC GATTGC GATTGC GATTGC GATTGC GATTGC G
4684793 GCGGCGAAGC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 77 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.31
Consensus pattern (6 bp):
GATTGC
Found at i:4685409 original size:5 final size:5
Alignment explanation
Indices: 4685401--4685428 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
4685391 AAAGAATCGC
4685401 AATAT AATAT AATAT AATAT AATAT AAT
1 AATAT AATAT AATAT AATAT AATAT AAT
4685429 CTAGCATCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:4686934 original size:41 final size:41
Alignment explanation
Indices: 4686875--4686953 Score: 133
Period size: 41 Copynumber: 1.9 Consensus size: 41
4686865 AGCCTAGTTT
*
4686875 AAGAAAATTATCACATATAATGCATAGCCTATAATAGCCAG
1 AAGAAAATTATCACATATAATGCATAACCTATAATAGCCAG
4686916 AAGAAAATTATCTA-ATATAATGCATAACCTATAATAGC
1 AAGAAAATTATC-ACATATAATGCATAACCTATAATAGC
4686954 TATAGGTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
41 35 0.97
42 1 0.03
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (41 bp):
AAGAAAATTATCACATATAATGCATAACCTATAATAGCCAG
Found at i:4694886 original size:54 final size:53
Alignment explanation
Indices: 4694826--4694933 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 53
4694816 TCTCCTCATA
*
4694826 ATTTTAACTATTTTTAACTAAGAGATAAGATTTGGGGGGAAAATACCCTTAATG
1 ATTTTAACTATTTTTAACTAAGAGATAAGATTT-GGGGAAAAATACCCTTAATG
*
4694880 ATTTTAACTATTTTTAACTAAGAGATAAGATTTGGGGAAAAATGCCCTTAATG
1 ATTTTAACTATTTTTAACTAAGAGATAAGATTTGGGGAAAAATACCCTTAATG
4694933 A
1 A
4694934 AGCTTTCTCA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
53 19 0.37
54 33 0.63
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (53 bp):
ATTTTAACTATTTTTAACTAAGAGATAAGATTTGGGGAAAAATACCCTTAATG
Found at i:4703116 original size:26 final size:26
Alignment explanation
Indices: 4703087--4703187 Score: 118
Period size: 26 Copynumber: 3.9 Consensus size: 26
4703077 AAAAAAAAAA
4703087 TCTACACGTCATTTTCATAAAAAATT
1 TCTACACGTCATTTTCATAAAAAATT
*
4703113 TCTACACATCATTTTCAT--AAAATT
1 TCTACACGTCATTTTCATAAAAAATT
* *
4703137 TCTACATGTCATGTTCA-AAAACAATT
1 TCTACACGTCATTTTCATAAAA-AATT
* *
4703163 TGCTACATGTCATTGTCATAAAAAA
1 T-CTACACGTCATTTTCATAAAAAA
4703188 ATTTTCACAC
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
24 20 0.31
25 2 0.03
26 22 0.34
27 16 0.25
28 4 0.06
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.37
Consensus pattern (26 bp):
TCTACACGTCATTTTCATAAAAAATT
Found at i:4703134 original size:24 final size:25
Alignment explanation
Indices: 4703087--4703211 Score: 94
Period size: 24 Copynumber: 4.9 Consensus size: 25
4703077 AAAAAAAAAA
*
4703087 TCTACACGTCATTTTCATAAAAAATT
1 TCTACACATCATTTTCAT-AAAAATT
4703113 TCTACACATCATTTTCAT-AAAATT
1 TCTACACATCATTTTCATAAAAATT
** * *
4703137 TCTACATGTCATGTTCAAAAACAATT
1 TCTACACATCATTTTCATAAA-AATT
** *
4703163 TGCTACATGTCATTGTCATAAAAAAATT
1 T-CTACACATCATTTTCAT--AAAAATT
*
4703191 T-TCACACATCATGTTCA-AAAA
1 TCT-ACACATCATTTTCATAAAA
4703212 TTTTGTTACA
Statistics
Matches: 81, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
24 24 0.30
25 2 0.02
26 23 0.28
27 24 0.30
28 5 0.06
29 3 0.04
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (25 bp):
TCTACACATCATTTTCATAAAAATT
Found at i:4703163 original size:50 final size:51
Alignment explanation
Indices: 4703087--4703185 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 51
4703077 AAAAAAAAAA
* *
4703087 TCTACACGTCATTTTCATAAAAAATTT-CTACACATCATTTTCATAAAATT
1 TCTACACGTCATGTTCATAAAAAATTTGCTACACATCATTGTCATAAAATT
* **
4703137 TCTACATGTCATGTTCA-AAAACAATTTGCTACATGTCATTGTCATAAAA
1 TCTACACGTCATGTTCATAAAA-AATTTGCTACACATCATTGTCATAAAA
4703186 AAATTTTCAC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 4 0.10
50 20 0.48
51 18 0.43
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.37
Consensus pattern (51 bp):
TCTACACGTCATGTTCATAAAAAATTTGCTACACATCATTGTCATAAAATT
Found at i:4703172 original size:27 final size:26
Alignment explanation
Indices: 4703077--4703211 Score: 98
Period size: 26 Copynumber: 5.2 Consensus size: 26
4703067 AATTTTGAGT
** * *
4703077 AAAAAAAAAATCTACACGTCATTTTC
1 AAAAAAAATTTCTACATGTCATGTTC
* ** *
4703103 ATAAAAAATTTCTACACATCATTTTC
1 AAAAAAAATTTCTACATGTCATGTTC
*
4703129 --ATAAAATTTCTACATGTCATGTTC
1 AAAAAAAATTTCTACATGTCATGTTC
*
4703153 AAAAACAATTTGCTACATGTCAT-TGTC
1 AAAAAAAATTT-CTACATGTCATGT-TC
**
4703180 ATAAAAAAATTT-TCACACATCATGTTC
1 A-AAAAAAATTTCT-ACATGTCATGTTC
4703207 AAAAA
1 AAAAA
4703212 TTTTGTTACA
Statistics
Matches: 89, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
24 20 0.22
26 35 0.39
27 24 0.27
28 10 0.11
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAAAAAATTTCTACATGTCATGTTC
Done.