Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 80 of 202
Found at i:23513500 original size:27 final size:27
Alignment explanation
Indices: 23513470--23513547 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
23513460 CACCAAAACG
23513470 ATCCTATCAGAGTATGCCACAAAGACA
1 ATCCTATCAGAGTATGCCACAAAGACA
* * * * *
23513497 ATCCAATCAGAAT-TCACCACAAAGGCT
1 ATCCTATCAGAGTAT-GCCACAAAGACA
23513524 AT-CTATACAGAGTATGCCACAAAG
1 ATCCTAT-CAGAGTATGCCACAAAG
23513548 GATGGCAGGA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
26 4 0.10
27 35 0.88
28 1 0.03
ACGTcount: A:0.41, C:0.26, G:0.14, T:0.19
Consensus pattern (27 bp):
ATCCTATCAGAGTATGCCACAAAGACA
Found at i:23515619 original size:17 final size:17
Alignment explanation
Indices: 23515593--23515639 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
23515583 AATTTGTTTG
*
23515593 ATATATTTTTTATTTAT
1 ATATAATTTTTATTTAT
*
23515610 ATATAATTTTTATATAT
1 ATATAATTTTTATTTAT
*
23515627 -TA-AATATTTATTT
1 ATATAATTTTTATTT
23515640 TCTCCAGCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 9 0.35
16 2 0.08
17 15 0.58
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATAATTTTTATTTAT
Found at i:23515794 original size:28 final size:28
Alignment explanation
Indices: 23515752--23515806 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
23515742 CATAATGATA
23515752 TATATAATATATATTTT-TATTATATAAT
1 TATATAATATATATTTTAT-TTATATAAT
23515780 TATATAAT-TATTATTTTATTTATATAA
1 TATATAATATA-TATTTTATTTATATAA
23515807 ATGAAAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 2 0.08
28 22 0.88
29 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TATATAATATATATTTTATTTATATAAT
Found at i:23522842 original size:51 final size:51
Alignment explanation
Indices: 23522769--23523056 Score: 287
Period size: 51 Copynumber: 5.7 Consensus size: 51
23522759 TATTGATGAA
* * *
23522769 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
* ** * * * * *
23522820 CACATGTGTAGTACTAAATGAAGGCTACAATGTGTACCGAGAAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAA-ATGTTGGT
* * * * *
23522871 CACGTGTGTAGTACTGTGTGAAGGCTACTATGTGAATCGATAAATGATGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
* * * *
23522922 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAA-GCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATG--TTGGT
* * ** *
23522973 CACGTGTGTAGTACTATATGAAGGCTACTACGTGAACAG-TAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
*
23523023 CACGTGTGTAGTACTATGTGAAGGTTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
23523057 TATCAAATGA
Statistics
Matches: 192, Mismatches: 39, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
49 1 0.01
50 40 0.21
51 150 0.78
52 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
Found at i:23522945 original size:102 final size:102
Alignment explanation
Indices: 23522769--23523046 Score: 425
Period size: 102 Copynumber: 2.7 Consensus size: 102
23522759 TATTGATGAA
*
23522769 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTAC
* *
23522834 TAAATGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
*
23522871 CACGTGTGTAGTACTGTGTGAAGGCTACTATGTGAATCGATAAATGATGATCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTAC
*
23522936 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
* * *** *
23522973 CACGTGTGTAGTACTATATGAAGGCTACTACGTGAA-C-AGTAAAACTTGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGA-TAAATGATGATCACATGTGTAGTA
*
23523036 CTATGTGAAGG
65 CTAAGTGAAGG
23523047 TTACTACGTG
Statistics
Matches: 162, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
100 1 0.01
101 31 0.19
102 130 0.80
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
Found at i:23523322 original size:37 final size:38
Alignment explanation
Indices: 23523253--23523333 Score: 110
Period size: 37 Copynumber: 2.1 Consensus size: 38
23523243 ATGTGTGGAA
* **
23523253 TTGAATTGAATATTGACTTGAAAATGGCAAAGTGAAAT
1 TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAAAT
*
23523291 TTGAATTGAATAGTGA-TTGAAAGTGAAAAAGTGAAAT
1 TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAAAT
23523328 TATGAA
1 T-TGAA
23523334 AAAGTAGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 19 0.50
38 19 0.50
ACGTcount: A:0.44, C:0.02, G:0.22, T:0.31
Consensus pattern (38 bp):
TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAAAT
Found at i:23527200 original size:6 final size:6
Alignment explanation
Indices: 23527140--23527198 Score: 73
Period size: 6 Copynumber: 9.8 Consensus size: 6
23527130 AGAACGACAT
* * * *
23527140 AGAAGA AGAAGA AAAAGG AGAATG AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
*
23527188 AGAAGA AGAAG
1 AGAAGG AGAAG
23527199 AAATAGACAC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.58, C:0.00, G:0.41, T:0.02
Consensus pattern (6 bp):
AGAAGG
Found at i:23541333 original size:19 final size:20
Alignment explanation
Indices: 23541309--23541355 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
23541299 GTTGAGAGAG
**
23541309 GAGAGAATGA-TGAATGAGT
1 GAGAGAATGATTGAAAAAGT
23541328 GAGAG-ATGATTGAAAAAGT
1 GAGAGAATGATTGAAAAAGT
23541347 GAGA-AATGA
1 GAGAGAATGA
23541356 GCTCTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.47, C:0.00, G:0.34, T:0.19
Consensus pattern (20 bp):
GAGAGAATGATTGAAAAAGT
Found at i:23543284 original size:36 final size:36
Alignment explanation
Indices: 23543243--23543315 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
23543233 AGTAACTATT
23543243 ACTTGAACAATACAAAGTTTTGTGTTTTACAAACTA
1 ACTTGAACAATACAAAGTTTTGTGTTTTACAAACTA
23543279 ACTTGAACAATACAAAGTTTTGTGTTTTACAAACTA
1 ACTTGAACAATACAAAGTTTTGTGTTTTACAAACTA
23543315 A
1 A
23543316 GTCACGTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.36
Consensus pattern (36 bp):
ACTTGAACAATACAAAGTTTTGTGTTTTACAAACTA
Found at i:23550834 original size:11 final size:11
Alignment explanation
Indices: 23550814--23550844 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
23550804 TTTAGAAATT
*
23550814 TTTGAAAAACC
1 TTTGATAAACC
23550825 TTTGATAAACC
1 TTTGATAAACC
23550836 TTTGATAAA
1 TTTGATAAA
23550845 TCTATCAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (11 bp):
TTTGATAAACC
Found at i:23553424 original size:15 final size:16
Alignment explanation
Indices: 23553393--23553427 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
23553383 AGAAGATCCC
*
23553393 AATGCAATTGAATCTA
1 AATGCAAATGAATCTA
23553409 AATGCAAATG-ATCTA
1 AATGCAAATGAATCTA
23553424 AATG
1 AATG
23553428 AATGAATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (16 bp):
AATGCAAATGAATCTA
Found at i:23564940 original size:35 final size:35
Alignment explanation
Indices: 23564901--23565003 Score: 95
Period size: 35 Copynumber: 3.0 Consensus size: 35
23564891 GGAGCAGCAT
* *
23564901 CGTGTAAA-AGATATATAGGTCCTACAGGGCGACAA
1 CGTGTAAATAG-TATACAAGTCCTACAGGGCGACAA
*
23564936 CGTGTAAATAGTATACAAGTCCTACAGGGTGAC-A
1 CGTGTAAATAGTATACAAGTCCTACAGGGCGACAA
* * * * *
23564970 CTTTGTAAA-GGTATACAATTCCTTCGGGGCGACA
1 C-GTGTAAATAGTATACAAGTCCTACAGGGCGACA
23565004 CCTCAAAAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
34 21 0.38
35 33 0.59
36 2 0.04
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (35 bp):
CGTGTAAATAGTATACAAGTCCTACAGGGCGACAA
Found at i:23577522 original size:14 final size:14
Alignment explanation
Indices: 23577503--23577591 Score: 78
Period size: 14 Copynumber: 6.4 Consensus size: 14
23577493 TAAATTACTC
23577503 CAACAATAGTTATA
1 CAACAATAGTTATA
*
23577517 CAACAAGAAGTTATA
1 CAACAA-TAGTTATA
* *
23577532 -AACAGTA-ATATTA
1 CAACAATAGTTA-TA
23577545 -AACAATAGTTATA
1 CAACAATAGTTATA
* *
23577558 CAACAAGAAGTCATA
1 CAACAA-TAGTTATA
23577573 -AACAATAGTTATA
1 CAACAATAGTTATA
23577586 CAACAA
1 CAACAA
23577592 GAAGTCATAA
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
12 2 0.03
13 17 0.29
14 27 0.46
15 13 0.22
ACGTcount: A:0.54, C:0.13, G:0.09, T:0.24
Consensus pattern (14 bp):
CAACAATAGTTATA
Found at i:23577577 original size:28 final size:28
Alignment explanation
Indices: 23577543--23577601 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
23577533 ACAGTAATAT
23577543 TAAACAATAGTTATACAACAAGAAGTCA
1 TAAACAATAGTTATACAACAAGAAGTCA
23577571 TAAACAATAGTTATACAACAAGAAGTCA
1 TAAACAATAGTTATACAACAAGAAGTCA
23577599 TAA
1 TAA
23577602 CCTTGTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.54, C:0.14, G:0.10, T:0.22
Consensus pattern (28 bp):
TAAACAATAGTTATACAACAAGAAGTCA
Found at i:23579199 original size:17 final size:17
Alignment explanation
Indices: 23579177--23579210 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
23579167 AGGTTTCAAG
*
23579177 TTTAAGGTAGTAAACAA
1 TTTAAGATAGTAAACAA
*
23579194 TTTAAGATAGTTAACAA
1 TTTAAGATAGTAAACAA
23579211 AAGGCCACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (17 bp):
TTTAAGATAGTAAACAA
Found at i:23580898 original size:25 final size:21
Alignment explanation
Indices: 23580850--23580894 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
23580840 ACCGATTTAC
*
23580850 AACAATCCTCTAATAGAGTCT
1 AACAATACTCTAATAGAGTCT
*
23580871 AACAATACTCTAATAGAGCCT
1 AACAATACTCTAATAGAGTCT
23580892 AAC
1 AAC
23580895 TAACATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.24
Consensus pattern (21 bp):
AACAATACTCTAATAGAGTCT
Found at i:23583144 original size:14 final size:14
Alignment explanation
Indices: 23583125--23583152 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
23583115 GGCAAGGAAT
23583125 TCTGAGCTAACAAC
1 TCTGAGCTAACAAC
23583139 TCTGAGCTAACAAC
1 TCTGAGCTAACAAC
23583153 ACCAGCCCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (14 bp):
TCTGAGCTAACAAC
Found at i:23584441 original size:36 final size:36
Alignment explanation
Indices: 23584389--23584458 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
23584379 GAGACTGTGG
23584389 CCCAAACCAATTCGATCCACCAT-TCGTATAACACGA
1 CCCAAACCAATTCGATCCACCATCT-GTATAACACGA
* *
23584425 CCCAGACCAATTCGATCCACTATCTGTATAACAC
1 CCCAAACCAATTCGATCCACCATCTGTATAACAC
23584459 ATATATACAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.34, C:0.36, G:0.09, T:0.21
Consensus pattern (36 bp):
CCCAAACCAATTCGATCCACCATCTGTATAACACGA
Found at i:23586999 original size:25 final size:25
Alignment explanation
Indices: 23586969--23587049 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 25
23586959 GTTCTAACCC
23586969 ACAGCTTGTGTGAGCATACCGATTT
1 ACAGCTTGTGTGAGCATACCGATTT
* * * * *
23586994 ATAGCTCGTGAGAGCATACTGATCT
1 ACAGCTTGTGTGAGCATACCGATTT
* * *
23587019 ACATCTTGAGTGAGCATACCGATTC
1 ACAGCTTGTGTGAGCATACCGATTT
23587044 ACAGCT
1 ACAGCT
23587050 CATATGAGCA
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (25 bp):
ACAGCTTGTGTGAGCATACCGATTT
Found at i:23588834 original size:35 final size:35
Alignment explanation
Indices: 23588764--23588864 Score: 130
Period size: 35 Copynumber: 2.9 Consensus size: 35
23588754 AAATGCGATG
* *
23588764 TTAAAAAGGTTTGGATAGACAAGTTCTAAGGCAACC
1 TTAAAAAGGTTAGGATAGACACG-TCTAAGGCAACC
* *
23588800 TTAAAAAGATTAGGATAGACTCGTCTAAGGCAACC
1 TTAAAAAGGTTAGGATAGACACGTCTAAGGCAACC
** *
23588835 TTCGAAAGGTTGGGATAGACACGTCTAAGG
1 TTAAAAAGGTTAGGATAGACACGTCTAAGG
23588865 GAATTTTTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
35 37 0.66
36 19 0.34
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.24
Consensus pattern (35 bp):
TTAAAAAGGTTAGGATAGACACGTCTAAGGCAACC
Found at i:23596157 original size:9 final size:9
Alignment explanation
Indices: 23596138--23596169 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
23596128 TTTAAACTAT
23596138 TTATTTATTA
1 TTATTT-TTA
23596148 TTATTTTTA
1 TTATTTTTA
23596157 TTATTTTTA
1 TTATTTTTA
23596166 TTAT
1 TTAT
23596170 AACTCTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
TTATTTTTA
Found at i:23597006 original size:18 final size:19
Alignment explanation
Indices: 23596972--23597007 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
23596962 AGGATCATAT
23596972 TTTTAAATTTCTTTTCGAA
1 TTTTAAATTTCTTTTCGAA
*
23596991 TTTTCAATTT-TTTTCGA
1 TTTTAAATTTCTTTTCGA
23597008 CATTAAGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.22, C:0.11, G:0.06, T:0.61
Consensus pattern (19 bp):
TTTTAAATTTCTTTTCGAA
Found at i:23601069 original size:212 final size:211
Alignment explanation
Indices: 23600623--23601121 Score: 615
Period size: 211 Copynumber: 2.4 Consensus size: 211
23600613 GTAGCAGATC
* * * * * * *
23600623 AAATATGCAAGTGATGAAGATAATAAAATGTGCACAATAAATTGAAATGTATAAAAAAAATCAAA
1 AAATATACAATTGATGGAGGTAATAAAATGCGTATAATAAATTGAAATGTAT-AAAAAAATCAAA
* * * * *
23600688 ATGAAGCTTTGATGCAATAATAAAGTACTCTTAAACAATATAATTTATTTTAAATACGAAAGGAT
65 ATCAAGCTTTGATACAATAATAAAGTACTCTCAAACAATATAACTTATTTTAAATACGAAAAGAT
** * * *
23600753 ATCAAAGTAATTTTCCTAACCATGTTGGTGCCTGGTTGACTTGTGACACCAACTCAGCCAATGTT
130 ATCAAAGTAATTTTCCTAACCACATTGATGCCTGGTTGAATTGTGACACCAACTCAGCCAAGGTT
*
23600818 TAAATAATAGTAAATAT
195 TAAACAATAGTAAATAT
* * *
23600835 AGATATACAATTGATAGAGGTAATAAAATGCGTATAATAGATTGAAATGTATAAAAAAATCAAAA
1 AAATATACAATTGATGGAGGTAATAAAATGCGTATAATAAATTGAAATGTATAAAAAAATCAAAA
* * *
23600900 TCAGGCTTTGATACAATACTAAAGTACTCTCAAATAATATAACTTATTTTAAATACGAAAAGATA
66 TCAAGCTTTGATACAATAATAAAGTACTCTCAAACAATATAACTTATTTTAAATACGAAAAGATA
* * * ** *
23600965 TCAAAGTAATTTTCTTAACCGCATTGATAGCCT-GTTGAATTGTGACACCAACTTAGTTAGGGGT
131 TCAAAGTAATTTTCCTAACCACATTGAT-GCCTGGTTGAATTGTGACACCAACTCAGCCA-AGGT
*
23601029 TTAAACAATAGTAAGTAT
194 TTAAACAATAGTAAATAT
* * *
23601047 AAATATACAATTGATGGAGGTAATAAATTGTGCATATAATAAATTAAAATGT-TAAAAAAATCAA
1 AAATATACAATTGATGGAGGTAATAAA--ATGCGTATAATAAATTGAAATGTATAAAAAAATCAA
* *
23601111 AGTGAAGCTTT
64 AATCAAGCTTT
23601122 AATTGAGTGG
Statistics
Matches: 243, Mismatches: 40, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
211 115 0.47
212 89 0.37
213 20 0.08
214 19 0.08
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (211 bp):
AAATATACAATTGATGGAGGTAATAAAATGCGTATAATAAATTGAAATGTATAAAAAAATCAAAA
TCAAGCTTTGATACAATAATAAAGTACTCTCAAACAATATAACTTATTTTAAATACGAAAAGATA
TCAAAGTAATTTTCCTAACCACATTGATGCCTGGTTGAATTGTGACACCAACTCAGCCAAGGTTT
AAACAATAGTAAATAT
Found at i:23603488 original size:44 final size:46
Alignment explanation
Indices: 23603398--23603489 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
23603388 TTTGGTTCGC
*
23603398 TGTAACGGAATAGAGGCGTAATGGGTAATTCTTTTGTTTGGTTGAA
1 TGTAACGGAATAGAGGCGTAATGGGTAATTCTTGTGTTTGGTTGAA
*
23603444 TGTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAA
1 TGTAACGGAATAGAGGCGTAATGGGTAATTCTTGTGTTTGGTTGAA
23603488 TG
1 TG
23603490 GAATACAGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 20 0.45
45 3 0.07
46 21 0.48
ACGTcount: A:0.25, C:0.05, G:0.32, T:0.38
Consensus pattern (46 bp):
TGTAACGGAATAGAGGCGTAATGGGTAATTCTTGTGTTTGGTTGAA
Found at i:23603490 original size:39 final size:44
Alignment explanation
Indices: 23603398--23603504 Score: 125
Period size: 46 Copynumber: 2.5 Consensus size: 44
23603388 TTTGGTTCGC
* *
23603398 TGTAACGGAATAGAGGCGTAATGGGTAATTCTTTTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATGGGTAATTCTTGTGTTTGGTT--A
23603444 TGTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGCGTAATGGGTAATTCTTGTGTTTGGTTA
* *
23603484 TG-AATGGAATACAGGTGTAAT
1 TGTAATGGAATAGAGGCGTAAT
23603505 AGCATAAGGA
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
39 17 0.30
40 2 0.04
43 1 0.02
44 13 0.23
45 3 0.05
46 21 0.37
ACGTcount: A:0.27, C:0.06, G:0.31, T:0.36
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATGGGTAATTCTTGTGTTTGGTTA
Found at i:23603740 original size:20 final size:21
Alignment explanation
Indices: 23603701--23603740 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
23603691 AATTTACTAA
*
23603701 TAAAATCATAATATATAATAC
1 TAAAATCATAATATAAAATAC
*
23603722 TAAAAT-ATAATTTAAAATA
1 TAAAATCATAATATAAAATA
23603741 ATTATTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATCATAATATAAAATAC
Found at i:23603753 original size:26 final size:28
Alignment explanation
Indices: 23603708--23603787 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 28
23603698 TAATAAAATC
23603708 ATAATATATAATACTAAAATATAATTTAA-A
1 ATAATATATAAT--T-AAATATAATTTAATA
*
23603738 ATAAT-TATTATTAAATATAATTTAATA
1 ATAATATATAATTAAATATAATTTAATA
* *
23603765 ATAATATATAATTTAATAAAATT
1 ATAATATATAATTAAATATAATT
23603788 CTTATTCTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
26 13 0.30
27 7 0.16
28 14 0.32
29 5 0.11
30 5 0.11
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
ATAATATATAATTAAATATAATTTAATA
Found at i:23603756 original size:100 final size:105
Alignment explanation
Indices: 23603632--23603874 Score: 308
Period size: 100 Copynumber: 2.3 Consensus size: 105
23603622 TTAATCATAT
* * *
23603632 TTTAACATAATTGTTATAAAATATAATTTAAT-A-AA-AT-T-GTTAAT-AAA-TATTCTTATAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAGTTAATAAAATTATTCTTATAT
23603690 GAATTTACTAATAAAATCATAATATATAATAC-TAAAATATAA
66 GAATTTAC---TAAAATCATAATATATAATACATAAAATATAA
*
23603732 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAATTCTTATTCTT
1 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATAT-AGTTAATAAAA---TTATTCTT
23603797 ATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
62 ATATGAATTTACTAAAATCATAATATATAATAC-ATAAAATATAA
23603842 TTT-AAATAATTATTATTAAATATAATTT-ATAAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAT
23603875 CTACTTTATT
Statistics
Matches: 126, Mismatches: 4, Indels: 18
0.85 0.03 0.12
Matches are distributed among these distances:
100 29 0.23
101 1 0.01
102 2 0.02
103 2 0.02
104 1 0.01
106 5 0.04
107 3 0.02
108 26 0.21
109 25 0.20
110 13 0.10
111 19 0.15
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (105 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAGTTAATAAAATTATTCTTATAT
GAATTTACTAAAATCATAATATATAATACATAAAATATAA
Found at i:23603820 original size:44 final size:41
Alignment explanation
Indices: 23603719--23603820 Score: 98
Period size: 44 Copynumber: 2.3 Consensus size: 41
23603709 TAATATATAA
23603719 TACTAAAATATAATTTAAAATAATTATTATTAAATATAATT
1 TACTAAAATATAATTTAAAATAATTATTATTAAATATAATT
* * **
23603760 TAATAATAATATATAATTTAATAA-AATTCTTATTCTTATATGAATT
1 TACT-A-AA-ATATAATTTAA-AATAATTATTATT-AAATAT-AATT
23603806 TACTAAAATCATAAT
1 TACTAAAAT-ATAAT
23603821 ATATAATACT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
41 3 0.06
42 1 0.02
43 4 0.08
44 27 0.55
45 7 0.14
46 7 0.14
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (41 bp):
TACTAAAATATAATTTAAAATAATTATTATTAAATATAATT
Found at i:23603866 original size:32 final size:32
Alignment explanation
Indices: 23603830--23603893 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
23603820 TATATAATAC
*
23603830 TATAAAATATAATTTAAATAATTATTATTAAA
1 TATAAAATATAATCTAAATAATTATTATTAAA
** ** *
23603862 TATAATTTATAATCTACTTTATTATTATTAAA
1 TATAAAATATAATCTAAATAATTATTATTAAA
23603894 CTGCAATACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (32 bp):
TATAAAATATAATCTAAATAATTATTATTAAA
Found at i:23604206 original size:64 final size:64
Alignment explanation
Indices: 23604097--23604312 Score: 373
Period size: 64 Copynumber: 3.4 Consensus size: 64
23604087 TAGAATCAAG
*
23604097 TTGATTATATCTAATGATCCAA--TTAATATATTATCCATATGTTTTTTAATCAAGTTGTTTAC
1 TTGATTATATCTAATGATCCAATTTTAATATATTATCCATATGTTTTTTAATCAATTTGTTTAC
* *
23604159 TTGATTATATCTAATGATTCAATTTTAATATATTATTCATATGTTTTTTAATCAATTTGTTTAC
1 TTGATTATATCTAATGATCCAATTTTAATATATTATCCATATGTTTTTTAATCAATTTGTTTAC
*
23604223 TTGATTATATGTAATGATCCAATTTTAATATATTATCCATATGTTTTTTAATCAATTTGTTTAC
1 TTGATTATATCTAATGATCCAATTTTAATATATTATCCATATGTTTTTTAATCAATTTGTTTAC
*
23604287 TTGATTATATGTAATGATCCAATTTT
1 TTGATTATATCTAATGATCCAATTTT
23604313 TATTTTATTT
Statistics
Matches: 146, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
62 21 0.14
64 125 0.86
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.51
Consensus pattern (64 bp):
TTGATTATATCTAATGATCCAATTTTAATATATTATCCATATGTTTTTTAATCAATTTGTTTAC
Found at i:23604508 original size:32 final size:32
Alignment explanation
Indices: 23604428--23604509 Score: 146
Period size: 32 Copynumber: 2.6 Consensus size: 32
23604418 TAGAAATATT
*
23604428 TTTAATTAATGAGTAGTATATGAATATACACA
1 TTTAATTAATGAGTTGTATATGAATATACACA
23604460 TTTAATTAATGAGTTGTATATGAATATACACA
1 TTTAATTAATGAGTTGTATATGAATATACACA
*
23604492 TTTAATTAATGCGTTGTA
1 TTTAATTAATGAGTTGTA
23604510 CAAGTCTCGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.41
Consensus pattern (32 bp):
TTTAATTAATGAGTTGTATATGAATATACACA
Found at i:23607083 original size:17 final size:17
Alignment explanation
Indices: 23607061--23607096 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
23607051 AAGTAATAAA
23607061 GAAAAAGGGAGGAAAAG
1 GAAAAAGGGAGGAAAAG
23607078 GAAAAAGGGAGGAAAAG
1 GAAAAAGGGAGGAAAAG
23607095 GA
1 GA
23607097 CTCACTTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (17 bp):
GAAAAAGGGAGGAAAAG
Found at i:23607883 original size:3 final size:3
Alignment explanation
Indices: 23607877--23607936 Score: 97
Period size: 3 Copynumber: 20.3 Consensus size: 3
23607867 TGTTACATCA
23607877 TAT TAT TAT T-T T-T GTAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
23607921 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
23607937 TACTCATCTA
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 3 0.05
3 51 0.93
4 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:23608011 original size:29 final size:29
Alignment explanation
Indices: 23607972--23608047 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 29
23607962 AAATTTTGCT
23607972 ATATATATACATTCATACAT-TTTTATAAA
1 ATATATATACA-TCATACATATTTTATAAA
* *
23608001 ATATATATACA-CATACATATTTTTTATA
1 ATATATATACATCATACATATTTTATAAA
*
23608029 ATTTATATACAT-ATACATA
1 ATATATATACATCATACATA
23608048 CTTATATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 7 0.17
28 24 0.57
29 11 0.26
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (29 bp):
ATATATATACATCATACATATTTTATAAA
Found at i:23608060 original size:28 final size:28
Alignment explanation
Indices: 23607975--23608057 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 28
23607965 TTTTGCTATA
* * *
23607975 TATATACATTCATACAT-TTTTATAAAATA
1 TATATACA--CATACATATTATATATAATT
* *
23608004 TATATACACATACATATTTTTTATAATT
1 TATATACACATACATATTATATATAATT
*
23608032 TATATACATATACATACTTATATATA
1 TATATACACATACATA-TTATATATA
23608058 TTTCTTATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 7 0.15
28 24 0.52
29 15 0.33
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (28 bp):
TATATACACATACATATTATATATAATT
Found at i:23608340 original size:24 final size:24
Alignment explanation
Indices: 23608313--23608363 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
23608303 TTTTACATTT
23608313 TTTATTAATTTTATTCTATTT-CTA
1 TTTATTAATTTTATT-TATTTACTA
*
23608337 TTTATTTATTTTATTTATTTACTA
1 TTTATTAATTTTATTTATTTACTA
23608361 TTT
1 TTT
23608364 CGAAAGAANN
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTATTAATTTTATTTATTTACTA
Found at i:23610823 original size:67 final size:67
Alignment explanation
Indices: 23610715--23610842 Score: 229
Period size: 67 Copynumber: 1.9 Consensus size: 67
23610705 CCAATTCAGT
* *
23610715 GAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAAGCTAAATCCCCTACAA
1 GAGCACACTCCCGCGAACATCATTTCTTACAGCGGGATTACCAATCCAAGCTAAATCCCCTACAA
23610780 GA
66 GA
*
23610782 GAGCACACTCCCGCGAACATCATTTCTTACAGCGGGATTACCAATCCAGGCTAAATCCCCT
1 GAGCACACTCCCGCGAACATCATTTCTTACAGCGGGATTACCAATCCAAGCTAAATCCCCT
23610843 GTAATATAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.29, C:0.34, G:0.16, T:0.20
Consensus pattern (67 bp):
GAGCACACTCCCGCGAACATCATTTCTTACAGCGGGATTACCAATCCAAGCTAAATCCCCTACAA
GA
Found at i:23614096 original size:31 final size:32
Alignment explanation
Indices: 23614058--23614136 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 32
23614048 CAAATTTTGT
*
23614058 TATATATATACATTCATACATTTTTATAA-TA
1 TATATATATACATACATACATTTTTATAATTA
* **
23614089 TATATATACACATACATATTTTTTTATAATTTA
1 TATATATATACATACATACATTTTTATAA-TTA
*
23614122 TATACATATACATAC
1 TATATATATACATAC
23614137 TTATATATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
31 25 0.62
33 15 0.38
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (32 bp):
TATATATATACATACATACATTTTTATAATTA
Found at i:23614145 original size:29 final size:30
Alignment explanation
Indices: 23614058--23614138 Score: 98
Period size: 29 Copynumber: 2.8 Consensus size: 30
23614048 CAAATTTTGT
23614058 TATATATATACAT-T-CATACATTTTTATAA
1 TATATATATACATATACATAC-TTTTTATAA
* *
23614087 TATATATATACACATACATATTTTTTTATAA
1 TATATATATACATATACATA-CTTTTTATAA
23614118 T-T-TATATACATATACATACTT
1 TATATATATACATATACATACTT
23614139 ATATATATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
28 2 0.04
29 27 0.60
30 2 0.04
31 14 0.31
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (30 bp):
TATATATATACATATACATACTTTTTATAA
Found at i:23615248 original size:32 final size:33
Alignment explanation
Indices: 23615198--23615264 Score: 109
Period size: 32 Copynumber: 2.0 Consensus size: 33
23615188 AACCCATGTT
23615198 ATTCGAGTTTTTTTTTTAATGATCATATTTTTAA
1 ATTCGAG-TTTTTTTTTAATGATCATATTTTTAA
*
23615232 ATTCGAG-TTTTTTTTAATGATCGTATTTTTAA
1 ATTCGAGTTTTTTTTTAATGATCATATTTTTAA
23615264 A
1 A
23615265 AAACGCTTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 25 0.78
34 7 0.22
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.57
Consensus pattern (33 bp):
ATTCGAGTTTTTTTTTAATGATCATATTTTTAA
Found at i:23621206 original size:97 final size:97
Alignment explanation
Indices: 23621030--23621223 Score: 280
Period size: 97 Copynumber: 2.0 Consensus size: 97
23621020 ATATTGTAAC
* * * * *
23621030 CTAAGTTTAATCGAGTTAGCTTATTTAAGATAACAACTCTTACACAACTCGTTGACCTATGTTCA
1 CTAAATTTAATCGAGTTAACTAATTTAAGATAACAACTCCTACACAACTCGCTGACCTATGTTCA
*
23621095 CAGGTGATTTTATTAAGGTTAACTGATTTAAG
66 CAAGTGATTTTATTAAGGTTAACTGATTTAAG
* * * *
23621127 CTAAATTTATTCGAGTTAACTAATTTAATATTACAACTCCTACACAGCTCGCTGACCTATGTTCA
1 CTAAATTTAATCGAGTTAACTAATTTAAGATAACAACTCCTACACAACTCGCTGACCTATGTTCA
**
23621192 CAAGTGATTTTATTAAGGTTAGTTGATTTAAG
66 CAAGTGATTTTATTAAGGTTAACTGATTTAAG
23621224 ATCGCATGTA
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 85 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (97 bp):
CTAAATTTAATCGAGTTAACTAATTTAAGATAACAACTCCTACACAACTCGCTGACCTATGTTCA
CAAGTGATTTTATTAAGGTTAACTGATTTAAG
Found at i:23622529 original size:50 final size:50
Alignment explanation
Indices: 23622420--23622666 Score: 248
Period size: 50 Copynumber: 4.8 Consensus size: 50
23622410 ATTTGGGTAA
23622420 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCCTTGAGGTCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GA-G--ATG
* *
23622476 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** * * *
23622526 AGAGCTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
23622576 AGA-ACTCCCATGTAAGACCATATCTGGGATATGGCATT-G-ACAGTACATG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* * * * *
23622625 AAACATCTCATGTAAGACCATGTCTGAGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
23622667 TGTTATTATC
Statistics
Matches: 162, Mismatches: 24, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
48 2 0.01
49 35 0.22
50 78 0.48
51 1 0.01
52 1 0.01
53 2 0.01
55 2 0.01
56 41 0.25
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:23624238 original size:105 final size:105
Alignment explanation
Indices: 23624052--23624812 Score: 575
Period size: 105 Copynumber: 7.1 Consensus size: 105
23624042 CGTTCACCGC
* *
23624052 TGATTTAAGATCGCAACCTAAATTTATTCAAGTTAG-TTGATTTAAGATTGCAACTCCTACATAG
1 TGATTTAAGATCGCAACCTAAATTTATTCGAGTTAGCTT-ATTTAAGATTGCAACTCCTACACAG
* * *
23624116 CTCACTGACCTAAGTTCACAGTTAATTTTATTAAGATTTGT
65 CTCACTGACCTAAGTTCACAGTTGATTTTATTAAGGTTAGT
23624157 TGATTTAAGATCGCAACCTAAATTTATTCGAGTTAGCTTATTTAAGATTGCAACTCCTACACAGC
1 TGATTTAAGATCGCAACCTAAATTTATTCGAGTTAGCTTATTTAAGATTGCAACTCCTACACAGC
* * * * * *
23624222 TCACTGACCTACGTTCAAAGCTAACTTTATTAAGGTTATT
66 TCACTGACCTAAGTTCACAGTTGATTTTATTAAGGTTAGT
* * * * *
23624262 TGATTTAAGATCACAATCTAAGTTTATTTGAGTTCA-CTTATTTAAGATCGCAACTCCTA-ACAG
1 TGATTTAAGATCGCAACCTAAATTTATTCGAGTT-AGCTTATTTAAGATTGCAACTCCTACACAG
** ** * * * * * *
23624325 CGT-GTTGATTTAAGATCGCAATTGATATTATTAAGGCTAGG
65 C-TCACTGACCTAAGTTCACAGTTGATTTTATTAAGGTTAGT
* * * * *
23624366 TGATTTACGATCGCAACTTAAGTTAATTTGAGTTTGTTGATTTAAGATCACTGATTTAAGATTGC
1 TGATTTAAGATCGCAACCT-A---AATTT-A---T-TCGAGTT-AG----CTTATTTAAGATTGC
* ** ** * * *
23624431 AACTCCTA-ACAACTCGTTGATTTAAGATCGCA-TCTAATTTTATTAAGGTTAGT
52 AACTCCTACACAGCTCACTGACCTAAGTTCACAGT-TGATTTTATTAAGGTTAGT
* * * * * * * * *
23624484 TGATTTACGATTGTAACCTAAATTTATTTGAGATAGCTTATTTAATATCGTAACTCCTCCACAGC
1 TGATTTAAGATCGCAACCTAAATTTATTCGAGTTAGCTTATTTAAGATTGCAACTCCTACACAGC
* *
23624549 TTACTGACCTACA-TTCACAGTTGATTTTATTAAAGGTTAAT
66 TCACTGACCTA-AGTTCACAGTTGATTTTATT-AAGGTTAGT
* * * *
23624590 TGATTTAAGATCGCAACCTAAATCTATTCAAGTTAGCTAATTTAAGATTGCAACTTCTACACCA-
1 TGATTTAAGATCGCAACCTAAATTTATTCGAGTTAGCTTATTTAAGATTGCAACTCCTACA-CAG
* * * * * *
23624654 CTCACTAACTTATGTTCATAGTTGATTTTATTAAGGGTAGC
65 CTCACTGACCTAAGTTCACAGTTGATTTTATTAAGGTTAGT
* * * * * * * * *
23624695 TAATTTAAGATCGCAACCTAAATTTTTTCAAGTTAGCTGATTTAATATTACAATTGCTACATAGC
1 TGATTTAAGATCGCAACCTAAATTTATTCGAGTTAGCTTATTTAAGATTGCAACTCCTACACAGC
** * * * * ** *
23624760 TCGTTGGCCTACGTTCATAGCTGATAATACTAAGGTTAGT
66 TCACTGACCTAAGTTCACAGTTGATTTTATTAAGGTTAGT
23624800 TGATTTAAGATCG
1 TGATTTAAGATCG
23624813 TAGCCCCCGA
Statistics
Matches: 523, Mismatches: 107, Indels: 52
0.77 0.16 0.08
Matches are distributed among these distances:
104 61 0.12
105 270 0.52
106 87 0.17
107 2 0.00
108 6 0.01
109 6 0.01
110 1 0.00
112 1 0.00
113 8 0.02
114 5 0.01
117 3 0.01
118 73 0.14
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (105 bp):
TGATTTAAGATCGCAACCTAAATTTATTCGAGTTAGCTTATTTAAGATTGCAACTCCTACACAGC
TCACTGACCTAAGTTCACAGTTGATTTTATTAAGGTTAGT
Found at i:23624513 original size:118 final size:118
Alignment explanation
Indices: 23624295--23624515 Score: 302
Period size: 118 Copynumber: 1.9 Consensus size: 118
23624285 TTATTTGAGT
* * *
23624295 TCACTTATTTAAGATCGCAACTCCTAACAGCGTGTTGATTTAAGATCGCAATTGATATTATTAAG
1 TCACTGATTTAAGATCGCAACTCCTAACAACGTGTTGATTTAAGATCGCAATTAATATTATTAAG
* *
23624360 GCTAGGTGATTTACGATCGCAACTTAAGTTAATTTGAGTTTGTTGATTTAAGA
66 GCTAGGTGATTTACGATCGCAACCTAAATTAATTTGAGTTTGTTGATTTAAGA
* *
23624413 TCACTGATTTAAGATTGCAACTCCTAACAAC-TCGTTGATTTAAGATCGC-ATCTAATTTTATTA
1 TCACTGATTTAAGATCGCAACTCCTAACAACGT-GTTGATTTAAGATCGCAAT-TAATATTATTA
* * * * *
23624476 AGGTTAGTTGATTTACGATTGTAACCTAAATTTATTTGAG
64 AGGCTAGGTGATTTACGATCGCAACCTAAATTAATTTGAG
23624516 ATAGCTTATT
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
117 3 0.03
118 86 0.97
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (118 bp):
TCACTGATTTAAGATCGCAACTCCTAACAACGTGTTGATTTAAGATCGCAATTAATATTATTAAG
GCTAGGTGATTTACGATCGCAACCTAAATTAATTTGAGTTTGTTGATTTAAGA
Found at i:23624627 original size:106 final size:105
Alignment explanation
Indices: 23624467--23624742 Score: 302
Period size: 106 Copynumber: 2.6 Consensus size: 105
23624457 ATCGCATCTA
* * * ** * *
23624467 ATTTTATTAAGGTTAGTTGATTTACGATTGTAACCTAAATTTATTTGAGATAGCTTATTTAATAT
1 ATTTTATTAAGGTTAGTTGATTTAAGATCGCAACCTAAATTTATTCAAGTTAGCTAATTTAATAT
* * * *
23624532 CGTAACTCCTCCA-CAGCTTACTGACCTACATTCACAGTTG
66 CGCAACTCCTACACCA-CTCACTAACCTACATTCACAGTTG
* * *
23624572 ATTTTATTAAAGGTTAATTGATTTAAGATCGCAACCTAAATCTATTCAAGTTAGCTAATTTAAGA
1 ATTTTATT-AAGGTTAGTTGATTTAAGATCGCAACCTAAATTTATTCAAGTTAGCTAATTTAATA
* * * ** *
23624637 TTGCAACTTCTACACCACTCACTAACTTATGTTCATAGTTG
65 TCGCAACTCCTACACCACTCACTAACCTACATTCACAGTTG
* * * * *
23624678 ATTTTATTAAGGGTAGCTAATTTAAGATCGCAACCTAAATTTTTTCAAGTTAGCTGATTTAATAT
1 ATTTTATTAAGGTTAGTTGATTTAAGATCGCAACCTAAATTTATTCAAGTTAGCTAATTTAATAT
23624743 TACAATTGCT
Statistics
Matches: 141, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
105 57 0.40
106 82 0.58
107 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (105 bp):
ATTTTATTAAGGTTAGTTGATTTAAGATCGCAACCTAAATTTATTCAAGTTAGCTAATTTAATAT
CGCAACTCCTACACCACTCACTAACCTACATTCACAGTTG
Found at i:23625819 original size:30 final size:30
Alignment explanation
Indices: 23625753--23625829 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 30
23625743 TTACACCACA
**
23625753 GGTCACCCAACTATGGGTTTGTTTCTTTTTT
1 GGTCA-CCAACTATGGAATTGTTTCTTTTTT
23625784 GGTCACTCAACTATGGAATTGTTTCTTTTTT
1 GGTCAC-CAACTATGGAATTGTTTCTTTTTT
23625815 -GTCACCAAACTATGG
1 GGTCACC-AACTATGG
23625830 TTGTTTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
29 1 0.02
30 14 0.33
31 27 0.64
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.43
Consensus pattern (30 bp):
GGTCACCAACTATGGAATTGTTTCTTTTTT
Found at i:23626150 original size:53 final size:49
Alignment explanation
Indices: 23626058--23626156 Score: 137
Period size: 53 Copynumber: 1.9 Consensus size: 49
23626048 AAATATACAT
*
23626058 AAATTTTGTCAAAAATATAATAATAAATTTAAAATTATATAAAAATAAA
1 AAATTTTGACAAAAATATAATAATAAATTTAAAATTATATAAAAATAAA
23626107 AAATTTTGACAAGAAATAATAATATATAAAATTTAAACA-TATATAAAAAT
1 AAATTTTGACAA-AAAT-ATAATA-AT-AAATTTAAA-ATTATATAAAAAT
23626157 GTATAAAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
49 11 0.25
50 4 0.09
51 6 0.14
52 2 0.05
53 20 0.45
54 1 0.02
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (49 bp):
AAATTTTGACAAAAATATAATAATAAATTTAAAATTATATAAAAATAAA
Found at i:23626860 original size:50 final size:49
Alignment explanation
Indices: 23626792--23626888 Score: 176
Period size: 50 Copynumber: 2.0 Consensus size: 49
23626782 ATTAGACTTC
23626792 AATTTCCTCTTTCATAAATCTTTGGGTTTTCATGGAGGAAATCAATTTT
1 AATTTCCTCTTTCATAAATCTTTGGGTTTTCATGGAGGAAATCAATTTT
*
23626841 AATTTCCCTTTTTCATAAATCTTTGGGTTTTCATGGAGGAAATCAATT
1 AATTT-CCTCTTTCATAAATCTTTGGGTTTTCATGGAGGAAATCAATT
23626889 GGGATACCCT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 5 0.11
50 41 0.89
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.44
Consensus pattern (49 bp):
AATTTCCTCTTTCATAAATCTTTGGGTTTTCATGGAGGAAATCAATTTT
Found at i:23627921 original size:30 final size:31
Alignment explanation
Indices: 23627867--23627936 Score: 99
Period size: 32 Copynumber: 2.3 Consensus size: 31
23627857 ACTGTTAATC
*
23627867 AGTGACTGTTTTGTCACTTTTTTTATAACGTT-
1 AGTGACTGTTTTGTCAC-TTTTTTA-AAAGTTG
23627899 AGTGACTGTTTTGTCA-TTTTTTAAAAGTTG
1 AGTGACTGTTTTGTCACTTTTTTAAAAGTTG
23627929 AGTGACTG
1 AGTGACTG
23627937 AAATGAAACC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 5 0.14
30 15 0.42
32 16 0.44
ACGTcount: A:0.21, C:0.10, G:0.20, T:0.49
Consensus pattern (31 bp):
AGTGACTGTTTTGTCACTTTTTTAAAAGTTG
Found at i:23628059 original size:29 final size:29
Alignment explanation
Indices: 23628027--23628091 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
23628017 ATATTAATAT
*
23628027 AAAATTTAAATTTATTATTATAT-TTTTTG
1 AAAATTT-AATGTATTATTATATATTTTTG
* * *
23628056 AAAATATTTATGTATTTTTATATATTTTTT
1 AAAAT-TTAATGTATTATTATATATTTTTG
23628086 AAAATT
1 AAAATT
23628092 ATATTATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
29 18 0.60
30 12 0.40
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (29 bp):
AAAATTTAATGTATTATTATATATTTTTG
Found at i:23628080 original size:31 final size:33
Alignment explanation
Indices: 23628036--23628103 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 33
23628026 TAAAATTTAA
23628036 ATTTATTATTATATTTTTTGAAAA-TAT-TTATGT
1 ATTTATTATTATATTTTTT-AAAATTATATTAT-T
23628069 ATTT-TTA-TATATTTTTTAAAATTATATTATT
1 ATTTATTATTATATTTTTTAAAATTATATTATT
23628100 ATTT
1 ATTT
23628104 CTTGTCAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
30 4 0.12
31 18 0.55
32 7 0.21
33 4 0.12
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (33 bp):
ATTTATTATTATATTTTTTAAAATTATATTATT
Found at i:23628141 original size:10 final size:10
Alignment explanation
Indices: 23628128--23628168 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
23628118 TTTTATTTTA
23628128 TTTTATATAT
1 TTTTATATAT
23628138 TTTTA-AT-T
1 TTTTATATAT
*
23628146 TGATTATATAT
1 T-TTTATATAT
23628157 TTTTATATAT
1 TTTTATATAT
23628167 TT
1 TT
23628169 CTTTGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
8 2 0.08
9 5 0.19
10 17 0.65
11 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (10 bp):
TTTTATATAT
Found at i:23631064 original size:23 final size:23
Alignment explanation
Indices: 23631032--23631075 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
23631022 ACTACCATTT
23631032 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
23631055 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
23631076 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:23631068 original size:13 final size:11
Alignment explanation
Indices: 23631036--23631078 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
23631026 CCATTTTCTA
*
23631036 AATAAAATAAT
1 AATAAAATATT
23631047 AAT-AAATATCT
1 AATAAAATAT-T
23631058 AAGTAAAATATT
1 AA-TAAAATATT
23631070 AATAAAATA
1 AATAAAATA
23631079 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:23632839 original size:27 final size:27
Alignment explanation
Indices: 23632775--23632839 Score: 62
Period size: 27 Copynumber: 2.4 Consensus size: 27
23632765 GGTGGTAAAA
* *
23632775 ACCACATA-TATCTATTTTGGTGGCTT
1 ACCACATATTATCTATTCTGGTAGCTT
* * *
23632801 AGCCACGT-TTATCTGTTCTGGTAGTTT
1 A-CCACATATTATCTATTCTGGTAGCTT
23632828 ACCACATATTAT
1 ACCACATATTAT
23632840 ATATGGCAGC
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
26 6 0.20
27 24 0.80
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (27 bp):
ACCACATATTATCTATTCTGGTAGCTT
Found at i:23633751 original size:13 final size:13
Alignment explanation
Indices: 23633733--23633757 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23633723 TCAAACGATG
23633733 TTTTTCCACATTC
1 TTTTTCCACATTC
23633746 TTTTTCCACATT
1 TTTTTCCACATT
23633758 TTGCACGTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.28, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTTCCACATTC
Found at i:23636255 original size:12 final size:13
Alignment explanation
Indices: 23636217--23636263 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
23636207 TTAATATAAA
23636217 ATTATTTTTATAT
1 ATTATTTTTATAT
* *
23636230 ATT-TTTTAAAAT
1 ATTATTTTTATAT
23636242 ATTTATTTTTATAT
1 A-TTATTTTTATAT
23636256 ATTTATTT
1 A-TTATTT
23636264 GTATTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 8 0.29
13 5 0.18
14 15 0.54
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTATTTTTATAT
Found at i:23638693 original size:21 final size:21
Alignment explanation
Indices: 23638669--23638711 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
23638659 TTTTGGTTGT
23638669 TATTTGAATCTTCAAATGATA
1 TATTTGAATCTTCAAATGATA
23638690 TATTTGAATCTTCAAATGATA
1 TATTTGAATCTTCAAATGATA
23638711 T
1 T
23638712 TCATAAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (21 bp):
TATTTGAATCTTCAAATGATA
Found at i:23645357 original size:21 final size:20
Alignment explanation
Indices: 23645333--23645375 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
23645323 TTTAATTAAT
23645333 TTTTTAAAATTAAAAAGAATA
1 TTTTTAAAATTAAAAA-AATA
*
23645354 TTTTTAAAATTTAAAAAATA
1 TTTTTAAAATTAAAAAAATA
23645374 TT
1 TT
23645376 AAAATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TTTTTAAAATTAAAAAAATA
Found at i:23645399 original size:20 final size:20
Alignment explanation
Indices: 23645362--23645399 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
23645352 TATTTTTAAA
*
23645362 ATTTAAAAAATATTAAAATT
1 ATTTAAAAAATATAAAAATT
23645382 ATTTAAAAAGA-ATAAAAA
1 ATTTAAAAA-ATATAAAAA
23645400 ATATATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
ATTTAAAAAATATAAAAATT
Found at i:23645948 original size:2 final size:2
Alignment explanation
Indices: 23645941--23645971 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23645931 AGTGCTTTAT
23645941 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23645972 TAAATACCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23649027 original size:17 final size:17
Alignment explanation
Indices: 23648981--23649028 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
23648971 AGATGTTGTA
* *
23648981 AATCGTATCCACCAGGT
1 AATCCTATCCGCCAGGT
23648998 AATCCTA-CTCGCCAGGT
1 AATCCTATC-CGCCAGGT
*
23649015 AATTCTATCCGCCA
1 AATCCTATCCGCCA
23649029 AGCTATACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 1 0.04
17 24 0.92
18 1 0.04
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25
Consensus pattern (17 bp):
AATCCTATCCGCCAGGT
Found at i:23649038 original size:125 final size:125
Alignment explanation
Indices: 23648816--23649072 Score: 453
Period size: 125 Copynumber: 2.1 Consensus size: 125
23648806 CTTTCCAAAA
*
23648816 GAATATTAACTTCTATAATTATCAACTTAAAGATGTTGTAAATCGTATCCACCAGGTAATCCTAC
1 GAATACTAACTTCTATAATTATCAACTTAAAGATGTTGTAAATCGTATCCACCAGGTAATCCTAC
* *
23648881 TCGCCAGGTCATTCTATCCGCTAAGCTATACTATTCGCCAGGCAATACTGTCCGCTAGGC
66 TCGCCAGGTAATTCTATCCGCCAAGCTATACTATTCGCCAGGCAATACTGTCCGCTAGGC
* *
23648941 GAATACTAACTTTTATAATTATTAACTTAAAGATGTTGTAAATCGTATCCACCAGGTAATCCTAC
1 GAATACTAACTTCTATAATTATCAACTTAAAGATGTTGTAAATCGTATCCACCAGGTAATCCTAC
*
23649006 TCGCCAGGTAATTCTATCCGCCAAGCTATACTATTTGCCAGGCAATACTGTCCGCTAGGC
66 TCGCCAGGTAATTCTATCCGCCAAGCTATACTATTCGCCAGGCAATACTGTCCGCTAGGC
23649066 G-ATACTA
1 GAATACTA
23649073 TCCACTAGAC
Statistics
Matches: 126, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
124 6 0.05
125 120 0.95
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (125 bp):
GAATACTAACTTCTATAATTATCAACTTAAAGATGTTGTAAATCGTATCCACCAGGTAATCCTAC
TCGCCAGGTAATTCTATCCGCCAAGCTATACTATTCGCCAGGCAATACTGTCCGCTAGGC
Found at i:23649131 original size:18 final size:17
Alignment explanation
Indices: 23649019--23649131 Score: 64
Period size: 17 Copynumber: 6.6 Consensus size: 17
23649009 CCAGGTAATT
* *
23649019 CTATCCGCCAAGCTATA
1 CTATCCGCCAGGCGATA
** *
23649036 CTATTTGCCAGGCAATA
1 CTATCCGCCAGGCGATA
* *
23649053 CTGTCCGCTAGGCGATA
1 CTATCCGCCAGGCGATA
* * * *
23649070 CTATCCACTAGACGGTA
1 CTATCCGCCAGGCGATA
* * * *
23649087 TTGTTCGTCAGGCGATA
1 CTATCCGCCAGGCGATA
* *
23649104 CTATCTGCCAGGTGATA
1 CTATCCGCCAGGCGATA
23649121 CTTATCCGCCA
1 C-TATCCGCCA
23649132 ATGATAAGAA
Statistics
Matches: 67, Mismatches: 28, Indels: 1
0.70 0.29 0.01
Matches are distributed among these distances:
17 59 0.88
18 8 0.12
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.27
Consensus pattern (17 bp):
CTATCCGCCAGGCGATA
Found at i:23663122 original size:4 final size:4
Alignment explanation
Indices: 23663113--23663187 Score: 54
Period size: 4 Copynumber: 19.5 Consensus size: 4
23663103 TATTTTTATT
*
23663113 TTTA TTTA TTTA TTT- TTTA -TTA -TTA TTTA -TTA TTTA -TTA TTATT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA
* *
23663157 TTTC TTTA CTTTA TTTTC TTTA -TTA TTTA TT
1 TTTA TTTA -TTTA -TTTA TTTA TTTA TTTA TT
23663188 ACTTATTTGG
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
3 18 0.31
4 30 0.52
5 10 0.17
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:23663122 original size:10 final size:10
Alignment explanation
Indices: 23663101--23663187 Score: 63
Period size: 10 Copynumber: 8.2 Consensus size: 10
23663091 CAACCCAATT
23663101 TTTATTTTTA
1 TTTATTTTTA
23663111 TTT-TTATTTA
1 TTTATT-TTTA
23663121 TTTATTTTTTA
1 TTTA-TTTTTA
23663132 TTATTATTTATTA
1 -T-TTATTT-TTA
*
23663145 TTTATTATTA
1 TTTATTTTTA
23663155 TTT-TTCTTTA
1 TTTATT-TTTA
*
23663165 CTTTA-TTTTC
1 -TTTATTTTTA
23663175 TTTATTATTTA
1 TTTATT-TTTA
23663186 TT
1 TT
23663188 ACTTATTTGG
Statistics
Matches: 62, Mismatches: 4, Indels: 21
0.71 0.05 0.24
Matches are distributed among these distances:
9 8 0.13
10 23 0.37
11 18 0.29
12 7 0.11
13 6 0.10
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:23663180 original size:44 final size:44
Alignment explanation
Indices: 23663101--23663194 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 44
23663091 CAACCCAATT
* *
23663101 TTTATTTTTATTTTTATTTATTTATTTTTTATTATTATTTATTA
1 TTTATTATTATTTTTATTTATTTATTTTCTATTATTATTTATTA
*
23663145 TTTATTATTATTTTTCTTTACTTTATTTTCT-TTATTATTTATTA
1 TTTATTATTATTTTTATTTA-TTTATTTTCTATTATTATTTATTA
*
23663189 CTTATT
1 TTTATT
23663195 TGGATATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 36 0.80
45 9 0.20
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.74
Consensus pattern (44 bp):
TTTATTATTATTTTTATTTATTTATTTTCTATTATTATTTATTA
Found at i:23663187 original size:7 final size:7
Alignment explanation
Indices: 23663098--23663194 Score: 71
Period size: 7 Copynumber: 14.0 Consensus size: 7
23663088 AGGCAACCCA
23663098 ATTT-TT
1 ATTTATT
23663104 ATTT-TT
1 ATTTATT
23663110 ATTT-TT
1 ATTTATT
23663116 ATTTATTT
1 ATTTA-TT
*
23663124 ATTTTTT
1 ATTTATT
23663131 A-TTATT
1 ATTTATT
23663137 ATTTATT
1 ATTTATT
23663144 ATTTATT
1 ATTTATT
23663151 A-TTATT
1 ATTTATT
*
23663157 -TTTCTTT
1 ATTT-ATT
23663164 ACTTTATTTT
1 A-TTTA--TT
*
23663174 CTTTATT
1 ATTTATT
23663181 ATTTATT
1 ATTTATT
*
23663188 ACTTATT
1 ATTTATT
23663195 TGGATATTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
6 28 0.37
7 32 0.43
8 6 0.08
9 7 0.09
10 2 0.03
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (7 bp):
ATTTATT
Found at i:23666582 original size:85 final size:85
Alignment explanation
Indices: 23666395--23666642 Score: 363
Period size: 85 Copynumber: 2.9 Consensus size: 85
23666385 CAGTTACTAT
* * **
23666395 CACTTGTTGTGGGTGCACAACATATTTGCAGATTAAACAAAATGCCACATGGTTCAT-ATCGAAC
1 CACTTGTTGTGAGTGCACAACATATTTGCAGATTAAACAAAATGCCACTTACTTCATAATCGAAC
* **
23666459 CACATATTTGCAGTTGTTGC
66 CACACATTTGCAGTTGCCGC
*
23666479 CACTTGTTGTGAGTGCACAACATATTTGCAGATTAAACAAAATGCCACTTATTTCATAATCGAAC
1 CACTTGTTGTGAGTGCACAACATATTTGCAGATTAAACAAAATGCCACTTACTTCATAATCGAAC
23666544 CACACATTTGCAGTTGCCGC
66 CACACATTTGCAGTTGCCGC
* * * * *
23666564 CACTTCTTGTGAGTGCACAACATATTTGCAAATTAAACAAACTACCACTTACTTCATAATGGAAC
1 CACTTGTTGTGAGTGCACAACATATTTGCAGATTAAACAAAATGCCACTTACTTCATAATCGAAC
23666629 CACACCATTTGCAG
66 CACA-CATTTGCAG
23666643 ATTAAACTGC
Statistics
Matches: 149, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
84 53 0.36
85 87 0.58
86 9 0.06
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (85 bp):
CACTTGTTGTGAGTGCACAACATATTTGCAGATTAAACAAAATGCCACTTACTTCATAATCGAAC
CACACATTTGCAGTTGCCGC
Found at i:23667195 original size:28 final size:27
Alignment explanation
Indices: 23667148--23667340 Score: 147
Period size: 28 Copynumber: 6.8 Consensus size: 27
23667138 ATTTTGGGTC
* * *
23667148 AAACTGTAAAATTTGAAAAATAGGAGACA
1 AAACTATAAAATCTAAAAAATAGG-G-CA
23667177 AAACTATAAAATCTAAAAAATTTAGGGCA
1 AAACTATAAAATCTAAAAAA--TAGGGCA
* * *
23667206 AAATTATAAAATCTAAAAATTATGGGTA
1 AAACTATAAAATCTAAAAAATA-GGGCA
** * * *
23667234 AATTTGTAAAAT-TTAAAAATCAAGGGTA
1 AAACTATAAAATCTAAAAAAT--AGGGCA
23667262 AAACTATAAAAATCTAAAAAATCAGGG-A
1 AAACTAT-AAAATCTAAAAAAT-AGGGCA
* * *
23667290 AAACTTTTAAATTTTAAAAAATAGGGGCA
1 AAAC-TATAAAATCTAAAAAATA-GGGCA
23667319 AAACTATAAAATCTAAAAAATA
1 AAACTATAAAATCTAAAAAATA
23667341 AGAGACACAC
Statistics
Matches: 133, Mismatches: 21, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
27 9 0.07
28 58 0.44
29 54 0.41
30 8 0.06
31 4 0.03
ACGTcount: A:0.55, C:0.07, G:0.11, T:0.26
Consensus pattern (27 bp):
AAACTATAAAATCTAAAAAATAGGGCA
Found at i:23667251 original size:57 final size:55
Alignment explanation
Indices: 23667183--23667337 Score: 163
Period size: 57 Copynumber: 2.7 Consensus size: 55
23667173 GACAAAACTA
* * * *
23667183 TAAAATCTAAAAAATTTAGGGCAAAATTATAAAATCTAAAAATTATGGGTAAA-TTT
1 TAAAATTTAAAAAA-TTAGGGCAAAACTATAAAATCTAAAAATCA-GGGAAAACTTT
* *
23667239 GTAAAATTT-AAAAATCAAGGGTAAAACTATAAAAATCTAAAAAATCAGGGAAAACTTT
1 -TAAAATTTAAAAAAT-TAGGGCAAAACTAT-AAAATCT-AAAAATCAGGGAAAACTTT
*
23667297 TAAATTTTAAAAAA-TAGGGGCAAAACTATAAAATCTAAAAA
1 TAAAATTTAAAAAATTA-GGGCAAAACTATAAAATCTAAAAA
23667338 ATAAGAGACA
Statistics
Matches: 83, Mismatches: 9, Indels: 14
0.78 0.08 0.13
Matches are distributed among these distances:
55 6 0.07
56 24 0.29
57 38 0.46
58 15 0.18
ACGTcount: A:0.55, C:0.07, G:0.11, T:0.27
Consensus pattern (55 bp):
TAAAATTTAAAAAATTAGGGCAAAACTATAAAATCTAAAAATCAGGGAAAACTTT
Found at i:23667338 original size:57 final size:57
Alignment explanation
Indices: 23667200--23667339 Score: 171
Period size: 57 Copynumber: 2.5 Consensus size: 57
23667190 TAAAAAATTT
* * *
23667200 AGGGCAAAATTATAAAATCT-AAAAATTATGGGTAAATTTGTAAAATTTAAAAATCA
1 AGGGCAAAACTATAAAATCTAAAAAATCATGGGAAAATTTGTAAAATTTAAAAATCA
* *
23667256 AGGGTAAAACTATAAAAATCTAAAAAATCA-GGGAAAACTTT-TAAATTTTAAAAAAT-A
1 AGGGCAAAACTAT-AAAATCTAAAAAATCATGGGAAAA-TTTGTAAAATTT-AAAAATCA
*
23667313 GGGGCAAAACTATAAAATCTAAAAAAT
1 AGGGCAAAACTATAAAATCTAAAAAAT
23667340 AAGAGACACA
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
56 25 0.34
57 32 0.44
58 16 0.22
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.26
Consensus pattern (57 bp):
AGGGCAAAACTATAAAATCTAAAAAATCATGGGAAAATTTGTAAAATTTAAAAATCA
Found at i:23667515 original size:12 final size:12
Alignment explanation
Indices: 23667479--23667509 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
23667469 GAGACACTGC
*
23667479 CGTGTGGCAAGT
1 CGTGTGGCAGGT
23667491 CGTGTGGCAGGT
1 CGTGTGGCAGGT
23667503 CGTGTGG
1 CGTGTGG
23667510 AGGGTCCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.16, G:0.48, T:0.26
Consensus pattern (12 bp):
CGTGTGGCAGGT
Found at i:23670059 original size:24 final size:25
Alignment explanation
Indices: 23670027--23670086 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 25
23670017 TAATTTATAT
*
23670027 TTTATATATC-ATTATATTAAATTA
1 TTTAAATATCTATTATATTAAATTA
23670051 TTTAAATATCATGTTATTATATTAAATTA
1 TTTAAATATC----TATTATATTAAATTA
23670080 TTTAAAT
1 TTTAAAT
23670087 CTTATTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 9 0.30
29 21 0.70
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (25 bp):
TTTAAATATCTATTATATTAAATTA
Found at i:23670884 original size:18 final size:17
Alignment explanation
Indices: 23670861--23670895 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
23670851 TCAATAAAAA
*
23670861 ATATATATTCTAAAATTT
1 ATATATAAT-TAAAATTT
23670879 ATATATAATTAAAATTT
1 ATATATAATTAAAATTT
23670896 TGAAAAAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATAATTAAAATTT
Found at i:23676711 original size:18 final size:19
Alignment explanation
Indices: 23676684--23676721 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
23676674 ATTCTAACCA
23676684 TTTGAATTT-AAATTGACT
1 TTTGAATTTAAAATTGACT
*
23676702 TTTGATTTTAAAATTGACT
1 TTTGAATTTAAAATTGACT
23676721 T
1 T
23676722 GAAGTACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTGAATTTAAAATTGACT
Found at i:23677154 original size:64 final size:66
Alignment explanation
Indices: 23677080--23677217 Score: 244
Period size: 66 Copynumber: 2.1 Consensus size: 66
23677070 GTGGGTGGGT
* *
23677080 TTAGGGTTAGCTTGTATTCA-TTTCTATTTGTTTAGGGTTTTTT-TTCATTTGGGCTAGATTTTT
1 TTAGGGTTAGCTTGTATTCATTTTCTATTTGCTTAGGGTTTTTTCCTCATTTGGGCTAGATTTTT
23677143 C
66 C
23677144 TTAGGGTTAGCTTGTATTCATTTTCTATTTGCTTAGGGTTTTTTCCTCATTTGGGCTAGATTTTT
1 TTAGGGTTAGCTTGTATTCATTTTCTATTTGCTTAGGGTTTTTTCCTCATTTGGGCTAGATTTTT
23677209 C
66 C
23677210 TTAGGGTT
1 TTAGGGTT
23677218 TAGGTAAAAT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
64 20 0.29
65 22 0.31
66 28 0.40
ACGTcount: A:0.14, C:0.11, G:0.21, T:0.54
Consensus pattern (66 bp):
TTAGGGTTAGCTTGTATTCATTTTCTATTTGCTTAGGGTTTTTTCCTCATTTGGGCTAGATTTTT
C
Found at i:23677182 original size:32 final size:32
Alignment explanation
Indices: 23677080--23677183 Score: 92
Period size: 32 Copynumber: 3.2 Consensus size: 32
23677070 GTGGGTGGGT
*
23677080 TTAGGGTTAGCTTGTATTCA-TTTCTATTTGT
1 TTAGGGTTAGCTTGTATTCATTTTCTATTTGC
* * *
23677111 TTAGGGTT---TT-TTTTCATTTGGGCTAGATTTTTC
1 TTAGGGTTAGCTTGTATTCATTT--TCT--A-TTTGC
23677144 TTAGGGTTAGCTTGTATTCATTTTCTATTTGC
1 TTAGGGTTAGCTTGTATTCATTTTCTATTTGC
23677176 TTAGGGTT
1 TTAGGGTT
23677184 TTTTCCTCAT
Statistics
Matches: 56, Mismatches: 7, Indels: 19
0.68 0.09 0.23
Matches are distributed among these distances:
27 5 0.09
28 4 0.07
30 2 0.04
31 8 0.14
32 13 0.23
33 12 0.21
35 2 0.04
36 2 0.04
37 8 0.14
ACGTcount: A:0.14, C:0.10, G:0.21, T:0.55
Consensus pattern (32 bp):
TTAGGGTTAGCTTGTATTCATTTTCTATTTGC
Found at i:23686551 original size:3 final size:3
Alignment explanation
Indices: 23686543--23686595 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
23686533 TCAAAAGGAA
23686543 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
23686591 AAT AA
1 AAT AA
23686596 AGAGAGAACA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:23690681 original size:126 final size:125
Alignment explanation
Indices: 23690250--23690817 Score: 665
Period size: 125 Copynumber: 4.5 Consensus size: 125
23690240 GATAAAATCA
* * * * * *
23690250 AAGCAGGATGCTTTATCAGAAGGATTTTTGCAGTCGCGCCCACGTGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * *
23690315 AGGTCCT-GGAAAAATAATTTTGAGTTGACGTTTCTAAGCAAATAGTATAAAAAACGCTTC
66 AGGTCCTAGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAAACGCTTC
* * * * * *
23690375 AAGCAGGATGATATATGCGAAGAATTTGTAAAATCGCGCCCTCCTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * * *
23690440 TGGTCTTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGATTC
66 AGGTCCTAGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTC
* * * * * *
23690500 TACCAGGATGCTTTATGAGAAGAATTTATGAAATCGAGCCCACGTGGACGTGCTTTTGCTATAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* *
23690565 AGGTCCT-GAAAAAATTATTTCGAGTTGACGTTTCTGAGTAAATAGTATAAAAAAACGCTTC
66 AGGTCCTAGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT--AAAAACGCTTC
* * * *** *
23690626 AAGCAGTATGCTATT-TGAGAAGAATTTCTGAAATCGCTCCTTTGTGGATGCGCTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
* * * *
23690690 TTGGTCCTAGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCACTTC
65 TAGGTCCTAGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTC
* * * * * *
23690751 TAGCAAGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCTACGTGGATGCACTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
23690816 AG
66 AG
23690818 CATGTTTGGG
Statistics
Matches: 370, Mismatches: 67, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
124 40 0.11
125 188 0.51
126 102 0.28
127 40 0.11
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (125 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTAGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTC
Found at i:23690715 original size:251 final size:250
Alignment explanation
Indices: 23690253--23690817 Score: 799
Period size: 251 Copynumber: 2.3 Consensus size: 250
23690243 AAAATCAAAG
* * * * * * *
23690253 CAGGATGCTTTATCAGAAGGATTTTTGCAGTCGCGCCCACGTGTACGCGCTTTTGCTACAGTAGG
1 CAGGATGCTTTATGAGAAGAATTTATGAAATCGAGCCCACGTGGACGCGCTTTTGCTACAGTAGG
* *
23690318 TCCTGGAAAAATAATTTTGAGTTGACGTTTCTAAGCAAATAGTATAAAAAACGCTTCAAGCAGGA
66 TCCTGAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAAACGCTTCAAGCAGGA
* * * *
23690383 TGATATATGCGAAGAATTTGTAAAATCGCGCCCTCCTGGACGCGCTTTTGCTACAGTTGGTCTTG
131 TGATATATGAGAAGAATTTCTAAAATCGCGCCCTCCTGGACGCGCTTTTGCTACAGTTGGTCCTA
23690448 GAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGA-TTCTAC
196 GAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATC-ACTTCTAC
* *
23690503 CAGGATGCTTTATGAGAAGAATTTATGAAATCGAGCCCACGTGGACGTGCTTTTGCTATAGTAGG
1 CAGGATGCTTTATGAGAAGAATTTATGAAATCGAGCCCACGTGGACGCGCTTTTGCTACAGTAGG
* * * *
23690568 TCCTGAAAAAATTATTTCGAGTTGACGTTTCTGAGTAAATAGTATAAAAAAACGCTTCAAGCAGT
66 TCCTGAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTAT-AAAAAACGCTTCAAGCAGG
* * * * * ** *
23690633 ATGCTATTTGAGAAGAATTTCTGAAATCGCTCCTTTGTGGATGCGCTTTTGCTACAGTTGGTCCT
130 ATGATATATGAGAAGAATTTCTAAAATCGCGCCCTCCTGGACGCGCTTTTGCTACAGTTGGTCCT
*
23690698 AGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCACTTCTAG
195 AGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCACTTCTAC
* * * * * *
23690754 CAAGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCTACGTGGATGCACTTTTGCTACAGTAG
1 CAGGATGCTTTATGAGAAGAATTTATGAAATCGAGCCCACGTGGACGCGCTTTTGCTACAGTAG
23690818 CATGTTTGGG
Statistics
Matches: 277, Mismatches: 36, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
250 97 0.35
251 180 0.65
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (250 bp):
CAGGATGCTTTATGAGAAGAATTTATGAAATCGAGCCCACGTGGACGCGCTTTTGCTACAGTAGG
TCCTGAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAAACGCTTCAAGCAGGA
TGATATATGAGAAGAATTTCTAAAATCGCGCCCTCCTGGACGCGCTTTTGCTACAGTTGGTCCTA
GAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCACTTCTAC
Found at i:23694030 original size:7 final size:7
Alignment explanation
Indices: 23694015--23694126 Score: 55
Period size: 7 Copynumber: 15.4 Consensus size: 7
23694005 AAGTTAAGGT
*
23694015 TTTAGGG
1 TTTATGG
23694022 TTTATGG
1 TTTATGG
* *
23694029 TTTTTAAG
1 TTTAT-GG
*
23694037 TTTAGGG
1 TTTATGG
23694044 TTTATGG
1 TTTATGG
23694051 TTTATGG
1 TTTATGG
*
23694058 TTTTTAGG
1 TTTAT-GG
23694066 TTTA-GG
1 TTTATGG
*
23694072 CTTTGTGG
1 -TTTATGG
* *
23694080 TTTTTAAG
1 TTTAT-GG
*
23694088 TTTAGGG
1 TTTATGG
*
23694095 TTTAGGG
1 TTTATGG
*
23694102 TTTTTAGG
1 TTTAT-GG
*
23694110 TTTAAGG
1 TTTATGG
*
23694117 TTTGTGG
1 TTTATGG
23694124 TTT
1 TTT
23694127 TTAAGTTTAG
Statistics
Matches: 78, Mismatches: 21, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
6 2 0.03
7 56 0.72
8 20 0.26
ACGTcount: A:0.14, C:0.01, G:0.30, T:0.54
Consensus pattern (7 bp):
TTTATGG
Found at i:23694032 original size:29 final size:29
Alignment explanation
Indices: 23693990--23694104 Score: 93
Period size: 29 Copynumber: 4.2 Consensus size: 29
23693980 ATTTAACTTA
* *
23693990 AGGG-TTAGGGTTTTAAAGTTAAGGTTTT
1 AGGGTTTATGGTTTTAAAGTTAAGGGTTT
* *
23694018 AGGGTTTATGGTTTTTAAGTTTAGGGTTT
1 AGGGTTTATGGTTTTAAAGTTAAGGGTTT
*
23694047 ATGGTTTATGG-TTT----TT-A-GGTTT
1 AGGGTTTATGGTTTTAAAGTTAAGGGTTT
* * * *
23694069 AGGCTTTGTGGTTTTTAAGTTTAGGGTTT
1 AGGGTTTATGGTTTTAAAGTTAAGGGTTT
23694098 AGGGTTT
1 AGGGTTT
23694105 TTAGGTTTAA
Statistics
Matches: 70, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
22 13 0.19
23 4 0.06
24 2 0.03
27 2 0.03
28 8 0.11
29 41 0.59
ACGTcount: A:0.17, C:0.01, G:0.31, T:0.50
Consensus pattern (29 bp):
AGGGTTTATGGTTTTAAAGTTAAGGGTTT
Found at i:23694060 original size:44 final size:43
Alignment explanation
Indices: 23694043--23694239 Score: 270
Period size: 44 Copynumber: 4.5 Consensus size: 43
23694033 TAAGTTTAGG
* *
23694043 GTTTATGGTTTATGGTTTTTAGGTTTAGGCTTTGTGGTTTTTAA
1 GTTTAGGGTTTA-GGTTTTTAGGTTTAGGGTTTGTGGTTTTTAA
*
23694087 GTTTAGGGTTTAGGGTTTTTAGGTTTAAGGTTTGTGGTTTTTAA
1 GTTTAGGGTTTA-GGTTTTTAGGTTTAGGGTTTGTGGTTTTTAA
23694131 GTTTAGGGTTTAGTGTTTTTAGGTTTAGGGTTTGTGGTTTTTAA
1 GTTTAGGGTTTAG-GTTTTTAGGTTTAGGGTTTGTGGTTTTTAA
* * *
23694175 GTTAAGGG-TTAGAGTTTTTAAGTTTAGGGTTTGATGTTTTTTAA
1 GTTTAGGGTTTAG-GTTTTTAGGTTTAGGGTTTG-TGGTTTTTAA
*
23694219 GTTTAGAGTTTAGGGTTTTTA
1 GTTTAGGGTTTA-GGTTTTTA
23694240 AGTTAAGTGT
Statistics
Matches: 138, Mismatches: 11, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
43 24 0.17
44 103 0.75
45 10 0.07
46 1 0.01
ACGTcount: A:0.17, C:0.01, G:0.29, T:0.53
Consensus pattern (43 bp):
GTTTAGGGTTTAGGTTTTTAGGTTTAGGGTTTGTGGTTTTTAA
Found at i:23694067 original size:22 final size:22
Alignment explanation
Indices: 23694043--23694243 Score: 228
Period size: 22 Copynumber: 9.1 Consensus size: 22
23694033 TAAGTTTAGG
* *
23694043 GTTTATGGTTTATGGTTTTTAG
1 GTTTAGGGTTTATGGTTTTTAA
* *
23694065 GTTTAGGCTTTGTGGTTTTTAA
1 GTTTAGGGTTTATGGTTTTTAA
* *
23694087 GTTTAGGGTTTAGGGTTTTTAG
1 GTTTAGGGTTTATGGTTTTTAA
* *
23694109 GTTTAAGGTTTGTGGTTTTTAA
1 GTTTAGGGTTTATGGTTTTTAA
*
23694131 GTTTAGGGTTTA-GTGTTTTTAG
1 GTTTAGGGTTTATG-GTTTTTAA
*
23694153 GTTTAGGGTTTGTGGTTTTTAA
1 GTTTAGGGTTTATGGTTTTTAA
*
23694175 GTTAAGGG-TTA-GAGTTTTTAA
1 GTTTAGGGTTTATG-GTTTTTAA
*
23694196 GTTTAGGGTTTGATGTTTTTTAA
1 GTTTAGGGTTT-ATGGTTTTTAA
* *
23694219 GTTTAGAGTTTAGGGTTTTTAA
1 GTTTAGGGTTTATGGTTTTTAA
23694241 GTT
1 GTT
23694244 AAGTGTTACC
Statistics
Matches: 149, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
20 1 0.01
21 18 0.12
22 110 0.74
23 19 0.13
24 1 0.01
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.53
Consensus pattern (22 bp):
GTTTAGGGTTTATGGTTTTTAA
Found at i:23694169 original size:29 final size:28
Alignment explanation
Indices: 23694020--23694170 Score: 101
Period size: 29 Copynumber: 5.2 Consensus size: 28
23694010 AAGGTTTTAG
* *
23694020 GGTTTATGGTTTTTAAGTTTAGGGTTTAT
1 GGTTTAT-GTTTTTAGGTTTAGGGTTTGT
*
23694049 GGTTTATGGTTTTTAGGTTTAGGCTTTGT
1 GGTTTAT-GTTTTTAGGTTTAGGGTTTGT
* *** *
23694078 GGTTTTTAAGTTTAGGGTTTAGGGTTTTT
1 GGTTTATGTTTTTA-GGTTTAGGGTTTGT
* * *
23694107 AGGTTTAAGGTTTGT-GGTTTTTA-AGTTTAG-
1 -GGTTT-ATGTTTTTAGG--TTTAGGGTTT-GT
23694137 GGTTTAGTGTTTTTAGGTTTAGGGTTTGT
1 GGTTTA-TGTTTTTAGGTTTAGGGTTTGT
23694166 GGTTT
1 GGTTT
23694171 TTAAGTTAAG
Statistics
Matches: 92, Mismatches: 20, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
28 10 0.11
29 65 0.71
30 11 0.12
31 6 0.07
ACGTcount: A:0.14, C:0.01, G:0.31, T:0.54
Consensus pattern (28 bp):
GGTTTATGTTTTTAGGTTTAGGGTTTGT
Found at i:23694270 original size:66 final size:64
Alignment explanation
Indices: 23694057--23694284 Score: 223
Period size: 66 Copynumber: 3.5 Consensus size: 64
23694047 ATGGTTTATG
* * * *
23694057 GTTTTTAGGTTTAGGCTTT-GTGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAGGTTTAAGGTTTG
1 GTTTTTAAGTTTAGGGTTTAGT-GTTTTTAAGTTTAGGGTTTAGGGTTTTTAAG-TTAAGG-TTA
**
23694121 TG
63 CA
* *
23694123 GTTTTTAAGTTTAGGGTTTAGTGTTTTTAGGTTTAGGGTTT-GTGGTTTTTAAGTTAAGGGTTAG
1 GTTTTTAAGTTTAGGGTTTAGTGTTTTTAAGTTTAGGGTTTAG-GGTTTTTAAGTTAA-GGTTAC
23694187 A
64 A
*
23694188 GTTTTTAAGTTTAGGGTTT-GATGTTTTTTAAGTTTAGAGTTTAGGGTTTTTAAGTTAAGTGTTA
1 GTTTTTAAGTTTAGGGTTTAG-TG-TTTTTAAGTTTAGGGTTTAGGGTTTTTAAGTTAAG-GTTA
*
23694252 CC
63 CA
* * *
23694254 CTTTTTGA-TTTAAGGG-TTAGGGTTTTTAAGT
1 GTTTTTAAGTTT-AGGGTTTAGTGTTTTTAAGT
23694285 GAAGGGTTAG
Statistics
Matches: 139, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
64 10 0.07
65 35 0.25
66 91 0.65
67 3 0.02
ACGTcount: A:0.18, C:0.02, G:0.29, T:0.52
Consensus pattern (64 bp):
GTTTTTAAGTTTAGGGTTTAGTGTTTTTAAGTTTAGGGTTTAGGGTTTTTAAGTTAAGGTTACA
Found at i:23694550 original size:21 final size:22
Alignment explanation
Indices: 23694526--23694573 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
23694516 TCAGTGCCAG
*
23694526 CTTCCGA-CGGCGG-TTGTGGTT
1 CTTCCGAGCGG-GGATTCTGGTT
23694547 CTTCC-AGCGGGGATTCTGGTT
1 CTTCCGAGCGGGGATTCTGGTT
23694568 CTTCCG
1 CTTCCG
23694574 GTAGGGCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.06, C:0.27, G:0.33, T:0.33
Consensus pattern (22 bp):
CTTCCGAGCGGGGATTCTGGTT
Found at i:23696770 original size:51 final size:51
Alignment explanation
Indices: 23696715--23696814 Score: 128
Period size: 51 Copynumber: 2.0 Consensus size: 51
23696705 AATTATTTAA
* *
23696715 AAATAGGGATTTAAGAGAAATTTAAAAGGAAATTGAGAGCTAATTGAGATT
1 AAATAGGAATTTAAGAGAAATTTAAAAGGAAATTGAGAGCAAATTGAGATT
* * ** * *
23696766 AAATATGAATTTGAGAGAAATTTGGAAGGAAATTTAGAGGAAATTGAGA
1 AAATAGGAATTTAAGAGAAATTTAAAAGGAAATTGAGAGCAAATTGAGA
23696815 GGAAATTTGA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.47, C:0.01, G:0.25, T:0.27
Consensus pattern (51 bp):
AAATAGGAATTTAAGAGAAATTTAAAAGGAAATTGAGAGCAAATTGAGATT
Found at i:23696826 original size:12 final size:12
Alignment explanation
Indices: 23696773--23696827 Score: 73
Period size: 11 Copynumber: 4.8 Consensus size: 12
23696763 ATTAAATATG
23696773 AATTTGAGA-GA
1 AATTTGAGAGGA
23696784 AATTTG-GAAGGA
1 AATTTGAG-AGGA
23696796 AATTT-AGAGGA
1 AATTTGAGAGGA
23696807 AA-TTGAGAGGA
1 AATTTGAGAGGA
23696818 AATTTGAGAG
1 AATTTGAGAG
23696828 AGGATTTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
10 3 0.08
11 21 0.54
12 15 0.38
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.25
Consensus pattern (12 bp):
AATTTGAGAGGA
Found at i:23702654 original size:105 final size:105
Alignment explanation
Indices: 23702472--23702687 Score: 387
Period size: 105 Copynumber: 2.1 Consensus size: 105
23702462 GTAATGAGAA
* *
23702472 AACGAATAAATGCATACATTGGTGCCAGTAGAGTTTGATGTGCAGATAAAAAATGCAATGGGGGC
1 AACGAATAAAAGCATACATTGGTGCCAGTAGAGTTTGATGTGCAGATAAAAAATGCAATGGGAGC
*
23702537 TAGGATTTAGGGAGTTAACCAAATTCAATGTGGCTTTTTT
66 TAGGATTTAGGGAGTTAACCAAATTCAATGTGGCCTTTTT
* *
23702577 AACGAATAAAAGCATACATTGGTGCTAGTGGAGTTTGATGTGCAGATAAAAAATGCAATGGGAGC
1 AACGAATAAAAGCATACATTGGTGCCAGTAGAGTTTGATGTGCAGATAAAAAATGCAATGGGAGC
23702642 TAGGATTTAGGGAGTTAACCAAATTCAATGTGGCCTTTTT
66 TAGGATTTAGGGAGTTAACCAAATTCAATGTGGCCTTTTT
23702682 AACGAA
1 AACGAA
23702688 ACAAGGTTAG
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 106 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (105 bp):
AACGAATAAAAGCATACATTGGTGCCAGTAGAGTTTGATGTGCAGATAAAAAATGCAATGGGAGC
TAGGATTTAGGGAGTTAACCAAATTCAATGTGGCCTTTTT
Found at i:23705354 original size:25 final size:25
Alignment explanation
Indices: 23705310--23705385 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
23705300 ATGAGTGATA
23705310 AACGGTAAGCTTC-T-CTGAGCTGAAT
1 AACGGTAAGC-TCATAC-GAGCTGAAT
*
23705335 AACGGTAAGCTCATACGAGCTGAGT
1 AACGGTAAGCTCATACGAGCTGAAT
* * *
23705360 ATCAGTAAGCTCATAAGAGCTAGAAT
1 AACGGTAAGCTCATACGAGCT-GAAT
23705386 CAGTAACCCT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
24 2 0.05
25 37 0.86
26 4 0.09
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (25 bp):
AACGGTAAGCTCATACGAGCTGAAT
Found at i:23708074 original size:46 final size:46
Alignment explanation
Indices: 23707879--23708063 Score: 264
Period size: 46 Copynumber: 4.0 Consensus size: 46
23707869 ACAATGCTAT
* * * *
23707879 AACTCAGTATGGTTTTCTTCACTGAAATACTATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTCCAC
*
23707925 AACTCAGTATGGTTTT-TGTGACTGAAATACCATACCTACGTTCCAC
1 AACTCAGTATGGTTTTCT-TTACTGAAATACCATACCTACGTTCCAC
* * *
23707971 AACTCAGTATGATTTTCTTTATTGAATTACCATACCTACGTTCCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTCCAC
* *
23708017 AACTCAGTATGGTTTTATTTACTGAATTACCATACCTACGTTCCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTCCAC
23708063 A
1 A
23708064 CTTTGCTATG
Statistics
Matches: 126, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
45 1 0.01
46 124 0.98
47 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTCCAC
Found at i:23723193 original size:24 final size:24
Alignment explanation
Indices: 23723178--23723229 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
23723168 AATCAAAGTC
23723178 AAATATATTATACTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
* *
23723202 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATGCT
23723226 AAAT
1 AAAT
23723230 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:23727509 original size:24 final size:24
Alignment explanation
Indices: 23727467--23727518 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
23727457 AATCAAATTC
* *
23727467 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
23727491 AAATATATTATATTCATAAATACT
1 AAATATATTATACTAATAAATACT
23727515 AAAT
1 AAAT
23727519 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:23728260 original size:31 final size:30
Alignment explanation
Indices: 23728225--23728302 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
23728215 TAATTCAAGC
*
23728225 TTTTAAAAACTTTTAGAGGCTTGATA-ATAAT
1 TTTTAAAAA-TTTTAGAGGCTTAATATA-AAT
* *
23728256 TTTTAAAAATTATGAGAGGCTTAATTTAAAT
1 TTTTAAAAATT-TTAGAGGCTTAATATAAAT
*
23728287 TTTCAAAAATTTTAGA
1 TTTTAAAAATTTTAGA
23728303 ACCATAATGA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 6 0.15
31 33 0.82
32 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.42
Consensus pattern (30 bp):
TTTTAAAAATTTTAGAGGCTTAATATAAAT
Found at i:23728263 original size:62 final size:61
Alignment explanation
Indices: 23728186--23728302 Score: 139
Period size: 62 Copynumber: 1.9 Consensus size: 61
23728176 GGGGGAGGTA
* *
23728186 ATAAGAATTTCTAAAATTTAGGA-AGGGCTTAATTCAAGCTTTT-AAAAACTTTTAGAGGCTTG
1 ATAAGAATTTCTAAAAATTAGGAGA-GGCTTAATTCAA-ATTTTCAAAAA-TTTTAGAGGCTTG
* * * *
23728248 ATAATAATTTTTAAAAATTATGAGAGGCTTAATTTAAATTTTCAAAAATTTTAGA
1 ATAAGAATTTCTAAAAATTAGGAGAGGCTTAATTCAAATTTTCAAAAATTTTAGA
23728303 ACCATAATGA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
61 11 0.23
62 35 0.74
63 1 0.02
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (61 bp):
ATAAGAATTTCTAAAAATTAGGAGAGGCTTAATTCAAATTTTCAAAAATTTTAGAGGCTTG
Found at i:23739837 original size:87 final size:87
Alignment explanation
Indices: 23739691--23739861 Score: 315
Period size: 87 Copynumber: 2.0 Consensus size: 87
23739681 TTTCATGGCA
23739691 TTTTTGCATTTTATTCAATTTGGTCCTTAATGTATGAAATTAATAATTAAGCTTTACAGTTTACC
1 TTTTTGCATTTTATTCAATTTGGTCCTTAATGTATGAAATTAATAATTAAGCTTTACAGTTTACC
*
23739756 CCTTTCTTAAACTAAGCTTTTT
66 CCTTTCTTAAAATAAGCTTTTT
* *
23739778 TTTTTTCATTTTATTCAATTTGGTTCTTAATGTATGAAATTAATAATTAAGCTTTACAGTTTACC
1 TTTTTGCATTTTATTCAATTTGGTCCTTAATGTATGAAATTAATAATTAAGCTTTACAGTTTACC
23739843 CCTTTCTTAAAATAAGCTT
66 CCTTTCTTAAAATAAGCTT
23739862 AATTTTTATC
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.49
Consensus pattern (87 bp):
TTTTTGCATTTTATTCAATTTGGTCCTTAATGTATGAAATTAATAATTAAGCTTTACAGTTTACC
CCTTTCTTAAAATAAGCTTTTT
Found at i:23742857 original size:10 final size:10
Alignment explanation
Indices: 23742838--23742880 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
23742828 AACAAATTTT
*
23742838 TTTAAATATA
1 TTTAATTATA
*
23742848 TATAATTATA
1 TTTAATTATA
23742858 TTTAATT-TAA
1 TTTAATTAT-A
23742868 TTTAATTATA
1 TTTAATTATA
23742878 TTT
1 TTT
23742881 TGTTTTGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
9 1 0.04
10 26 0.93
11 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTAATTATA
Found at i:23744830 original size:3 final size:3
Alignment explanation
Indices: 23744822--23744878 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
23744812 ATTTGACATT
* ** *
23744822 TTA TTA TTA TTA TTA TTA CTA CCA TTA TTAA TCA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
23744867 TTA CTTA TTA TT
1 TTA -TTA TTA TT
23744879 CTTGTTATAC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 2 0.04
3 38 0.84
4 5 0.11
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:23754178 original size:10 final size:10
Alignment explanation
Indices: 23754155--23754187 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
23754145 AATTATTTAA
23754155 AAAAAATTAT
1 AAAAAATTAT
23754165 -AAAAATTAT
1 AAAAAATTAT
*
23754174 AAAAAAATAT
1 AAAAAATTAT
23754184 AAAA
1 AAAA
23754188 TTTTTCAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:23760538 original size:20 final size:20
Alignment explanation
Indices: 23760513--23760560 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
23760503 GGAACTTAGG
23760513 AAATTTTTAGCAAAATTTCA
1 AAATTTTTAGCAAAATTTCA
23760533 AAATTTTTAGCAAAATTTCA
1 AAATTTTTAGCAAAATTTCA
23760553 AAATTTTT
1 AAATTTTT
23760561 CCAAGGTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (20 bp):
AAATTTTTAGCAAAATTTCA
Found at i:23761839 original size:32 final size:32
Alignment explanation
Indices: 23761793--23761854 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
23761783 ATTTTACACC
23761793 TTTCATTTACAAAAGTTGTTTATCTATCAAAA
1 TTTCATTTACAAAAGTTGTTTATCTATCAAAA
*
23761825 TTTCCTTTACAAAAGTTGTTTATCTATCAA
1 TTTCATTTACAAAAGTTGTTTATCTATCAA
23761855 CAACCTTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.34, C:0.15, G:0.06, T:0.45
Consensus pattern (32 bp):
TTTCATTTACAAAAGTTGTTTATCTATCAAAA
Found at i:23762652 original size:25 final size:25
Alignment explanation
Indices: 23762616--23762669 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
23762606 GACATTACGT
* * *
23762616 CACATAGCCTTTATAGGTAACTTGC
1 CACATAGACTTTACAGATAACTTGC
23762641 CACATAGACTTTACAGATAACTTGC
1 CACATAGACTTTACAGATAACTTGC
23762666 CACA
1 CACA
23762670 AAGGCTTCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (25 bp):
CACATAGACTTTACAGATAACTTGC
Found at i:23762685 original size:25 final size:25
Alignment explanation
Indices: 23762657--23762732 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
23762647 GACTTTACAG
*
23762657 ATAACTTGCCACAAAGGCTTCCCAA
1 ATAAATTGCCACAAAGGCTTCCCAA
* *
23762682 ATAAATAGCCACAAAGGCTTCCAAAA
1 ATAAATTGCCACAAAGGCTTCC-CAA
* * *
23762708 ATAAATCGCCATAAAGGCTTTCCAA
1 ATAAATTGCCACAAAGGCTTCCCAA
23762733 CCAATTCGCC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 22 0.51
26 21 0.49
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.20
Consensus pattern (25 bp):
ATAAATTGCCACAAAGGCTTCCCAA
Found at i:23762718 original size:26 final size:26
Alignment explanation
Indices: 23762664--23762732 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
23762654 CAGATAACTT
*
23762664 GCCACAAAGGCTTCC-CAAATAAATA
1 GCCACAAAGGCTTCCAAAAATAAATA
*
23762689 GCCACAAAGGCTTCCAAAAATAAATC
1 GCCACAAAGGCTTCCAAAAATAAATA
*
23762715 GCCATAAAGGCTTTCCAA
1 GCCACAAAGGC-TTCCAA
23762733 CCAATTCGCC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
25 15 0.38
26 18 0.46
27 6 0.15
ACGTcount: A:0.42, C:0.28, G:0.13, T:0.17
Consensus pattern (26 bp):
GCCACAAAGGCTTCCAAAAATAAATA
Found at i:23764791 original size:26 final size:26
Alignment explanation
Indices: 23764756--23764818 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
23764746 GTAGCTCTTA
* *
23764756 TGAGCGTCCC-ATTATATGGCTCTTCG
1 TGAGCTTCCCGATTA-AAGGCTCTTCG
*
23764782 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTTCCCGATTAAAGGCTCTTCG
*
23764808 TAAGCTTCCCG
1 TGAGCTTCCCG
23764819 TTAGTGCTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 28 0.88
27 4 0.12
ACGTcount: A:0.17, C:0.27, G:0.22, T:0.33
Consensus pattern (26 bp):
TGAGCTTCCCGATTAAAGGCTCTTCG
Found at i:23764890 original size:24 final size:24
Alignment explanation
Indices: 23764863--23764922 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
23764853 TCTGGTGCTT
23764863 CCGTTAATTGCTCTTCGGAGCTAC
1 CCGTTAATTGCTCTTCGGAGCTAC
* *
23764887 CCGTTAATTACTCTTTGGAGCTAC
1 CCGTTAATTGCTCTTCGGAGCTAC
23764911 CCGTTATATTGC
1 CCGTTA-ATTGC
23764923 CCGGATAAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 28 0.88
25 4 0.12
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.37
Consensus pattern (24 bp):
CCGTTAATTGCTCTTCGGAGCTAC
Found at i:23766071 original size:40 final size:40
Alignment explanation
Indices: 23766027--23766106 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
23766017 CCTTACTTCA
*
23766027 AATACCACGCGACCTAAGTTATGGGTGTGTCACTTGGCCG
1 AATACAACGCGACCTAAGTTATGGGTGTGTCACTTGGCCG
*
23766067 AATACAATGCGACCTAAGTTATGGGTGTGTCACTTGGCCG
1 AATACAACGCGACCTAAGTTATGGGTGTGTCACTTGGCCG
23766107 TGTGAGCCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
AATACAACGCGACCTAAGTTATGGGTGTGTCACTTGGCCG
Found at i:23772052 original size:20 final size:21
Alignment explanation
Indices: 23772007--23772052 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
23771997 ATAATGTTGC
23772007 ATAGAGGAACTGAAGTGCAAA
1 ATAGAGGAACTGAAGTGCAAA
* *
23772028 A-AGAGGCACTGAAG-GGAAA
1 ATAGAGGAACTGAAGTGCAAA
23772047 ATAGAG
1 ATAGAG
23772053 AGCAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 5 0.23
20 16 0.73
21 1 0.05
ACGTcount: A:0.48, C:0.09, G:0.33, T:0.11
Consensus pattern (21 bp):
ATAGAGGAACTGAAGTGCAAA
Found at i:23774278 original size:17 final size:17
Alignment explanation
Indices: 23774228--23774278 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
23774218 AAATAATTGA
*
23774228 GATAAAAATAAATAAAT
1 GATAAAAATAAATAAAC
* * *
23774245 AAGAAAAATAAACAAAC
1 GATAAAAATAAATAAAC
*
23774262 GATAAAAATCAATAAAC
1 GATAAAAATAAATAAAC
23774279 CAATCAGGAA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.71, C:0.08, G:0.06, T:0.16
Consensus pattern (17 bp):
GATAAAAATAAATAAAC
Found at i:23779460 original size:8 final size:8
Alignment explanation
Indices: 23779443--23779486 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
23779433 AAAAAAAAAG
*
23779443 CAAACGTA
1 CAAACATA
23779451 CAAACATA
1 CAAACATA
*
23779459 CAAACAAA
1 CAAACATA
*
23779467 CAAACAAA
1 CAAACATA
23779475 CAAACCATA
1 CAAA-CATA
23779484 CAA
1 CAA
23779487 TTTGTTCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
8 26 0.81
9 6 0.19
ACGTcount: A:0.64, C:0.27, G:0.02, T:0.07
Consensus pattern (8 bp):
CAAACATA
Found at i:23779467 original size:4 final size:4
Alignment explanation
Indices: 23779429--23779479 Score: 52
Period size: 4 Copynumber: 13.0 Consensus size: 4
23779419 TCTTATTGAT
** *
23779429 AAAC AAA- AAA- AAAGC AAAC GTAC AAAC ATAC AAAC AAAC AAAC AAAC
1 AAAC AAAC AAAC AAA-C AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC
23779476 AAAC
1 AAAC
23779480 CATACAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 6 0.15
4 30 0.77
5 3 0.08
ACGTcount: A:0.71, C:0.22, G:0.04, T:0.04
Consensus pattern (4 bp):
AAAC
Found at i:23779467 original size:12 final size:12
Alignment explanation
Indices: 23779450--23779486 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
23779440 AAGCAAACGT
23779450 ACAAACATACAA
1 ACAAACATACAA
*
23779462 ACAAACAAACAA
1 ACAAACATACAA
23779474 ACAAACCATACAA
1 ACAAA-CATACAA
23779487 TTTGTTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.68, C:0.27, G:0.00, T:0.05
Consensus pattern (12 bp):
ACAAACATACAA
Found at i:23789161 original size:20 final size:18
Alignment explanation
Indices: 23789113--23789167 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 18
23789103 GCAATAAAAT
23789113 AAAATAAAAA-AAGATTTA
1 AAAATAAAAATAA-ATTTA
23789131 AAAATGCAAAAATAAATTTA
1 AAAAT--AAAAATAAATTTA
23789151 AGAAA-ATAAAATAAATT
1 A-AAATA-AAAATAAATT
23789168 GTTAAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
18 6 0.19
19 10 0.31
20 11 0.34
21 5 0.16
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (18 bp):
AAAATAAAAATAAATTTA
Found at i:23790035 original size:13 final size:13
Alignment explanation
Indices: 23790017--23790095 Score: 107
Period size: 13 Copynumber: 6.5 Consensus size: 13
23790007 TAGATTTTTT
23790017 CTAAATATTATCA
1 CTAAATATTATCA
23790030 CTAAATA--ATC-
1 CTAAATATTATCA
23790040 CTAAATATTATCA
1 CTAAATATTATCA
*
23790053 CTAAATA--AT-T
1 CTAAATATTATCA
23790063 CTAAATATTATCA
1 CTAAATATTATCA
23790076 CTAAATATTATCA
1 CTAAATATTATCA
23790089 CTAAATA
1 CTAAATA
23790096 ATTCAAAATT
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
10 14 0.24
11 5 0.09
12 5 0.09
13 34 0.59
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:23790047 original size:23 final size:23
Alignment explanation
Indices: 23790017--23790082 Score: 123
Period size: 23 Copynumber: 2.9 Consensus size: 23
23790007 TAGATTTTTT
23790017 CTAAATATTATCACTAAATAATC
1 CTAAATATTATCACTAAATAATC
*
23790040 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATC
23790063 CTAAATATTATCACTAAATA
1 CTAAATATTATCACTAAATA
23790083 TTATCACTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATC
Found at i:23803621 original size:21 final size:21
Alignment explanation
Indices: 23803596--23803636 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
23803586 TTTAAAATAA
*
23803596 AAAAATAAAAACAAGTATTTT
1 AAAAATAAAAACAAATATTTT
*
23803617 AAAAATAAAAATAAATATTT
1 AAAAATAAAAACAAATATTT
23803637 ATTATATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAATAAAAACAAATATTTT
Found at i:23809510 original size:8 final size:8
Alignment explanation
Indices: 23809462--23809519 Score: 59
Period size: 8 Copynumber: 7.4 Consensus size: 8
23809452 AAAAATTATA
23809462 AATTTAAT
1 AATTTAAT
*
23809470 AATGTTAAC
1 AAT-TTAAT
*
23809479 AATATAAT
1 AATTTAAT
23809487 AA-TTAACT
1 AATTTAA-T
23809495 AA-TT-AT
1 AATTTAAT
23809501 AATTTAAT
1 AATTTAAT
23809509 AATTTAAT
1 AATTTAAT
23809517 AAT
1 AAT
23809520 ATTTTCTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
6 3 0.07
7 6 0.14
8 26 0.62
9 7 0.17
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (8 bp):
AATTTAAT
Done.