Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 18 of 216
Found at i:5671890 original size:27 final size:26
Alignment explanation
Indices: 5671859--5671918 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
5671849 AATTCTACAA
5671859 ATAAAATA-AAAAATTAATAAATATTTT
1 ATAAAATATAAAAA--AATAAATATTTT
*
5671886 ATAAAAATATAATAAAATAAATATTTT
1 AT-AAAATATAAAAAAATAAATATTTT
*
5671913 AAAAAA
1 ATAAAA
5671919 ACTGATAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 4 0.14
27 15 0.52
28 6 0.21
29 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
ATAAAATATAAAAAAATAAATATTTT
Found at i:5671915 original size:14 final size:14
Alignment explanation
Indices: 5671874--5671916 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5671864 ATAAAAAATT
*
5671874 AATAAATATTTTAT
1 AATAAATATTTTAA
**
5671888 AA-AAATATAATAA
1 AATAAATATTTTAA
5671901 AATAAATATTTTAA
1 AATAAATATTTTAA
5671915 AA
1 AA
5671917 AAACTGATAG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATAAATATTTTAA
Found at i:5672245 original size:6 final size:7
Alignment explanation
Indices: 5672230--5672265 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
5672220 CTAGTTTAAA
5672230 TTTAATT
1 TTTAATT
5672237 TTTAATT
1 TTTAATT
5672244 TTTAATT
1 TTTAATT
5672251 TTTAAATT
1 TTT-AATT
5672259 ATTTAAT
1 -TTTAAT
5672266 GATAATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 17 0.63
8 7 0.26
9 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTAATT
Found at i:5672249 original size:14 final size:16
Alignment explanation
Indices: 5672229--5672265 Score: 60
Period size: 14 Copynumber: 2.4 Consensus size: 16
5672219 TCTAGTTTAA
5672229 ATTTAATTTTT-AATT
1 ATTTAATTTTTAAATT
5672244 -TTTAATTTTTAAATT
1 ATTTAATTTTTAAATT
5672259 ATTTAAT
1 ATTTAAT
5672266 GATAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 10 0.50
15 4 0.20
16 6 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTAATTTTTAAATT
Found at i:5672281 original size:23 final size:22
Alignment explanation
Indices: 5672246--5672301 Score: 85
Period size: 23 Copynumber: 2.5 Consensus size: 22
5672236 TTTTAATTTT
*
5672246 TAATTTTTAAATTATTTAATGA
1 TAATATTTAAATTATTTAATGA
*
5672268 TAATATTTAGAATTATTTAGTGA
1 TAATATTTA-AATTATTTAATGA
5672291 TAATATTTAAA
1 TAATATTTAAA
5672302 AAAAATCTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 10 0.32
23 21 0.68
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (22 bp):
TAATATTTAAATTATTTAATGA
Found at i:5676118 original size:21 final size:21
Alignment explanation
Indices: 5676092--5676136 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
5676082 ATGCTCACCT
5676092 AAGTATAGAAACATGAATTCA
1 AAGTATAGAAACATGAATTCA
5676113 AAGTATAGAAACATGAATTCA
1 AAGTATAGAAACATGAATTCA
5676134 AAG
1 AAG
5676137 GATTAGGAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.53, C:0.09, G:0.16, T:0.22
Consensus pattern (21 bp):
AAGTATAGAAACATGAATTCA
Found at i:5677499 original size:36 final size:36
Alignment explanation
Indices: 5677450--5677520 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
5677440 AAAACTTAGC
** *
5677450 CCGTGTGGTCCACACGGTCTGCATTATTTCACACGA
1 CCGTGTGACCCACACGGTCTGCATGATTTCACACGA
*
5677486 CCGTGTGACCCACACGGTTTGCATGATTTCACACG
1 CCGTGTGACCCACACGGTCTGCATGATTTCACACG
5677521 GCCTACCCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.27
Consensus pattern (36 bp):
CCGTGTGACCCACACGGTCTGCATGATTTCACACGA
Found at i:5679391 original size:15 final size:15
Alignment explanation
Indices: 5679371--5679399 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5679361 CAACCCTTTG
5679371 CAATTATTTTGAATA
1 CAATTATTTTGAATA
5679386 CAATTATTTTGAAT
1 CAATTATTTTGAAT
5679400 TTTAAAACCA
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:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (15 bp):
CAATTATTTTGAATA
Found at i:5693077 original size:40 final size:40
Alignment explanation
Indices: 5693033--5693108 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
5693023 GTGTGTCTCA
* *
5693033 TCCACATGGGTGTGTAGGCCTCCACACGGCCAGGGCCACG
1 TCCACATAGGCGTGTAGGCCTCCACACGGCCAGGGCCACG
* *
5693073 TCCACATAGGCGTGTAGGCCTCTACACGGCTAGGGC
1 TCCACATAGGCGTGTAGGCCTCCACACGGCCAGGGC
5693109 AAACGGCCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.17
Consensus pattern (40 bp):
TCCACATAGGCGTGTAGGCCTCCACACGGCCAGGGCCACG
Found at i:5693756 original size:21 final size:21
Alignment explanation
Indices: 5693731--5693771 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5693721 CTGAATATAC
5693731 GTCTGTTTGTCAGAACATTTT
1 GTCTGTTTGTCAGAACATTTT
**
5693752 GTCTGTTTGTGTGAACATTT
1 GTCTGTTTGTCAGAACATTT
5693772 GGTTATTGAA
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:0.17, C:0.12, G:0.22, T:0.49
Consensus pattern (21 bp):
GTCTGTTTGTCAGAACATTTT
Found at i:5706320 original size:89 final size:89
Alignment explanation
Indices: 5706215--5706391 Score: 327
Period size: 89 Copynumber: 2.0 Consensus size: 89
5706205 GTAAGTTAAT
* *
5706215 TTGGTTCAATGGATAGGTGTTGTGCTTGTGTCTATGAGGTTTTGGGTTTGAATTTTTCCCTTGAA
1 TTGGTTCAATGGATAGGTGTTGTGCTTGTGTATATGAGGTTTTGGGTTTGAATCTTTCCCTTGAA
5706280 TTTTTGTTATTTTTGTCTTAATCA
66 TTTTTGTTATTTTTGTCTTAATCA
*
5706304 TTGGTTCAATGGATAGGTGTTGTGCTTGTGTATGTGAGGTTTTGGGTTTGAATCTTTCCCTTGAA
1 TTGGTTCAATGGATAGGTGTTGTGCTTGTGTATATGAGGTTTTGGGTTTGAATCTTTCCCTTGAA
5706369 TTTTTGTTATTTTTGTCTTAATC
66 TTTTTGTTATTTTTGTCTTAATC
5706392 CCTATCTTTG
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 85 1.00
ACGTcount: A:0.15, C:0.09, G:0.24, T:0.51
Consensus pattern (89 bp):
TTGGTTCAATGGATAGGTGTTGTGCTTGTGTATATGAGGTTTTGGGTTTGAATCTTTCCCTTGAA
TTTTTGTTATTTTTGTCTTAATCA
Found at i:5707569 original size:42 final size:42
Alignment explanation
Indices: 5707522--5707612 Score: 182
Period size: 42 Copynumber: 2.2 Consensus size: 42
5707512 TTTATGGAAT
5707522 ATATGTGTTAGTTTTTTATGCATGTGCATCGGGGTGGGTTTA
1 ATATGTGTTAGTTTTTTATGCATGTGCATCGGGGTGGGTTTA
5707564 ATATGTGTTAGTTTTTTATGCATGTGCATCGGGGTGGGTTTA
1 ATATGTGTTAGTTTTTTATGCATGTGCATCGGGGTGGGTTTA
5707606 ATATGTG
1 ATATGTG
5707613 ATGGAGAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.18, C:0.07, G:0.31, T:0.45
Consensus pattern (42 bp):
ATATGTGTTAGTTTTTTATGCATGTGCATCGGGGTGGGTTTA
Found at i:5707853 original size:24 final size:24
Alignment explanation
Indices: 5707800--5707869 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
5707790 GGATGGGGTA
*
5707800 GGATCTGTGATTGCATCTGTATCT
1 GGATCTGTGATTGCATCTGTATAT
* * *
5707824 GAATCTGTG-TCTGTATTTGTATAT
1 GGATCTGTGAT-TGCATCTGTATAT
*
5707848 GGATCT-AGATATGCATCTGTAT
1 GGATCTGTGAT-TGCATCTGTAT
5707870 TTGGTTATGA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
23 2 0.06
24 33 0.94
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (24 bp):
GGATCTGTGATTGCATCTGTATAT
Found at i:5710869 original size:30 final size:31
Alignment explanation
Indices: 5710835--5710892 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
5710825 GCCCTTGAAC
*
5710835 TTTTT-AAAAATTACATTTTAACCCCTATTT
1 TTTTTCAAAAATTACATCTTAACCCCTATTT
* *
5710865 TTTTTCTAAATTTACATCTTAACCCCTA
1 TTTTTCAAAAATTACATCTTAACCCCTA
5710893 ATAATTTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (31 bp):
TTTTTCAAAAATTACATCTTAACCCCTATTT
Found at i:5711193 original size:22 final size:23
Alignment explanation
Indices: 5711168--5711212 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5711158 GGCAGCAAAG
5711168 AAAAAATT-AAAAAAATAGCAGC
1 AAAAAATTCAAAAAAATAGCAGC
*
5711190 AAAATATTCAAAAAAATAGCAGC
1 AAAAAATTCAAAAAAATAGCAGC
5711213 CCAAAACCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.64, C:0.11, G:0.09, T:0.16
Consensus pattern (23 bp):
AAAAAATTCAAAAAAATAGCAGC
Found at i:5711489 original size:9 final size:9
Alignment explanation
Indices: 5711474--5711518 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
5711464 GGTTCGGCCC
5711474 AAAGAAGAA
1 AAAGAAGAA
*
5711483 GAAGAAGAA
1 AAAGAAGAA
5711492 AAAGAAGAA
1 AAAGAAGAA
5711501 AAAGAAGAA
1 AAAGAAGAA
5711510 AAAG-AGAA
1 AAAGAAGAA
5711518 A
1 A
5711519 GAAAAAAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
8 5 0.15
9 29 0.85
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AAAGAAGAA
Found at i:5711530 original size:6 final size:6
Alignment explanation
Indices: 5711474--5711531 Score: 55
Period size: 6 Copynumber: 9.5 Consensus size: 6
5711464 GGTTCGGCCC
* * * *
5711474 AAAGAA GAAGAA GAAGAA AAAGAA GAAA-AA GAAGAA AAAGAG AAAGAAA
1 AAAGAA AAAGAA AAAGAA AAAGAA -AAAGAA AAAGAA AAAGAA AAAG-AA
5711523 AAAGAA AAA
1 AAAGAA AAA
5711532 AATATCATAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
5 2 0.05
6 33 0.77
7 8 0.19
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:5711652 original size:17 final size:17
Alignment explanation
Indices: 5711632--5711668 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5711622 AAACAGCAAC
5711632 CAGCAAAAAAAAAGCAG
1 CAGCAAAAAAAAAGCAG
* *
5711649 CAGCAGAAAAAAGGCAG
1 CAGCAAAAAAAAAGCAG
5711666 CAG
1 CAG
5711669 GCCTGTCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.19, G:0.24, T:0.00
Consensus pattern (17 bp):
CAGCAAAAAAAAAGCAG
Found at i:5711691 original size:19 final size:19
Alignment explanation
Indices: 5711663--5711709 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5711653 AGAAAAAAGG
*
5711663 CAGCAGGCCTG-TCCAAGCC
1 CAGCAAGCCTGATCC-AGCC
*
5711682 CAGCAAGCCTGATCCAGTC
1 CAGCAAGCCTGATCCAGCC
5711701 CAGCAAGCC
1 CAGCAAGCC
5711710 CAGAACAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 22 0.88
20 3 0.12
ACGTcount: A:0.26, C:0.40, G:0.23, T:0.11
Consensus pattern (19 bp):
CAGCAAGCCTGATCCAGCC
Found at i:5712337 original size:16 final size:17
Alignment explanation
Indices: 5712293--5712407 Score: 103
Period size: 19 Copynumber: 6.5 Consensus size: 17
5712283 CGATATTTCT
5712293 TTTCAAAAAATT-TCGTG
1 TTTC-AAAAATTCTCGTG
5712310 TTTTCAAAAAAATTCTCGTG
1 -TTTC--AAAAATTCTCGTG
*
5712330 TTTC-AAAATTTTCGTG
1 TTTCAAAAATTCTCGTG
5712346 TTTCCAAAAATT-TCCGTG
1 TTT-CAAAAATTCT-CGTG
*
5712364 TTTCAAAAATT-TTGTG
1 TTTCAAAAATTCTCGTG
5712380 TTTTCAAAAAAATTCTCGTG
1 -TTTC--AAAAATTCTCGTG
5712400 TTTCAAAA
1 TTTCAAAA
5712408 TCTTCGTGTT
Statistics
Matches: 85, Mismatches: 3, Indels: 19
0.79 0.03 0.18
Matches are distributed among these distances:
16 17 0.20
17 19 0.22
18 17 0.20
19 23 0.27
20 9 0.11
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (17 bp):
TTTCAAAAATTCTCGTG
Found at i:5712346 original size:36 final size:37
Alignment explanation
Indices: 5712293--5712420 Score: 185
Period size: 35 Copynumber: 3.6 Consensus size: 37
5712283 CGATATTTCT
*
5712293 TTTCAAAAAATTTCGTGTTTTCAAAAAAATTCTCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAATTCTCGTG
* *
5712330 TTTC-AAAATTTTCGTG-TTTCCAAAAATTTC-CGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAATTCTCGTG
5712364 TTTCAAAAATTTT-GTGTTTTCAAAAAAATTCTCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAATTCTCGTG
*
5712400 TTTC-AAAATCTTCGTGTTTTC
1 TTTCAAAAATTTTCGTGTTTTC
5712421 TTTCTTTTTT
Statistics
Matches: 81, Mismatches: 6, Indels: 9
0.84 0.06 0.09
Matches are distributed among these distances:
34 11 0.14
35 39 0.48
36 27 0.33
37 4 0.05
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.45
Consensus pattern (37 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAAAATTCTCGTG
Found at i:5712414 original size:16 final size:16
Alignment explanation
Indices: 5712293--5712418 Score: 119
Period size: 17 Copynumber: 7.2 Consensus size: 16
5712283 CGATATTTCT
5712293 TTTCAAAAAATTTCGTG
1 TTTC-AAAAATTTCGTG
5712310 TTTTCAAAAAAATTCTCGTG
1 -TTTC--AAAAATT-TCGTG
*
5712330 TTTCAAAATTTTCGTG
1 TTTCAAAAATTTCGTG
5712346 TTTCCAAAAATTTCCGTG
1 TTT-CAAAAATTT-CGTG
*
5712364 TTTCAAAAATTTTGTG
1 TTTCAAAAATTTCGTG
5712380 TTTTCAAAAAAATTCTCGTG
1 -TTTC--AAAAATT-TCGTG
5712400 TTTC-AAAATCTTCGTG
1 TTTCAAAAAT-TTCGTG
5712416 TTT
1 TTT
5712419 TCTTTCTTTT
Statistics
Matches: 95, Mismatches: 4, Indels: 20
0.80 0.03 0.17
Matches are distributed among these distances:
16 24 0.25
17 28 0.29
18 11 0.12
19 23 0.24
20 9 0.09
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.44
Consensus pattern (16 bp):
TTTCAAAAATTTCGTG
Found at i:5714327 original size:15 final size:17
Alignment explanation
Indices: 5714296--5714327 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
5714286 TTTACCACTG
5714296 TTTAATAAGTCTTTTGT
1 TTTAATAAGTCTTTTGT
5714313 TTTAA-AAGT-TTTTGT
1 TTTAATAAGTCTTTTGT
5714328 CTGCTCTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.59
Consensus pattern (17 bp):
TTTAATAAGTCTTTTGT
Found at i:5716436 original size:102 final size:102
Alignment explanation
Indices: 5716288--5716665 Score: 488
Period size: 102 Copynumber: 3.7 Consensus size: 102
5716278 GCTCATATGC
* * * * ** * * * * *
5716288 TGGAGGCTCATAAACTGGTGGTTTAGGTTTTGGCTTTTCTTCCTTTGGTGGTGCATAAACTGGTG
1 TGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTTTTCTTTCTTTGGAGGTGTATAAACCGGTG
* * * * * * * * *
5716353 GCTTAGGTGGTTTGGGCTCATATATTGGTGGGTTGTT
66 GCTTTGGTGGCTTAGGTTCGTACATTGGAGGCTTTTT
* * * *
5716390 GGGAGGTTGATACATTGGTGGCTTGGGTTCTGGTTTTTCTTTCTTTGGAGGTGTATAAACCGGTG
1 TGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTTTTCTTTCTTTGGAGGTGTATAAACCGGTG
*
5716455 GTTTTGGTGGCTTAGGTTCGTACATTGGAGGCTTTTT
66 GCTTTGGTGGCTTAGGTTCGTACATTGGAGGCTTTTT
*
5716492 TGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTTCTT-TTTCTTTGGAGGTGTATAAACCGAT
1 TGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTT-TTCTTTCTTTGGAGGTGTATAAACCGGT
*
5716556 GGTTTTGGTGGCTTAGGTTCGTACATTGGAGGCTTTTT
65 GGCTTTGGTGGCTTAGGTTCGTACATTGGAGGCTTTTT
*
5716594 TGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGGTG
1 TGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTTTTCTTTCTTTGGAGGTGTATAAACCGGTG
5716659 GCTTTGG
66 GCTTTGG
5716666 CTCGGGCTTC
Statistics
Matches: 243, Mismatches: 31, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
101 1 0.00
102 240 0.99
103 2 0.01
ACGTcount: A:0.14, C:0.11, G:0.33, T:0.42
Consensus pattern (102 bp):
TGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTTTTCTTTCTTTGGAGGTGTATAAACCGGTG
GCTTTGGTGGCTTAGGTTCGTACATTGGAGGCTTTTT
Found at i:5716659 original size:45 final size:45
Alignment explanation
Indices: 5716592--5716894 Score: 301
Period size: 45 Copynumber: 6.7 Consensus size: 45
5716582 TGGAGGCTTT
* ** *
5716592 TTTGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTTCTCTTTC
1 TTTGGAGGTTCATAAACCGGTGGTTTGGGTTCAGGTTTCTCCTTC
* * *
5716637 TTTGGAGGTGT-ATAAACCGGTGGCTTT-GGCTCGGGCTTCTCCTTC
1 TTTGGAGGT-TCATAAACCGGTGG-TTTGGGTTCAGGTTTCTCCTTC
* * *
5716682 TTTGGAGGTTCATATACGGGTGGTTTGGGTTCAGGTTTCTCTTTC
1 TTTGGAGGTTCATAAACCGGTGGTTTGGGTTCAGGTTTCTCCTTC
* * * *
5716727 TTTGGAGGTGT-ATAAACCGGTGATTTTGGCTCAAGTTTCTCCTTC
1 TTTGGAGGT-TCATAAACCGGTGGTTTGGGTTCAGGTTTCTCCTTC
* * * *
5716772 TTTGGAGGTTCATATACTGGTGGTTTAGGTTCAGGCTTCTCCTTC
1 TTTGGAGGTTCATAAACCGGTGGTTTGGGTTCAGGTTTCTCCTTC
* * * * *
5716817 TTAGGAGGTTCATACACTGGTGGTTTGGGTTCAGGCTTT-TCTTTT
1 TTTGGAGGTTCATAAACCGGTGGTTTGGGTTCAGG-TTTCTCCTTC
* *
5716862 TTTGGAGGTGT-ATAAACCGGTGGCTTAGGTTCA
1 TTTGGAGGT-TCATAAACCGGTGGTTTGGGTTCA
5716895 TATGGTGGTG
Statistics
Matches: 212, Mismatches: 38, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
44 5 0.02
45 199 0.94
46 8 0.04
ACGTcount: A:0.14, C:0.16, G:0.29, T:0.41
Consensus pattern (45 bp):
TTTGGAGGTTCATAAACCGGTGGTTTGGGTTCAGGTTTCTCCTTC
Found at i:5716687 original size:102 final size:100
Alignment explanation
Indices: 5716288--5716755 Score: 442
Period size: 102 Copynumber: 4.7 Consensus size: 100
5716278 GCTCATATGC
* * * * ** * * * *
5716288 TGGAGGCTCATAAACTGGTGGTTTAGGTTTTGGCTTT-TCTTCCTTTGGTGGTGCATAAACTGGT
1 TGGAGGTTCATACATTGGTGGTTTGGGTTCAGG-TTTCTCTTTCTTTGGAGGTGTATAAACCGGT
* * * * * * * *
5716352 GGCTTAGGTGGTTTGGGCTCATATATTGGTGGGTTGTT
65 GGTTTTGGTGGCTT--GCTCCTACATTGGAGGCTTTTT
* * * * *
5716390 GGGAGGTTGATACATTGGTGGCTTGGGTTCTGGTTTTTCTTTCTTTGGAGGTGTATAAACCGGTG
1 TGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGGTG
* *
5716455 GTTTTGGTGGCTTAGGTTCGTACATTGGAGGCTTTTT
66 GTTTTGGTGGCTT--GCTCCTACATTGGAGGCTTTTT
* *
5716492 TGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTTCTTTTTCTTTGGAGGTGTATAAACCGATG
1 TGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGGTG
* *
5716557 GTTTTGGTGGCTTAGGTTCGTACATTGGAGGCTTTTT
66 GTTTTGGTGGCTT--GCTCCTACATTGGAGGCTTTTT
5716594 TGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGGTG
1 TGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGGTG
*
5716659 GCTTTGGCTCGGGCTT-CT-C--C-TT-----C---TT
66 GTTTTGG-T--GGCTTGCTCCTACATTGGAGGCTTTTT
* **
5716684 TGGAGGTTCATATACGGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGGTG
1 TGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGGTG
*
5716749 ATTTTGG
66 GTTTTGG
5716756 CTCAAGTTTC
Statistics
Matches: 323, Mismatches: 39, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
90 69 0.21
93 1 0.00
98 2 0.01
99 1 0.00
101 3 0.01
102 241 0.75
103 1 0.00
105 5 0.02
ACGTcount: A:0.13, C:0.12, G:0.32, T:0.42
Consensus pattern (100 bp):
TGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGGTG
GTTTTGGTGGCTTGCTCCTACATTGGAGGCTTTTT
Found at i:5716704 original size:90 final size:90
Alignment explanation
Indices: 5716592--5716825 Score: 360
Period size: 90 Copynumber: 2.6 Consensus size: 90
5716582 TGGAGGCTTT
* *
5716592 TTTGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGG
1 TTTGGAGGTTCATATACTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGG
* **
5716657 TGGCTTTGGCTCGGGCTTCTCCTTC
66 TGACTTTGGCTCAAGCTTCTCCTTC
*
5716682 TTTGGAGGTTCATATACGGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGG
1 TTTGGAGGTTCATATACTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGG
* *
5716747 TGATTTTGGCTCAAGTTTCTCCTTC
66 TGACTTTGGCTCAAGCTTCTCCTTC
* * * *
5716772 TTTGGAGGTTCATATACTGGTGGTTTAGGTTCAGGCTTCTCCTTCTTAGGAGGT
1 TTTGGAGGTTCATATACTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGT
5716826 TCATACACTG
Statistics
Matches: 131, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 131 1.00
ACGTcount: A:0.13, C:0.16, G:0.29, T:0.41
Consensus pattern (90 bp):
TTTGGAGGTTCATATACTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGG
TGACTTTGGCTCAAGCTTCTCCTTC
Found at i:5716839 original size:135 final size:135
Alignment explanation
Indices: 5716626--5716883 Score: 387
Period size: 135 Copynumber: 1.9 Consensus size: 135
5716616 TTGGGTTCAG
* * *
5716626 GTTTCTCTTTCTTTGGAGGTGTATAAACCGGTGGCTTTGGCTCGGGCTTCTCCTTCTTTGGAGGT
1 GTTTCTCCTTCTTTGGAGGTGTATAAACCGGTGGCTTTGGCTCAGGCTTCTCCTTCTTAGGAGGT
*
5716691 TCATATACGGGTGGTTTGGGTTCAGG-TTTCTCTTTCTTTGGAGGTGTATAAACCGGTGATTTTG
66 TCATACACGGGTGGTTTGGGTTCAGGCTTT-TCTTTCTTTGGAGGTGTATAAACCGGTGATTTTG
5716755 GCTCAA
130 GCTCAA
* * *
5716761 GTTTCTCCTTCTTTGGAGGT-TCATATACTGGTGG-TTTAGGTTCAGGCTTCTCCTTCTTAGGAG
1 GTTTCTCCTTCTTTGGAGGTGT-ATAAACCGGTGGCTTT-GGCTCAGGCTTCTCCTTCTTAGGAG
* *
5716824 GTTCATACACTGGTGGTTTGGGTTCAGGCTTTTCTTTTTTTGGAGGTGTATAAACCGGTG
64 GTTCATACACGGGTGGTTTGGGTTCAGGCTTTTCTTTCTTTGGAGGTGTATAAACCGGTG
5716884 GCTTAGGTTC
Statistics
Matches: 111, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
134 4 0.04
135 104 0.94
136 3 0.03
ACGTcount: A:0.14, C:0.17, G:0.28, T:0.41
Consensus pattern (135 bp):
GTTTCTCCTTCTTTGGAGGTGTATAAACCGGTGGCTTTGGCTCAGGCTTCTCCTTCTTAGGAGGT
TCATACACGGGTGGTTTGGGTTCAGGCTTTTCTTTCTTTGGAGGTGTATAAACCGGTGATTTTGG
CTCAA
Found at i:5716866 original size:90 final size:89
Alignment explanation
Indices: 5716592--5716894 Score: 351
Period size: 90 Copynumber: 3.4 Consensus size: 89
5716582 TGGAGGCTTT
* * *
5716592 TTTGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGG
1 TTTGGAGGTTCATATACTGGTGGTTTAGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGG
* *
5716657 TGGCTTTGGCTCGGGCTTCTCCTTC
66 TGG-TTTGGCTCAGGCTTTTCCTTC
* *
5716682 TTTGGAGGTTCATATACGGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGG
1 TTTGGAGGTTCATATACTGGTGGTTTAGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGG
* *
5716747 TGATTTTGGCTCAAG-TTTCTCCTTC
66 TG-GTTTGGCTCAGGCTTT-TCCTTC
* * * * *
5716772 TTTGGAGGTTCATATACTGGTGGTTTAGGTTCAGGCTTCTCCTTCTTAGGAGGT-TCATACACTG
1 TTTGGAGGTTCATATACTGGTGGTTTAGGTTCAGGTTTCTCTTTCTTTGGAGGTGT-ATAAACCG
* * *
5716836 GTGGTTTGGGTTCAGGCTTTTCTTTT
65 GTGGTTT-GGCTCAGGCTTTTCCTTC
* * *
5716862 TTTGGAGGTGT-ATAAACCGGTGGCTTAGGTTCA
1 TTTGGAGGT-TCATATACTGGTGGTTTAGGTTCA
5716895 TATGGTGGTG
Statistics
Matches: 185, Mismatches: 22, Indels: 12
0.84 0.10 0.05
Matches are distributed among these distances:
89 6 0.03
90 175 0.95
91 4 0.02
ACGTcount: A:0.14, C:0.16, G:0.29, T:0.41
Consensus pattern (89 bp):
TTTGGAGGTTCATATACTGGTGGTTTAGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGG
TGGTTTGGCTCAGGCTTTTCCTTC
Found at i:5718133 original size:74 final size:74
Alignment explanation
Indices: 5718011--5718154 Score: 209
Period size: 74 Copynumber: 1.9 Consensus size: 74
5718001 TTCAGATTTT
* * ** *
5718011 AAAAAGGGATCATGCTCAGTAAGTTAGGATGCGATCTTTTCTTCATTCCCGAGACCGTTTAAAAC
1 AAAAAGGGATCATGCCCAATAAGTTAGGACACGATCTTTTCTTAATTCCCGAGACCGTTTAAAAC
5718076 TTGAGAAAA
66 TTGAGAAAA
* *
5718085 AAAAAGGGATCATGCCCAATAAGTTAGGACACGAT-TTCTTCTTAATTCCCGAGATCGTTTATAA
1 AAAAAGGGATCATGCCCAATAAGTTAGGACACGATCTT-TTCTTAATTCCCGAGACCGTTTAAAA
5718149 CTTGAG
65 CTTGAG
5718155 TTTGAAAAGA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
73 2 0.03
74 60 0.97
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (74 bp):
AAAAAGGGATCATGCCCAATAAGTTAGGACACGATCTTTTCTTAATTCCCGAGACCGTTTAAAAC
TTGAGAAAA
Found at i:5718639 original size:12 final size:12
Alignment explanation
Indices: 5718624--5718649 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5718614 TAAATAAATG
5718624 TATATAGATATA
1 TATATAGATATA
5718636 TATATAGATATA
1 TATATAGATATA
5718648 TA
1 TA
5718650 GATATGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (12 bp):
TATATAGATATA
Found at i:5718649 original size:20 final size:20
Alignment explanation
Indices: 5718624--5718661 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5718614 TAAATAAATG
5718624 TATATAGATATATATATAGA
1 TATATAGATATATATATAGA
*
5718644 TATATAGATATGTATATA
1 TATATAGATATATATATA
5718662 AATTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TATATAGATATATATATAGA
Found at i:5721095 original size:50 final size:50
Alignment explanation
Indices: 5720971--5721219 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
5720961 GATAATAACA
* * ** * *
5720971 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
5721022 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
5721072 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
5721122 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
5721177 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
5721220 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:5721149 original size:100 final size:104
Alignment explanation
Indices: 5720970--5721219 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
5720960 TGATAATAAC
**
5720970 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
5721035 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
5721072 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
5721135 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
5721177 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
5721220 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:5721334 original size:13 final size:13
Alignment explanation
Indices: 5721313--5721344 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5721303 GCTTGGATCA
*
5721313 TCATCAAATAAAT
1 TCATAAAATAAAT
5721326 TCATAAAATAAAT
1 TCATAAAATAAAT
5721339 TCATAA
1 TCATAA
5721345 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:5721589 original size:30 final size:30
Alignment explanation
Indices: 5721555--5721612 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5721545 CCTCGACTCT
*
5721555 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
5721585 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
5721613 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:5727211 original size:19 final size:19
Alignment explanation
Indices: 5727187--5727228 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
5727177 TTAACAATAT
5727187 TAAAAAT-TCATAAAATTAA
1 TAAAAATATCA-AAAATTAA
*
5727206 TAAAAATATTAAAAATTAA
1 TAAAAATATCAAAAATTAA
5727225 TAAA
1 TAAA
5727229 CCGATTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAAATATCAAAAATTAA
Found at i:5728631 original size:45 final size:45
Alignment explanation
Indices: 5728568--5729059 Score: 304
Period size: 45 Copynumber: 10.7 Consensus size: 45
5728558 CATACGGTGG
*
5728568 TTTCTTTGGAT-GTTCATAAACTGGTGGCTTGGGTCCTGGTTTCTC
1 TTTCTTTGG-TGGTTCATAAACTGGTGGCTTGGGTTCTGGTTTCTC
* * * *
5728613 TTTCTTTGGTGGTACATAAACTGGTGGTTTTGGTGGTT-TAGGCTCATAAACTGG
1 TTTCTTTGGTGGTTCATAAACTGGTGG-CTT-G-GGTTCT-GG-T--T--TCT-C
* * * * * *
5728667 TGGCTTCTTCGGAGGCTGATAAACTGGTGGTTTGGGTTCTGGTTTTTC
1 T---TTCTTTGGTGGTTCATAAACTGGTGGCTTGGGTTCTGGTTTCTC
* * * *
5728715 TTTCTTTGTTGGTGT-ATAAACCGGTGGCTTAGGCTT-AGGCTTT-TC
1 TTTCTTTGGTGGT-TCATAAACTGGTGGCTT-GGGTTCTGG-TTTCTC
* * * *
5728760 CTTCTTTGGTGGTTCATACACTGGTGGCTTGGGTTCAGGCTTCTC
1 TTTCTTTGGTGGTTCATAAACTGGTGGCTTGGGTTCTGGTTTCTC
* * * *
5728805 TTTCTTTGGTGGGGT-ATAAACTGGTGGCTTAGGCTCAGGCTTT-TC
1 TTTCTTTGGT-GGTTCATAAACTGGTGGCTTGGGTTCTGG-TTTCTC
* * * * ** *
5728850 CTTCTTTGGTGGTTCATATACTGGTGGTTTGTGTTCAAGCTTCTC
1 TTTCTTTGGTGGTTCATAAACTGGTGGCTTGGGTTCTGGTTTCTC
* * *
5728895 TTTCTTTGGAGGTGT-ATAAACTGGTGGCTTTGGTTCGGGCTTT-TCC
1 TTTCTTTGGTGGT-TCATAAACTGGTGGCTTGGGTTCTGG-TTTCT-C
* * *
5728941 TTT-TTTGGTGATTCATATACTGGTGGCTTGGGTTCTGGCTTCTC
1 TTTCTTTGGTGGTTCATAAACTGGTGGCTTGGGTTCTGGTTTCTC
* * * *
5728985 TTTCTTTGGTGGTGT-ATAAACTGGTGGTTTAGGTTCAGGTTTTTC
1 TTTCTTTGGTGGT-TCATAAACTGGTGGCTTGGGTTCTGGTTTCTC
* * * *
5729030 CTTCTTTGGAGGTTCATAGACAGGTGGCTT
1 TTTCTTTGGTGGTTCATAAACTGGTGGCTT
5729060 ATGTTCATAA
Statistics
Matches: 345, Mismatches: 69, Indels: 66
0.72 0.14 0.14
Matches are distributed among these distances:
44 21 0.06
45 253 0.73
46 23 0.07
47 2 0.01
48 6 0.02
49 2 0.01
51 2 0.01
53 3 0.01
54 7 0.02
55 2 0.01
56 3 0.01
57 21 0.06
ACGTcount: A:0.12, C:0.15, G:0.29, T:0.43
Consensus pattern (45 bp):
TTTCTTTGGTGGTTCATAAACTGGTGGCTTGGGTTCTGGTTTCTC
Found at i:5728765 original size:90 final size:90
Alignment explanation
Indices: 5728689--5729059 Score: 519
Period size: 90 Copynumber: 4.1 Consensus size: 90
5728679 AGGCTGATAA
* * * * * *
5728689 ACTGGTGGTTTGGGTTCTGGTTTTTCTTTCTTTGTTGGTGTATAAACCGGTGGCTTAGGCTT-AG
1 ACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGTATAAACTGGTGGCTTAGG-TTCAG
*
5728753 GCTTTTCCTTCTTTGGTGGTTCATAC
65 GCTTTTCCTTCTTTGGTGGTTCATAT
* *
5728779 ACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGGGTATAAACTGGTGGCTTAGGCTCAGG
1 ACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGTATAAACTGGTGGCTTAGGTTCAGG
5728844 CTTTTCCTTCTTTGGTGGTTCATAT
66 CTTTTCCTTCTTTGGTGGTTCATAT
* * * * * *
5728869 ACTGGTGGTTTGTGTTCAAGCTTCTCTTTCTTTGGAGGTGTATAAACTGGTGGCTTTGGTTCGGG
1 ACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGTATAAACTGGTGGCTTAGGTTCAGG
* *
5728934 CTTTTCCTTTTTTGGTGATTCATAT
66 CTTTTCCTTCTTTGGTGGTTCATAT
* *
5728959 ACTGGTGGCTTGGGTTCTGGCTTCTCTTTCTTTGGTGGTGTATAAACTGGTGGTTTAGGTTCAGG
1 ACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGTATAAACTGGTGGCTTAGGTTCAGG
* * *
5729024 TTTTTCCTTCTTTGGAGGTTCATAG
66 CTTTTCCTTCTTTGGTGGTTCATAT
*
5729049 ACAGGTGGCTT
1 ACTGGTGGCTT
5729060 ATGTTCATAA
Statistics
Matches: 247, Mismatches: 33, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
89 1 0.00
90 246 1.00
ACGTcount: A:0.11, C:0.16, G:0.29, T:0.44
Consensus pattern (90 bp):
ACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGTATAAACTGGTGGCTTAGGTTCAGG
CTTTTCCTTCTTTGGTGGTTCATAT
Found at i:5729066 original size:45 final size:44
Alignment explanation
Indices: 5728685--5729066 Score: 354
Period size: 45 Copynumber: 8.5 Consensus size: 44
5728675 TCGGAGGCTG
* * * * * *
5728685 ATAAACTGGTGGTTTGGGTTCTGGTTTTTCTTTCTTTGTTGGTGT
1 ATAAACTGGTGGCTTAGGTTCAGGCTTTTCCTTCTTTGGTGGT-T
*
5728730 ATAAACCGGTGGCTTAGGCTT-AGGCTTTTCCTTCTTTGGTGGTT
1 ATAAACTGGTGGCTTAGG-TTCAGGCTTTTCCTTCTTTGGTGGTT
* * * * *
5728774 CATACACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGGGT
1 -ATAAACTGGTGGCTTAGGTTCAGGCTTTTCCTTCTTTGGT-GGTT
*
5728820 ATAAACTGGTGGCTTAGGCTCAGGCTTTTCCTTCTTTGGTGGTT
1 ATAAACTGGTGGCTTAGGTTCAGGCTTTTCCTTCTTTGGTGGTT
* * * * * *
5728864 CATATACTGGTGG-TTTGTGTTCAAGCTTCTCTTTCTTTGGAGGTGT
1 -ATAAACTGGTGGCTTAG-GTTCAGGCTTTTCCTTCTTTGGTGGT-T
* * * *
5728910 ATAAACTGGTGGCTTTGGTTCGGGCTTTTCCTTTTTTGGTGATT
1 ATAAACTGGTGGCTTAGGTTCAGGCTTTTCCTTCTTTGGTGGTT
* * * * *
5728954 CATATACTGGTGGCTTGGGTTCTGGCTTCTCTTTCTTTGGTGGTGT
1 -ATAAACTGGTGGCTTAGGTTCAGGCTTTTCCTTCTTTGGTGGT-T
* * *
5729000 ATAAACTGGTGGTTTAGGTTCAGGTTTTTCCTTCTTTGGAGGTT
1 ATAAACTGGTGGCTTAGGTTCAGGCTTTTCCTTCTTTGGTGGTT
* * *
5729044 CATAGACAGGTGGCTTATGTTCA
1 -ATAAACTGGTGGCTTAGGTTCA
5729067 TAAGGTGGGG
Statistics
Matches: 273, Mismatches: 53, Indels: 22
0.78 0.15 0.06
Matches are distributed among these distances:
44 11 0.04
45 251 0.92
46 11 0.04
ACGTcount: A:0.12, C:0.15, G:0.28, T:0.44
Consensus pattern (44 bp):
ATAAACTGGTGGCTTAGGTTCAGGCTTTTCCTTCTTTGGTGGTT
Found at i:5731480 original size:19 final size:18
Alignment explanation
Indices: 5731451--5731490 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
5731441 ATTAGCAAGT
*
5731451 TTTGAAAACTTCTATATA
1 TTTGAAAACTTCTATAAA
*
5731469 TTTGAGAAACTTGTATAAA
1 TTTGA-AAACTTCTATAAA
5731488 TTT
1 TTT
5731491 ATTTACTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (18 bp):
TTTGAAAACTTCTATAAA
Found at i:5735356 original size:14 final size:14
Alignment explanation
Indices: 5735337--5735364 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5735327 AATAGCTCTA
5735337 CAACCCCAAACCTT
1 CAACCCCAAACCTT
5735351 CAACCCCAAACCTT
1 CAACCCCAAACCTT
5735365 TAAATAATTA
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:0.50, G:0.00, T:0.14
Consensus pattern (14 bp):
CAACCCCAAACCTT
Found at i:5737025 original size:16 final size:18
Alignment explanation
Indices: 5737004--5737041 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5736994 ATTATAAAAA
5737004 ATATAAA-A-GTACATAT
1 ATATAAATATGTACATAT
5737020 ATATAAATATGTACATAT
1 ATATAAATATGTACATAT
5737038 ATAT
1 ATAT
5737042 GTAAGCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
17 1 0.05
18 12 0.60
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (18 bp):
ATATAAATATGTACATAT
Found at i:5738310 original size:30 final size:30
Alignment explanation
Indices: 5738288--5738352 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
5738278 TTTGTTTGTA
5738288 ATTGGG-CTGAGGGTATTGGGTTTGTGGGT
1 ATTGGGTCTGAGGGTATTGGGTTTGTGGGT
* *
5738317 ATTGGGTTTGTGGGTATTGGGTTTGTGGGT
1 ATTGGGTCTGAGGGTATTGGGTTTGTGGGT
5738347 ATTGGG
1 ATTGGG
5738353 CCGGACAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
29 6 0.18
30 27 0.82
ACGTcount: A:0.09, C:0.02, G:0.48, T:0.42
Consensus pattern (30 bp):
ATTGGGTCTGAGGGTATTGGGTTTGTGGGT
Found at i:5738318 original size:15 final size:15
Alignment explanation
Indices: 5738298--5738352 Score: 110
Period size: 15 Copynumber: 3.7 Consensus size: 15
5738288 ATTGGGCTGA
5738298 GGGTATTGGGTTTGT
1 GGGTATTGGGTTTGT
5738313 GGGTATTGGGTTTGT
1 GGGTATTGGGTTTGT
5738328 GGGTATTGGGTTTGT
1 GGGTATTGGGTTTGT
5738343 GGGTATTGGG
1 GGGTATTGGG
5738353 CCGGACAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.07, C:0.00, G:0.49, T:0.44
Consensus pattern (15 bp):
GGGTATTGGGTTTGT
Found at i:5738322 original size:7 final size:7
Alignment explanation
Indices: 5738298--5738352 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
5738288 ATTGGGCTGA
5738298 GGGTATT
1 GGGTATT
*
5738305 GGGTTTGT
1 GGGTAT-T
5738313 GGGTATT
1 GGGTATT
*
5738320 GGGTTTGT
1 GGGTAT-T
5738328 GGGTATT
1 GGGTATT
*
5738335 GGGTTTGT
1 GGGTAT-T
5738343 GGGTATT
1 GGGTATT
5738350 GGG
1 GGG
5738353 CCGGACAGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
7 21 0.54
8 18 0.46
ACGTcount: A:0.07, C:0.00, G:0.49, T:0.44
Consensus pattern (7 bp):
GGGTATT
Found at i:5738330 original size:8 final size:8
Alignment explanation
Indices: 5738304--5738346 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
5738294 CTGAGGGTAT
5738304 TGGGTTTG
1 TGGGTTTG
*
5738312 TGGGTAT-
1 TGGGTTTG
5738319 TGGGTTTG
1 TGGGTTTG
*
5738327 TGGGTAT-
1 TGGGTTTG
5738334 TGGGTTTG
1 TGGGTTTG
5738342 TGGGT
1 TGGGT
5738347 ATTGGGCCGG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 12 0.41
8 17 0.59
ACGTcount: A:0.05, C:0.00, G:0.49, T:0.47
Consensus pattern (8 bp):
TGGGTTTG
Found at i:5738589 original size:41 final size:41
Alignment explanation
Indices: 5738524--5738717 Score: 140
Period size: 41 Copynumber: 4.6 Consensus size: 41
5738514 GTCGCTTCAA
* *
5738524 TCCATTGT-ACTTCAGGGAAATAAGACTTGATGCGATCTGC
1 TCCACTGTAACTTCAGGGAGATAAGACTTGATGCGATCTGC
* * * *** *
5738564 TCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGC
1 TCCACTGTAACTTCAGGGAGATAAGA-CT-TGA-TGCGATCTGC
* * * *
5738608 TCCACTGTAACTTCAGGGAGATAGGACAGTGTCTTCGATCTGC
1 TCCACTGTAACTTCAGGGAGATAAGAC-TTG-ATGCGATCTGC
* * * *
5738651 TCCGCTGTAA-TCTCAGGGAGATAAGACCTGATGCGGTCTAC
1 TCCACTGTAACT-TCAGGGAGATAAGACTTGATGCGATCTGC
** *
5738692 TCTGCTGTAACTTCAGAGAGATAAGA
1 TCCACTGTAACTTCAGGGAGATAAGA
5738718 TCTTTTAATC
Statistics
Matches: 119, Mismatches: 27, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
40 5 0.04
41 44 0.37
42 6 0.05
43 36 0.30
44 28 0.24
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (41 bp):
TCCACTGTAACTTCAGGGAGATAAGACTTGATGCGATCTGC
Found at i:5777447 original size:19 final size:19
Alignment explanation
Indices: 5777415--5777451 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5777405 TTTTTAATAT
5777415 TTTCCCTCCAAACTATTTAC
1 TTTCCCTCCAAACT-TTTAC
5777435 TTTCCCT-CAAACTTTTA
1 TTTCCCTCCAAACTTTTA
5777452 TCCTCCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTCCCTCCAAACTTTTAC
Found at i:5778625 original size:32 final size:32
Alignment explanation
Indices: 5778533--5778668 Score: 134
Period size: 32 Copynumber: 4.3 Consensus size: 32
5778523 GAATGGCTAC
* * * *
5778533 AAGCCATAAGT-ACAGTAATATGATTGACACA
1 AAGCCATCAGTAACAGTAATATAATCGGCACA
* * * *
5778564 AAGCCATCAGTAGCAGTGATATGACCGGCACA
1 AAGCCATCAGTAACAGTAATATAATCGGCACA
*
5778596 CAA-CTATCAGTAAC-GATAATATAATCGGCACA
1 -AAGCCATCAGTAACAG-TAATATAATCGGCACA
* *
5778628 AAGCCATCAGTAACAGTCATATAATCGGTACA
1 AAGCCATCAGTAACAGTAATATAATCGGCACA
5778660 AAGCCATCA
1 AAGCCATCA
5778669 ATAGCATTGC
Statistics
Matches: 86, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
31 13 0.15
32 70 0.81
33 3 0.03
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATAATCGGCACA
Found at i:5778696 original size:26 final size:26
Alignment explanation
Indices: 5778662--5778724 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
5778652 TCGGTACAAA
* * *
5778662 GCCATCAATAGCATTGCAACAAAGCT
1 GCCAGCAATAGCATCGCAACAAAACT
* *
5778688 GCCAGCAATAGTATCGCAGCAAAACT
1 GCCAGCAATAGCATCGCAACAAAACT
*
5778714 GCCAGTAATAG
1 GCCAGCAATAG
5778725 TATATGTGGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.17
Consensus pattern (26 bp):
GCCAGCAATAGCATCGCAACAAAACT
Found at i:5778771 original size:27 final size:27
Alignment explanation
Indices: 5778715--5778779 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 27
5778705 AGCAAAACTG
* *
5778715 CCAGTAATAGTATATGTGGCCAAGCTA
1 CCAGTAACAGTATATGTGGCCAAGCCA
5778742 CCAGTAACAGTGAT-TGTGG-CAGAGCCA
1 CCAGTAACAGT-ATATGTGGCCA-AGCCA
*
5778769 CCAAT-ACAGTA
1 CCAGTAACAGTA
5778780 CTTCTTCCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 1 0.03
26 7 0.21
27 23 0.70
28 2 0.06
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (27 bp):
CCAGTAACAGTATATGTGGCCAAGCCA
Found at i:5778870 original size:24 final size:24
Alignment explanation
Indices: 5778843--5778948 Score: 104
Period size: 24 Copynumber: 4.4 Consensus size: 24
5778833 CCATACTCAG
5778843 AATCAGTCATACAAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
* *
5778867 AATCAGTCATACCATTCACAGACA
1 AATCAGTCATACAAATCACAGACA
* ** *
5778891 AATCAATCATTTAAATCACAGGCA
1 AATCAGTCATACAAATCACAGACA
* ** * *
5778915 CATCAGTCATTTACATCACATACA
1 AATCAGTCATACAAATCACAGACA
*
5778939 AATCAATCAT
1 AATCAGTCAT
5778949 TTACACTCGA
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.44, C:0.25, G:0.07, T:0.24
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAGACA
Found at i:5778920 original size:48 final size:47
Alignment explanation
Indices: 5778855--5778951 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 47
5778845 TCAGTCATAC
5778855 AAATCACAGACAAATCAGTCA-TACCATTCACAGACAAATCAATCATTT
1 AAATCACAGACAAATCAGTCATTA-CA-TCACAGACAAATCAATCATTT
* * *
5778903 AAATCACAGGCACATCAGTCATTTACATCACATACAAATCAATCATTT
1 AAATCACAGACAAATCAGTCA-TTACATCACAGACAAATCAATCATTT
5778951 A
1 A
5778952 CACTCGAGGG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
48 40 0.91
49 2 0.05
50 2 0.05
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (47 bp):
AAATCACAGACAAATCAGTCATTACATCACAGACAAATCAATCATTT
Found at i:5778949 original size:24 final size:24
Alignment explanation
Indices: 5778857--5778953 Score: 108
Period size: 24 Copynumber: 4.0 Consensus size: 24
5778847 AGTCATACAA
*
5778857 ATCACAGACAAATCAGTCA--TACC
1 ATCACAGACAAATCAATCATTTA-C
*
5778880 ATTCACAGACAAATCAATCATTTAA
1 A-TCACAGACAAATCAATCATTTAC
* * *
5778905 ATCACAGGCACATCAGTCATTTAC
1 ATCACAGACAAATCAATCATTTAC
*
5778929 ATCACATACAAATCAATCATTTAC
1 ATCACAGACAAATCAATCATTTAC
5778953 A
1 A
5778954 CTCGAGGGGC
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
23 1 0.02
24 57 0.93
25 1 0.02
26 2 0.03
ACGTcount: A:0.43, C:0.26, G:0.06, T:0.25
Consensus pattern (24 bp):
ATCACAGACAAATCAATCATTTAC
Found at i:5778973 original size:26 final size:27
Alignment explanation
Indices: 5778938--5778990 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
5778928 CATCACATAC
*
5778938 AAATCAATCATTTACACTCGAGGGGCA
1 AAATCAATCATTTACACTCCAGGGGCA
*
5778965 AAAT-AATCATTTACCCTCCAGGGGCA
1 AAATCAATCATTTACACTCCAGGGGCA
5778991 TTATGGTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.23
Consensus pattern (27 bp):
AAATCAATCATTTACACTCCAGGGGCA
Found at i:5779013 original size:27 final size:27
Alignment explanation
Indices: 5778974--5779163 Score: 125
Period size: 27 Copynumber: 7.1 Consensus size: 27
5778964 AAAATAATCA
*
5778974 TTTACCCTCCAGGGGCATTAT-GGTCAT
1 TTTACCCTACAGGGGCATT-TCGGTCAT
* *
5779001 TTTACCTTACAGGGGTATTTCGGTCAT
1 TTTACCCTACAGGGGCATTTCGGTCAT
* * * * *
5779028 TTAACCCTA-TGGAGGTATTACGATCAT
1 TTTACCCTACAGG-GGCATTTCGGTCAT
** * *
5779055 TTTACCCTATTGGGGTATTTTGGTCAT
1 TTTACCCTACAGGGGCATTTCGGTCAT
* ** *
5779082 TTTATCCTATTGGGGTATTTCGGTCAT
1 TTTACCCTACAGGGGCATTTCGGTCAT
* * *
5779109 TTTACCCTA-TGGGGTATTTCCGTCAT
1 TTTACCCTACAGGGGCATTTCGGTCAT
* ** * *
5779135 TCTACCCTATGGGGGTATTTCAGTCAT
1 TTTACCCTACAGGGGCATTTCGGTCAT
5779162 TT
1 TT
5779164 AACAATATTT
Statistics
Matches: 139, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
26 27 0.19
27 109 0.78
28 3 0.02
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.41
Consensus pattern (27 bp):
TTTACCCTACAGGGGCATTTCGGTCAT
Found at i:5779058 original size:54 final size:51
Alignment explanation
Indices: 5778971--5779153 Score: 179
Period size: 54 Copynumber: 3.4 Consensus size: 51
5778961 GGCAAAATAA
* * * * *
5778971 TCATTTACCCTCCA-GGGGCATTATGGTCATTTTACCTTACAGGGGTATTTCGG
1 TCATTTACCCT--ATGGGGTATTACGATCATTTTACCCTA-TGGGGTATTTCGG
*
5779024 TCATTTAACCCTATGGAGGTATTACGATCATTTTACCCTATTGGGGTATTTTGG
1 TCATTT-ACCCTATGG-GGTATTACGATCATTTTACCCTA-TGGGGTATTTCGG
* * * *
5779078 TCATTTTATCCTATTGGGGTATTTCGGTCATTTTACCCTATGGGGTATTTCCG
1 TCA-TTTACCCTA-TGGGGTATTACGATCATTTTACCCTATGGGGTATTTCGG
5779131 TCATTCTACCCTATGGGGGTATT
1 TCATT-TACCCTAT-GGGGTATT
5779154 TCAGTCATTT
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
52 4 0.04
53 36 0.33
54 64 0.58
55 6 0.05
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (51 bp):
TCATTTACCCTATGGGGTATTACGATCATTTTACCCTATGGGGTATTTCGG
Found at i:5779061 original size:81 final size:79
Alignment explanation
Indices: 5778970--5779143 Score: 208
Period size: 81 Copynumber: 2.2 Consensus size: 79
5778960 GGGCAAAATA
*
5778970 ATCATTTACCCTCCAGGGGCATTATGGTCATTTTA-CCTTACAGGGGTATTTCGGTCATTTAACC
1 ATCATTTACCCTACAGGGGCATTATGGTCATTTTATCC-TACAGGGGTATTTCGGTCATTTAACC
5779034 CTATGGAGGTATTACG
65 CTATGG-GGTATTACG
** * * ** *
5779050 ATCATTTTACCCTATTGGGGTATTTTGGTCATTTTATCCTATTGGGGTATTTCGGTCATTTTACC
1 ATCA-TTTACCCTACAGGGGCATTATGGTCATTTTATCCTACAGGGGTATTTCGGTCATTTAACC
*
5779115 CTATGGGGTATTTCCG
65 CTATGGGGTA-TTACG
5779131 -TCATTCTACCCTA
1 ATCATT-TACCCTA
5779144 TGGGGGTATT
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
79 2 0.02
80 18 0.22
81 59 0.73
82 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.40
Consensus pattern (79 bp):
ATCATTTACCCTACAGGGGCATTATGGTCATTTTATCCTACAGGGGTATTTCGGTCATTTAACCC
TATGGGGTATTACG
Found at i:5780114 original size:13 final size:13
Alignment explanation
Indices: 5780096--5780152 Score: 77
Period size: 13 Copynumber: 4.7 Consensus size: 13
5780086 TTATCCAACT
5780096 CAACCCAATTACC
1 CAACCCAATTACC
5780109 CAACCCAATTA-C
1 CAACCCAATTACC
5780121 CAACCC-A--ACC
1 CAACCCAATTACC
*
5780131 CAACCTAATTACC
1 CAACCCAATTACC
5780144 CAACCCAAT
1 CAACCCAAT
5780153 AAAACTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 1 0.03
10 6 0.16
11 2 0.05
12 7 0.18
13 22 0.58
ACGTcount: A:0.40, C:0.46, G:0.00, T:0.14
Consensus pattern (13 bp):
CAACCCAATTACC
Found at i:5780134 original size:22 final size:23
Alignment explanation
Indices: 5780106--5780151 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
5780096 CAACCCAATT
5780106 ACCCAACCCAATTA-CCAACCCA
1 ACCCAACCCAATTACCCAACCCA
*
5780128 ACCCAACCTAATTACCCAACCCA
1 ACCCAACCCAATTACCCAACCCA
5780151 A
1 A
5780152 TAAAACTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.41, C:0.48, G:0.00, T:0.11
Consensus pattern (23 bp):
ACCCAACCCAATTACCCAACCCA
Found at i:5780146 original size:18 final size:18
Alignment explanation
Indices: 5780084--5780151 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
5780074 TAATAAATAA
* * *
5780084 AATTATCCAACTCAACCC
1 AATTACCCAACCCAACCT
*
5780102 AATTACCCAACCCAA-TT
1 AATTACCCAACCCAACCT
***
5780119 ACCAACCCAACCCAACCT
1 AATTACCCAACCCAACCT
5780137 AATTACCCAACCCAA
1 AATTACCCAACCCAA
5780152 TAAAACTAAA
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
17 12 0.32
18 26 0.68
ACGTcount: A:0.41, C:0.43, G:0.00, T:0.16
Consensus pattern (18 bp):
AATTACCCAACCCAACCT
Found at i:5780536 original size:24 final size:22
Alignment explanation
Indices: 5780469--5780560 Score: 125
Period size: 22 Copynumber: 4.2 Consensus size: 22
5780459 AAATTCAATA
*
5780469 TCAATTTCTTTCAAAAATTCTC
1 TCAATTCCTTTCAAAAATTCTC
5780491 TCAATTCCTTTCAAAAATTCTC
1 TCAATTCCTTTCAAAAATTCTC
*
5780513 TCAATTCCCTTT-AAAATTTCTC
1 TCAATT-CCTTTCAAAAATTCTC
*
5780535 TCAATTTCC-TTCCAAAATTCTC
1 TCAA-TTCCTTTCAAAAATTCTC
5780557 TCAA
1 TCAA
5780561 ACTCTCAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
21 2 0.03
22 54 0.86
23 7 0.11
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (22 bp):
TCAATTCCTTTCAAAAATTCTC
Found at i:5780566 original size:30 final size:30
Alignment explanation
Indices: 5780532--5780590 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
5780522 TTTAAAATTT
* *
5780532 CTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
5780562 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
5780591 TTTCCTTCAA
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:0.31, C:0.36, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:5780609 original size:22 final size:22
Alignment explanation
Indices: 5780562--5780603 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5780552 TTCTCTCAAA
*
5780562 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCAAAAATC
*
5780584 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCAAAAA
5780604 ATCTCTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCAAAAATC
Found at i:5780665 original size:25 final size:24
Alignment explanation
Indices: 5780636--5780690 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 24
5780626 TCTTTTTCCA
5780636 TTAAATTTCA-TTTTTTAAGAAAATT
1 TTAAATTT-ATTTTTTTAA-AAAATT
*
5780661 TTAAAATTTATTTTTTTAAATAATT
1 TT-AAATTTATTTTTTTAAAAAATT
5780686 TTAAA
1 TTAAA
5780691 ATTTTTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 3 0.11
25 10 0.37
26 14 0.52
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TTAAATTTATTTTTTTAAAAAATT
Found at i:5780691 original size:25 final size:26
Alignment explanation
Indices: 5780638--5780694 Score: 82
Period size: 25 Copynumber: 2.2 Consensus size: 26
5780628 TTTTTCCATT
5780638 AAATTTCATTTTTTAAGAAAATTTTA
1 AAATTTCATTTTTTAAGAAAATTTTA
*
5780664 AAATTT-ATTTTTTTAA-ATAATTTTA
1 AAATTTCA-TTTTTTAAGAAAATTTTA
5780689 AAATTT
1 AAATTT
5780695 TTAATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 15 0.52
26 14 0.48
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
AAATTTCATTTTTTAAGAAAATTTTA
Found at i:5783010 original size:23 final size:23
Alignment explanation
Indices: 5782984--5783188 Score: 225
Period size: 23 Copynumber: 8.4 Consensus size: 23
5782974 TAAAAACCCT
*
5782984 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAACTTAATTAAA
5783007 AACCCTAACCCT-ACTTAATTAAA
1 AACCCTAA-CCTAACTTAATTAAA
5783030 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAA-CCTAA-C----TTAATTAAA
*
5783059 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAACTTAATTAAA
* *
5783082 AACCCTAACATAACTTAATAAAA
1 AACCCTAACCTAACTTAATTAAA
*
5783105 AAACCTAACCTAACTTAATTAAATTAAA
1 AACCCTAACCTAAC----TT-AATTAAA
*
5783133 AACCCTAACATAACTTAATTAAA
1 AACCCTAACCTAACTTAATTAAA
5783156 AACCCTAACCCT-ACTTAATTAAA
1 AACCCTAA-CCTAACTTAATTAAA
5783179 AACCCTAACC
1 AACCCTAACC
5783189 CAAAGCAACG
Statistics
Matches: 158, Mismatches: 11, Indels: 27
0.81 0.06 0.14
Matches are distributed among these distances:
22 2 0.01
23 105 0.66
24 8 0.05
25 1 0.01
27 2 0.01
28 23 0.15
29 17 0.11
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.26
Consensus pattern (23 bp):
AACCCTAACCTAACTTAATTAAA
Found at i:5783034 original size:52 final size:52
Alignment explanation
Indices: 5782972--5783189 Score: 269
Period size: 52 Copynumber: 4.3 Consensus size: 52
5782962 ACATTATTTG
5782972 ATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCT-ACTTA
1 ATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA-CCTAACTTA
*
5783024 ATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTA
1 ATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAACTTA
* *
5783076 ATTAAAAACCCTAA-CATAACTTAA--TAA--AAAAA-CCTAACCTAACTTA
1 ATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAACTTA
* * *
5783122 ATTAAATTAA---AAACCCTAACATAACTTAATTAAAAACCCTAACCCT-ACTTA
1 ATTAAA--AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA-CCTAACTTA
5783173 ATTAAAAACCCTAACCC
1 ATTAAAAACCCTAACCC
5783190 AAAGCAACGT
Statistics
Matches: 145, Mismatches: 8, Indels: 26
0.81 0.04 0.15
Matches are distributed among these distances:
45 2 0.01
46 27 0.19
47 5 0.03
48 5 0.03
49 5 0.03
50 5 0.03
51 27 0.19
52 69 0.48
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (52 bp):
ATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAACTTA
Found at i:5783087 original size:46 final size:46
Alignment explanation
Indices: 5782984--5783188 Score: 232
Period size: 51 Copynumber: 4.2 Consensus size: 46
5782974 TAAAAACCCT
*
5782984 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTACTTAATTAAA
1 AACCCTAACCTAACTTAATTAAAAACCCTAACCCTACTTAATTAAA
*
5783030 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA-CCTAATTTAATTAAA
1 AACCCTAA-CCTAA-C----TTAATTAAAAACCCTAACCCT-ACTTAATTAAA
* * * *
5783082 AACCCTAACATAACTTAATAAAAAAACCTAACCTAACTTAATTAAATTAAA
1 AACCCTAACCTAACTTAATTAAAAACCCTAACC---C-TACTT-AATTAAA
*
5783133 AACCCTAACATAACTTAATTAAAAACCCTAACCCTACTTAATTAAA
1 AACCCTAACCTAACTTAATTAAAAACCCTAACCCTACTTAATTAAA
5783179 AACCCTAACC
1 AACCCTAACC
5783189 CAAAGCAACG
Statistics
Matches: 136, Mismatches: 10, Indels: 26
0.79 0.06 0.15
Matches are distributed among these distances:
46 39 0.29
47 10 0.07
48 1 0.01
50 5 0.04
51 46 0.34
52 35 0.26
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.26
Consensus pattern (46 bp):
AACCCTAACCTAACTTAATTAAAAACCCTAACCCTACTTAATTAAA
Found at i:5785447 original size:123 final size:124
Alignment explanation
Indices: 5785225--5785503 Score: 384
Period size: 123 Copynumber: 2.3 Consensus size: 124
5785215 CCACGAGGGC
*
5785225 GCGATTTGACACTATTTACTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAATTGTAGCG
1 GCGATTTGACACTATTTACTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
* * * **
5785290 AAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 AAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
* * * *
5785349 GCGATTTTATACTATTTGCTCAGGAAACGTC-AAAAAAATTATTTCTTACATGACC-ACTGTAGC
1 GCGATTTGACACTATTTACTCA-GAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGC
* *
5785412 GAAATCGCGTCCACGAGGCCACTATTTCACAATTTCTTCTTAAATAGCATCCTGGTAGAA
65 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
** *
5785472 GCGATTTCCCACTATTTAAC-CAGATACGTCAA
1 GCGATTTGACACTATTT-ACTCAGAAACGTCAA
5785504 CTCGAAAAAA
Statistics
Matches: 135, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
122 7 0.05
123 77 0.57
124 43 0.32
125 8 0.06
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (124 bp):
GCGATTTGACACTATTTACTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
AAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
Found at i:5786034 original size:37 final size:37
Alignment explanation
Indices: 5786007--5786081 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
5785997 TGTTAATTTC
* *
5786007 AAGAATTATGTAATGCTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATACTTTTAATTATGTAGTAATTCA
* * *
5786044 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATACTTTTAATTATGTAGTAATTCA
5786081 A
1 A
5786082 TTCGGGTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (37 bp):
AAGAATTATGTAATACTTTTAATTATGTAGTAATTCA
Found at i:5786115 original size:9 final size:9
Alignment explanation
Indices: 5786097--5786138 Score: 75
Period size: 9 Copynumber: 4.7 Consensus size: 9
5786087 GTAATTCGAG
*
5786097 TAATTCGGT
1 TAATTTGGT
5786106 TAATTTGGT
1 TAATTTGGT
5786115 TAATTTGGT
1 TAATTTGGT
5786124 TAATTTGGT
1 TAATTTGGT
5786133 TAATTT
1 TAATTT
5786139 TTAACCAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.24, C:0.02, G:0.19, T:0.55
Consensus pattern (9 bp):
TAATTTGGT
Found at i:5789117 original size:15 final size:15
Alignment explanation
Indices: 5789099--5789130 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5789089 CATTTTACTA
*
5789099 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
5789114 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
5789129 TT
1 TT
5789131 TGCACGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:5792911 original size:21 final size:18
Alignment explanation
Indices: 5792878--5792924 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
5792868 TGCATAAAAT
*
5792878 TTAATT-TGAATTTAGGATA
1 TTAATTATGGATTTA-GA-A
5792897 TTGAATTATGGATTTAGAA
1 TT-AATTATGGATTTAGAA
5792916 TTAATTATG
1 TTAATTATG
5792925 TATACAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.28
19 5 0.20
20 6 0.24
21 7 0.28
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (18 bp):
TTAATTATGGATTTAGAA
Found at i:5795352 original size:4 final size:4
Alignment explanation
Indices: 5795275--5795411 Score: 82
Period size: 4 Copynumber: 33.5 Consensus size: 4
5795265 TTTTAATTCT
* * * * *
5795275 TTTA TTCA TTGA TTTA CTTA TTTA CTTA TTTA -TTA TTTCT TTTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA -TTTA
* * * * * *
5795324 TTCA TTTA TTTA CTTA TTTA CTTA TTTA TTTA TATA -TTA TTCA TCTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* *
5795371 TTTA CTTTT TTTA TTTTAA TTCT- TTTA TTCA TTTA TTTA TT
1 TTTA -TTTA TTTA -TTT-A TT-TA TTTA TTTA TTTA TTTA TT
5795412 ATTCCTTCAC
Statistics
Matches: 99, Mismatches: 25, Indels: 18
0.70 0.18 0.13
Matches are distributed among these distances:
3 6 0.06
4 76 0.77
5 15 0.15
6 2 0.02
ACGTcount: A:0.23, C:0.09, G:0.01, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:5795527 original size:14 final size:15
Alignment explanation
Indices: 5795508--5795537 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5795498 GCCTTTACTA
5795508 TTATTATTA-CTATT
1 TTATTATTATCTATT
5795522 TTATTATTATCTATT
1 TTATTATTATCTATT
5795537 T
1 T
5795538 ATCTACTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTATTATCTATT
Found at i:5795824 original size:26 final size:25
Alignment explanation
Indices: 5795764--5795832 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
5795754 TTAAATTACT
*
5795764 TTATTTATTAATACTA-TAATATGA
1 TTATTTATTAATACTATTAATATAA
*
5795788 TTATTAATATTAATACTATTATTATAA
1 TTATT--TATTAATACTATTAATATAA
*
5795815 TTATGTTATTATTACTAT
1 TTAT-TTATTAATACTAT
5795833 AGGATTCCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
24 5 0.13
26 22 0.58
27 10 0.26
28 1 0.03
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (25 bp):
TTATTTATTAATACTATTAATATAA
Found at i:5806237 original size:102 final size:101
Alignment explanation
Indices: 5806028--5806219 Score: 262
Period size: 102 Copynumber: 1.9 Consensus size: 101
5806018 AGTGACCATA
* *
5806028 TGGTGGCTTCTTGGGAGACTCATATACTGGTGGTTTAGGTTCTGGCTTCTCTTTCTTTGGTGGTG
1 TGGTGGCTTCTTGGGAGACTCATAAACTGGTGGTTTAGGTTCTGGCTTCTCTTTCTTTGGAGGTG
* *
5806093 CATAAACCGGTGGCTTTGGTGGCTTAGGCTCATACAC
66 CATAAACCGGTGGCTTT-GAGGCTCAGGCTCATACAC
* * * * * *
5806130 TGGTGGCTTCTTTGGAGGCTTATAAACTGGTGGTTTGGGTTCTGGTTTTTCTTTCTTTGGAGGTG
1 TGGTGGCTTCTTGGGAGACTCATAAACTGGTGGTTTAGGTTCTGGCTTCTCTTTCTTTGGAGGTG
*
5806195 CATAAACTGGTGG-TTT-AGGCTCAGG
66 CATAAACCGGTGGCTTTGAGGCTCAGG
5806220 TTTTTCCTTC
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
99 7 0.09
101 3 0.04
102 69 0.87
ACGTcount: A:0.14, C:0.16, G:0.32, T:0.39
Consensus pattern (101 bp):
TGGTGGCTTCTTGGGAGACTCATAAACTGGTGGTTTAGGTTCTGGCTTCTCTTTCTTTGGAGGTG
CATAAACCGGTGGCTTTGAGGCTCAGGCTCATACAC
Found at i:5806270 original size:90 final size:90
Alignment explanation
Indices: 5806136--5806443 Score: 379
Period size: 90 Copynumber: 3.4 Consensus size: 90
5806126 ACACTGGTGG
* * * * * *
5806136 CTTCTTTGGAGGCTT-ATAAACTGGTGGTTTGGGTTC-TGGTTTTTCTTTCTTTGGAGGTGCATA
1 CTTCTTTGGTGG-TTCATACACCGGTGGTTTGTGTTCAT-GCTTTTCTTTCTTTGGAGGTGTATA
*
5806199 AACTGGTGGTTTAGGCTCAGGTTTTTC
64 AACTGGTGGTTTAGGCTCAGGCTTTTC
* *
5806226 CTTCTTTGGTGGTTCATACACCGGTGGCTTGTGTTCATGCTTTTCTTTCTTTGGTGGTGTATAAA
1 CTTCTTTGGTGGTTCATACACCGGTGGTTTGTGTTCATGCTTTTCTTTCTTTGGAGGTGTATAAA
*
5806291 CCGGTGGTTTAGGCTCAGGCTTTTC
66 CTGGTGGTTTAGGCTCAGGCTTTTC
* * * * *
5806316 CTTCTTTGGAGGTTCATATACTGGTGGTTTCG-GTTCAGGCTTCTCTTTCTTTGGAGGTGTATAA
1 CTTCTTTGGTGGTTCATACACCGGTGGTTT-GTGTTCATGCTTTTCTTTCTTTGGAGGTGTATAA
* * *
5806380 ACTGGTGGCTTAGGTTCAGGCTTCTC
65 ACTGGTGGTTTAGGCTCAGGCTTTTC
* * *
5806406 CTTCTTTGGTGGTTCATAGACCGGAGGTTTATGTTCAT
1 CTTCTTTGGTGGTTCATACACCGGTGGTTTGTGTTCAT
5806444 ATGGTGGCGG
Statistics
Matches: 187, Mismatches: 27, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
89 2 0.01
90 183 0.98
91 2 0.01
ACGTcount: A:0.13, C:0.17, G:0.28, T:0.43
Consensus pattern (90 bp):
CTTCTTTGGTGGTTCATACACCGGTGGTTTGTGTTCATGCTTTTCTTTCTTTGGAGGTGTATAAA
CTGGTGGTTTAGGCTCAGGCTTTTC
Found at i:5806387 original size:135 final size:134
Alignment explanation
Indices: 5806136--5806436 Score: 345
Period size: 135 Copynumber: 2.2 Consensus size: 134
5806126 ACACTGGTGG
* * * * * * *
5806136 CTTCTTTGGAGGCTTATAAACTGGTGGTTTGGGTTCTGGTTTTTCTTTCTTTGGAGGTGCATAAA
1 CTTCTTTGGTGG-TTATAAACCGGTGGTTTAGGCTCAGGCTTTTCCTTCTTTGGAGGTGCATAAA
* * * * *
5806201 CTGGTGGTTTAGGCTCAGGTTTTTCCTTCTTTGGTGGTTCATACACCGGTGGCTT-GTGTTCATG
65 CTGGTGGTTTAGGCTCAGGCTTCTCCTTCTTTGGAGGTTCATAAACCGGTGGCTTAG-GTTCAGG
*
5806265 CTTTTC
129 CTTCTC
* * *
5806271 TTTCTTTGGTGGTGTATAAACCGGTGGTTTAGGCTCAGGCTTTTCCTTCTTTGGAGGTTCATATA
1 CTTCTTTGGTGGT-TATAAACCGGTGGTTTAGGCTCAGGCTTTTCCTTCTTTGGAGGTGCATAAA
* * * *
5806336 CTGGTGGTTTCGGTTCAGGCTTCTCTTTCTTTGGAGGTGT-ATAAACTGGTGGCTTAGGTTCAGG
65 CTGGTGGTTTAGGCTCAGGCTTCTCCTTCTTTGGAGGT-TCATAAACCGGTGGCTTAGGTTCAGG
5806400 CTTCTC
129 CTTCTC
* *
5806406 CTTCTTTGGTGGTTCATAGACCGGAGGTTTA
1 CTTCTTTGGTGGTT-ATAAACCGGTGGTTTA
5806437 TGTTCATATG
Statistics
Matches: 139, Mismatches: 23, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
134 2 0.01
135 135 0.97
136 2 0.01
ACGTcount: A:0.13, C:0.17, G:0.28, T:0.43
Consensus pattern (134 bp):
CTTCTTTGGTGGTTATAAACCGGTGGTTTAGGCTCAGGCTTTTCCTTCTTTGGAGGTGCATAAAC
TGGTGGTTTAGGCTCAGGCTTCTCCTTCTTTGGAGGTTCATAAACCGGTGGCTTAGGTTCAGGCT
TCTC
Found at i:5806442 original size:45 final size:45
Alignment explanation
Indices: 5806136--5806442 Score: 298
Period size: 45 Copynumber: 6.8 Consensus size: 45
5806126 ACACTGGTGG
* * * *
5806136 CTTCTTTGGAGGCTT-ATAAACTGGTGGTTTGGGTTCTGGTTTTTC
1 CTTCTTTGGAGG-TTCATAAACCGGTGGTTTAGGTTCAGGCTTTTC
* * * * *
5806181 TTTCTTTGGAGGTGCATAAACTGGTGGTTTAGGCTCAGGTTTTTC
1 CTTCTTTGGAGGTTCATAAACCGGTGGTTTAGGTTCAGGCTTTTC
* * * *
5806226 CTTCTTTGGTGGTTCATACACCGGTGGCTT-GTGTTCATGCTTTTC
1 CTTCTTTGGAGGTTCATAAACCGGTGGTTTAG-GTTCAGGCTTTTC
* * *
5806271 TTTCTTTGGTGGTGT-ATAAACCGGTGGTTTAGGCTCAGGCTTTTC
1 CTTCTTTGGAGGT-TCATAAACCGGTGGTTTAGGTTCAGGCTTTTC
* * * *
5806316 CTTCTTTGGAGGTTCATATACTGGTGGTTTCGGTTCAGGCTTCTC
1 CTTCTTTGGAGGTTCATAAACCGGTGGTTTAGGTTCAGGCTTTTC
* * * *
5806361 TTTCTTTGGAGGTGT-ATAAACTGGTGGCTTAGGTTCAGGCTTCTC
1 CTTCTTTGGAGGT-TCATAAACCGGTGGTTTAGGTTCAGGCTTTTC
* * * *
5806406 CTTCTTTGGTGGTTCATAGACCGGAGGTTTATGTTCA
1 CTTCTTTGGAGGTTCATAAACCGGTGGTTTAGGTTCA
5806443 TATGGTGGCG
Statistics
Matches: 218, Mismatches: 37, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
44 4 0.02
45 211 0.97
46 3 0.01
ACGTcount: A:0.13, C:0.17, G:0.28, T:0.43
Consensus pattern (45 bp):
CTTCTTTGGAGGTTCATAAACCGGTGGTTTAGGTTCAGGCTTTTC
Found at i:5808983 original size:19 final size:19
Alignment explanation
Indices: 5808955--5808992 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5808945 ATTGTTTAAA
*
5808955 TATAATAATT-TAAAGAAAT
1 TATAAAAATTATAAA-AAAT
5808974 TATAAAAATTATAAAAAAT
1 TATAAAAATTATAAAAAAT
5808993 CTTTTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
TATAAAAATTATAAAAAAT
Found at i:5810321 original size:14 final size:14
Alignment explanation
Indices: 5810304--5810350 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
5810294 AACATATTAG
5810304 ACAAAATAAAAATC
1 ACAAAATAAAAATC
* *
5810318 ACAAAA-AAATATTG
1 ACAAAATAAA-AATC
5810332 ACAAAAT-AAAATC
1 ACAAAATAAAAATC
5810345 ACAAAA
1 ACAAAA
5810351 CTATGAACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.70, C:0.13, G:0.02, T:0.15
Consensus pattern (14 bp):
ACAAAATAAAAATC
Found at i:5810350 original size:27 final size:29
Alignment explanation
Indices: 5810292--5810350 Score: 95
Period size: 27 Copynumber: 2.1 Consensus size: 29
5810282 TACTTAAAAG
*
5810292 AAAACATATTAGACAAAATAAAAATCACA
1 AAAAAATATTAGACAAAATAAAAATCACA
5810321 AAAAAATATT-GACAAAAT-AAAATCACA
1 AAAAAATATTAGACAAAATAAAAATCACA
5810348 AAA
1 AAA
5810351 CTATGAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 12 0.41
28 8 0.28
29 9 0.31
ACGTcount: A:0.68, C:0.12, G:0.03, T:0.17
Consensus pattern (29 bp):
AAAAAATATTAGACAAAATAAAAATCACA
Found at i:5810363 original size:25 final size:27
Alignment explanation
Indices: 5810292--5810350 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 27
5810282 TACTTAAAAG
*
5810292 AAAACATATTAGACAAAATAAAAATCAC
1 AAAAAATATT-GACAAAATAAAAATCAC
5810320 AAAAAAATATTGACAAAAT-AAAATCAC
1 -AAAAAATATTGACAAAATAAAAATCAC
5810347 AAAA
1 AAAA
5810351 CTATGAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 4 0.14
27 8 0.28
28 8 0.28
29 9 0.31
ACGTcount: A:0.68, C:0.12, G:0.03, T:0.17
Consensus pattern (27 bp):
AAAAAATATTGACAAAATAAAAATCAC
Found at i:5811427 original size:23 final size:23
Alignment explanation
Indices: 5811393--5811438 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5811383 TTATTTTTTC
*
5811393 TTTTTAATATTTTTTTTA-TAAA
1 TTTTTAATATTTATTTTACTAAA
*
5811415 TTTTTAGTGATTTATTTTACTAAA
1 TTTTTAAT-ATTTATTTTACTAAA
5811439 CCCTAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
23 9 0.45
24 4 0.20
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.63
Consensus pattern (23 bp):
TTTTTAATATTTATTTTACTAAA
Found at i:5816158 original size:19 final size:18
Alignment explanation
Indices: 5816123--5816158 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5816113 AAATTTTTTA
*
5816123 TCAAATTAACCCTAAAAC
1 TCAAATTAACACTAAAAC
5816141 TCAAATTAAACACTAAAA
1 TCAAATT-AACACTAAAA
5816159 AGTTAACAGT
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:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (18 bp):
TCAAATTAACACTAAAAC
Found at i:5821879 original size:12 final size:12
Alignment explanation
Indices: 5821828--5821882 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
5821818 TTTCTTTTGT
5821828 TTCTTTTTCTAA-
1 TTCTTTTTC-AAC
* *
5821840 TTCATTTTC-TC
1 TTCTTTTTCAAC
5821851 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
*
5821864 TTCTTTTTCAAT
1 TTCTTTTTCAAC
5821876 TTCTTTT
1 TTCTTTT
5821883 CTGTTTCACA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 5 0.14
12 23 0.66
13 7 0.20
ACGTcount: A:0.13, C:0.22, G:0.00, T:0.65
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:5821889 original size:17 final size:18
Alignment explanation
Indices: 5821864--5821901 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5821854 TTTCTTCAAC
* *
5821864 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
5821881 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
5821899 TTC
1 TTC
5821902 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Found at i:5827411 original size:31 final size:31
Alignment explanation
Indices: 5827376--5827438 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
5827366 AAGGGTTAGG
5827376 TAAGAAAAAAAAGAAACATGATTGATGATAT
1 TAAGAAAAAAAAGAAACATGATTGATGATAT
5827407 TAAGAAAAAAAAGAAACATGATTGATGATAT
1 TAAGAAAAAAAAGAAACATGATTGATGATAT
5827438 T
1 T
5827439 TTGTTCATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.57, C:0.03, G:0.16, T:0.24
Consensus pattern (31 bp):
TAAGAAAAAAAAGAAACATGATTGATGATAT
Found at i:5837674 original size:18 final size:21
Alignment explanation
Indices: 5837638--5837677 Score: 59
Period size: 18 Copynumber: 2.0 Consensus size: 21
5837628 TTTTATAATT
5837638 ATTTCTATATATTTCATTATA
1 ATTTCTATATATTTCATTATA
5837659 ATTTCT-TA-ATTT-ATTATA
1 ATTTCTATATATTTCATTATA
5837677 A
1 A
5837678 GATTTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 4 0.21
20 2 0.11
21 6 0.32
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTCTATATATTTCATTATA
Found at i:5844264 original size:30 final size:30
Alignment explanation
Indices: 5844220--5844279 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
5844210 ATTTAACAAG
5844220 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
5844250 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
5844280 TAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:5845469 original size:18 final size:18
Alignment explanation
Indices: 5845446--5845486 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
5845436 CTCTGCCACC
5845446 ATTATGTAATTACAAGTA
1 ATTATGTAATTACAAGTA
5845464 ATTATGTAATTACAAGTA
1 ATTATGTAATTACAAGTA
5845482 ATTAT
1 ATTAT
5845487 ACCTAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (18 bp):
ATTATGTAATTACAAGTA
Found at i:5851624 original size:10 final size:10
Alignment explanation
Indices: 5851595--5851629 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
5851585 TTTCAATTGT
*
5851595 TATATATATA
1 TATATATATG
5851605 TATATATATG
1 TATATATATG
5851615 TATATATATG
1 TATATATATG
*
5851625 AATAT
1 TATAT
5851630 GAAGTAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (10 bp):
TATATATATG
Found at i:5855015 original size:16 final size:16
Alignment explanation
Indices: 5854991--5855028 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
5854981 TTTGGTTCGC
* *
5854991 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
5855007 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
5855023 TGTAAT
1 TGTAAT
5855029 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:5855073 original size:45 final size:44
Alignment explanation
Indices: 5855007--5855097 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
5854997 GGATTAGAGG
*
5855007 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
5855052 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
5855096 TG
1 TG
5855098 GAATAGAGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 18 0.44
45 23 0.56
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:5855112 original size:39 final size:42
Alignment explanation
Indices: 5855007--5855116 Score: 127
Period size: 45 Copynumber: 2.6 Consensus size: 42
5854997 GGATTAGAGG
*
5855007 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAG-TAATCAACTGTTTGGTT--A
* ***
5855052 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGTAATCAACTGTTTGGTTA
5855092 TG-AATGGAATAGAGGTGTAATAGTA
1 TGTAATGGAATAGAGGTGTAATAGTA
5855117 TAATGGAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
39 22 0.37
40 2 0.03
43 1 0.02
44 11 0.19
45 23 0.39
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.33
Consensus pattern (42 bp):
TGTAATGGAATAGAGGTGTAATAGTAATCAACTGTTTGGTTA
Found at i:5855273 original size:16 final size:16
Alignment explanation
Indices: 5855236--5855277 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5855226 TTAATCATAT
*
5855236 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
5855252 TT-AAATATATTATAA
1 TTAAAATATATTATAA
5855267 TTAAAATATAT
1 TTAAAATATAT
5855278 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:5855284 original size:14 final size:15
Alignment explanation
Indices: 5855245--5855286 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5855235 TTTAAACATA
*
5855245 ATTATTATTAAATAT
1 ATTATAATTAAATAT
5855260 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
5855274 A-TATAATTTAATA
1 ATTATAATTAAATA
5855287 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:5859047 original size:12 final size:12
Alignment explanation
Indices: 5859030--5859068 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
5859020 TTAAATCATT
5859030 TCTCTAATTTCC
1 TCTCTAATTTCC
5859042 TCTCTAATTTCC
1 TCTCTAATTTCC
*
5859054 TCTCAAATTT-C
1 TCTCTAATTTCC
5859065 TCTC
1 TCTC
5859069 AAATCCCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 5 0.19
12 21 0.81
ACGTcount: A:0.18, C:0.33, G:0.00, T:0.49
Consensus pattern (12 bp):
TCTCTAATTTCC
Found at i:5860900 original size:18 final size:18
Alignment explanation
Indices: 5860877--5860919 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5860867 TGCCAGGTGC
* *
5860877 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
5860895 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
5860913 GTTTCCT
1 GTATCCT
5860920 TTTTCGAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:5861185 original size:21 final size:21
Alignment explanation
Indices: 5861160--5861207 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5861150 CCAACACCGA
*
5861160 CAACCA-AATACCCTACCGGAG
1 CAACCAGAAT-CCCCACCGGAG
*
5861181 GAACCAGAATCCCCACCGGAG
1 CAACCAGAATCCCCACCGGAG
5861202 CAACCA
1 CAACCA
5861208 CAACCCCCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.38, C:0.40, G:0.17, T:0.06
Consensus pattern (21 bp):
CAACCAGAATCCCCACCGGAG
Found at i:5861215 original size:21 final size:21
Alignment explanation
Indices: 5861174--5861215 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5861164 CAAATACCCT
* * *
5861174 ACCGGAGGAACCAGAATCCCC
1 ACCGGAGCAACCACAACCCCC
5861195 ACCGGAGCAACCACAACCCCC
1 ACCGGAGCAACCACAACCCCC
5861216 GCCGAAAGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.45, G:0.19, T:0.02
Consensus pattern (21 bp):
ACCGGAGCAACCACAACCCCC
Found at i:5864751 original size:8 final size:8
Alignment explanation
Indices: 5864731--5864760 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
5864721 GTTGATAAAG
5864731 AAAATAA-
1 AAAATAAT
5864738 AAAATAAT
1 AAAATAAT
5864746 AAAATAAT
1 AAAATAAT
5864754 AAAATAA
1 AAAATAA
5864761 AAACAGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (8 bp):
AAAATAAT
Found at i:5872823 original size:18 final size:18
Alignment explanation
Indices: 5872796--5872831 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5872786 ATATTTCACA
*
5872796 TCTTTTTTTTTTTACTTC
1 TCTTTGTTTTTTTACTTC
*
5872814 TCTTTGTTTTTTTCCTTC
1 TCTTTGTTTTTTTACTTC
5872832 AAACTGGAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (18 bp):
TCTTTGTTTTTTTACTTC
Found at i:5891504 original size:55 final size:55
Alignment explanation
Indices: 5891420--5891526 Score: 196
Period size: 55 Copynumber: 1.9 Consensus size: 55
5891410 ATCTAAAGCA
*
5891420 CCAAGCAAAGGCTTAATCTAAAGTACTAGTAATCCAAACGAAACACAAAGAAATT
1 CCAAGCAAAGGCATAATCTAAAGTACTAGTAATCCAAACGAAACACAAAGAAATT
*
5891475 CCAAGCAAAGGCATAATCTAAAGTACTAGTAATCCAAATGAAACACAAAGAA
1 CCAAGCAAAGGCATAATCTAAAGTACTAGTAATCCAAACGAAACACAAAGAA
5891527 CTACATCACA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.50, C:0.20, G:0.13, T:0.17
Consensus pattern (55 bp):
CCAAGCAAAGGCATAATCTAAAGTACTAGTAATCCAAACGAAACACAAAGAAATT
Found at i:5898232 original size:41 final size:41
Alignment explanation
Indices: 5898187--5898271 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
5898177 AAAAGTTGTG
5898187 ATAATTATAATTATAAATTGAGTTACATTTATTAGTTAAAA
1 ATAATTATAATTATAAATTGAGTTACATTTATTAGTTAAAA
* *
5898228 ATAATTATAGTTATAAATTGATTTACATTTATTAGTTAAAA
1 ATAATTATAATTATAAATTGAGTTACATTTATTAGTTAAAA
5898269 ATA
1 ATA
5898272 TGTGTATTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (41 bp):
ATAATTATAATTATAAATTGAGTTACATTTATTAGTTAAAA
Found at i:5901909 original size:8 final size:8
Alignment explanation
Indices: 5901898--5901944 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
5901888 TTTTAATTTT
5901898 TTAAAATA
1 TTAAAATA
*
5901906 TTAAATTA
1 TTAAAATA
*
5901914 TTAAATTA
1 TTAAAATA
5901922 TT-AAA-A
1 TTAAAATA
5901928 TT-AAATA
1 TTAAAATA
5901935 TTAAAATA
1 TTAAAATA
5901943 TT
1 TT
5901945 CAGAATTACT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 6 0.17
7 5 0.14
8 24 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
TTAAAATA
Found at i:5901936 original size:13 final size:13
Alignment explanation
Indices: 5901901--5901941 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 13
5901891 TAATTTTTTA
5901901 AAATATTAAATTATT
1 AAATATTAAA--ATT
5901916 AAATTATTAAAATT
1 AAA-TATTAAAATT
5901930 AAATATTAAAAT
1 AAATATTAAAAT
5901942 ATTCAGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.36
14 6 0.24
15 3 0.12
16 7 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATATTAAAATT
Found at i:5902536 original size:4 final size:4
Alignment explanation
Indices: 5902527--5902551 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5902517 ATTGGACCAC
5902527 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
5902552 GGAATTACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:5904463 original size:23 final size:21
Alignment explanation
Indices: 5904415--5904460 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
5904405 TGCTCACAAT
5904415 GGCGTGTGTCCCCTCCACATG
1 GGCGTGTGTCCCCTCCACATG
** *
5904436 GGCGTGTGTGGCCTTCACATG
1 GGCGTGTGTCCCCTCCACATG
5904457 GGCG
1 GGCG
5904461 CGTAGACCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.30, G:0.37, T:0.24
Consensus pattern (21 bp):
GGCGTGTGTCCCCTCCACATG
Found at i:5905149 original size:21 final size:20
Alignment explanation
Indices: 5905113--5905154 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5905103 CTGAATATAC
5905113 GTCTGTTTGTCAGAACATTTT
1 GTCTGTTTGTCAGAAC-TTTT
**
5905134 GTCTGTTTGTGTGAACTTTT
1 GTCTGTTTGTCAGAACTTTT
5905154 G
1 G
5905155 GTTATTGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.24, T:0.50
Consensus pattern (20 bp):
GTCTGTTTGTCAGAACTTTT
Found at i:5906472 original size:23 final size:23
Alignment explanation
Indices: 5906411--5906470 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
5906401 TTTTAATTTG
* * *
5906411 TTAAAATATCAATTAAT-GATAC
1 TTAAAAAATAAATAAATAGATAC
5906433 TTAAAAAATAAATAAATAGATA-
1 TTAAAAAATAAATAAATAGATAC
*
5906455 TTAAAAATTAAATAAA
1 TTAAAAAATAAATAAA
5906471 ATTTAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (23 bp):
TTAAAAAATAAATAAATAGATAC
Found at i:5916867 original size:13 final size:15
Alignment explanation
Indices: 5916849--5916880 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5916839 CACCAAATTT
5916849 AAACCC-AAT-TAAA
1 AAACCCTAATATAAA
5916862 AAACCCTAATATAAA
1 AAACCCTAATATAAA
5916877 AAAC
1 AAAC
5916881 TTCAAAACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 3 0.18
15 8 0.47
ACGTcount: A:0.62, C:0.22, G:0.00, T:0.16
Consensus pattern (15 bp):
AAACCCTAATATAAA
Found at i:5921976 original size:15 final size:15
Alignment explanation
Indices: 5921956--5921993 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5921946 GTTTTCCAGA
5921956 GGAGTCAATGGTAGT
1 GGAGTCAATGGTAGT
*
5921971 GGAGTCAATTGTAGT
1 GGAGTCAATGGTAGT
*
5921986 GGACTCAA
1 GGAGTCAA
5921994 GGGGAGATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (15 bp):
GGAGTCAATGGTAGT
Found at i:5925678 original size:5 final size:5
Alignment explanation
Indices: 5925659--5925689 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
5925649 AAATAAACCC
5925659 CAAAA CAAAA TCAAAA CAAAA CAAAA CAAAA
1 CAAAA CAAAA -CAAAA CAAAA CAAAA CAAAA
5925690 GAGAATAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.77, C:0.19, G:0.00, T:0.03
Consensus pattern (5 bp):
CAAAA
Found at i:5925680 original size:16 final size:15
Alignment explanation
Indices: 5925659--5925689 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5925649 AAATAAACCC
5925659 CAAAACAAAATCAAAA
1 CAAAACAAAA-CAAAA
5925675 CAAAACAAAACAAAA
1 CAAAACAAAACAAAA
5925690 GAGAATAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.77, C:0.19, G:0.00, T:0.03
Consensus pattern (15 bp):
CAAAACAAAACAAAA
Found at i:5926591 original size:40 final size:40
Alignment explanation
Indices: 5926547--5926673 Score: 120
Period size: 37 Copynumber: 3.2 Consensus size: 40
5926537 ACCAGTTTGG
* *
5926547 CACCCAATGCTTTATCGGA-TAATTCGAAGTAATAAATTGA
1 CACCCAGTGCTTCATCGGACTAATTCGAAGT-ATAAATTGA
** *
5926587 CACCCAGTG-TCTCATC-GACTAAACCGAAG--TAAATTGG
1 CACCCAGTGCT-TCATCGGACTAATTCGAAGTATAAATTGA
* * *
5926624 CACCCAGTGCCTCATCGAATTAATTCGAAGTAGTAAATTGA
1 CACCCAGTGCTTCATCGGACTAATTCGAAGTA-TAAATTGA
5926665 CACCCAGTG
1 CACCCAGTG
5926674 TCTCATCAAC
Statistics
Matches: 69, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
37 21 0.30
38 9 0.13
39 3 0.04
40 20 0.29
41 16 0.23
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (40 bp):
CACCCAGTGCTTCATCGGACTAATTCGAAGTATAAATTGA
Found at i:5926629 original size:37 final size:40
Alignment explanation
Indices: 5926579--5926684 Score: 130
Period size: 41 Copynumber: 2.7 Consensus size: 40
5926569 TTCGAAGTAA
5926579 TAAATTGACACCCAGTGTCTCATCG-ACTAAACCG-A-AG
1 TAAATTGACACCCAGTGTCTCATCGAACTAAACCGAAGAG
* * * **
5926616 TAAATTGGCACCCAGTGCCTCATCGAATTAATTCGAAGTAG
1 TAAATTGACACCCAGTGTCTCATCGAACTAAACCGAAG-AG
5926657 TAAATTGACACCCAGTGTCTCATC-AACT
1 TAAATTGACACCCAGTGTCTCATCGAACT
5926685 CGAAGTCGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
37 23 0.40
38 6 0.11
39 1 0.02
40 3 0.05
41 24 0.42
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (40 bp):
TAAATTGACACCCAGTGTCTCATCGAACTAAACCGAAGAG
Done.