Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 61 of 205
Found at i:18276917 original size:17 final size:17
Alignment explanation
Indices: 18276895--18276930 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
18276885 CTTGGGCTGA
18276895 ATTGATTGAA-ATGTTAT
1 ATTGATT-AACATGTTAT
18276912 ATTGATTAACATGTTAT
1 ATTGATTAACATGTTAT
18276929 AT
1 AT
18276931 GGTTTTACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 16 0.89
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (17 bp):
ATTGATTAACATGTTAT
Found at i:18278431 original size:15 final size:15
Alignment explanation
Indices: 18278411--18278441 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18278401 AATGGCATGA
*
18278411 TTGAATAAGTTGAAT
1 TTGAATAAATTGAAT
18278426 TTGAATAAATTGAAT
1 TTGAATAAATTGAAT
18278441 T
1 T
18278442 GATATCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (15 bp):
TTGAATAAATTGAAT
Found at i:18295536 original size:42 final size:41
Alignment explanation
Indices: 18295434--18295619 Score: 160
Period size: 42 Copynumber: 4.5 Consensus size: 41
18295424 CGAAGGCTGT
* * * * **
18295434 ACTGAAGCACATAAGTGCTAAACAGAAACCTGTAAGGGTTAA
1 ACTGAAGCTCAGAAGAGCTGAACAGAAACCCATAAGGGTT-A
* * *
18295476 ACGGAAGCTCATAGGAGCTGAACAGAAACCCATAAGGGTTA
1 ACTGAAGCTCAGAAGAGCTGAACAGAAACCCATAAGGGTTA
* * *
18295517 ATCTGAAGCTCAGAAGAGCT-AAAATAAAACCCATTAGGGTTA
1 A-CTGAAGCTCAGAAGAGCTGAACA-GAAACCCATAAGGGTTA
* * * * *
18295559 AGCTGAAGCTCAAAAGAGCTGAACTGAAACTCATATGAGTTA
1 A-CTGAAGCTCAGAAGAGCTGAACAGAAACCCATAAGGGTTA
18295601 ACTGAAGCTCATG-AGAGCT
1 ACTGAAGCTCA-GAAGAGCT
18295620 AAATGGAAAG
Statistics
Matches: 117, Mismatches: 23, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
41 21 0.18
42 94 0.80
43 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
ACTGAAGCTCAGAAGAGCTGAACAGAAACCCATAAGGGTTA
Found at i:18295578 original size:84 final size:83
Alignment explanation
Indices: 18295468--18295622 Score: 213
Period size: 84 Copynumber: 1.9 Consensus size: 83
18295458 GAAACCTGTA
* * *
18295468 AGGGTTAAACGGAAGCTCATAGGAGCTGAACAGAAACCCATAAGGGTTAATCTGAAGCTCA-GAA
1 AGGGTTAAACGGAAGCTCAAAAGAGCTGAACAGAAACCCATAAGAGTTAA-CTGAAGCTCATG-A
18295532 GAGCTAAAATAAAACCCATT
64 GAGCTAAAATAAAACCCATT
* * * * *
18295552 AGGGTTAAGCTGAAGCTCAAAAGAGCTGAACTGAAACTCATATGAGTTAACTGAAGCTCATGAGA
1 AGGGTTAAACGGAAGCTCAAAAGAGCTGAACAGAAACCCATAAGAGTTAACTGAAGCTCATGAGA
18295617 GCTAAA
66 GCTAAA
18295623 TGGAAAGCAA
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
83 19 0.31
84 43 0.69
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (83 bp):
AGGGTTAAACGGAAGCTCAAAAGAGCTGAACAGAAACCCATAAGAGTTAACTGAAGCTCATGAGA
GCTAAAATAAAACCCATT
Found at i:18295982 original size:15 final size:15
Alignment explanation
Indices: 18295962--18295996 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18295952 ACAAACCCAC
*
18295962 CAGAACAGGATAGAG
1 CAGAACAGGATAGAA
*
18295977 CAGAACATGATAGAA
1 CAGAACAGGATAGAA
18295992 CAGAA
1 CAGAA
18295997 TAGAGCAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.14, G:0.26, T:0.09
Consensus pattern (15 bp):
CAGAACAGGATAGAA
Found at i:18297910 original size:13 final size:13
Alignment explanation
Indices: 18297892--18297917 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18297882 ACCTGAAAGC
18297892 AATTTAATTCATA
1 AATTTAATTCATA
18297905 AATTTAATTCATA
1 AATTTAATTCATA
18297918 TTAGGACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:18304767 original size:31 final size:30
Alignment explanation
Indices: 18304725--18304815 Score: 96
Period size: 31 Copynumber: 2.9 Consensus size: 30
18304715 ACCAAAACTT
18304725 TATTTTAAAAATTAAAACAAAAATTTTAAAAA-
1 TATTTT-AAAATT-AAA-AAAAATTTTAAAAAG
* *
18304757 TATTTTAAAATT-TAAAAAATTTAAAAAAAAG
1 TATTTTAAAATTAAAAAAAATTT--TAAAAAG
*
18304788 TATTTTAAAATGAAAAAAAATTTTAAAA
1 TATTTTAAAATTAAAAAAAATTTTAAAA
18304816 TAAAAATATT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
28 8 0.16
29 1 0.02
30 9 0.18
31 17 0.34
32 15 0.30
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (30 bp):
TATTTTAAAATTAAAAAAAATTTTAAAAAG
Found at i:18304772 original size:18 final size:17
Alignment explanation
Indices: 18304750--18304826 Score: 74
Period size: 18 Copynumber: 4.7 Consensus size: 17
18304740 AACAAAAATT
18304750 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
18304767 TTTAAAAA-A-TTTAAAA
1 -TTAAAAATATTTTAAAA
*
18304783 --AAAAGTATTTTAAAA
1 TTAAAAATATTTTAAAA
* *
18304798 TGAAAAAAAATTTTAAAA
1 T-TAAAAATATTTTAAAA
18304816 -TAAAAATATTT
1 TTAAAAATATTT
18304827 ATTATATTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
13 4 0.08
14 1 0.02
15 7 0.14
16 16 0.33
17 1 0.02
18 20 0.41
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:18304785 original size:10 final size:9
Alignment explanation
Indices: 18304743--18304784 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
18304733 AAATTAAAAC
*
18304743 AAAAATTTT
1 AAAAAATTT
18304752 AAAAATATTT
1 AAAAA-ATTT
*
18304762 -TAAAATTT
1 AAAAAATTT
18304770 AAAAAATTT
1 AAAAAATTT
18304779 AAAAAA
1 AAAAAA
18304785 AAGTATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 4 0.14
9 21 0.75
10 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAAAATTT
Found at i:18306542 original size:37 final size:38
Alignment explanation
Indices: 18306491--18306566 Score: 145
Period size: 37 Copynumber: 2.0 Consensus size: 38
18306481 AATATATCAC
18306491 ATAGTTTTTTCTAGATAATTCGTCCCAAGGACTTTACA
1 ATAGTTTTTTCTAGATAATTCGTCCCAAGGACTTTACA
18306529 ATAG-TTTTTCTAGATAATTCGTCCCAAGGACTTTACA
1 ATAGTTTTTTCTAGATAATTCGTCCCAAGGACTTTACA
18306566 A
1 A
18306567 ATAATTTGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 34 0.89
38 4 0.11
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (38 bp):
ATAGTTTTTTCTAGATAATTCGTCCCAAGGACTTTACA
Found at i:18307641 original size:16 final size:16
Alignment explanation
Indices: 18307617--18307648 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18307607 CAAAACTCTA
*
18307617 GGGCTTAGTCTTTCTT
1 GGGCGTAGTCTTTCTT
18307633 GGGCGTAGTCTTTCTT
1 GGGCGTAGTCTTTCTT
18307649 CACTTGAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.19, G:0.28, T:0.47
Consensus pattern (16 bp):
GGGCGTAGTCTTTCTT
Found at i:18309150 original size:29 final size:29
Alignment explanation
Indices: 18309118--18309185 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
18309108 TATTTGTTAT
18309118 TTTTTTATTTAAAAATATTTTGAAAATAC
1 TTTTTTATTTAAAAATATTTTGAAAATAC
* * *
18309147 TTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTATTTAAAAATATTTTGAAAATAC
18309176 TTTTTT-TTTA
1 TTTTTTATTTA
18309186 TTTTTTAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (29 bp):
TTTTTTATTTAAAAATATTTTGAAAATAC
Found at i:18309169 original size:17 final size:19
Alignment explanation
Indices: 18309134--18309170 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
18309124 ATTTAAAAAT
18309134 ATTTTGAAAATACTTTTTA
1 ATTTTGAAAATACTTTTTA
18309153 ATTTT-AAAATA-TTTTTA
1 ATTTTGAAAATACTTTTTA
18309170 A
1 A
18309171 AATACTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 6 0.33
19 5 0.28
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTTTGAAAATACTTTTTA
Found at i:18309173 original size:40 final size:40
Alignment explanation
Indices: 18309129--18309219 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
18309119 TTTTTATTTA
18309129 AAAATA-TTTTGAAAATACTTTTTAATTTTAAAATATTTTT
1 AAAATACTTTT-AAAATACTTTTTAATTTTAAAATATTTTT
**** *
18309169 AAAATACTTTTTTTTTATTTTTTAATTTTAAAATATTTTT
1 AAAATACTTTTAAAATACTTTTTAATTTTAAAATATTTTT
18309209 AAAATACTTTT
1 AAAATACTTTT
18309220 TTTATTTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
40 41 0.91
41 4 0.09
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (40 bp):
AAAATACTTTTAAAATACTTTTTAATTTTAAAATATTTTT
Found at i:18309220 original size:40 final size:40
Alignment explanation
Indices: 18309147--18309243 Score: 169
Period size: 40 Copynumber: 2.4 Consensus size: 40
18309137 TTGAAAATAC
18309147 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT-TTAT
1 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTATT-T
18309187 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTATTT
1 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTATTT
*
18309227 TTTTTATTTTTAAAATA
1 TTTTTAATTTTAAAATA
18309244 AATTTTTGGT
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
40 53 0.96
41 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (40 bp):
TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTATTT
Found at i:18309250 original size:69 final size:69
Alignment explanation
Indices: 18309114--18309250 Score: 177
Period size: 69 Copynumber: 2.0 Consensus size: 69
18309104 TATATATTTG
* **
18309114 TTATTTTTTTATTTAAAAATATTTTGAAAATACTTTTTAATTTTAAAATATTTTTAAAATACTTT
1 TTATTTTTTAATTTAAAAATATTTTGAAAATACTTTTTAATTTTAAAATATTTTTAAAATAAATT
18309179 TTTT
66 TTTT
* * * ***
18309183 TTATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTATTTT-TTTTATTTTTAAAATAAAT
1 TTATTTTTTAATTTAAAAATATTTTGAAAATAC-TTTTTAATTTTAAAATATTTTTAAAATAAAT
18309247 TTTT
65 TTTT
18309251 GGTGTTTATT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
69 48 0.83
70 10 0.17
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (69 bp):
TTATTTTTTAATTTAAAAATATTTTGAAAATACTTTTTAATTTTAAAATATTTTTAAAATAAATT
TTTT
Found at i:18312237 original size:27 final size:27
Alignment explanation
Indices: 18312184--18312260 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 27
18312174 CCCTCCACAA
* * *
18312184 TTCACCACAAAGGC-ATTCATTTGATA-
1 TTCAACACAAAGGCTCTTC-TTTCATAT
*
18312210 TTCAAACACGAAGGCTCTTCTTTCATAT
1 TTC-AACACAAAGGCTCTTCTTTCATAT
* *
18312238 TTCACCACAAAGGCTTTTCTTTC
1 TTCAACACAAAGGCTCTTCTTTC
18312261 CTGTCGTGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
26 3 0.07
27 32 0.78
28 6 0.15
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (27 bp):
TTCAACACAAAGGCTCTTCTTTCATAT
Found at i:18330591 original size:11 final size:11
Alignment explanation
Indices: 18330575--18330665 Score: 57
Period size: 11 Copynumber: 8.5 Consensus size: 11
18330565 TTTTTTTTAA
18330575 TTTTAAAATAT
1 TTTTAAAATAT
18330586 TTTTAAAATACT
1 TTTTAAAATA-T
** *
18330598 TTTTTTATTAT
1 TTTTAAAATAT
*
18330609 TTTT----TAA
1 TTTTAAAATAT
18330616 TTTTAAAATAT
1 TTTTAAAATAT
18330627 TTTTAAAATACT
1 TTTTAAAATA-T
**
18330639 TTTTTTAAT-T
1 TTTTAAAATAT
*
18330649 TTTTAAATAAAT
1 TTTTAAA-ATAT
18330661 TTTTA
1 TTTTA
18330666 GTATTTATTA
Statistics
Matches: 62, Mismatches: 10, Indels: 15
0.71 0.11 0.17
Matches are distributed among these distances:
7 6 0.10
10 6 0.10
11 28 0.45
12 22 0.35
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:18330614 original size:41 final size:39
Alignment explanation
Indices: 18330567--18330654 Score: 158
Period size: 41 Copynumber: 2.2 Consensus size: 39
18330557 CACTTTAATT
18330567 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTATTA
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA--A
18330608 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA
18330647 TTTTTTAA
1 TTTTTTAA
18330655 ATAAATTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
39 9 0.19
41 38 0.81
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (39 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA
Found at i:18330642 original size:30 final size:31
Alignment explanation
Indices: 18330586--18330650 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
18330576 TTTAAAATAT
** *
18330586 TTTTAAAATACTTTTTTTATTA-TTTTTTAA
1 TTTTAAAATACTTTTTAAAATATTTTTTTAA
18330616 TTTTAAAATA-TTTTTAAAATACTTTTTTTAA
1 TTTTAAAATACTTTTTAAAATA-TTTTTTTAA
18330647 TTTT
1 TTTT
18330651 TTAAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 8 0.27
30 10 0.33
31 12 0.40
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (31 bp):
TTTTAAAATACTTTTTAAAATATTTTTTTAA
Found at i:18330663 original size:21 final size:21
Alignment explanation
Indices: 18330625--18330664 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18330615 ATTTTAAAAT
**
18330625 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
*
18330646 ATTTTTTAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
18330665 AGTATTTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:18341287 original size:15 final size:14
Alignment explanation
Indices: 18341256--18341302 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
18341246 ATATTTTTCT
* *
18341256 TTATTTTTATTTTC
1 TTATTTTTATATAC
18341270 TTAGTTTTTATATAC
1 TTA-TTTTTATATAC
*
18341285 TTA-TTATATATAC
1 TTATTTTTATATAC
18341298 TTATT
1 TTATT
18341303 CATTTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 12 0.43
14 4 0.14
15 12 0.43
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (14 bp):
TTATTTTTATATAC
Found at i:18341506 original size:12 final size:12
Alignment explanation
Indices: 18341489--18341517 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
18341479 TATGCATACC
18341489 TACATATTTTAA
1 TACATATTTTAA
18341501 TACATATTTTAA
1 TACATATTTTAA
18341513 TACAT
1 TACAT
18341518 TCATTTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (12 bp):
TACATATTTTAA
Found at i:18341642 original size:18 final size:19
Alignment explanation
Indices: 18341606--18341644 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
18341596 TTTTATATGC
* *
18341606 ATATTGTACATATATACAT
1 ATATTGTACATACACACAT
18341625 ATATT-TACATACACACAT
1 ATATTGTACATACACACAT
18341643 AT
1 AT
18341645 TTCATGATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (19 bp):
ATATTGTACATACACACAT
Found at i:18345783 original size:5 final size:5
Alignment explanation
Indices: 18345773--18345854 Score: 89
Period size: 5 Copynumber: 16.4 Consensus size: 5
18345763 AAAACGCTTC
* *
18345773 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA AAGAA TATTTAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TA--TAA
*
18345825 TATATA GATAA -ATAA TA-AA TAT-A TATAA TA
1 TATA-A TATAA TATAA TATAA TATAA TATAA TA
18345855 AAAAAGTTTA
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
4 12 0.18
5 46 0.70
6 4 0.06
7 4 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (5 bp):
TATAA
Found at i:18345888 original size:24 final size:23
Alignment explanation
Indices: 18345861--18345922 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
18345851 AATAAAAAAG
18345861 TTTAAAATATAATGAAT-TTTTATA
1 TTTAAAATAT-AT-AATATTTTATA
*
18345885 TTTATAAT-TATAATATTTTATA
1 TTTAAAATATATAATATTTTATA
*
18345907 TATAAAATATTATAAT
1 TTTAAAATA-TATAAT
18345923 TATAAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 3 0.09
22 15 0.47
23 1 0.03
24 13 0.41
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTAAAATATATAATATTTTATA
Found at i:18345906 original size:16 final size:16
Alignment explanation
Indices: 18345885--18345928 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 16
18345875 AATTTTTATA
*
18345885 TTTATAATTATAATAT
1 TTTATAATTATAAAAT
18345901 TTTAT-A-TATAAAAT
1 TTTATAATTATAAAAT
*
18345915 ATTATAATTATAAA
1 TTTATAATTATAAA
18345929 TATAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 11 0.46
15 2 0.08
16 11 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTATAATTATAAAAT
Found at i:18345952 original size:24 final size:21
Alignment explanation
Indices: 18345897--18345952 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
18345887 TATAATTATA
*
18345897 ATATTTTATATATAAAATATT
1 ATATTTTAAATATAAAATATT
*
18345918 ATAATTATAAATATAAAAATTCATT
1 AT-ATTTTAAATAT-AAAA-T-ATT
18345943 ATATTTTAAA
1 ATATTTTAAA
18345953 CTTTTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 2 0.07
22 9 0.32
23 4 0.14
24 8 0.29
25 5 0.18
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATTTTAAATATAAAATATT
Found at i:18346011 original size:5 final size:5
Alignment explanation
Indices: 18345959--18346041 Score: 91
Period size: 5 Copynumber: 16.6 Consensus size: 5
18345949 TAAACTTTTT
* * *
18345959 TATTA TA-TA TATT- TATTA T-TTA TCTATA TATTAAA TATTC TTTTA
1 TATTA TATTA TATTA TATTA TATTA TAT-TA TATT--A TATTA TATTA
18346004 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
18346042 GTTATATTGA
Statistics
Matches: 67, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
4 12 0.18
5 46 0.69
6 4 0.06
7 5 0.07
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:18346135 original size:17 final size:17
Alignment explanation
Indices: 18346113--18346151 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
18346103 CTACCTCCAT
* *
18346113 TTTTATTTTTTAGTTTA
1 TTTTATATTTTAGTATA
18346130 TTTTATATTTTAGTATA
1 TTTTATATTTTAGTATA
18346147 TTTTA
1 TTTTA
18346152 CATCTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (17 bp):
TTTTATATTTTAGTATA
Found at i:18348352 original size:43 final size:43
Alignment explanation
Indices: 18348290--18348388 Score: 137
Period size: 43 Copynumber: 2.3 Consensus size: 43
18348280 TCTTTCACAT
*
18348290 AAACGCCGCAAAAGAACATGACCTTTAGCGGCG-CTTTTATCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCCTTTT-TCAC
* * *
18348333 AAACACCGCTAAAGAACATGACTTTTAGTGGCGCCTTTTTCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCCTTTTTCAC
*
18348376 AAACGCTGCTAAA
1 AAACGCCGCTAAA
18348389 AGCATCGTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
43 44 0.90
44 5 0.10
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCCTTTTTCAC
Found at i:18354216 original size:9 final size:9
Alignment explanation
Indices: 18354164--18354233 Score: 65
Period size: 9 Copynumber: 8.0 Consensus size: 9
18354154 CAAGTATAAA
*
18354164 TAAGTTCTG
1 TAAGTTATG
18354173 TAAGTTATG
1 TAAGTTATG
* * *
18354182 ATATGATATA
1 -TAAGTTATG
*
18354192 T-ATTTATG
1 TAAGTTATG
18354200 T-A-TTATG
1 TAAGTTATG
18354207 TAAGTTATG
1 TAAGTTATG
18354216 TAAGTTATG
1 TAAGTTATG
18354225 TAAGTTATG
1 TAAGTTATG
18354234 ATATGATATA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
7 6 0.12
8 6 0.12
9 32 0.64
10 6 0.12
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:18354381 original size:21 final size:21
Alignment explanation
Indices: 18354357--18354396 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
18354347 TCAAATTTCG
18354357 AATAATAATACAAAGTTGTAA
1 AATAATAATACAAAGTTGTAA
18354378 AATAATAATACAAAGTTGT
1 AATAATAATACAAAGTTGT
18354397 CTTCAAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.30
Consensus pattern (21 bp):
AATAATAATACAAAGTTGTAA
Found at i:18355972 original size:28 final size:29
Alignment explanation
Indices: 18355925--18355980 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
18355915 AAGGATTTCG
*
18355925 GGGGGAAAAAAGAATAAGGAGAAAAGGTT
1 GGGGGAAAAAAGAATAAGGAAAAAAGGTT
* *
18355954 GGGGGAAAAAAG-TTGAGGAAAAAAGGT
1 GGGGGAAAAAAGAATAAGGAAAAAAGGT
18355981 CGGGCTGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.50, C:0.00, G:0.39, T:0.11
Consensus pattern (29 bp):
GGGGGAAAAAAGAATAAGGAAAAAAGGTT
Found at i:18356300 original size:113 final size:114
Alignment explanation
Indices: 18356157--18356377 Score: 268
Period size: 114 Copynumber: 1.9 Consensus size: 114
18356147 TTTATCCACA
* ** *
18356157 AGCGCCGCTAAATCCCTACATATTGCGGCG-TTTAACCG-AAATGCCACTAAAAAACCTACA-AA
1 AGCGCCGCTAAATCCCGACATATTGCGGCGTTTTAA-CGAAAACACCACTAAAAAACC-AAATAA
* *
18356219 AACGGCACCATTTTTATTAAAACAAAATAACATGTTGCGGCGTTTTTTGGT
64 AACGACACCATTTTGATTAAAACAAAATAACATGTTGCGGCGTTTTTTGGT
* * * *
18356270 AGCGTCGCTAAATCCCGACCTATTGCGGCGTTTTGACGAAAACACCACTAAAAAATCAAATAAAA
1 AGCGCCGCTAAATCCCGACATATTGCGGCGTTTTAACGAAAACACCACTAAAAAACCAAATAAAA
* * * * *
18356335 CGACTCTATTTTGATTAAAACAAATTAACCTTTTGCGGCGTTT
66 CGACACCATTTTGATTAAAACAAAATAACATGTTGCGGCGTTT
18356378 CACCAAAAAC
Statistics
Matches: 90, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
113 31 0.34
114 59 0.66
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (114 bp):
AGCGCCGCTAAATCCCGACATATTGCGGCGTTTTAACGAAAACACCACTAAAAAACCAAATAAAA
CGACACCATTTTGATTAAAACAAAATAACATGTTGCGGCGTTTTTTGGT
Found at i:18356957 original size:7 final size:7
Alignment explanation
Indices: 18356945--18357116 Score: 66
Period size: 7 Copynumber: 24.1 Consensus size: 7
18356935 ACTAATTAAT
18356945 CTAAACC
1 CTAAACC
18356952 CTAAACCC
1 CTAAA-CC
18356960 CT-AACTC
1 CTAAAC-C
18356967 CT-AACC
1 CTAAACC
18356973 CTTAAACC
1 C-TAAACC
**
18356981 CTAAATT
1 CTAAACC
** *
18356988 AAAAAAC
1 CTAAACC
*
18356995 ATAAACC
1 CTAAACC
18357002 CTAAACCC
1 CTAAA-CC
*
18357010 CTAACCC
1 CTAAACC
*
18357017 CCAAACC
1 CTAAACC
*
18357024 TTAAACC
1 CTAAACC
18357031 CT-AACC
1 CTAAACC
18357037 CTTAAACC
1 C-TAAACC
*
18357045 ATAAACC
1 CTAAACC
*
18357052 ATAAACC
1 CTAAACC
*
18357059 TTAAA--
1 CTAAACC
*
18357064 ATAGTAACTC
1 CTA--AAC-C
18357074 CTAAACC
1 CTAAACC
*
18357081 TTAAACC
1 CTAAACC
*
18357088 ATAAACC
1 CTAAACC
* *
18357095 ATAAATC
1 CTAAACC
* *
18357102 ATAATCC
1 CTAAACC
18357109 CTAAACC
1 CTAAACC
18357116 C
1 C
18357117 ATAATCCATC
Statistics
Matches: 127, Mismatches: 26, Indels: 24
0.72 0.15 0.14
Matches are distributed among these distances:
5 2 0.02
6 8 0.06
7 93 0.73
8 22 0.17
10 2 0.02
ACGTcount: A:0.45, C:0.35, G:0.01, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:18357186 original size:72 final size:72
Alignment explanation
Indices: 18357019--18357198 Score: 215
Period size: 72 Copynumber: 2.5 Consensus size: 72
18357009 CCTAACCCCC
* * * *
18357019 AAACCTTAAACCCTAACCCTTAAA-CCATAAACCATAAACCTTAAAATAGTAACTCCTAAACCTT
1 AAACCATAAACCATAATCCATAAACCCATAAACCATAAACCTTAAAATAGTAACTCCTAAACCTT
18357083 AAACCAT
66 AAACCAT
* * * * *
18357090 AAACCATAAATCATAATCCCTAAACCCATAATCCATCAACCTTAAAATAGTAATTCCTAAACCTT
1 AAACCATAAACCATAATCCATAAACCCATAAACCATAAACCTTAAAATAGTAACTCCTAAACCTT
18357155 AAACTC-T
66 AAAC-CAT
* *
18357162 AAACCATATACCATTAA-CCATAAACCC-TAAACTATAA
1 AAACCATAAACCA-TAATCCATAAACCCATAAACCATAA
18357199 TGGTAATTAA
Statistics
Matches: 92, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
71 26 0.28
72 62 0.67
73 4 0.04
ACGTcount: A:0.47, C:0.28, G:0.01, T:0.24
Consensus pattern (72 bp):
AAACCATAAACCATAATCCATAAACCCATAAACCATAAACCTTAAAATAGTAACTCCTAAACCTT
AAACCAT
Found at i:18357198 original size:14 final size:14
Alignment explanation
Indices: 18356994--18357198 Score: 99
Period size: 14 Copynumber: 14.4 Consensus size: 14
18356984 AATTAAAAAA
18356994 CATAAACCCTAAACC
1 CATAAACCCTAAA-C
* * *
18357009 CCTAACCCCCAAAC
1 CATAAACCCTAAAC
* *
18357023 CTTAAACCCTAACC
1 CATAAACCCTAAAC
* *
18357037 CTTAAACCATAAAC
1 CATAAACCCTAAAC
*
18357051 CATAAACCTTAAA-
1 CATAAACCCTAAAC
18357064 -ATAGTAACTCCTAAAC
1 CATA--AAC-CCTAAAC
* *
18357080 CTTAAACCATAAAC
1 CATAAACCCTAAAC
* * *
18357094 CATAAATCATAATC
1 CATAAACCCTAAAC
* *
18357108 CCTAAACCCATAATC
1 CATAAACCC-TAAAC
* * *
18357123 CATCAACCTTAAAA
1 CATAAACCCTAAAC
* **
18357137 TAGTAATTCCTAAAC
1 CA-TAAACCCTAAAC
* *
18357152 CTTAAACTCTAAAC
1 CATAAACCCTAAAC
* * *
18357166 CATATACCATTAAC
1 CATAAACCCTAAAC
18357180 CATAAACCCTAAAC
1 CATAAACCCTAAAC
*
18357194 TATAA
1 CATAA
18357199 TGGTAATTAA
Statistics
Matches: 138, Mismatches: 45, Indels: 15
0.70 0.23 0.08
Matches are distributed among these distances:
12 3 0.02
14 97 0.70
15 36 0.26
17 2 0.01
ACGTcount: A:0.45, C:0.31, G:0.01, T:0.22
Consensus pattern (14 bp):
CATAAACCCTAAAC
Found at i:18357878 original size:40 final size:40
Alignment explanation
Indices: 18357749--18357878 Score: 118
Period size: 40 Copynumber: 3.2 Consensus size: 40
18357739 ATTTTTTTGT
* * * * *
18357749 GGCGTTTTTCATAAAGCGTCGCTAATTG-TTGACCTATAGC
1 GGCGTTTTTTAAAAAGCGCCGCTAA-TGCTCGATCTATAGC
** * * * *
18357789 GGCGTTTTCCAAGAAGCGCCGCTAATGGTCTATCTATAGT
1 GGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGC
* * *
18357829 GGCGATTTTTAAAAAGTGCTGCTAATGCTCGATCTATAGC
1 GGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGC
18357869 GGCGTTTTTT
1 GGCGTTTTTT
18357879 GTCCGCCGCT
Statistics
Matches: 71, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (40 bp):
GGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGC
Found at i:18358263 original size:20 final size:20
Alignment explanation
Indices: 18358238--18358280 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
18358228 TTATTTTTTT
*
18358238 ATTTTATGAGAGTTTAATTG
1 ATTTTACGAGAGTTTAATTG
*
18358258 ATTTTACGAGGGTTTAATTG
1 ATTTTACGAGAGTTTAATTG
18358278 ATT
1 ATT
18358281 ATTTAAGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (20 bp):
ATTTTACGAGAGTTTAATTG
Found at i:18358847 original size:11 final size:11
Alignment explanation
Indices: 18358831--18358864 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
18358821 TCGCCCATAT
18358831 TATTATTTTTA
1 TATTATTTTTA
18358842 TATTATTTTTTA
1 TATTA-TTTTTA
*
18358854 TATAATTTTTA
1 TATTATTTTTA
18358865 AAAAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:18358853 original size:12 final size:12
Alignment explanation
Indices: 18358831--18358863 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
18358821 TCGCCCATAT
18358831 TATTA-TTTTTA
1 TATTATTTTTTA
18358842 TATTATTTTTTA
1 TATTATTTTTTA
*
18358854 TATAATTTTT
1 TATTATTTTT
18358864 AAAAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TATTATTTTTTA
Found at i:18360297 original size:20 final size:20
Alignment explanation
Indices: 18360272--18360310 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
18360262 TATTTTTTTC
18360272 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
18360292 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
18360311 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:18360653 original size:50 final size:50
Alignment explanation
Indices: 18360599--18360701 Score: 134
Period size: 50 Copynumber: 2.1 Consensus size: 50
18360589 ACATGAGAGT
* * * *
18360599 TCTCATATCGGTGCCCATGCCATGTCCCATACATGGTCTTACGGGGGACC
1 TCTCATATCGGTACCAACGCCATGTCCCAGACATGGTCTTACGGGGGACC
* ** *
18360649 TCTCATCTCGGTACCAACGCCATGTCTTAGACATGGTCTTACGTGGGACC
1 TCTCATATCGGTACCAACGCCATGTCCCAGACATGGTCTTACGGGGGACC
18360699 TCT
1 TCT
18360702 TATAACCTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.18, C:0.31, G:0.22, T:0.28
Consensus pattern (50 bp):
TCTCATATCGGTACCAACGCCATGTCCCAGACATGGTCTTACGGGGGACC
Found at i:18362151 original size:19 final size:20
Alignment explanation
Indices: 18362115--18362153 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
18362105 TTTAAAACTT
*
18362115 TTCTATACTTTTTTTTAAAA
1 TTCTATACTTTTTCTTAAAA
18362135 TTCTATA-TTTTTCTTAAAA
1 TTCTATACTTTTTCTTAAAA
18362154 AATTTATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (20 bp):
TTCTATACTTTTTCTTAAAA
Found at i:18362153 original size:60 final size:60
Alignment explanation
Indices: 18362070--18362187 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 60
18362060 ATAATTTTAA
** * *
18362070 TAAAATTTATATATTATTCTAAAATCTTTATAACATTTAAAACTTTTCTATACTTTTTTT
1 TAAAATTTATATATTATTCTAAAAAATTTATAACATTTAAAAATTTTCTATAATTTTTTT
18362130 TAAAATTCTATAT-TT-TTCTTAAAAAATTTATAACATTTAAAAATTTTCTATAATTTTT
1 TAAAATT-TATATATTATTC-TAAAAAATTTATAACATTTAAAAATTTTCTATAATTTTT
18362188 AATAATTTGT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
59 3 0.06
60 44 0.85
61 5 0.10
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (60 bp):
TAAAATTTATATATTATTCTAAAAAATTTATAACATTTAAAAATTTTCTATAATTTTTTT
Found at i:18362154 original size:20 final size:20
Alignment explanation
Indices: 18362115--18362154 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
18362105 TTTAAAACTT
*
18362115 TTCTATACTTTTTTTTAAAA
1 TTCTATACTTTTTTTAAAAA
18362135 TTCTATA-TTTTTCTTAAAAA
1 TTCTATACTTTTT-TTAAAAA
18362155 ATTTATAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (20 bp):
TTCTATACTTTTTTTAAAAA
Found at i:18371480 original size:19 final size:19
Alignment explanation
Indices: 18371453--18371500 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
18371443 GCACTTATGA
* *
18371453 GCCAAGATGTACTTCGTGT
1 GCCAGGATGTACTTCATGT
18371472 GCCAGGATGTACTTCATGT
1 GCCAGGATGTACTTCATGT
*
18371491 GCCAGTATGT
1 GCCAGGATGT
18371501 GCTTTGTGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (19 bp):
GCCAGGATGTACTTCATGT
Found at i:18374823 original size:13 final size:13
Alignment explanation
Indices: 18374807--18374831 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18374797 AAAATGCATA
18374807 AGTAAATACAACG
1 AGTAAATACAACG
18374820 AGTAAATACAAC
1 AGTAAATACAAC
18374832 TACAATGATT
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:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (13 bp):
AGTAAATACAACG
Found at i:18386047 original size:66 final size:66
Alignment explanation
Indices: 18385940--18386077 Score: 188
Period size: 66 Copynumber: 2.1 Consensus size: 66
18385930 TCATATTTTG
* * * *
18385940 AAGTTGTAGTTGGAGTTCGTCATATTTTCTTGTTGCATCTACTTCCGTCGCTGCTGCCTCAACTT
1 AAGTTGTAGCTGGAGTTCATCATATTTTCTTGTAGCATCTACTTCCGTCGATGCTGCCTCAACTT
18386005 T
66 T
* ** *
18386006 AAGTTGTAGCTGGAGTTCATCATATTTTCTT-TGAGCCTCTACTTCTTTCGATGCTGCCTCCACT
1 AAGTTGTAGCTGGAGTTCATCATATTTTCTTGT-AGCATCTACTTCCGTCGATGCTGCCTCAACT
18386070 TT
65 TT
18386072 AAGTTG
1 AAGTTG
18386078 AGCAATTTGC
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
65 1 0.02
66 62 0.98
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAGTTGTAGCTGGAGTTCATCATATTTTCTTGTAGCATCTACTTCCGTCGATGCTGCCTCAACTT
T
Found at i:18387129 original size:45 final size:45
Alignment explanation
Indices: 18387065--18387154 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
18387055 GAAAGTAAAT
* *
18387065 ATAAATTAAACTTAAACCAAAGTATTGTAAATTACATTCACGTTA
1 ATAAATGAAACTTAAACCAAAGTATTATAAATTACATTCACGTTA
18387110 ATAAATGAAACTTAAACCAAAGTATTATAAATTACATTCACGTTA
1 ATAAATGAAACTTAAACCAAAGTATTATAAATTACATTCACGTTA
18387155 TTACCTTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.32
Consensus pattern (45 bp):
ATAAATGAAACTTAAACCAAAGTATTATAAATTACATTCACGTTA
Found at i:18392139 original size:23 final size:24
Alignment explanation
Indices: 18392075--18392146 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 24
18392065 TTATTCATAA
*
18392075 AATTATTATGAAATATAATTATTT
1 AATTATTATGAAATATAATTAATT
* * *
18392099 AATTAAATCATCAAAAATTAATTAATT
1 AATT--ATTATGAAATA-TAATTAATT
*
18392126 AATTATTATGAAATATGATTA
1 AATTATTATGAAATATAATTA
18392147 TTTATTTAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
24 9 0.24
25 8 0.22
26 8 0.22
27 12 0.32
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (24 bp):
AATTATTATGAAATATAATTAATT
Found at i:18392258 original size:5 final size:5
Alignment explanation
Indices: 18392234--18392276 Score: 59
Period size: 5 Copynumber: 8.2 Consensus size: 5
18392224 ATAAACTATT
*
18392234 ATTTA ATTATA TAATTA ATTTA ATTTA ATTTA ATTTA ATTTA A
1 ATTTA ATT-TA -ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA A
18392277 AAATAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 28 0.82
6 4 0.12
7 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
ATTTA
Found at i:18400735 original size:11 final size:11
Alignment explanation
Indices: 18400715--18400747 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
18400705 GTTAAATTCG
18400715 TAATTGGTTGT
1 TAATTGGTTGT
*
18400726 TAATTTGTTGT
1 TAATTGGTTGT
18400737 TAATTGGTTGT
1 TAATTGGTTGT
18400748 GGTAATACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.58
Consensus pattern (11 bp):
TAATTGGTTGT
Found at i:18402226 original size:37 final size:38
Alignment explanation
Indices: 18402152--18402247 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 38
18402142 ACCCCTTCGA
* *
18402152 CCACCCTACACACCACAATTGGGCTATGGTAGGCCCAT
1 CCACCCTACACACCACAATAGGGCTATGGTAGACCCAT
*
18402190 CCACTCTACACACCACAA-AGGGCTATGGTAGACCCAT
1 CCACCCTACACACCACAATAGGGCTATGGTAGACCCAT
* *
18402227 CTACCCTACACACCACGATAG
1 CCACCCTACACACCACAATAG
18402248 TGGATCTAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
37 32 0.63
38 19 0.37
ACGTcount: A:0.30, C:0.38, G:0.16, T:0.17
Consensus pattern (38 bp):
CCACCCTACACACCACAATAGGGCTATGGTAGACCCAT
Found at i:18405132 original size:19 final size:18
Alignment explanation
Indices: 18405108--18405150 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
18405098 TATATGTTGA
18405108 ATAAAATGAACAAAAATAG
1 ATAAAATG-ACAAAAATAG
* *
18405127 ATAAAAATGATAAAATTAG
1 AT-AAAATGACAAAAATAG
18405146 ATAAA
1 ATAAA
18405151 TAGATTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 12 0.57
20 6 0.29
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.21
Consensus pattern (18 bp):
ATAAAATGACAAAAATAG
Found at i:18407214 original size:3 final size:3
Alignment explanation
Indices: 18407201--18407345 Score: 281
Period size: 3 Copynumber: 48.0 Consensus size: 3
18407191 TTTAATTATG
18407201 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18407247 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18407295 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18407343 TTA
1 TTA
18407346 NNNNNNNNNN
Statistics
Matches: 141, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
3 138 0.98
4 3 0.02
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:18413540 original size:50 final size:50
Alignment explanation
Indices: 18413410--18413560 Score: 153
Period size: 50 Copynumber: 3.0 Consensus size: 50
18413400 ACCATAGATT
* *
18413410 TTACTTTCTTAGCAGTGCAGTAGAACAGATTGAAGCTACGACGGCGGATC
1 TTACTTCCTTAGCAGTACAGTAGAACAGATTGAAGCTACGACGGCGGATC
*** * * * * * * *
18413460 TGGTTTCCCT-GATATTACAATTA-AAAAGATTGAAGCCACAACGGCGGATC
1 TTACTTCCTTAG-CAGTAC-AGTAGAACAGATTGAAGCTACGACGGCGGATC
*
18413510 TTACTTCCTTAGCAGTACAGTGGAACAGATTGAAGCTACGACGGCGGATC
1 TTACTTCCTTAGCAGTACAGTAGAACAGATTGAAGCTACGACGGCGGATC
18413560 T
1 T
18413561 GGTTTCCCCA
Statistics
Matches: 74, Mismatches: 23, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
49 3 0.04
50 67 0.91
51 4 0.05
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26
Consensus pattern (50 bp):
TTACTTCCTTAGCAGTACAGTAGAACAGATTGAAGCTACGACGGCGGATC
Found at i:18413586 original size:50 final size:50
Alignment explanation
Indices: 18413427--18413594 Score: 174
Period size: 50 Copynumber: 3.4 Consensus size: 50
18413417 CTTAGCAGTG
* * *
18413427 CAGTAGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTA
1 CAGTTGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAACATTA
* * * * * *** * * *
18413477 CAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTA
1 CAGTTGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAACATTA
* * *
18413527 CAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCCAACATTG
1 CAGTTGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAACATTA
*
18413577 CAGTTGAACAAATTGAAG
1 CAGTTGAACAGATTGAAG
18413595 ATTTCAGATC
Statistics
Matches: 88, Mismatches: 30, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
50 88 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (50 bp):
CAGTTGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAACATTA
Found at i:18413747 original size:132 final size:132
Alignment explanation
Indices: 18413588--18414035 Score: 736
Period size: 132 Copynumber: 3.4 Consensus size: 132
18413578 AGTTGAACAA
* ** *
18413588 ATTGAAGATTTCAGATCTTGTCTCCCTAAGTAGTAGTGGAGCAGATTGAAGATGGCGGATTTTAC
1 ATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTAC
* * *
18413653 CTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGCGGAAT
66 CTCCCCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGCGGAAT
18413718 AG
131 AG
18413720 ATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTAC
1 ATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTAC
18413785 CTCCCCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGCGGAAT
66 CTCCCCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGCGGAAT
18413850 AG
131 AG
18413852 ATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTAC
1 ATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTAC
* * *
18413917 CTCCCCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-TCTCCCTGGGCAGCAGTGAAA
66 CTCCCCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGACAGCAGCGGAA
18413981 TAG
130 TAG
* ** * * *
18413984 ATTGAAGATTACAGATCTTACCTCCCTAGGCAGTAATGGAGCAGATCGAAGA
1 ATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGA
18414036 CCCCAGTCTT
Statistics
Matches: 299, Mismatches: 16, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
131 1 0.00
132 298 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (132 bp):
ATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTAC
CTCCCCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGCGGAAT
AG
Found at i:18421803 original size:22 final size:22
Alignment explanation
Indices: 18421763--18421829 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
18421753 CGGAACAAAT
*
18421763 ACAGAGAGCACAAATGTGCTGA
1 ACAGAGAGCACAAACGTGCTGA
** *
18421785 ACAGAGAGCACTGACGTGCTAAA
1 ACAGAGAGCACAAACGTGCT-GA
*
18421808 TATCAGAGAGCACCAACGTGCT
1 -A-CAGAGAGCACAAACGTGCT
18421830 AATAATCAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
22 17 0.47
23 1 0.03
24 1 0.03
25 17 0.47
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.15
Consensus pattern (22 bp):
ACAGAGAGCACAAACGTGCTGA
Found at i:18421817 original size:25 final size:25
Alignment explanation
Indices: 18421786--18421868 Score: 123
Period size: 25 Copynumber: 3.3 Consensus size: 25
18421776 ATGTGCTGAA
**
18421786 CAGAGAGCACTGACGTGCTAA-ATAT
1 CAGAGAGCACCAACGTGCTAATA-AT
18421811 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAATAAT
*
18421836 CAGAGAGCACCAACGTACTAATAAT
1 CAGAGAGCACCAACGTGCTAATAAT
18421861 CAGAGAGC
1 CAGAGAGC
18421869 GCGCTAAAGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
25 53 0.98
26 1 0.02
ACGTcount: A:0.40, C:0.23, G:0.22, T:0.16
Consensus pattern (25 bp):
CAGAGAGCACCAACGTGCTAATAAT
Found at i:18422196 original size:11 final size:11
Alignment explanation
Indices: 18422169--18422202 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
18422159 GGTTCCATAA
18422169 TATTTTA-TTT
1 TATTTTATTTT
*
18422179 TACTTTATTTT
1 TATTTTATTTT
18422190 TATTTTATTTT
1 TATTTTATTTT
18422201 TA
1 TA
18422203 AATAAATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:18422715 original size:12 final size:13
Alignment explanation
Indices: 18422698--18422729 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
18422688 GATTTCCATC
18422698 AATTCAAT-CACT
1 AATTCAATCCACT
18422710 AATTC-ATCCACT
1 AATTCAATCCACT
18422722 AATTCAAT
1 AATTCAAT
18422730 ATAAGCTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 14 0.78
13 2 0.11
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (13 bp):
AATTCAATCCACT
Found at i:18422922 original size:11 final size:11
Alignment explanation
Indices: 18422906--18422931 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18422896 TCTTTCTTTC
18422906 TTTCTCCCCTG
1 TTTCTCCCCTG
18422917 TTTCTCCCCTG
1 TTTCTCCCCTG
18422928 TTTC
1 TTTC
18422932 GTTTCAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:18423001 original size:5 final size:5
Alignment explanation
Indices: 18422991--18423025 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
18422981 TATATATATA
*
18422991 ATAAT ATAAT ATAAT ATTAT AATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAA
18423026 CAACTCACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:18423011 original size:21 final size:22
Alignment explanation
Indices: 18422982--18423025 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
18422972 CTTTTGCTTT
18422982 ATATATATAATAATATAATATA
1 ATATATATAATAATATAATATA
18423004 ATAT-TATAATAATATAATATA
1 ATATATATAATAATATAATATA
18423025 A
1 A
18423026 CAACTCACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATATATAATAATATAATATA
Found at i:18423859 original size:64 final size:65
Alignment explanation
Indices: 18423782--18423992 Score: 175
Period size: 64 Copynumber: 3.3 Consensus size: 65
18423772 GCTATTCAGA
*
18423782 GTTGCGATCTTAAATCAACTAACTCAAATAAAATTATTCATGATCTGAAATC-GAATGAACTTAG
1 GTTGCGATCTTAAATCAGCTAACTCAAATAAAATTATTCATGATCTGAAATCAGAATGAACTTAG
* * * * * * * * *
18423846 GTTGCGATATTAAATCAGCGAAC-CTTAATAATATGAATT-GTGATCTTAAATCAGCTAGTTG-C
1 GTTGCGATCTTAAATCAGCTAACTC-AAATAAAAT-TATTCATGATCTGAAATCAG--A-ATGAA
**
18423908 CGGA-
61 CTTAG
* * * * *
18423912 GTTGTGATCTTAAATTAGCTAACTCAAATAAAATTGTTCATGAACTGAAA-CTGAATGAACTTAG
1 GTTGCGATCTTAAATCAGCTAACTCAAATAAAATTATTCATGATCTGAAATCAGAATGAACTTAG
18423976 GTTGCGAT-TTAAATCAG
1 GTTGCGATCTTAAATCAG
18423993 TGAACCTTAA
Statistics
Matches: 107, Mismatches: 30, Indels: 21
0.68 0.19 0.13
Matches are distributed among these distances:
62 2 0.02
63 12 0.11
64 45 0.42
65 8 0.07
66 34 0.32
67 4 0.04
68 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (65 bp):
GTTGCGATCTTAAATCAGCTAACTCAAATAAAATTATTCATGATCTGAAATCAGAATGAACTTAG
Found at i:18423960 original size:130 final size:130
Alignment explanation
Indices: 18423780--18424083 Score: 477
Period size: 130 Copynumber: 2.3 Consensus size: 130
18423770 GAGCTATTCA
* * * *
18423780 GAGTTGCGATCTTAAATCAACTAACTCAAATAAAATTATTCATGATCTGAAA-TCGAATGAACTT
1 GAGTTGCGATCTTAAATTAGCTAACTCAAATAAAATTGTTCATGAACTGAAACT-GAATGAACTT
* *
18423844 AGGTTGCGATATTAAATCAGCGAACCTTAATAATATGAATTGTGATCTTAAATCAGCTAGTTG-C
65 AGGTTGCGAT-TTAAATCAGCGAACCTTAATAATATCAATTGTGATCTTAAATCAGCAAGTTGTC
18423908 CG
129 CG
*
18423910 GAGTTGTGATCTTAAATTAGCTAACTCAAATAAAATTGTTCATGAACTGAAACTGAATGAACTTA
1 GAGTTGCGATCTTAAATTAGCTAACTCAAATAAAATTGTTCATGAACTGAAACTGAATGAACTTA
* * *
18423975 GGTTGCGATTTAAATCAGTGAACCTTAATAATATCAGTTGTGATCTTAAATCAGCAAGTTGTTCG
66 GGTTGCGATTTAAATCAGCGAACCTTAATAATATCAATTGTGATCTTAAATCAGCAAGTTGTCCG
*
18424040 GAGTTGCGATCTTAAATTAGCAAACTCAAATAAAATTGTTCATG
1 GAGTTGCGATCTTAAATTAGCTAACTCAAATAAAATTGTTCATG
18424084 TTAAATAAAG
Statistics
Matches: 160, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
129 48 0.30
130 111 0.69
131 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.33
Consensus pattern (130 bp):
GAGTTGCGATCTTAAATTAGCTAACTCAAATAAAATTGTTCATGAACTGAAACTGAATGAACTTA
GGTTGCGATTTAAATCAGCGAACCTTAATAATATCAATTGTGATCTTAAATCAGCAAGTTGTCCG
Found at i:18427345 original size:24 final size:24
Alignment explanation
Indices: 18427288--18427351 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
18427278 ACACAAATGT
* ** *
18427288 AGATACAAAAACAGGTTCAGTTAC
1 AGATACAAATACAAATTCAATTAC
*
18427312 AGATGCAAATACAAATTCAATTAC
1 AGATACAAATACAAATTCAATTAC
*
18427336 AGATACAAATGCAAAT
1 AGATACAAATACAAAT
18427352 GCAAACACAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (24 bp):
AGATACAAATACAAATTCAATTAC
Found at i:18428639 original size:40 final size:42
Alignment explanation
Indices: 18428595--18428672 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
18428585 GGAACACTTG
*
18428595 TGACAAAAATTG-AA-AAAAAAAACCAAGCAAACAAAAGTTT
1 TGACAAAAATTGAAAGAAAAAAAAACAAGCAAACAAAAGTTT
*
18428635 TGACAAAAATTGAAAGAAAAAAAAACAAGCAAAGAAAA
1 TGACAAAAATTGAAAGAAAAAAAAACAAGCAAACAAAA
18428673 CTTATAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 12 0.35
41 2 0.06
42 20 0.59
ACGTcount: A:0.67, C:0.10, G:0.12, T:0.12
Consensus pattern (42 bp):
TGACAAAAATTGAAAGAAAAAAAAACAAGCAAACAAAAGTTT
Found at i:18431447 original size:112 final size:109
Alignment explanation
Indices: 18431220--18431426 Score: 245
Period size: 112 Copynumber: 1.8 Consensus size: 109
18431210 AAATAATTTC
* * *
18431220 TTTTTTTTGTGCTGGCACACTGATGGCCAACTCCCACTTTATCAGATAAAAAAATTTTGGTTTGG
1 TTTTTTTTGTGCTGGCACACTAATGGCCAACACCCACTTTATCAAATAAAAAAATTTTGGTTTGG
* * * * **
18431285 GAGAATTAGATGGCCAGCATCACCTTTGTCATATTAAAAAAATAA
66 GAGAACTAAATGGACAACATCACCTTTGTCATAGGAAAAAAAT-A
*
18431330 TTTTTTTTAGATGCTGGCACACTAATGGCTAACACCCACTTTATCAAATAAAAAAAATTTCTTAG
1 TTTTTTTT-G-TGCTGGCACACTAATGGCCAACACCCACTTTATCAAAT-AAAAAAA-TT-TT-G
*
18431395 G-TTGGGGGAACTAAATGGACAACATCACCTTT
60 GTTTGGGAGAACTAAATGGACAACATCACCTTT
18431427 TTTAGGAATA
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
110 8 0.10
111 1 0.01
112 34 0.41
113 7 0.09
114 2 0.02
115 28 0.34
116 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (109 bp):
TTTTTTTTGTGCTGGCACACTAATGGCCAACACCCACTTTATCAAATAAAAAAATTTTGGTTTGG
GAGAACTAAATGGACAACATCACCTTTGTCATAGGAAAAAAATA
Found at i:18434451 original size:24 final size:24
Alignment explanation
Indices: 18434424--18434473 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
18434414 CACATGATTC
* * *
18434424 AATTTAATTTATAGTGTAAATAAA
1 AATTCAATTAATAGTATAAATAAA
18434448 AATTCAATTAATAGTATAAATAAA
1 AATTCAATTAATAGTATAAATAAA
18434472 AA
1 AA
18434474 AATAATTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (24 bp):
AATTCAATTAATAGTATAAATAAA
Found at i:18434480 original size:24 final size:23
Alignment explanation
Indices: 18434428--18434480 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
18434418 TGATTCAATT
* * *
18434428 TAATTTATAGTGTAAATAAAAAT
1 TAATTAATAGTATAAATAAAAAA
18434451 TCAATTAATAGTATAAATAAAAAAA
1 T-AATTAATAGTATAAAT-AAAAAA
18434476 TAATT
1 TAATT
18434481 TGATACATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 1 0.04
24 18 0.72
25 6 0.24
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.36
Consensus pattern (23 bp):
TAATTAATAGTATAAATAAAAAA
Found at i:18437671 original size:90 final size:88
Alignment explanation
Indices: 18437561--18437838 Score: 272
Period size: 90 Copynumber: 3.1 Consensus size: 88
18437551 AGAAAATACA
*
18437561 AACATTCTACAAAACTAATATACGAAAATATATAATTCGACCAACAAATAATACCGACTAAATTT
1 AACATTTTACAAAACTAATATACGAAAATATA-AATTCGACCAACAAATAATA-CGACTAAATTT
*
18437626 TATTTATAGATACAAAACTCATATG
64 TATTTATAGATACAAAACTAATATG
* * * *
18437651 AACATTTTAGAAAATTAATATACGAAAATATAATATTCGATCAGA-AAATAATACAAGCTAAAAT
1 AACATTTTACAAAACTAATATACGAAAATATAA-ATTCGACCA-ACAAATAATACGA-CT-AAAT
* * * * **
18437715 ATT-TTTACAGATCCAAAAATAATACA
62 TTTATTTATAGATACAAAACTAATATG
* * * * * *
18437741 AACATTTTACAGAACTGATATAGGAAAATATAAAAATCGACCAACAAATAATATGGACTAAAATT
1 AACATTTTACAAAACTAATATACGAAAATAT-AAATTCGACCAACAAATAATA-CGACTAAATTT
* * *
18437806 GATTTATGGACACAAAACTAATATG
64 TATTTATAGATACAAAACTAATATG
*
18437831 AATATTTT
1 AACATTTT
18437839 GAATAATAGT
Statistics
Matches: 148, Mismatches: 32, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
89 8 0.05
90 130 0.88
91 10 0.07
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29
Consensus pattern (88 bp):
AACATTTTACAAAACTAATATACGAAAATATAAATTCGACCAACAAATAATACGACTAAATTTTA
TTTATAGATACAAAACTAATATG
Found at i:18457444 original size:11 final size:13
Alignment explanation
Indices: 18457436--18457475 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
18457426 ATAATTTAAA
*
18457436 ATTTTTTTATATAT
1 ATTTTTTAATA-AT
*
18457450 ATATTTTAATAAT
1 ATTTTTTAATAAT
18457463 ATTTTTTAATAAT
1 ATTTTTTAATAAT
18457476 TTACTATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTTTTAATAAT
Found at i:18457446 original size:22 final size:23
Alignment explanation
Indices: 18457418--18457478 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
18457408 TATTTTTTTA
*
18457418 TTTTATAAATAATTTAA-AATTT
1 TTTTATAAATAATTTAATAATAT
*
18457440 TTTTATATATATATTTTAATAATAT
1 TTTTATA-A-ATAATTTAATAATAT
18457465 TTTT-T-AATAATTTA
1 TTTTATAAATAATTTA
18457479 CTATATTCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 7 0.21
22 8 0.24
23 1 0.03
24 9 0.27
25 8 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTTATAAATAATTTAATAATAT
Found at i:18458202 original size:51 final size:51
Alignment explanation
Indices: 18458147--18458283 Score: 175
Period size: 51 Copynumber: 2.7 Consensus size: 51
18458137 TATGGTAACC
*
18458147 AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATATGATATGG
1 AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
* * * ** * * **
18458198 AATCTTATAAGATATTATTTTATAAGATTACATATCTTATCTAAGATATGG
1 AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
*
18458249 AATCTTAGAAGATATGATATTATATTCTTAGAGAT
1 AATCTTAGAAGATATGATATTATAATCTTAGAGAT
18458284 TTGATGGTAG
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (51 bp):
AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
Found at i:18461845 original size:11 final size:11
Alignment explanation
Indices: 18461829--18461853 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18461819 GATCCCTAAA
18461829 TGATTGCTCAT
1 TGATTGCTCAT
18461840 TGATTGCTCAT
1 TGATTGCTCAT
18461851 TGA
1 TGA
18461854 AGATGTGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.44
Consensus pattern (11 bp):
TGATTGCTCAT
Found at i:18464289 original size:16 final size:16
Alignment explanation
Indices: 18464254--18464300 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 16
18464244 AAAAAAGTTT
*
18464254 TTTAACAATTTTTAAAAA
1 TTTAA-AATATTT-AAAA
18464272 TTTAAAATATTTAAAA
1 TTTAAAATATTTAAAA
18464288 TTTAAAATATTTA
1 TTTAAAATATTTA
18464301 TAAAAATTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 17 0.61
17 6 0.21
18 5 0.18
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAAATATTTAAAA
Found at i:18464379 original size:19 final size:19
Alignment explanation
Indices: 18464347--18464399 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
18464337 AAAGTTTTTT
*
18464347 TAAAAAATATTTAAAGAA-TA
1 TAAAAAA-AGTTAAA-AATTA
18464367 TAAAAAAAGTTAAAAATTA
1 TAAAAAAAGTTAAAAATTA
*
18464386 AAAAAAAAGTTAAA
1 TAAAAAAAGTTAAA
18464400 TGATAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 21 0.70
20 7 0.23
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.25
Consensus pattern (19 bp):
TAAAAAAAGTTAAAAATTA
Found at i:18466409 original size:15 final size:13
Alignment explanation
Indices: 18466376--18466416 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
18466366 TCGACCAAAG
18466376 TTTATATAAAAAA
1 TTTATATAAAAAA
18466389 -TTATATAACATAAA
1 TTTATATAA-A-AAA
18466403 TTTATATAAAAAA
1 TTTATATAAAAAA
18466416 T
1 T
18466417 GATTTAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.32
13 5 0.20
14 4 0.16
15 8 0.32
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (13 bp):
TTTATATAAAAAA
Found at i:18470922 original size:44 final size:43
Alignment explanation
Indices: 18470862--18470979 Score: 130
Period size: 44 Copynumber: 2.7 Consensus size: 43
18470852 GATGTGATCT
* * * * *
18470862 ACTCTACTGCACCTTCAGAGAGATAAGATCTGA-GGTTTTAATCC
1 ACTCCACTGCAACTTCAGGGAGATAAGAT-T-ATGGCTTCAATCC
* *
18470906 ACTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTCAATCT
1 ACTCCACTGCAACTTCAGGGAGATAAGATTA-TGGCTTCAATCC
*
18470950 ACTCCACTACAACTTCAGGGAGATAAGATT
1 ACTCCACTGCAACTTCAGGGAGATAAGATT
18470980 CGTCATCTTC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 1 0.02
43 1 0.02
44 61 0.97
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (43 bp):
ACTCCACTGCAACTTCAGGGAGATAAGATTATGGCTTCAATCC
Found at i:18471124 original size:100 final size:100
Alignment explanation
Indices: 18470994--18471174 Score: 308
Period size: 100 Copynumber: 1.8 Consensus size: 100
18470984 ATCTTCAGTC
18470994 TTTTAAATTGCAATGTTGGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTACACCG
1 TTTTAAATTGCAATGTTGGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTACACCG
18471059 CCAGAGAAGTAAGATTTGCCGTTGCGACTTCAATT
66 CCAGAGAAGTAAGATTTGCCGTTGCGACTTCAATT
* * * *
18471094 TTTTTAATTGCAATGTTGGGGAAACGAGATTCGCCGTTGTAGCTTCAATCTGTTCTACTACACCG
1 TTTTAAATTGCAATGTTGGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTACACCG
* *
18471159 CCAGGGGAGTAAGATT
66 CCAGAGAAGTAAGATT
18471175 CATCGTTGTG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 75 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (100 bp):
TTTTAAATTGCAATGTTGGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTACACCG
CCAGAGAAGTAAGATTTGCCGTTGCGACTTCAATT
Found at i:18471174 original size:50 final size:50
Alignment explanation
Indices: 18471019--18471195 Score: 119
Period size: 50 Copynumber: 3.5 Consensus size: 50
18471009 TTGGGGAAAC
* * *
18471019 AAGATTCACCGTTGTAGCTTCAATCTGTTCCACTACACCGCCAGAGAAGT
1 AAGATTCACCGTTGTAGCTTCAATCTGTTCTACTACACCGCCAGGGGAGT
** * * * * * ** ** *
18471069 AAGATTTGCCGTTG-CGACTTCAAT-TTTTTTAATTGCAATG-TTGGGGA-A
1 AAGATTCACCGTTGTAG-CTTCAATCTGTTCT-ACTACACCGCCAGGGGAGT
*
18471117 ACGAGATTCGCCGTTGTAGCTTCAATCTGTTCTACTACACCGCCAGGGGAGT
1 A--AGATTCACCGTTGTAGCTTCAATCTGTTCTACTACACCGCCAGGGGAGT
* * *
18471169 AAGATTCATCGTTGTGGCTTTAATCTG
1 AAGATTCACCGTTGTAGCTTCAATCTG
18471196 CTCCACTGTA
Statistics
Matches: 89, Mismatches: 30, Indels: 16
0.66 0.22 0.12
Matches are distributed among these distances:
48 1 0.01
49 7 0.08
50 70 0.79
51 10 0.11
52 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.32
Consensus pattern (50 bp):
AAGATTCACCGTTGTAGCTTCAATCTGTTCTACTACACCGCCAGGGGAGT
Found at i:18471341 original size:51 final size:50
Alignment explanation
Indices: 18471286--18471422 Score: 139
Period size: 51 Copynumber: 2.7 Consensus size: 50
18471276 CCAGGGAGAT
* * * **
18471286 AAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGTAATGCTAGGGAAAC
1 AAGATTCGCTGCC-TCAGCTTTAATCTGCTCCACTATAATGCCAAAGAAAC
* * *
18471337 AAGATTCGCTACCTCTAGCTTTAATCTGTTCCACTATAATGCCAAAGAAAT
1 AAGATTCGCTGCCTC-AGCTTTAATCTGCTCCACTATAATGCCAAAGAAAC
* * * *
18471388 AGGATTCGCTGCCCACAACTTTAATCCGCTCCACT
1 AAGATTCGCTG-CCTCAGCTTTAATCTGCTCCACT
18471423 TCAGCTATTT
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
50 2 0.03
51 65 0.93
52 3 0.04
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (50 bp):
AAGATTCGCTGCCTCAGCTTTAATCTGCTCCACTATAATGCCAAAGAAAC
Found at i:18471475 original size:169 final size:169
Alignment explanation
Indices: 18471185--18471653 Score: 749
Period size: 169 Copynumber: 2.8 Consensus size: 169
18471175 CATCGTTGTG
* * * **
18471185 GCTTTAATCTGCTCCACTGTAATGCCAAAGAGATAGGATTTGCTGCCCATAGCTTTAATCTACTC
1 GCTTTAATCTGTTCCACTATAATGCCAAAGAGATAGGATTTGCTGCCCACAGCTTTAATCCGCTC
* * * *
18471250 CGCTTTAGCTATTTCAAGTCTTAACGCCAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGC
66 CACTTCAGCTATTTCAAGTCTTAACGCCAGGGAGATAAGATTCGTTGCCCTCAGCTTTAATCTGC
* * *
18471315 TCCGCTGTAATGCTAGGGAAACAAGATTCGCTACCTCTA
131 TCCGCCGCAATGCTAGGGAAACAAGATTCACTACCTCTA
* * *
18471354 GCTTTAATCTGTTCCACTATAATGCCAAAGAAATAGGATTCGCTGCCCACAACTTTAATCCGCTC
1 GCTTTAATCTGTTCCACTATAATGCCAAAGAGATAGGATTTGCTGCCCACAGCTTTAATCCGCTC
* *
18471419 CACTTCAGCTATTTCAAGTCTTAACACCAAGGAGATAAGATTCGTTGCCCTCAGCTTTAATCTGC
66 CACTTCAGCTATTTCAAGTCTTAACGCCAGGGAGATAAGATTCGTTGCCCTCAGCTTTAATCTGC
* *
18471484 TCCGCCGCAATGCTAGGGAAACAAGATTCATTACCTTTA
131 TCCGCCGCAATGCTAGGGAAACAAGATTCACTACCTCTA
18471523 GCTTTAATCTGTTCCACTATAATGCCAAAGAGATAGGATTTGCTGCCCACAGCTTTAATCCGCTC
1 GCTTTAATCTGTTCCACTATAATGCCAAAGAGATAGGATTTGCTGCCCACAGCTTTAATCCGCTC
* *
18471588 CACTTCAGCTTTTTCAAGTCTTAACGCCTGGGAGATAAGATTCGTTGCCCTCAGCTTTAATCTGC
66 CACTTCAGCTATTTCAAGTCTTAACGCCAGGGAGATAAGATTCGTTGCCCTCAGCTTTAATCTGC
18471653 T
131 T
18471654 TTGTTATAAC
Statistics
Matches: 274, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
169 274 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (169 bp):
GCTTTAATCTGTTCCACTATAATGCCAAAGAGATAGGATTTGCTGCCCACAGCTTTAATCCGCTC
CACTTCAGCTATTTCAAGTCTTAACGCCAGGGAGATAAGATTCGTTGCCCTCAGCTTTAATCTGC
TCCGCCGCAATGCTAGGGAAACAAGATTCACTACCTCTA
Found at i:18471756 original size:44 final size:44
Alignment explanation
Indices: 18471678--18471812 Score: 193
Period size: 44 Copynumber: 3.1 Consensus size: 44
18471668 GAAAAGTAAA
* * * *
18471678 ATTCGCAATCTTCAACCTATTTCATTGCTAACCAGGGAGATAGG
1 ATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGG
18471722 ATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGG
1 ATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGG
*
18471766 ACTT-ACAAAT-TTCAACCTATTCCACTGCTGACTAGGGAGATAGG
1 A-TTCAC-AATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGG
18471810 ATT
1 ATT
18471813 TATTATCTTC
Statistics
Matches: 84, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
43 2 0.02
44 77 0.92
45 5 0.06
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (44 bp):
ATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGG
Found at i:18472423 original size:12 final size:12
Alignment explanation
Indices: 18472406--18472430 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18472396 TGACAACAAA
18472406 ATCTGAAGGGAT
1 ATCTGAAGGGAT
18472418 ATCTGAAGGGAT
1 ATCTGAAGGGAT
18472430 A
1 A
18472431 GTCTCAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.32, T:0.24
Consensus pattern (12 bp):
ATCTGAAGGGAT
Found at i:18478019 original size:51 final size:50
Alignment explanation
Indices: 18477964--18478100 Score: 139
Period size: 51 Copynumber: 2.7 Consensus size: 50
18477954 CCAGGGAGAT
* * * **
18477964 AAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGTAATGCTAGGGAAAC
1 AAGATTCGCTGCC-TCAGCTTTAATCTGCTCCACTATAATGCCAAAGAAAC
* * *
18478015 AAGATTCGCTACCTCTAGCTTTAATCTGTTCCACTATAATGCCAAAGAAAT
1 AAGATTCGCTGCCTC-AGCTTTAATCTGCTCCACTATAATGCCAAAGAAAC
* * * *
18478066 AGGATTCGCTGCCCACAACTTTAATCCGCTCCACT
1 AAGATTCGCTG-CCTCAGCTTTAATCTGCTCCACT
18478101 TCAGCTATTT
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
50 2 0.03
51 65 0.93
52 3 0.04
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (50 bp):
AAGATTCGCTGCCTCAGCTTTAATCTGCTCCACTATAATGCCAAAGAAAC
Found at i:18478153 original size:169 final size:169
Alignment explanation
Indices: 18477863--18478331 Score: 749
Period size: 169 Copynumber: 2.8 Consensus size: 169
18477853 CATCGTTGTG
* * * **
18477863 GCTTTAATCTGCTCCACTGTAATGCCAAAGAGATAGGATTTGCTGCCCATAGCTTTAATCTACTC
1 GCTTTAATCTGTTCCACTATAATGCCAAAGAGATAGGATTTGCTGCCCACAGCTTTAATCCGCTC
* * * *
18477928 CGCTTTAGCTATTTCAAGTCTTAACGCCAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGC
66 CACTTCAGCTATTTCAAGTCTTAACGCCAGGGAGATAAGATTCGTTGCCCTCAGCTTTAATCTGC
* * *
18477993 TCCGCTGTAATGCTAGGGAAACAAGATTCGCTACCTCTA
131 TCCGCCGCAATGCTAGGGAAACAAGATTCACTACCTCTA
* * *
18478032 GCTTTAATCTGTTCCACTATAATGCCAAAGAAATAGGATTCGCTGCCCACAACTTTAATCCGCTC
1 GCTTTAATCTGTTCCACTATAATGCCAAAGAGATAGGATTTGCTGCCCACAGCTTTAATCCGCTC
* *
18478097 CACTTCAGCTATTTCAAGTCTTAACACCAAGGAGATAAGATTCGTTGCCCTCAGCTTTAATCTGC
66 CACTTCAGCTATTTCAAGTCTTAACGCCAGGGAGATAAGATTCGTTGCCCTCAGCTTTAATCTGC
* *
18478162 TCCGCCGCAATGCTAGGGAAACAAGATTCATTACCTTTA
131 TCCGCCGCAATGCTAGGGAAACAAGATTCACTACCTCTA
18478201 GCTTTAATCTGTTCCACTATAATGCCAAAGAGATAGGATTTGCTGCCCACAGCTTTAATCCGCTC
1 GCTTTAATCTGTTCCACTATAATGCCAAAGAGATAGGATTTGCTGCCCACAGCTTTAATCCGCTC
* *
18478266 CACTTCAGCTTTTTCAAGTCTTAACGCCTGGGAGATAAGATTCGTTGCCCTCAGCTTTAATCTGC
66 CACTTCAGCTATTTCAAGTCTTAACGCCAGGGAGATAAGATTCGTTGCCCTCAGCTTTAATCTGC
18478331 T
131 T
18478332 TTGTTATAAC
Statistics
Matches: 274, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
169 274 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (169 bp):
GCTTTAATCTGTTCCACTATAATGCCAAAGAGATAGGATTTGCTGCCCACAGCTTTAATCCGCTC
CACTTCAGCTATTTCAAGTCTTAACGCCAGGGAGATAAGATTCGTTGCCCTCAGCTTTAATCTGC
TCCGCCGCAATGCTAGGGAAACAAGATTCACTACCTCTA
Found at i:18478434 original size:44 final size:44
Alignment explanation
Indices: 18478356--18478490 Score: 193
Period size: 44 Copynumber: 3.1 Consensus size: 44
18478346 GAAAAGTAAA
* * * *
18478356 ATTCGCAATCTTCAACCTATTTCATTGCTAACCAGGGAGATAGG
1 ATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGG
18478400 ATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGG
1 ATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGG
*
18478444 ACTT-ACAAAT-TTCAACCTATTCCACTGCTGACTAGGGAGATAGG
1 A-TTCAC-AATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGG
18478488 ATT
1 ATT
18478491 TATTATCTTC
Statistics
Matches: 84, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
43 2 0.02
44 77 0.92
45 5 0.06
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (44 bp):
ATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGG
Found at i:18479101 original size:12 final size:12
Alignment explanation
Indices: 18479084--18479108 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18479074 TGACAACAAA
18479084 ATCTGAAGGGAT
1 ATCTGAAGGGAT
18479096 ATCTGAAGGGAT
1 ATCTGAAGGGAT
18479108 A
1 A
18479109 GTCTCAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.32, T:0.24
Consensus pattern (12 bp):
ATCTGAAGGGAT
Found at i:18491728 original size:15 final size:13
Alignment explanation
Indices: 18491695--18491721 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18491685 CACAAACGAT
18491695 AAAATTTTCACAC
1 AAAATTTTCACAC
18491708 AAAATTTTCACAC
1 AAAATTTTCACAC
18491721 A
1 A
18491722 CATAATTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:18494523 original size:16 final size:18
Alignment explanation
Indices: 18494504--18494544 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
18494494 AATTAATCGC
18494504 ATTTTAAAT-A-AAAATA
1 ATTTTAAATAATAAAATA
*
18494520 ATTTAAAATAATAAAATA
1 ATTTTAAATAATAAAATA
18494538 ATGTTTA
1 AT-TTTA
18494545 TTGATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 8 0.40
17 1 0.05
18 8 0.40
19 3 0.15
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
ATTTTAAATAATAAAATA
Found at i:18494918 original size:26 final size:26
Alignment explanation
Indices: 18494889--18494960 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 26
18494879 TTTTTCTAAT
* *
18494889 TTAAAACAAAATAAAAATTTTATTAA
1 TTAAAACAAAATTAAAATTTTATCAA
*
18494915 TTAAAA-ATAAATTCAAATTTTATCAA
1 TTAAAACA-AAATTAAAATTTTATCAA
* * *
18494941 ATATAACTAAATTAAAATTT
1 TTAAAACAAAATTAAAATTT
18494961 ATGAATCTTG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
25 1 0.03
26 36 0.97
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (26 bp):
TTAAAACAAAATTAAAATTTTATCAA
Found at i:18495209 original size:18 final size:18
Alignment explanation
Indices: 18495167--18495201 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18495157 TTCAACTTCC
*
18495167 TAAAAAATTAAAATAAAA
1 TAAAATATTAAAATAAAA
18495185 TAAAATATTAAAATAAA
1 TAAAATATTAAAATAAA
18495202 TACCAATAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAAATATTAAAATAAAA
Found at i:18505934 original size:46 final size:46
Alignment explanation
Indices: 18505814--18506031 Score: 253
Period size: 46 Copynumber: 4.8 Consensus size: 46
18505804 TGCCCAAGTT
*
18505814 CCAGCTCCTGCATATGTTGTAGACTGGAGAATACAGATTCAGGTTC
1 CCAGCTCCTGCATATGTTGTAGACTGGAGAATATAGATTCAGGTTC
* * * * *
18505860 CTAG-T-CTGTATATGTT-TCAGACTAGAGAATATAGATTTAGGTTT
1 CCAGCTCCTGCATATGTTGT-AGACTGGAGAATATAGATTCAGGTTC
* * *
18505904 CTAGCTCCTGCATATGTTGTAGACTGGAGAATACAAATTCAGGTTC
1 CCAGCTCCTGCATATGTTGTAGACTGGAGAATATAGATTCAGGTTC
* ** * * *
18505950 CCAACTCCTGCATATGTTGCGGACTGGAGAATATAGGTTTAGATTC
1 CCAGCTCCTGCATATGTTGTAGACTGGAGAATATAGATTCAGGTTC
* *
18505996 CCAACTCCTGCATATGTTGTGGACTGGAGAATATAG
1 CCAGCTCCTGCATATGTTGTAGACTGGAGAATATAG
18506032 TAATAATAAG
Statistics
Matches: 146, Mismatches: 22, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
43 1 0.01
44 36 0.25
45 2 0.01
46 106 0.73
47 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (46 bp):
CCAGCTCCTGCATATGTTGTAGACTGGAGAATATAGATTCAGGTTC
Found at i:18506022 original size:92 final size:90
Alignment explanation
Indices: 18505818--18506028 Score: 287
Period size: 92 Copynumber: 2.3 Consensus size: 90
18505808 CAAGTTCCAG
* * * * *
18505818 CTCCTGCATATGTTGTAGACTGGAGAATACAGATTCAGGTTCCTAGTCTGTATATGTTTCAGACT
1 CTCCTGCATATGTTGTAGACTGGAGAATACAAATTCAGGTTCCAACTCTGCATATGTTGCAGACT
* * * *
18505883 AGAGAATATAGATTTAGGTTTCTAG
66 AGAGAATATAGATTTAGATTCCCAA
*
18505908 CTCCTGCATATGTTGTAGACTGGAGAATACAAATTCAGGTTCCCAACTCCTGCATATGTTGCGGA
1 CTCCTGCATATGTTGTAGACTGGAGAATACAAATTCAGGTT-CCAACT-CTGCATATGTTGCAGA
* *
18505973 CTGGAGAATATAGGTTTAGATTCCCAA
64 CTAGAGAATATAGATTTAGATTCCCAA
*
18506000 CTCCTGCATATGTTGTGGACTGGAGAATA
1 CTCCTGCATATGTTGTAGACTGGAGAATA
18506029 TAGTAATAAT
Statistics
Matches: 106, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
90 40 0.38
91 4 0.04
92 62 0.58
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (90 bp):
CTCCTGCATATGTTGTAGACTGGAGAATACAAATTCAGGTTCCAACTCTGCATATGTTGCAGACT
AGAGAATATAGATTTAGATTCCCAA
Found at i:18513219 original size:15 final size:15
Alignment explanation
Indices: 18513176--18513221 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
18513166 AAACAATTTG
* *
18513176 AAAAAAATAAAAAAC
1 AAAAAAATTAAAAAT
*
18513191 AAAAAAAATAAAAAT
1 AAAAAAATTAAAAAT
*
18513206 AAAAAAATTGAAAAT
1 AAAAAAATTAAAAAT
18513221 A
1 A
18513222 TCATATCTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (15 bp):
AAAAAAATTAAAAAT
Found at i:18517092 original size:24 final size:24
Alignment explanation
Indices: 18517048--18517094 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
18517038 AAATTTATGT
* *
18517048 AATTTTTTATTTATTATTTTTTTG
1 AATTTTTTATTAATCATTTTTTTG
18517072 AATTTTTTA-TAATCATATTTTTT
1 AATTTTTTATTAATCAT-TTTTTT
18517095 TTGAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (24 bp):
AATTTTTTATTAATCATTTTTTTG
Found at i:18517594 original size:22 final size:20
Alignment explanation
Indices: 18517552--18517598 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
18517542 AAAGTATTTT
* *
18517552 TATTTAAAATTAATTATAAA
1 TATTTAAAATTAATAAAAAA
18517572 TATTATAAATATTAATAAAAAA
1 TATT-TAAA-ATTAATAAAAAA
18517594 TATTT
1 TATTT
18517599 TTATATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 5 0.22
22 14 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTTAAAATTAATAAAAAA
Found at i:18519638 original size:3 final size:3
Alignment explanation
Indices: 18519612--18519691 Score: 110
Period size: 3 Copynumber: 26.7 Consensus size: 3
18519602 AACATGCACG
* *
18519612 AAT AAG AAT AAT GAT -AT AAAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
18519657 AAT AAT AAT AAT AAT AAT AAT AAT AACT -AT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AA
18519692 GAACAAATCT
Statistics
Matches: 70, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
2 3 0.04
3 64 0.91
4 3 0.04
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:18528696 original size:43 final size:43
Alignment explanation
Indices: 18528645--18528970 Score: 288
Period size: 43 Copynumber: 7.6 Consensus size: 43
18528635 TTATGTGAAA
* * *
18528645 AAACGCCGCTAAAGATTATGACCTTTAGCGGTGCTTTTATAAC
1 AAACGCCGCTAAAGAATATGACCTTTAGCGGCGCTTTTATCAC
* *
18528688 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTGTCAC
1 AAACGCCGCTAAAGAATATGACCTTTAGCGGCGCTTTTATCAC
** * **
18528731 AAACGATGCTAAAGAGCT-TGACCTTTAGCGGCATTTTTATCAC
1 AAACGCCGCTAAAGA-ATATGACCTTTAGCGGCGCTTTTATCAC
* * *
18528774 AAACGCCGCTAAA-AATCGTGATCTTTAGCGGCGCTTTAGAT-AC
1 AAACGCCGCTAAAGAAT-ATGACCTTTAGCGGCGCTTT-TATCAC
* * * * *
18528817 AAACACCGCTAAAG-ATCGTGAGCTTTAGTGGCGC-TTTAGCCAC
1 AAACGCCGCTAAAGAAT-ATGACCTTTAGCGGCGCTTTTA-TCAC
* * *
18528860 AAACGCCGCTAAAGAATATGATCTTTAACGGCGCTTTTGTCAC
1 AAACGCCGCTAAAGAATATGACCTTTAGCGGCGCTTTTATCAC
* * * * ** *
18528903 AAACGCCGCTAAAGAATA-AACCTGTAGCGACGCTTCTAGAAA
1 AAACGCCGCTAAAGAATATGACCTTTAGCGGCGCTTTTATCAC
* *
18528945 AAACGCCGCTAAA-AACATAACCTTTA
1 AAACGCCGCTAAAGAATATGACCTTTA
18528971 AAAAATTTAT
Statistics
Matches: 230, Mismatches: 43, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
41 5 0.02
42 37 0.16
43 181 0.79
44 7 0.03
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAATATGACCTTTAGCGGCGCTTTTATCAC
Found at i:18528810 original size:129 final size:129
Alignment explanation
Indices: 18528645--18528970 Score: 331
Period size: 129 Copynumber: 2.5 Consensus size: 129
18528635 TTATGTGAAA
* * * * *
18528645 AAACGCCGCTAAAGATTATGACCTTTAGCGGTGCTTT-TATAACAAACGCCGCTAAAGAACATGA
1 AAACGCCGCTAAAAATCATGACCTTTAGCGGCGCTTTAGAT-ACAAACACCGCTAAAGAACATGA
* * * * * *
18528709 CCTTTAGCGGCGCTTTTGTCACAAACGATGCTAAAGAGCT-TGACCTTTAGCGGCATTTTTATCA
65 CCTTTAGCGGCGCTTTAGCCACAAACGACGCTAAAGA-ATATGACCTTTAACGGCACTTTTATCA
18528773 C
129 C
* * * * *
18528774 AAACGCCGCTAAAAATCGTGATCTTTAGCGGCGCTTTAGATACAAACACCGCTAAAGATCGTGAG
1 AAACGCCGCTAAAAATCATGACCTTTAGCGGCGCTTTAGATACAAACACCGCTAAAGAACATGAC
* * * * *
18528839 CTTTAGTGGCGCTTTAGCCACAAACGCCGCTAAAGAATATGATCTTTAACGGCGCTTTTGTCAC
66 CTTTAGCGGCGCTTTAGCCACAAACGACGCTAAAGAATATGACCTTTAACGGCACTTTTATCAC
* * * * * *
18528903 AAACGCCGCTAAAGAAT-A-AACCTGTAGCGACGCTTCTAGA-AAAAACGCCGCTAAA-AACATA
1 AAACGCCGCTAAA-AATCATGACCTTTAGCGGCGCTT-TAGATACAAACACCGCTAAAGAACATG
18528964 ACCTTTA
64 ACCTTTA
18528971 AAAAATTTAT
Statistics
Matches: 161, Mismatches: 32, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
127 9 0.06
128 27 0.17
129 120 0.75
130 5 0.03
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (129 bp):
AAACGCCGCTAAAAATCATGACCTTTAGCGGCGCTTTAGATACAAACACCGCTAAAGAACATGAC
CTTTAGCGGCGCTTTAGCCACAAACGACGCTAAAGAATATGACCTTTAACGGCACTTTTATCAC
Found at i:18531709 original size:3 final size:3
Alignment explanation
Indices: 18531701--18531726 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
18531691 CAATGAATCA
18531701 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
18531727 ATGAATCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:18537345 original size:30 final size:29
Alignment explanation
Indices: 18537311--18537406 Score: 72
Period size: 30 Copynumber: 3.3 Consensus size: 29
18537301 GCACTAGTTG
18537311 CCGGTGATTACAGTTTCCAGGTATTATGTA
1 CCGGTGATTACA-TTTCCAGGTATTATGTA
* * *
18537341 CCGGTG-TTTCAATTCCAGGCACTCTATG--
1 CCGGTGATTACATTTCCAGGTA-T-TATGTA
* **
18537369 CCGGTGATTACAATTTCCAAGTACAATGTA
1 CCGGTGATTAC-ATTTCCAGGTATTATGTA
*
18537399 TCGGTGAT
1 CCGGTGAT
18537407 GGGTACCATA
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
28 17 0.34
29 8 0.16
30 25 0.50
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (29 bp):
CCGGTGATTACATTTCCAGGTATTATGTA
Found at i:18553930 original size:26 final size:26
Alignment explanation
Indices: 18553901--18553953 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
18553891 CTAGTAATAA
*
18553901 TAACTCAGCAAAGCTGCCAATAACAG
1 TAACACAGCAAAGCTGCCAATAACAG
* * *
18553927 TAACACAGCAATGCTGTCAGTAACAG
1 TAACACAGCAAAGCTGCCAATAACAG
18553953 T
1 T
18553954 GTATGTGGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (26 bp):
TAACACAGCAAAGCTGCCAATAACAG
Found at i:18554209 original size:27 final size:26
Alignment explanation
Indices: 18554147--18554532 Score: 359
Period size: 27 Copynumber: 14.3 Consensus size: 26
18554137 GGGTATAATG
*
18554147 GTCATTTTACCCTAC-AGGGTTATTTCA
1 GTCATTTTA-CCTTCGAGGG-TATTTCA
* *
18554174 ATAATTTTATCCTTCGAGGGTATTTCA
1 GTCATTTTA-CCTTCGAGGGTATTTCA
*
18554201 GTCAGTTTATCC-TCGAGGGTATTTCA
1 GTCATTTTA-CCTTCGAGGGTATTTCA
* *
18554227 GTCATTTTACCTTTTGGGGGTATTTC-
1 GTCATTTTACC-TTCGAGGGTATTTCA
* *
18554253 GATTATTTTACCCTTCGAGGGTATTTCG
1 G-TCATTTTA-CCTTCGAGGGTATTTCA
*
18554281 GTTATTTTACCATTCGAGGGTATTTC-
1 GTCATTTTACC-TTCGAGGGTATTTCA
* *
18554307 GATCATTTTACCTTTCGAGGGTGTTTCG
1 G-TCATTTTACC-TTCGAGGGTATTTCA
* * *
18554335 GTCATTTTACCCTTCAAGGGTCTTTCG
1 GTCATTTTA-CCTTCGAGGGTATTTCA
*
18554362 GTCATTTTACCTTTCGAAGGTATTTCA
1 GTCATTTTACC-TTCGAGGGTATTTCA
* * * *
18554389 ATTATTTTACCCTTCGGGGGTATTTCG
1 GTCATTTTA-CCTTCGAGGGTATTTCA
*
18554416 GTTATTTTACCCTTCGAGGGTATTTCA
1 GTCATTTTA-CCTTCGAGGGTATTTCA
* * *
18554443 ATCAGTTTACCTTTCGGGGGTATTTC-
1 GTCATTTTACC-TTCGAGGGTATTTCA
*
18554469 GATCATTTTACCCTTCGAGGGTATTTCG
1 G-TCATTTTA-CCTTCGAGGGTATTTCA
18554497 GTCATTTTACCTTTCGAGGGTATTTCA
1 GTCATTTTACC-TTCGAGGGTATTTCA
18554524 GTCATTTTA
1 GTCATTTTA
18554533 GGCCTATTAC
Statistics
Matches: 304, Mismatches: 38, Indels: 34
0.81 0.10 0.09
Matches are distributed among these distances:
25 2 0.01
26 32 0.11
27 255 0.84
28 15 0.05
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.44
Consensus pattern (26 bp):
GTCATTTTACCTTCGAGGGTATTTCA
Found at i:18554288 original size:54 final size:54
Alignment explanation
Indices: 18554148--18554532 Score: 429
Period size: 54 Copynumber: 7.1 Consensus size: 54
18554138 GGTATAATGG
* * *
18554148 TCATTTTACCCTAC-AGGGTTATTTCAATAATTTTATCC-TTCGAGGGTATTTC-A
1 TCATTTTACCCTTCGAGGG-TATTTCAGTCATTTTA-CCTTTCGAGGGTATTTCGA
* * * *
18554201 GTCAGTTTATCC-TCGAGGGTATTTCAGTCATTTTACCTTTTGGGGGTATTTCGA
1 -TCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCTTTCGAGGGTATTTCGA
* * * *
18554255 TTATTTTACCCTTCGAGGGTATTTCGGTTATTTTACCATTCGAGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCTTTCGAGGGTATTTCGA
* * * * * * *
18554309 TCATTTTACCTTTCGAGGGTGTTTCGGTCATTTTACCCTTCAAGGGTCTTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCTTTCGAGGGTATTTCGA
* * * * * * *
18554363 TCATTTTACCTTTCGAAGGTATTTCAATTATTTTACCCTTCGGGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCTTTCGAGGGTATTTCGA
* * * *
18554417 TTATTTTACCCTTCGAGGGTATTTCAATCAGTTTACCTTTCGGGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCTTTCGAGGGTATTTCGA
*
18554471 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCTTTCGAGGGTATTTC-A
1 TCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCTTTCGAGGGTATTTCGA
18554524 GTCATTTTA
1 -TCATTTTA
18554533 GGCCTATTAC
Statistics
Matches: 283, Mismatches: 43, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
52 2 0.01
53 36 0.13
54 245 0.87
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (54 bp):
TCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCTTTCGAGGGTATTTCGA
Found at i:18554334 original size:81 final size:81
Alignment explanation
Indices: 18554148--18554532 Score: 463
Period size: 81 Copynumber: 4.8 Consensus size: 81
18554138 GGTATAATGG
* ** * * *
18554148 TCATTTTACCCTAC-AGGGTTATTTCAATAATTTTATCCTTCGAGGGTATTTCAGTCAGTTTATC
1 TCATTTTACCCTTCGAGGG-TATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTA-C
18554212 C--TCGAGGGTATTTC-A
64 CTTTCGAGGGTATTTCGA
* * * * * * *
18554227 GTCATTTTACCTTTTGGGGGTATTTCGATTATTTTACCCTTCGAGGGTATTTCGGTTATTTTACC
1 -TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACC
*
18554292 ATTCGAGGGTATTTCGA
65 TTTCGAGGGTATTTCGA
* * * * *
18554309 TCATTTTACCTTTCGAGGGTGTTTCGGTCATTTTACCCTTCAAGGGTCTTTCGGTCATTTTACCT
1 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCT
* *
18554374 TTCGAAGGTATTTCAA
66 TTCGAGGGTATTTCGA
* * * * *
18554390 TTATTTTACCCTTCGGGGGTATTTCGGTTATTTTACCCTTCGAGGGTATTTCAATCAGTTTACCT
1 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCT
*
18554455 TTCGGGGGTATTTCGA
66 TTCGAGGGTATTTCGA
*
18554471 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCTTTCGAGGGTATTTCAGTCATTTTA
1 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTA
18554533 GGCCTATTAC
Statistics
Matches: 261, Mismatches: 40, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
79 2 0.01
80 48 0.18
81 210 0.80
82 1 0.00
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (81 bp):
TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCT
TTCGAGGGTATTTCGA
Found at i:18561540 original size:30 final size:28
Alignment explanation
Indices: 18561499--18561581 Score: 87
Period size: 30 Copynumber: 2.9 Consensus size: 28
18561489 AGCAGCACAA
* *
18561499 TGTGGGTCTTAGCCCATTACAGTAACAGTG
1 TGTGGGCCTTAGCCCAATACAGTAACA--G
* *
18561529 TGTGGGCCTTAGCCCAATATAGTAATAG
1 TGTGGGCCTTAGCCCAATACAGTAACAG
*
18561557 TATGGGCCTTAGCCCAA-AGCAGTAA
1 TGTGGGCCTTAGCCCAATA-CAGTAA
18561582 TTAGAACAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 1 0.02
28 22 0.48
30 23 0.50
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAATACAGTAACAG
Found at i:18561759 original size:26 final size:26
Alignment explanation
Indices: 18561707--18561782 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 26
18561697 ACACCAATAG
* * *
18561707 CGCAACAAAGTTGCCAGTAATAATAA
1 CGCAGCAAAGTTGCCAGTAACAGTAA
18561733 CGCAGCAAAGTTGCCAGTAACAGTAA
1 CGCAGCAAAGTTGCCAGTAACAGTAA
* * *
18561759 CGTAGCAATGCTGCCAGTAACAGT
1 CGCAGCAAAGTTGCCAGTAACAGT
18561783 GTATGTGTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.18
Consensus pattern (26 bp):
CGCAGCAAAGTTGCCAGTAACAGTAA
Found at i:18562051 original size:27 final size:27
Alignment explanation
Indices: 18562014--18562336 Score: 357
Period size: 27 Copynumber: 12.0 Consensus size: 27
18562004 TAATTATAAA
* * *
18562014 CTTCGAAGGTATTTTGGTCATTTTACC
1 CTTCGAGGGTATTTCGATCATTTTACC
* ** * *
18562041 TTTTAAGGGTATTTCAATCAATTTACC
1 CTTCGAGGGTATTTCGATCATTTTACC
*
18562068 CTTCGAGGGTATTTC-AGCCATTTTACC
1 CTTCGAGGGTATTTCGA-TCATTTTACC
*
18562095 CTTCGAGGCTATTTCGATCATTTTACC
1 CTTCGAGGGTATTTCGATCATTTTACC
* * *
18562122 CTTCGAGGCTATTTCAATCATTTTACT
1 CTTCGAGGGTATTTCGATCATTTTACC
* *
18562149 CTTTGAGGGTATTTTGATCATTTTACC
1 CTTCGAGGGTATTTCGATCATTTTACC
** *
18562176 CTTTAAGGGTATTTCGGTCATTTTACC
1 CTTCGAGGGTATTTCGATCATTTTACC
18562203 CTTCGAGGGTATTTCGATCATTTTACC
1 CTTCGAGGGTATTTCGATCATTTTACC
*
18562230 CTTTG-GGAGTATTTCGATCATTTTACC
1 CTTCGAGG-GTATTTCGATCATTTTACC
*
18562257 TTTCGAGGGTATTTCGATCATTTTACC
1 CTTCGAGGGTATTTCGATCATTTTACC
* * *
18562284 CTT-TAGGGGTATTTTGGTCATTTTACC
1 CTTCGA-GGGTATTTCGATCATTTTACC
* *
18562311 CTTCGCGGGT-TTTCCGGTCATTTTAC
1 CTTCGAGGGTATTT-CGATCATTTTAC
18562337 GCCCATTACA
Statistics
Matches: 251, Mismatches: 38, Indels: 14
0.83 0.13 0.05
Matches are distributed among these distances:
26 7 0.03
27 241 0.96
28 3 0.01
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.44
Consensus pattern (27 bp):
CTTCGAGGGTATTTCGATCATTTTACC
Found at i:18562072 original size:54 final size:54
Alignment explanation
Indices: 18561975--18562336 Score: 342
Period size: 54 Copynumber: 6.7 Consensus size: 54
18561965 GGGGTATAAT
* * * ** *
18561975 GGTCATTTTACCCTATAG-GGGTATTTC-AGTAATTATAAACTTCGAAGGTATTTT
1 GGTCATTTTACCCT-TCGAGGGTATTTCGA-TCATTTTACCCTTCGAAGGTATTTC
* ** * * *
18562029 GGTCATTTTACCTTTTAAGGGTATTTCAATCAATTTACCCTTCGAGGGTATTTC
1 GGTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCGAAGGTATTTC
* * *
18562083 AGCCATTTTACCCTTCGAGGCTATTTCGATCATTTTACCCTTCG-AGGCTATTTC
1 GGTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCGAAGG-TATTTC
** * * * *
18562137 AATCATTTTACTCTTTGAGGGTATTTTGATCATTTTACCCTT-TAAGGGTATTTC
1 GGTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCGAA-GGTATTTC
* *
18562191 GGTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTTG-GGAGTATTTC
1 GGTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCGAAG-GTATTTC
* * * * *
18562245 GATCATTTTACCTTTCGAGGGTATTTCGATCATTTTACCCTT-TAGGGGTATTTT
1 GGTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCGA-AGGTATTTC
* *
18562299 GGTCATTTTACCCTTCGCGGGT-TTTCCGGTCATTTTAC
1 GGTCATTTTACCCTTCGAGGGTATTT-CGATCATTTTAC
18562337 GCCCATTACA
Statistics
Matches: 257, Mismatches: 41, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
53 7 0.03
54 245 0.95
55 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Consensus pattern (54 bp):
GGTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCGAAGGTATTTC
Found at i:18563041 original size:13 final size:13
Alignment explanation
Indices: 18563023--18563048 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18563013 AGGTTCGGCC
18563023 ATAAGAAAAGAGA
1 ATAAGAAAAGAGA
18563036 ATAAGAAAAGAGA
1 ATAAGAAAAGAGA
18563049 GTAAAAGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (13 bp):
ATAAGAAAAGAGA
Found at i:18574906 original size:16 final size:18
Alignment explanation
Indices: 18574875--18574907 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
18574865 GAATTTTATG
18574875 TTTATGTTTTGAGGGTTC
1 TTTATGTTTTGAGGGTTC
18574893 TTTAT-TTTTG-GGGTT
1 TTTATGTTTTGAGGGTT
18574908 TCGGGGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.09, C:0.03, G:0.27, T:0.61
Consensus pattern (18 bp):
TTTATGTTTTGAGGGTTC
Found at i:18576831 original size:22 final size:22
Alignment explanation
Indices: 18576801--18576852 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
18576791 AATCAGTGTT
* *
18576801 ATCAGTGGCAGTTTATCTGC-A
1 ATCAGTGGCAATTTATATGCAA
18576822 ATCCAGTGGCAATTTATATGCAA
1 AT-CAGTGGCAATTTATATGCAA
18576845 ATCAGTGG
1 ATCAGTGG
18576853 TGACTTGTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 2 0.07
22 22 0.81
23 3 0.11
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (22 bp):
ATCAGTGGCAATTTATATGCAA
Found at i:18582698 original size:6 final size:6
Alignment explanation
Indices: 18582687--18582711 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
18582677 CAGGTACCTT
18582687 AAAATG AAAATG AAAATG AAAATG A
1 AAAATG AAAATG AAAATG AAAATG A
18582712 TATAAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:18584064 original size:33 final size:33
Alignment explanation
Indices: 18584027--18584092 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
18584017 AGTATTAGTC
18584027 TGGG-CTTGAGCCCTATT-CAATAACAGTACAGTG
1 TGGGCCTT-AGCCC-ATTACAATAACAGTACAGTG
* *
18584060 TGGGCCTTAGCCCATTACAGTATCAGTACAGTG
1 TGGGCCTTAGCCCATTACAATAACAGTACAGTG
18584093 CAATAATGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 3 0.10
33 23 0.79
34 3 0.10
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (33 bp):
TGGGCCTTAGCCCATTACAATAACAGTACAGTG
Done.