Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 96 of 109
Found at i:19202003 original size:41 final size:41
Alignment explanation
Indices: 19201958--19202334 Score: 560
Period size: 41 Copynumber: 9.1 Consensus size: 41
19201948 ATGATTGTCA
19201958 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
19201999 AGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGCTTAG
1 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
* *
19202041 AGGAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
19202082 AGGAGCAATTTACTTTCCAAAGTTTCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG--TCGTGGTGCCTCTGTTTAG
*
19202123 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
19202164 AGGAGCCATTTACTTTTCAAAGTTGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
19202205 AGGAGCAATTTATTTTTTAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
19202246 AGGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTTTGTTTAG
1 AGGAGCAATTTAC-TTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * * * *
19202288 AGGAGCAATTTATTTTTCAAAGTCATTGAGCCTCTGCTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
19202329 AAGAGC
1 AGGAGC
19202335 TTTGGTAAAA
Statistics
Matches: 306, Mismatches: 24, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
39 4 0.01
41 222 0.73
42 77 0.25
43 3 0.01
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:19202347 original size:1 final size:1
Alignment explanation
Indices: 19202341--19202397 Score: 60
Period size: 1 Copynumber: 57.0 Consensus size: 1
19202331 GAGCTTTGGT
* * * ** *
19202341 AAAAAAAAAAAAACAAAAAAATAAAAAAATAAAAAAAACCAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19202398 CATAAAATGA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.89, C:0.07, G:0.00, T:0.04
Consensus pattern (1 bp):
A
Found at i:19202404 original size:10 final size:9
Alignment explanation
Indices: 19202341--19202404 Score: 71
Period size: 9 Copynumber: 7.3 Consensus size: 9
19202331 GAGCTTTGGT
19202341 AAAAA-AAA
1 AAAAACAAA
19202349 AAAAACAAA
1 AAAAACAAA
19202358 AAAATA-AAA
1 AAAA-ACAAA
*
19202367 AAATA-AAA
1 AAAAACAAA
*
19202375 AAAACCAAA
1 AAAAACAAA
19202384 AAAAACAAA
1 AAAAACAAA
*
19202393 AAAAACATA
1 AAAAACAAA
19202402 AAA
1 AAA
19202405 TGAAAATGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
8 12 0.25
9 35 0.73
10 1 0.02
ACGTcount: A:0.88, C:0.08, G:0.00, T:0.05
Consensus pattern (9 bp):
AAAAACAAA
Found at i:19202576 original size:6 final size:6
Alignment explanation
Indices: 19202565--19202599 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
19202555 TATCTTTGTC
19202565 ATTTTT ATTTTT ATTTTT A-TTTT ATTTTAT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT-T ATTTT
19202600 ATGTATATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:19202587 original size:11 final size:11
Alignment explanation
Indices: 19202565--19202688 Score: 58
Period size: 11 Copynumber: 10.9 Consensus size: 11
19202555 TATCTTTGTC
19202565 ATTTTTATTTTT
1 ATTTTTA-TTTT
19202577 ATTTTTATTTT
1 ATTTTTATTTT
19202588 ATTTTATATTTT
1 ATTTT-TATTTT
* * **
19202600 ATGTATATCCT
1 ATTTTTATTTT
19202611 ATGTATTTATTATT
1 AT-T-TTTATT-TT
*
19202625 -TATTTATTATT
1 ATTTTTATT-TT
* ** *
19202636 ACTAATA-TAT
1 ATTTTTATTTT
*
19202646 ATTTTTATTAT
1 ATTTTTATTTT
19202657 -TTTTTATTTT
1 ATTTTTATTTT
19202667 ATTTATT-TTTGT
1 ATTT-TTATTT-T
19202679 ATTTTTATTT
1 ATTTTTATTT
19202689 ATCTAATTAT
Statistics
Matches: 84, Mismatches: 18, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
10 14 0.17
11 36 0.43
12 28 0.33
13 5 0.06
14 1 0.01
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:19202731 original size:28 final size:27
Alignment explanation
Indices: 19202695--19202750 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
19202685 ATTTATCTAA
*
19202695 TTATATATCTGATATTATTATTATTATT
1 TTATATATCTGATAATATT-TTATTATT
* * *
19202723 TTATTTATCTTATAATATTTTTTTATT
1 TTATATATCTGATAATATTTTATTATT
19202750 T
1 T
19202751 ATCTTTTCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.66
Consensus pattern (27 bp):
TTATATATCTGATAATATTTTATTATT
Found at i:19203662 original size:15 final size:15
Alignment explanation
Indices: 19203604--19203672 Score: 61
Period size: 16 Copynumber: 4.4 Consensus size: 15
19203594 TTATTTAATA
19203604 TTTTTTTATCTTTAT
1 TTTTTTTATCTTTAT
*
19203619 CTTATTTTTAT-TTTGGT
1 -TT-TTTTTATCTTT-AT
*
19203636 TTTACTTT-TCTTTAT
1 TTT-TTTTATCTTTAT
19203651 TTTTTTTATCTTTAT
1 TTTTTTTATCTTTAT
19203666 TTATTTT
1 TT-TTTT
19203673 CACTTTTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
14 3 0.07
15 15 0.35
16 17 0.40
17 8 0.19
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTTTTTATCTTTAT
Found at i:19203692 original size:22 final size:22
Alignment explanation
Indices: 19203654--19203695 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
19203644 TCTTTATTTT
19203654 TTTTATCTTTATTTATTTTCAC
1 TTTTATCTTTATTTATTTTCAC
*
19203676 TTTTAT-TTTGTTCTATTTTC
1 TTTTATCTTTATT-TATTTTC
19203696 TTTAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTATCTTTATTTATTTTCAC
Found at i:19203918 original size:62 final size:60
Alignment explanation
Indices: 19203710--19204117 Score: 299
Period size: 59 Copynumber: 6.7 Consensus size: 60
19203700 AATAAAAATC
* * *
19203710 AAAAA-ATATTTTTG-GGAAAAAGTTAAAAGTATCAATTTTCCTTAAAAAT-AAATTTTC--
1 AAAAATATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTTCTT-AAAATCAAAATTTCAA
* ***
19203767 AAAAA-ATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTTTG
1 AAAAATATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTTCTT-AAAATCAAAATTTCAA
* * * *
19203827 AAAAATAT-TTTTAGA-GAAAAGTTGAAAGTATCAGTTTTTCTTGGAAATCAAAGTTTCAAA
1 AAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT-AAAATCAAAATTTC-AA
*
19203887 AAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT--AAATTTCCAA
1 AAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTA-AAATCAAAATTT-CAA
* *
19203947 AAAAATAT-TTTTTTAGGAAAAGTTGAAAAGCTAAATCAATTTTTCTTAAAATAATAAAATTTCA
1 AAAAATATATTTTTGAGGAAAAGTTG-AAAG-T--ATCAATTTTTCTTAAAAT--CAAAATTTCA
19204011 A
60 A
*** * ** * * *
19204012 AAAAA-GGGTTTTTGAGAAAAAGTTGAAAAGTATCTGTGTGTTT-TTGAAATCAGAGTTTCAA
1 AAAAATATATTTTTGAGGAAAAGTTG-AAAGTATCAAT-T-TTTCTTAAAATCAAAATTTCAA
19204073 AAAAA-ATATATTTTG-GGAGAAAGTTGCGAAAGTTATCAATTTTTC
1 AAAAATATAT-TTTTGAGGA-AAAGTT--GAAAG-TATCAATTTTTC
19204118 CTTACACGAA
Statistics
Matches: 289, Mismatches: 35, Indels: 48
0.78 0.09 0.13
Matches are distributed among these distances:
57 47 0.16
58 6 0.02
59 52 0.18
60 38 0.13
61 26 0.09
62 51 0.18
63 25 0.09
64 10 0.03
65 28 0.10
66 6 0.02
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.36
Consensus pattern (60 bp):
AAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAATCAAAATTTCAA
Found at i:19207279 original size:23 final size:25
Alignment explanation
Indices: 19207249--19207294 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
19207239 TGTTGCGCTT
*
19207249 GAAGCAATA-ATCACAA-CAATACA
1 GAAGCAATAGATAACAATCAATACA
19207272 GAAGCAATAGATAACAATCAATA
1 GAAGCAATAGATAACAATCAATA
19207295 ATCAAATACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 6 0.30
25 5 0.25
ACGTcount: A:0.57, C:0.17, G:0.11, T:0.15
Consensus pattern (25 bp):
GAAGCAATAGATAACAATCAATACA
Found at i:19209024 original size:25 final size:27
Alignment explanation
Indices: 19208969--19209025 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
19208959 TTAATGATTC
*
19208969 ATTGAAAGATAATATAATTAGTAATTC
1 ATTGAAAGATAATATAATTAGTAATTA
*
19208996 ATTGAAA-AT-ATATAATATA-TTATTA
1 ATTGAAAGATAATATAAT-TAGTAATTA
19209021 ATTGA
1 ATTGA
19209026 CCCCTCAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 16 0.59
26 4 0.15
27 7 0.26
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (27 bp):
ATTGAAAGATAATATAATTAGTAATTA
Found at i:19209850 original size:83 final size:82
Alignment explanation
Indices: 19209741--19209930 Score: 317
Period size: 83 Copynumber: 2.3 Consensus size: 82
19209731 ATGAATAGTC
* * * *
19209741 AGAGCTTTCTAGTCTCTTTTCGCAGAGTGATGACATAGAGATTGCATAGTTATACGGTTTCCATA
1 AGAGCTTTCTAGTCTATTTTCTCAGAGTGATGACATAGAGATTGCATAGTTAGACGGCTTCCATA
19209806 TGTCCCAATGGTTGGTA
66 TGTCCCAATGGTTGGTA
*
19209823 AGAGCCTTTCTAGTCTATTTTATCAGAGTGATGACATAGAGATTGCATAGTTAGACGGCTTCCAT
1 AGAG-CTTTCTAGTCTATTTTCTCAGAGTGATGACATAGAGATTGCATAGTTAGACGGCTTCCAT
19209888 ATGTCCCAATGGTTGGTA
65 ATGTCCCAATGGTTGGTA
*
19209906 AGAGCTTTCTAATCTATTTTCTCAG
1 AGAGCTTTCTAGTCTATTTTCTCAG
19209931 TGAAATCCAA
Statistics
Matches: 100, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
82 23 0.23
83 77 0.77
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (82 bp):
AGAGCTTTCTAGTCTATTTTCTCAGAGTGATGACATAGAGATTGCATAGTTAGACGGCTTCCATA
TGTCCCAATGGTTGGTA
Found at i:19211906 original size:27 final size:28
Alignment explanation
Indices: 19211876--19211939 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
19211866 AAATATTAAT
19211876 AAAATTATATGTAAT-TTTAATAAATTA
1 AAAATTATATGTAATATTTAATAAATTA
* * *
19211903 AAAA-TATATTTTATATTTAATATATTA
1 AAAATTATATGTAATATTTAATAAATTA
19211930 ATATAATTAT
1 A-A-AATTAT
19211940 TATTCAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 8 0.27
27 16 0.53
28 1 0.03
29 2 0.07
30 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
AAAATTATATGTAATATTTAATAAATTA
Found at i:19211910 original size:26 final size:27
Alignment explanation
Indices: 19211875--19211930 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
19211865 AAAATATTAA
*
19211875 TAAAATTATATGTAAT-TTTAATAAAT
1 TAAAAATATATGTAATATTTAATAAAT
* * *
19211901 TAAAAATATATTTTATATTTAATATAT
1 TAAAAATATATGTAATATTTAATAAAT
19211928 TAA
1 TAA
19211931 TATAATTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
TAAAAATATATGTAATATTTAATAAAT
Found at i:19214328 original size:2 final size:2
Alignment explanation
Indices: 19214321--19214372 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
19214311 CAAACTTGTT
19214321 TA TA TA TA T- TA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19214360 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
19214373 TAGATTTGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 44 0.94
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19221663 original size:60 final size:60
Alignment explanation
Indices: 19221599--19221932 Score: 229
Period size: 62 Copynumber: 5.5 Consensus size: 60
19221589 TCTTTTTTTT
* * *
19221599 AAATTTAAACCTTTCGATATGTTGGTGAGACTCATTTTTTATTCATAAATTTATTTTTAA
1 AAATTTAAACCTTTCAATATGTTGGTAAGACTTATTTTTTATTCATAAATTTATTTTTAA
* * * * ** *
19221659 AAATTTAAACCTTCCAATATCCTT-ATAAGATTTATTCATTATTCAAAAAATTGT-TTTTTAA
1 AAATTTAAACCTTTCAATAT-GTTGGTAAGACTTATTTTTTATTC-ATAAATT-TATTTTTAA
* * *
19221720 GAAATTTAAACC-TTCTAATATGTTGGTAAGGCTTATCTTTCTATT-TTGAAATTTCATTTTTAA
1 -AAATTTAAACCTTTC-AATATGTTGGTAAGACTTAT-TTTTTATTCAT-AAATTT-ATTTTTAA
* ** ** * * * *
19221783 AAATTTAAACCTTTTAATATGTTGGTAAGGTTTATTCATTATTCAAAAAGTAATTTTTTAG
1 AAATTTAAACCTTTCAATATGTTGGTAAGACTTATTTTTTATTCATAAATTTA-TTTTTAA
** *
19221844 AAATTTAAACCTTT---TA-GTTGGTAAGGTTTATTTCTTTATTTGGA-AAATTTATTTTTTAA
1 AAATTTAAACCTTTCAATATGTTGGTAAGACTTATTT-TTTA-TT-CATAAATTTA-TTTTTAA
*
19221903 AATATTTAAACC-TTCTAATATATTGGTAAG
1 AA-ATTTAAACCTTTC-AATATGTTGGTAAG
19221933 TTTTATTTGT
Statistics
Matches: 215, Mismatches: 37, Indels: 40
0.74 0.13 0.14
Matches are distributed among these distances:
57 16 0.07
58 5 0.02
59 18 0.08
60 43 0.20
61 49 0.23
62 60 0.28
63 16 0.07
64 8 0.04
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (60 bp):
AAATTTAAACCTTTCAATATGTTGGTAAGACTTATTTTTTATTCATAAATTTATTTTTAA
Found at i:19221817 original size:124 final size:119
Alignment explanation
Indices: 19221645--19221939 Score: 362
Period size: 124 Copynumber: 2.4 Consensus size: 119
19221635 TTTTATTCAT
* * *
19221645 AAATTTATTTTTAAAAATTTAAACCTTCCAATATCCTT-ATAAGATTTATTCATTATTCAAAAAA
1 AAATTTATTTTTAAAAATTTAAACCTTCTAATAT-ATTGGTAAGATTTATTCATTATTCAAAAAA
** *
19221709 TTGTTTTTTAAGAAATTTAAACCTTCTAATATGTTGGTAAGGCTTATCTT-TCTATTTTG-
65 TAATTTTTT-AGAAATTTAAACCTT-T--TA-GTTGGTAAGGCTTAT-TTCTCTATTTGGA
* * * *
19221768 AAATTTCATTTTTAAAAATTTAAACCTTTTAATATGTTGGTAAGGTTTATTCATTATTCAAAAAG
1 AAATTT-ATTTTTAAAAATTTAAACCTTCTAATATATTGGTAAGATTTATTCATTATTCAAAAAA
* *
19221833 TAATTTTTTAGAAATTTAAACCTTTTAGTTGGTAAGGTTTATTTCTTTATTTGGA
65 TAATTTTTTAGAAATTTAAACCTTTTAGTTGGTAAGGCTTATTTCTCTATTTGGA
*
19221888 AAATTTATTTTTTAAAATATTTAAACCTTCTAATATATTGGTAAGTTTTATT
1 AAATTTA-TTTTTAAAA-ATTTAAACCTTCTAATATATTGGTAAGATTTATT
19221940 TGTCTAAAAA
Statistics
Matches: 152, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
118 2 0.01
119 22 0.14
120 17 0.11
121 31 0.20
122 1 0.01
123 23 0.15
124 56 0.37
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.48
Consensus pattern (119 bp):
AAATTTATTTTTAAAAATTTAAACCTTCTAATATATTGGTAAGATTTATTCATTATTCAAAAAAT
AATTTTTTAGAAATTTAAACCTTTTAGTTGGTAAGGCTTATTTCTCTATTTGGA
Found at i:19222007 original size:12 final size:12
Alignment explanation
Indices: 19221989--19222029 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
19221979 ATATTTATCG
*
19221989 ATAAACAAATAC
1 ATAAACAAATAA
* *
19222001 GTAAACAAACAA
1 ATAAACAAATAA
19222013 ATAAACAAATAA
1 ATAAACAAATAA
19222025 ATAAA
1 ATAAA
19222030 TAAACTAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.71, C:0.12, G:0.02, T:0.15
Consensus pattern (12 bp):
ATAAACAAATAA
Found at i:19222020 original size:8 final size:8
Alignment explanation
Indices: 19222007--19222044 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
19221997 ATACGTAAAC
19222007 AAACAAAT
1 AAACAAAT
19222015 AAACAAAT
1 AAACAAAT
*
19222023 AAATAAAT
1 AAACAAAT
*
19222031 AAACTAA-
1 AAACAAAT
19222038 AAACAAA
1 AAACAAA
19222045 AGAAATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.13
Consensus pattern (8 bp):
AAACAAAT
Found at i:19222029 original size:24 final size:24
Alignment explanation
Indices: 19221989--19222053 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
19221979 ATATTTATCG
**
19221989 ATAAACAAATACGTAAACAAACAA
1 ATAAACAAATAAATAAACAAACAA
* *
19222013 ATAAACAAATAAATAAATAAACTA
1 ATAAACAAATAAATAAACAAACAA
*
19222037 A-AAACAAAAGAAATAAA
1 ATAAAC-AAATAAATAAA
19222054 TAATTAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 4 0.11
24 31 0.89
ACGTcount: A:0.72, C:0.11, G:0.03, T:0.14
Consensus pattern (24 bp):
ATAAACAAATAAATAAACAAACAA
Found at i:19222073 original size:28 final size:27
Alignment explanation
Indices: 19222002--19222072 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
19221992 AACAAATACG
*
19222002 TAAACAAACAA-ATAAACAAATAAATAAA
1 TAAACAAA-AACA-AAAGAAATAAATAAA
*
19222030 TAAACTAAAAACAAAAGAAATAAATAAT
1 TAAAC-AAAAACAAAAGAAATAAATAAA
19222058 TAAA-AAAATACAAAA
1 TAAACAAAA-ACAAAA
19222073 AATGCGGCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 4 0.11
27 6 0.16
28 24 0.63
29 4 0.11
ACGTcount: A:0.75, C:0.08, G:0.01, T:0.15
Consensus pattern (27 bp):
TAAACAAAAACAAAAGAAATAAATAAA
Found at i:19222855 original size:2 final size:2
Alignment explanation
Indices: 19222848--19222877 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19222838 CAATTTGCTT
19222848 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19222878 ACAAATAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19224673 original size:61 final size:62
Alignment explanation
Indices: 19224573--19224705 Score: 162
Period size: 61 Copynumber: 2.2 Consensus size: 62
19224563 TAAAAAACGC
** * * * **
19224573 CTTAAATAATCCTTTAAAAGAATTGAATGAGATTATTTAAGATATTTTTTGGCAAAAAATAT
1 CTTAAATAATCCCCTAAAAGAATTGAATCAGATTATTTAAGACATTTTCTAACAAAAAATAT
* *
19224635 CTTAAATAATCCCCTAAAA-AATTG-ATCAGTATTATTTAAGACATTTTCTAACCATAAATAT
1 CTTAAATAATCCCCTAAAAGAATTGAATCAG-ATTATTTAAGACATTTTCTAACAAAAAATAT
19224696 CTTAAATAAT
1 CTTAAATAAT
19224706 GTTGATCCAT
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
60 4 0.07
61 40 0.66
62 17 0.28
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.38
Consensus pattern (62 bp):
CTTAAATAATCCCCTAAAAGAATTGAATCAGATTATTTAAGACATTTTCTAACAAAAAATAT
Found at i:19230315 original size:2 final size:2
Alignment explanation
Indices: 19230308--19230338 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19230298 ATAGGTTTAA
19230308 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19230339 GAGTCGATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19233036 original size:5 final size:5
Alignment explanation
Indices: 19233026--19233052 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
19233016 CCTCAGACCC
19233026 TTTCT TTTCT TTTCT TTTCT TTTCT TT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TT
19233053 CATCATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:19238890 original size:28 final size:26
Alignment explanation
Indices: 19238850--19238913 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 26
19238840 CTTTAACAAA
* *
19238850 ATTTTTTTTATTTTCTGTTTTGATTTTG
1 ATTTTATTTATTTTATG--TTGATTTTG
*
19238878 ATTTTATTTATTTTATGTTGATTTTT
1 ATTTTATTTATTTTATGTTGATTTTG
19238904 ATTTTTATTT
1 A-TTTTATTT
19238914 GTTGGTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 9 0.28
27 8 0.25
28 15 0.47
ACGTcount: A:0.16, C:0.02, G:0.08, T:0.75
Consensus pattern (26 bp):
ATTTTATTTATTTTATGTTGATTTTG
Found at i:19238891 original size:21 final size:21
Alignment explanation
Indices: 19238875--19238929 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
19238865 TGTTTTGATT
19238875 TTGA-TTTTATTTATTTTATG
1 TTGATTTTTATTTATTTTATG
19238895 TTGATTTTTATTT-TTATT-TG
1 TTGATTTTTATTTATT-TTATG
* *
19238915 TTGGTTTTTTTTTAT
1 TTGATTTTTATTTAT
19238930 GATGATGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.15, C:0.00, G:0.11, T:0.75
Consensus pattern (21 bp):
TTGATTTTTATTTATTTTATG
Found at i:19238906 original size:17 final size:17
Alignment explanation
Indices: 19238884--19238935 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
19238874 TTTGATTTTA
19238884 TTTATTTTATGTTGATT
1 TTTATTTTATGTTGATT
*
19238901 TTTATTTTTATTTGTTGGTT
1 TTTA-TTTTA--TGTTGATT
*
19238921 TTT-TTTTATGATGAT
1 TTTATTTTATGTTGAT
19238936 GATGATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 5 0.17
17 4 0.14
18 10 0.34
20 10 0.34
ACGTcount: A:0.15, C:0.00, G:0.13, T:0.71
Consensus pattern (17 bp):
TTTATTTTATGTTGATT
Found at i:19238947 original size:3 final size:3
Alignment explanation
Indices: 19238941--19238967 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
19238931 ATGATGATGA
19238941 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
19238968 GCTATTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:19239521 original size:20 final size:20
Alignment explanation
Indices: 19239485--19239543 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
19239475 TATTCATTTA
*
19239485 AATAATAAAAAAGATTAAAAT
1 AATAACAAAAAA-ATTAAAAT
19239506 AATAACAAAAAAATTAAAAT
1 AATAACAAAAAAATTAAAAT
* *
19239526 AATCACAATAACAATTAA
1 AATAACAA-AAAAATTAA
19239544 TTAATTAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.22
Consensus pattern (20 bp):
AATAACAAAAAAATTAAAAT
Found at i:19251465 original size:36 final size:35
Alignment explanation
Indices: 19251424--19251523 Score: 92
Period size: 37 Copynumber: 2.7 Consensus size: 35
19251414 GATTTTTAAA
*
19251424 TTTAAAGTTTCGTTACCTTTGGTCAGAAGAGATTTC
1 TTTAAAGTATC-TTACCTTTGGTCAGAAGAGATTTC
* * ** *
19251460 TTTAAAAGTATCATAGCCTATACTCAGAAGAGCTTTC
1 TTT-AAAGTATCTTA-CCTTTGGTCAGAAGAGATTTC
* *
19251497 TTTAAAGTATCATTGCTTTTGGTCAGA
1 TTTAAAGTATC-TTACCTTTGGTCAGA
19251524 TGAGCCATTT
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
36 21 0.43
37 28 0.57
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (35 bp):
TTTAAAGTATCTTACCTTTGGTCAGAAGAGATTTC
Found at i:19251777 original size:40 final size:40
Alignment explanation
Indices: 19251732--19251912 Score: 202
Period size: 40 Copynumber: 4.5 Consensus size: 40
19251722 GAAACTTTCT
*
19251732 TTTAAAGTTTCATAGCCTCTAGTCAGATGAGCCTTTTAAA
1 TTTAAAGTTTTATAGCCTCTAGTCAGATGAGCCTTTTAAA
* *
19251772 TTTAAAGTTTTATAGCCTCTGGTTAGA-GAAGCCTTTTAAA
1 TTTAAAGTTTTATAGCCTCTAGTCAGATG-AGCCTTTTAAA
* * *
19251812 TTTAAAGTTTTATAACCTCTAGTTAGATGAGCCTTTTGAA
1 TTTAAAGTTTTATAGCCTCTAGTCAGATGAGCCTTTTAAA
* * * * * * **
19251852 TTTAAAGTTTTGTTGCTTTTGGTCAGAGGAATCTTTTAAA
1 TTTAAAGTTTTATAGCCTCTAGTCAGATGAGCCTTTTAAA
* *
19251892 TTTAAAATTTCATAGCCTCTA
1 TTTAAAGTTTTATAGCCTCTA
19251913 ATCATAAGAG
Statistics
Matches: 115, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
39 1 0.01
40 113 0.98
41 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (40 bp):
TTTAAAGTTTTATAGCCTCTAGTCAGATGAGCCTTTTAAA
Found at i:19251831 original size:80 final size:80
Alignment explanation
Indices: 19251732--19251912 Score: 247
Period size: 80 Copynumber: 2.3 Consensus size: 80
19251722 GAAACTTTCT
*
19251732 TTTAAAGTTTCATAGCCTCTAGTCAGATGAGCCTTTTAAATTTAAAGTTTTATAGCCTCTGGTTA
1 TTTAAAGTTTCATAGCCTCTAGTCAGATGAGCCTTTTAAATTTAAAGTTTTATAGCCTCTGGTCA
19251797 GA-GAAGCCTTTTAAA
66 GAGGAA-CCTTTTAAA
* * * * * * * *
19251812 TTTAAAGTTTTATAACCTCTAGTTAGATGAGCCTTTTGAATTTAAAGTTTTGTTGCTTTTGGTCA
1 TTTAAAGTTTCATAGCCTCTAGTCAGATGAGCCTTTTAAATTTAAAGTTTTATAGCCTCTGGTCA
*
19251877 GAGGAATCTTTTAAA
66 GAGGAACCTTTTAAA
*
19251892 TTTAAAATTTCATAGCCTCTA
1 TTTAAAGTTTCATAGCCTCTA
19251913 ATCATAAGAG
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
80 84 0.97
81 3 0.03
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (80 bp):
TTTAAAGTTTCATAGCCTCTAGTCAGATGAGCCTTTTAAATTTAAAGTTTTATAGCCTCTGGTCA
GAGGAACCTTTTAAA
Found at i:19253094 original size:12 final size:13
Alignment explanation
Indices: 19253073--19253101 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
19253063 GTTTAGCAGG
19253073 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
19253086 TTTTC-TTTTTCT
1 TTTTCTTTTTTCT
19253098 TTTT
1 TTTT
19253102 ATTTCTAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTCTTTTTTCT
Found at i:19253139 original size:26 final size:29
Alignment explanation
Indices: 19253099--19253159 Score: 101
Period size: 27 Copynumber: 2.2 Consensus size: 29
19253089 TCTTTTTCTT
19253099 TTTATTTCTAGTGTTGATTTTTA-TTTTA
1 TTTATTTCTAGTGTTGATTTTTATTTTTA
19253127 TTTATTT-TA-TGTTGATTTTTATTTTTA
1 TTTATTTCTAGTGTTGATTTTTATTTTTA
19253154 TTTATT
1 TTTATT
19253160 GTTGATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 12 0.38
27 13 0.41
28 7 0.22
ACGTcount: A:0.18, C:0.02, G:0.08, T:0.72
Consensus pattern (29 bp):
TTTATTTCTAGTGTTGATTTTTATTTTTA
Found at i:19253162 original size:23 final size:23
Alignment explanation
Indices: 19253091--19253169 Score: 79
Period size: 23 Copynumber: 3.2 Consensus size: 23
19253081 TTTCTTTTTC
* *
19253091 TTTTTCTTTTTATTTCTAGTGTTGA
1 TTTTTATTTTTA-TT-TATTGTTGA
19253116 TTTTTA-TTTTATTTATTTTATGTTGA
1 TTTTTATTTTTATTTA---T-TGTTGA
19253142 TTTTTATTTTTATTTATTGTTGA
1 TTTTTATTTTTATTTATTGTTGA
19253165 TTTTT
1 TTTTT
19253170 TTTATGATGA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
22 2 0.04
23 13 0.28
24 6 0.13
25 5 0.11
26 12 0.26
27 9 0.19
ACGTcount: A:0.15, C:0.03, G:0.09, T:0.73
Consensus pattern (23 bp):
TTTTTATTTTTATTTATTGTTGA
Found at i:19253179 original size:3 final size:3
Alignment explanation
Indices: 19253173--19253201 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19253163 GATTTTTTTT
19253173 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
19253202 ATTATTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:19253207 original size:3 final size:3
Alignment explanation
Indices: 19253201--19253235 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
19253191 ATGATGATGA
19253201 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
19253236 ATTTTTTAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:19253763 original size:20 final size:20
Alignment explanation
Indices: 19253740--19253788 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
19253730 TAATAAATAG
19253740 TAAATAATAACAAAAAAAAT
1 TAAATAATAACAAAAAAAAT
* *
19253760 TAAAATAATCACAATAAAAAT
1 T-AAATAATAACAAAAAAAAT
*
19253781 TAATTAAT
1 TAAATAAT
19253789 TAATTAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (20 bp):
TAAATAATAACAAAAAAAAT
Found at i:19253792 original size:24 final size:21
Alignment explanation
Indices: 19253741--19253783 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
19253731 AATAAATAGT
19253741 AAATAATAACAAAAAAAATTA
1 AAATAATAACAAAAAAAATTA
* *
19253762 AAATAATCACAATAAAAATTA
1 AAATAATAACAAAAAAAATTA
19253783 A
1 A
19253784 TTAATTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (21 bp):
AAATAATAACAAAAAAAATTA
Found at i:19261764 original size:61 final size:61
Alignment explanation
Indices: 19261669--19261787 Score: 193
Period size: 61 Copynumber: 2.0 Consensus size: 61
19261659 GGTGGATAAA
* * *
19261669 ATATTTTTTATTTTTATTATTAGATTTTTATATTATATTAATCTCGTATTCATAATTAATG
1 ATATTTTTAATTTTTATTATTAAATTTTTATATTATATTAATCTCATATTCATAATTAATG
* *
19261730 ATATTTTTAATTTTTATTATTAAATTTTTATATTATATTTATCTCATATTCTTAATTA
1 ATATTTTTAATTTTTATTATTAAATTTTTATATTATATTAATCTCATATTCATAATTA
19261788 TTGAATACTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (61 bp):
ATATTTTTAATTTTTATTATTAAATTTTTATATTATATTAATCTCATATTCATAATTAATG
Found at i:19265414 original size:23 final size:23
Alignment explanation
Indices: 19265384--19265428 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
19265374 TTTGCATTAG
19265384 AAAGTTTTTTTACTTGATTCTTA
1 AAAGTTTTTTTACTTGATTCTTA
*
19265407 AAAGTTTTTTTCCTTGATTCTT
1 AAAGTTTTTTTACTTGATTCTT
19265429 GCCCGAGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.58
Consensus pattern (23 bp):
AAAGTTTTTTTACTTGATTCTTA
Found at i:19266879 original size:3 final size:3
Alignment explanation
Indices: 19266871--19266898 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
19266861 TTTATAGCCA
19266871 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
19266899 TCCAAATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19275412 original size:25 final size:26
Alignment explanation
Indices: 19275364--19275414 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
19275354 GTAACTTATT
*
19275364 TGTGGAAAAACTAAGAAATTAAACTG
1 TGTGGAAAAACTAAGAAATAAAACTG
19275390 TGTGG-AAAACTAAGAGAA-AAAACTG
1 TGTGGAAAAACTAAGA-AATAAAACTG
19275415 AATGTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.51, C:0.08, G:0.22, T:0.20
Consensus pattern (26 bp):
TGTGGAAAAACTAAGAAATAAAACTG
Found at i:19275583 original size:22 final size:22
Alignment explanation
Indices: 19275558--19275600 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
19275548 TTTTTTGTCA
*
19275558 TTAATTCTAGGGATACAAATAC
1 TTAATTCTAGAGATACAAATAC
19275580 TTAATTCTAGAGATACAAATA
1 TTAATTCTAGAGATACAAATA
19275601 TAAATATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (22 bp):
TTAATTCTAGAGATACAAATAC
Found at i:19284155 original size:18 final size:18
Alignment explanation
Indices: 19284107--19284158 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
19284097 TTTAATGTCA
*
19284107 ATATAAAAAAT-AATATG
1 ATATAAAAAATAAAAATG
* *
19284124 ATAATATAATATAAAAATG
1 AT-ATAAAAAATAAAAATG
19284143 ATATAAAAAATAAAAA
1 ATATAAAAAATAAAAA
19284159 ATGACACGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 2 0.07
18 19 0.68
19 7 0.25
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (18 bp):
ATATAAAAAATAAAAATG
Found at i:19285913 original size:22 final size:22
Alignment explanation
Indices: 19285885--19285943 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 22
19285875 CTCAAAATTA
*
19285885 ATAAAATATTATTTTTTTAGAT
1 ATAAAATATTATTTTTTTAAAT
19285907 ATAAAATATTATTTTTTTAAAT
1 ATAAAATATTATTTTTTTAAAT
*
19285929 ATAAATATATAATTT
1 ATAAA-ATATTATTT
19285944 AAAATTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 26 0.76
23 8 0.24
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATAAAATATTATTTTTTTAAAT
Found at i:19293459 original size:3 final size:3
Alignment explanation
Indices: 19293444--19293494 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
19293434 TTATATATAG
*
19293444 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19293492 ATT
1 ATT
19293495 TGAAATTAGC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:19295810 original size:20 final size:21
Alignment explanation
Indices: 19295779--19295819 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
19295769 AAAACTTCAT
19295779 AATTTTTAATATAAAAAATAA
1 AATTTTTAATATAAAAAATAA
*
19295800 AATTTTT-ATATTAAAAATAA
1 AATTTTTAATATAAAAAATAA
19295820 CATAATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATTTTTAATATAAAAAATAA
Found at i:19298483 original size:10 final size:10
Alignment explanation
Indices: 19298470--19298522 Score: 63
Period size: 10 Copynumber: 5.4 Consensus size: 10
19298460 TTCTCTGTTT
19298470 TTTTATCTTA
1 TTTTATCTTA
*
19298480 TTTTATGTTA
1 TTTTATCTTA
* *
19298490 TTTT-TTTTT
1 TTTTATCTTA
19298499 TTTTATCTTA
1 TTTTATCTTA
*
19298509 TTTTATGTTA
1 TTTTATCTTA
19298519 TTTT
1 TTTT
19298523 TTTAAATGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
9 7 0.19
10 29 0.81
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (10 bp):
TTTTATCTTA
Found at i:19298485 original size:5 final size:5
Alignment explanation
Indices: 19298470--19298522 Score: 54
Period size: 5 Copynumber: 10.8 Consensus size: 5
19298460 TTCTCTGTTT
* * * * *
19298470 TTTTA TCTTA TTTTA TGTTA TTTT- TTTTT TTTTA TCTTA TTTTA TGTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
19298519 TTTT
1 TTTT
19298523 TTTAAATGCA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
4 4 0.11
5 34 0.89
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:19298525 original size:29 final size:29
Alignment explanation
Indices: 19298438--19298525 Score: 126
Period size: 29 Copynumber: 3.0 Consensus size: 29
19298428 ATTATTAATA
*
19298438 TTTTTTAT-TT-TTATATGTTATTTTCTCTGT
1 TTTTTTATCTTATTTTATGTTATTTT-T-T-T
19298468 TTTTTTATCTTATTTTATGTTATTTTTTT
1 TTTTTTATCTTATTTTATGTTATTTTTTT
19298497 TTTTTTATCTTATTTTATGTTATTTTTTT
1 TTTTTTATCTTATTTTATGTTATTTTTTT
19298526 AAATGCAATT
Statistics
Matches: 55, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
29 30 0.55
30 9 0.16
31 3 0.05
32 13 0.24
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.77
Consensus pattern (29 bp):
TTTTTTATCTTATTTTATGTTATTTTTTT
Found at i:19304792 original size:20 final size:20
Alignment explanation
Indices: 19304767--19304806 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19304757 CATATCTTTG
19304767 AAGTAAACTACAAAG-TAAAA
1 AAGTAAA-TACAAAGCTAAAA
*
19304787 AAGTAAATGCAAAGCTAAAA
1 AAGTAAATACAAAGCTAAAA
19304807 CTCTAAGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.15
Consensus pattern (20 bp):
AAGTAAATACAAAGCTAAAA
Found at i:19313422 original size:2 final size:2
Alignment explanation
Indices: 19313415--19313463 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
19313405 AAGATTACAT
* *
19313415 TC TC TC TC TC TC TC TC TC TC TC TC TC T- TC TT TC T- TC TC AC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19313455 TC TC TC TC T
1 TC TC TC TC T
19313464 TAGATTGCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.02, C:0.45, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:19318153 original size:11 final size:11
Alignment explanation
Indices: 19318135--19318173 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
19318125 TATATAAATT
19318135 AATATATTTAA
1 AATATATTTAA
** *
19318146 TTTATATTGAA
1 AATATATTTAA
19318157 AATATATTTAA
1 AATATATTTAA
19318168 AATATA
1 AATATA
19318174 ACATAAAATA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
AATATATTTAA
Found at i:19320417 original size:21 final size:22
Alignment explanation
Indices: 19320393--19320449 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
19320383 TTTTTTGTAT
*
19320393 ATAAAATTATAATAAG-ATAAG
1 ATAAAATTATAATAAGAATAAA
* *
19320414 ATAAAATGATAATATGAATAAA
1 ATAAAATTATAATAAGAATAAA
*
19320436 ATTAAATTA-AATAA
1 ATAAAATTATAATAA
19320450 TATCATCTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (22 bp):
ATAAAATTATAATAAGAATAAA
Found at i:19322546 original size:38 final size:38
Alignment explanation
Indices: 19322495--19322573 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
19322485 TCACGGTTTG
**
19322495 ATTTTAATTAAATTAATGGATCGAATCAATTTAATTTA
1 ATTTTAATTAAATTAATAAATCGAATCAATTTAATTTA
* **
19322533 ATTTTAGTTAAATTAATAAATTTAATCAATTTAATTTA
1 ATTTTAATTAAATTAATAAATCGAATCAATTTAATTTA
19322571 ATT
1 ATT
19322574 AATCGATTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (38 bp):
ATTTTAATTAAATTAATAAATCGAATCAATTTAATTTA
Found at i:19322859 original size:23 final size:23
Alignment explanation
Indices: 19322800--19322859 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
19322790 AGATAATTTT
19322800 ATTTAATTT--ATTTAAAATATA
1 ATTTAATTTAAATTTAAAATATA
* *
19322821 A--AAAATTAAGAGTTTAAAATATA
1 ATTTAATTTAA-A-TTTAAAATATA
19322844 ATTTAATTTAAATTTA
1 ATTTAATTTAAATTTA
19322860 TTTATTATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
19 4 0.14
21 1 0.03
22 1 0.03
23 16 0.55
24 1 0.03
25 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (23 bp):
ATTTAATTTAAATTTAAAATATA
Found at i:19322996 original size:15 final size:16
Alignment explanation
Indices: 19322974--19323018 Score: 74
Period size: 15 Copynumber: 2.9 Consensus size: 16
19322964 AAATAATTTG
19322974 ATTAATTTAATTTAAA
1 ATTAATTTAATTTAAA
19322990 A-TAATTTAATTTAAA
1 ATTAATTTAATTTAAA
*
19323005 ATTAATTGAATTTA
1 ATTAATTTAATTTA
19323019 CCGGATGAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATTAATTTAATTTAAA
Found at i:19327915 original size:21 final size:22
Alignment explanation
Indices: 19327891--19327936 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
19327881 TTCTTCATCT
*
19327891 AAATTCATGCTC-TCTTTCTAA
1 AAATTCATACTCTTCTTTCTAA
19327912 AAATTCATACTCTTTCTTTCTAA
1 AAATTCATACTC-TTCTTTCTAA
19327935 AA
1 AA
19327937 TCAAATCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.50
23 11 0.50
ACGTcount: A:0.33, C:0.22, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATTCATACTCTTCTTTCTAA
Found at i:19328715 original size:19 final size:19
Alignment explanation
Indices: 19328688--19328727 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
19328678 GTATGAATTT
*
19328688 AAATGAAAAAAAAATGAAA
1 AAATGAAAAAAAAACGAAA
* *
19328707 AAATTAAAAAGAAACGAAA
1 AAATGAAAAAAAAACGAAA
19328726 AA
1 AA
19328728 CGTAACAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.78, C:0.03, G:0.10, T:0.10
Consensus pattern (19 bp):
AAATGAAAAAAAAACGAAA
Found at i:19329341 original size:21 final size:21
Alignment explanation
Indices: 19329317--19329359 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
19329307 TTTTCATATG
19329317 AATTCATACTT-TTTCTCTAAA
1 AATTCAT-CTTCTTTCTCTAAA
*
19329338 AATTCATTTTCTTTCTCTAAA
1 AATTCATCTTCTTTCTCTAAA
19329359 A
1 A
19329360 TCAAATCAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTCATCTTCTTTCTCTAAA
Found at i:19329565 original size:23 final size:23
Alignment explanation
Indices: 19329536--19329581 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
19329526 ATCTCTCTAA
19329536 AAATTCATACTTTCTACCTTAAT
1 AAATTCATACTTTCTACCTTAAT
19329559 AAATTCATACTTTCTACCTTAAT
1 AAATTCATACTTTCTACCTTAAT
19329582 CACCTACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATTCATACTTTCTACCTTAAT
Found at i:19331707 original size:10 final size:10
Alignment explanation
Indices: 19331692--19331721 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
19331682 ATAATATGAC
19331692 TATTTTTAAT
1 TATTTTTAAT
19331702 TATTTTTAA-
1 TATTTTTAAT
19331711 TATTTTTAAT
1 TATTTTTAAT
19331721 T
1 T
19331722 TAAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTTTTAAT
Found at i:19331810 original size:22 final size:22
Alignment explanation
Indices: 19331784--19331825 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
19331774 TAATAATAAA
*
19331784 TATAAATAAATAATACATATGC
1 TATAAATAAATAATAAATATGC
* *
19331806 TATAATTTAATAATAAATAT
1 TATAAATAAATAATAAATAT
19331826 TGTCAATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (22 bp):
TATAAATAAATAATAAATATGC
Found at i:19331890 original size:21 final size:21
Alignment explanation
Indices: 19331864--19331912 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
19331854 GTAATTTTTT
19331864 TAATATTTA-AATAATAAATAA
1 TAATATTTATAATAATAAA-AA
* *
19331885 TAATA-TTATATTAATAGAAA
1 TAATATTTATAATAATAAAAA
19331905 TAATATTT
1 TAATATTT
19331913 CAAGGTAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TAATATTTATAATAATAAAAA
Found at i:19332003 original size:9 final size:9
Alignment explanation
Indices: 19331991--19332032 Score: 52
Period size: 8 Copynumber: 4.9 Consensus size: 9
19331981 ATTAAAATAC
19331991 TTAATAATT
1 TTAATAATT
19332000 TTAATAA-T
1 TTAATAATT
* *
19332008 TAAATTATT
1 TTAATAATT
19332017 TTAAT-ATT
1 TTAATAATT
19332025 TTAATAAT
1 TTAATAAT
19332033 AAATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 14 0.50
9 14 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TTAATAATT
Found at i:19332009 original size:25 final size:25
Alignment explanation
Indices: 19331981--19332058 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
19331971 AATATTAGTT
19331981 ATTAAAATA-CTTAATAATTTTAATA
1 ATTAAAATATCTTAAT-ATTTTAATA
* *
19332006 ATTAAATTATTTTAATATTTTAATA
1 ATTAAAATATCTTAATATTTTAATA
* * *
19332031 A-T-AAATTTTTTAAATATTTTCATA
1 ATTAAAATATCTT-AATATTTTAATA
19332055 ATTA
1 ATTA
19332059 TGTTAATATT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
23 7 0.16
24 13 0.30
25 19 0.43
26 5 0.11
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTAAAATATCTTAATATTTTAATA
Found at i:19332035 original size:24 final size:23
Alignment explanation
Indices: 19331991--19332056 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 23
19331981 ATTAAAATAC
19331991 TTAATAATTTTAATAATTAAATTATT
1 TTAAT-ATTTTAATAA-TAAATT-TT
19332017 TTAATATTTTAATAATAAATTTT
1 TTAATATTTTAATAATAAATTTT
*
19332040 TTAAATATTTTCATAAT
1 TT-AATATTTTAATAAT
19332057 TATGTTAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
23 4 0.11
24 19 0.50
25 10 0.26
26 5 0.13
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAATATTTTAATAATAAATTTT
Found at i:19332182 original size:20 final size:20
Alignment explanation
Indices: 19332144--19332182 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19332134 AACAATATTA
**
19332144 ACTATTTTATACACTTAAAG
1 ACTATTTTATACAAATAAAG
*
19332164 ACTATTTTATTCAAATAAA
1 ACTATTTTATACAAATAAA
19332183 ATCCTACAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.41
Consensus pattern (20 bp):
ACTATTTTATACAAATAAAG
Found at i:19334756 original size:14 final size:14
Alignment explanation
Indices: 19334737--19334769 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
19334727 AGTATTTTTA
*
19334737 CTAAAAATATCTAT
1 CTAAAAATATATAT
19334751 CTAAAAATATATAT
1 CTAAAAATATATAT
19334765 -TAAAA
1 CTAAAA
19334770 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (14 bp):
CTAAAAATATATAT
Found at i:19338651 original size:15 final size:15
Alignment explanation
Indices: 19338633--19338666 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
19338623 CGAGACCATT
19338633 TCCTGCGAAAACAAA
1 TCCTGCGAAAACAAA
* *
19338648 TCCTGTGAAAGCAAA
1 TCCTGCGAAAACAAA
19338663 TCCT
1 TCCT
19338667 AACGTGATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (15 bp):
TCCTGCGAAAACAAA
Found at i:19347502 original size:28 final size:30
Alignment explanation
Indices: 19347471--19347539 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 30
19347461 TAAAAATAAG
19347471 AAATTTATTAATTTAA-TAATTAAATT-AT-
1 AAATTTATTAATTTAACT-ATTAAATTAATA
*
19347499 AAA-TTATAAATTTTAACTATTAAATTAATA
1 AAATTTATTAA-TTTAACTATTAAATTAATA
19347529 AAATTT-TTAAT
1 AAATTTATTAAT
19347540 CTTTGCTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
27 6 0.18
28 16 0.47
29 4 0.12
30 6 0.18
31 2 0.06
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (30 bp):
AAATTTATTAATTTAACTATTAAATTAATA
Found at i:19348763 original size:2 final size:2
Alignment explanation
Indices: 19348756--19348781 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19348746 ACAAGAGTGA
19348756 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
19348782 GAATAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19348866 original size:49 final size:49
Alignment explanation
Indices: 19348812--19348909 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
19348802 TAGTGTAAAA
19348812 GGTCTACATTTTTTTTGGATCATTGAATCTAAATTAAATTTATAGTGCT
1 GGTCTACATTTTTTTTGGATCATTGAATCTAAATTAAATTTATAGTGCT
19348861 GGTCTACATTTTTTTTGGATCATTGAATCTAAATTAAATTTATAGTGCT
1 GGTCTACATTTTTTTTGGATCATTGAATCTAAATTAAATTTATAGTGCT
19348910 TACATTTAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (49 bp):
GGTCTACATTTTTTTTGGATCATTGAATCTAAATTAAATTTATAGTGCT
Found at i:19349260 original size:11 final size:11
Alignment explanation
Indices: 19349244--19349280 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
19349234 TTTTGTTATA
19349244 ATTATTAATTG
1 ATTATTAATTG
19349255 ATTATTAA-TG
1 ATTATTAATTG
19349265 ATTA-TAATTTG
1 ATTATTAA-TTG
19349276 ATTAT
1 ATTAT
19349281 AATGTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 3 0.13
10 6 0.26
11 14 0.61
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (11 bp):
ATTATTAATTG
Found at i:19349268 original size:18 final size:17
Alignment explanation
Indices: 19349239--19349296 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 17
19349229 TCTAGTTTTG
*
19349239 TTATAATTATTAATTGA
1 TTATAATGATTAATTGA
19349256 TTATTAATGATTATAATTTGA
1 TTA-TAATGA-T-TAA-TTGA
*
19349277 TTATAATGTAATAATTGA
1 TTATAATG-ATTAATTGA
19349295 TT
1 TT
19349297 TTTTAATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 3 0.09
18 11 0.32
19 4 0.12
20 8 0.24
21 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.52
Consensus pattern (17 bp):
TTATAATGATTAATTGA
Found at i:19349276 original size:21 final size:20
Alignment explanation
Indices: 19349244--19349296 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
19349234 TTTTGTTATA
19349244 ATTATTAATTGATTATTAATG
1 ATTA-TAATTGATTATTAATG
19349265 ATTATAATTTGATTA-TAATG
1 ATTATAA-TTGATTATTAATG
*
19349285 -TAATAATTGATT
1 ATTATAATTGATT
19349297 TTTTAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.20
19 5 0.17
20 8 0.27
21 11 0.37
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (20 bp):
ATTATAATTGATTATTAATG
Found at i:19349311 original size:40 final size:37
Alignment explanation
Indices: 19349235--19349314 Score: 97
Period size: 40 Copynumber: 2.1 Consensus size: 37
19349225 ACTATCTAGT
* *
19349235 TTTGTTATAATTATTAATTGATTATTAATGATTATAA
1 TTTGTTATAATTAATAATTGATTATTAATGAATATAA
* *
19349272 TTTGATTATAATGTAATAATTGATTTTTTAATTAATATAA
1 TTTG-TTATAAT-TAATAATTGA-TTATTAATGAATATAA
19349312 TTT
1 TTT
19349315 ATCAGTTGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 4 0.11
38 7 0.19
39 9 0.25
40 16 0.44
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (37 bp):
TTTGTTATAATTAATAATTGATTATTAATGAATATAA
Found at i:19350066 original size:15 final size:15
Alignment explanation
Indices: 19350046--19350080 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
19350036 CAATTGTAAT
*
19350046 TTAAAAAT-TAAAAA
1 TTAAAAATATTAAAA
19350060 TTAAAAATATTAAAA
1 TTAAAAATATTAAAA
19350075 TTAAAA
1 TTAAAA
19350081 TTTTAGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAAAATATTAAAA
Found at i:19350082 original size:6 final size:7
Alignment explanation
Indices: 19350046--19350080 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
19350036 CAATTGTAAT
19350046 TTAAAAA
1 TTAAAAA
19350053 TTAAAAA
1 TTAAAAA
19350060 TTAAAAA
1 TTAAAAA
*
19350067 TATTAAAA
1 T-TAAAAA
19350075 TTAAAA
1 TTAAAA
19350081 TTTTAGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TTAAAAA
Found at i:19350302 original size:28 final size:28
Alignment explanation
Indices: 19350258--19350313 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
19350248 CAAGCGCGAC
*
19350258 TTTGTTGACCTTTTGGCTAAAATTAATT
1 TTTGTTGACCTTATGGCTAAAATTAATT
19350286 TTTGTTGACCTTATGGCTAAAATTAATT
1 TTTGTTGACCTTATGGCTAAAATTAATT
19350314 GTAGTATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (28 bp):
TTTGTTGACCTTATGGCTAAAATTAATT
Found at i:19351121 original size:21 final size:21
Alignment explanation
Indices: 19351087--19351137 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
19351077 AATTTATCTC
* * *
19351087 AAAA-TTTATTTAAATATATT
1 AAAATTTTATATAAAAATAAT
19351107 AAAATTTTATATAAAAATAAT
1 AAAATTTTATATAAAAATAAT
19351128 ATAAATTTTA
1 A-AAATTTTA
19351138 AAAAATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 4 0.15
21 14 0.54
22 8 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAATTTTATATAAAAATAAT
Found at i:19352389 original size:35 final size:36
Alignment explanation
Indices: 19352350--19352418 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 36
19352340 AATATATTGA
* *
19352350 AATTAT-TTATTATTAATATTA-TTAATATTAAAAAT
1 AATTATATT-TTAATAATAATATTTAATATTAAAAAT
19352385 AATTATATTTTAATAATAATATTTAATATTAAAA
1 AATTATATTTTAATAATAATATTTAATATTAAAA
19352419 TATTATGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 16 0.53
36 14 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (36 bp):
AATTATATTTTAATAATAATATTTAATATTAAAAAT
Found at i:19352479 original size:18 final size:18
Alignment explanation
Indices: 19352467--19352529 Score: 78
Period size: 18 Copynumber: 3.7 Consensus size: 18
19352457 TTATTATTTT
19352467 TATATTATTTATTAATAG
1 TATATTATTTATTAATAG
19352485 TATATTATTTATT-A-A-
1 TATATTATTTATTAATAG
* *
19352500 TATATGATTTATTAATAC
1 TATATTATTTATTAATAG
*
19352518 AATATTATTTAT
1 TATATTATTTAT
19352530 AAGTAAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
15 12 0.31
16 2 0.05
17 2 0.05
18 23 0.59
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.56
Consensus pattern (18 bp):
TATATTATTTATTAATAG
Found at i:19352504 original size:33 final size:33
Alignment explanation
Indices: 19352467--19352529 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
19352457 TTATTATTTT
* **
19352467 TATATTATTTATTAATAGTATATTATTTATTAA
1 TATATGATTTATTAATACAATATTATTTATTAA
19352500 TATATGATTTATTAATACAATATTATTTAT
1 TATATGATTTATTAATACAATATTATTTAT
19352530 AAGTAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.56
Consensus pattern (33 bp):
TATATGATTTATTAATACAATATTATTTATTAA
Found at i:19353855 original size:25 final size:25
Alignment explanation
Indices: 19353801--19353855 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
19353791 GATTTTTATG
* ** *
19353801 AAATTTAATTTTTTTAATGTATTTA
1 AAATTAAATTTTTTTAATAAAATTA
*
19353826 TAATTAAATTTTTTTAATAAAATTA
1 AAATTAAATTTTTTTAATAAAATTA
19353851 AAATT
1 AAATT
19353856 CCATAACTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
AAATTAAATTTTTTTAATAAAATTA
Found at i:19354559 original size:13 final size:14
Alignment explanation
Indices: 19354509--19354558 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 14
19354499 ATGATATAAC
19354509 TTTTATATATTTTA
1 TTTTATATATTTTA
19354523 -TTTATATCATTTT-
1 TTTTATAT-ATTTTA
19354536 TGTATTATATTATTTTA
1 T-T-TTATA-TATTTTA
19354553 TTTTAT
1 TTTTAT
19354559 TTAAATTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
13 7 0.23
14 5 0.17
15 5 0.17
16 11 0.37
17 2 0.07
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTTATATATTTTA
Found at i:19355399 original size:2 final size:2
Alignment explanation
Indices: 19355387--19355421 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
19355377 GTATGTTCCC
19355387 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19355422 TCCTTTGCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19368931 original size:33 final size:33
Alignment explanation
Indices: 19368894--19368959 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
19368884 AATAATTTAT
*
19368894 ATATAATAATTAGAT-TATTATGTTTAGTAAGTA
1 ATATAATAATT-GATATATTATGATTAGTAAGTA
*
19368927 ATATAATAATTTATATATTATGATTAGTAAGTA
1 ATATAATAATTGATATATTATGATTAGTAAGTA
19368960 TTTTATGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (33 bp):
ATATAATAATTGATATATTATGATTAGTAAGTA
Found at i:19369023 original size:17 final size:17
Alignment explanation
Indices: 19368993--19369048 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
19368983 GTATCTTAAA
19368993 ATTAT-AATTATTTTAT
1 ATTATAAATTATTTTAT
*
19369009 ATTATAAATTTTTTTAT
1 ATTATAAATTATTTTAT
* *
19369026 -TTTTAAATTAATATT-T
1 ATTATAAATT-ATTTTAT
19369042 ATTATAA
1 ATTATAA
19369049 TAAGTTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 14 0.44
17 18 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATAAATTATTTTAT
Found at i:19369086 original size:26 final size:27
Alignment explanation
Indices: 19369057--19369110 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
19369047 AATAAGTTTA
* * *
19369057 AAATAATTTGTATTTTAT-TATTTTTT
1 AAATAATTTATATATAATATATTTTTT
*
19369083 AAATATTTTATATATAATATATTTTTT
1 AAATAATTTATATATAATATATTTTTT
19369110 A
1 A
19369111 TTTTTATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (27 bp):
AAATAATTTATATATAATATATTTTTT
Found at i:19371570 original size:231 final size:231
Alignment explanation
Indices: 19371180--19371606 Score: 549
Period size: 231 Copynumber: 1.8 Consensus size: 231
19371170 ATGACCTGAT
* *
19371180 GATTCAATCCTCTTCATTAAAGAAGCTGTCCTCTCACGTTCTTCAGTCAGTTCAAGTTTTACAGT
1 GATTCAACCCTCTTCATCAAAGAAGCTGTCCTCTCACGTTCTTCAGTCAGTTCAAGTTTTACAGT
* * * ** * *
19371245 TTCTAAAGCATCACAAACTTTTCGAAGTTTCTCTCCAAATTCATTTTTCATATGCACAGCTTGCT
66 ATCTAAAGCATCACAAACTTCTCCAAGTTTCTCTCCAAATTCACCTTCCATATGCAAAGCTTGCT
* * *
19371310 CTTCTAACTGACGTTGACTCCTGGATGCTTCCTTAAGCATTTCCTTATACCTCTCAAGCTCTTCC
131 CTTCGAACTGACGTTGACTCCTAGATGCTTCCTCAAGCATTTCCTTATACCTCTCAAGCTCTTCC
19371375 TCTGTCTGGAGCCACTGCTCTTCAGTGTGATCCAAA
196 TCTGTCTGGAGCCACTGCTCTTCAGTGTGATCCAAA
* * * *
19371411 GATTCAACCCTCTTCATCAAAGAAGCTGTTCTCTCTCGTTCTTCAGTCAGTTC-AGATTTTGCTG
1 GATTCAACCCTCTTCATCAAAGAAGCTGTCCTCTCACGTTCTTCAGTCAGTTCAAG-TTTTACAG
* *
19371475 TATCTAAAGCATCACAAACTTCTCCAAGTTTCT-TCCTGGAA-TCACCTTCCATTTGCAAAGCTT
65 TATCTAAAGCATCACAAACTTCTCCAAGTTTCTCTCC--AAATTCACCTTCCATATGCAAAGCTT
* * * * * * *
19371538 TCTCTTCGAAGTG-TGTTTGA-TACCTAGATGCTTCCTCGATCCTTTCTTTATACCTCTCAAGCT
128 GCTCTTCGAACTGACG-TTGACT-CCTAGATGCTTCCTCAAGCATTTCCTTATACCTCTCAAGCT
19371601 CTTCCT
191 CTTCCT
19371607 GCATCTGGAG
Statistics
Matches: 166, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
230 7 0.04
231 157 0.95
232 2 0.01
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.37
Consensus pattern (231 bp):
GATTCAACCCTCTTCATCAAAGAAGCTGTCCTCTCACGTTCTTCAGTCAGTTCAAGTTTTACAGT
ATCTAAAGCATCACAAACTTCTCCAAGTTTCTCTCCAAATTCACCTTCCATATGCAAAGCTTGCT
CTTCGAACTGACGTTGACTCCTAGATGCTTCCTCAAGCATTTCCTTATACCTCTCAAGCTCTTCC
TCTGTCTGGAGCCACTGCTCTTCAGTGTGATCCAAA
Found at i:19371640 original size:231 final size:230
Alignment explanation
Indices: 19371180--19371729 Score: 528
Period size: 231 Copynumber: 2.4 Consensus size: 230
19371170 ATGACCTGAT
* * * *
19371180 GATTCAATCCTCTTCATTAAAGAAGCTGTCCTCTCACGTTCTTCAGTCAGTTCA-AGTTTTACAG
1 GATTCAACCCTCTTCATCAAAGAAGCTGTTCTCTC-CGTTCTTCAGTCAGTTCAGA-TTTTGCAG
* * * ** * *
19371244 TTTCTAAAGCATCACAAACTTTTCGAAGTTTCTCTCCAAATTCATTTTTCATATGCACAGCTTGC
64 TATCTAAAGCATCACAAACTTCTCCAAGTTTCTCTCCAAATTCACCTTCCATATGCAAAGCTTGC
* * *
19371309 TCTTCTAACTGACGTTGACTCCTGGATGCTTCCTTAAGCATTTCCTTATACCTCTCAAGCTCTTC
129 TCTTCGAACTGACGTTGACTCCTAGATGCTTCCTCAAGCATTTCCTTATACCTCTCAAGCTCTTC
* * * **
19371374 CTCTGTCTGGAGCCACTGCTCTTCAGTGTGATCCAAA
194 CTCTATCTGGAGCCACTGCTCTGCAATAAGATCCAAA
*
19371411 GATTCAACCCTCTTCATCAAAGAAGCTGTTCTCTCTCGTTCTTCAGTCAGTTCAGATTTTGCTGT
1 GATTCAACCCTCTTCATCAAAGAAGCTGTTCTCTC-CGTTCTTCAGTCAGTTCAGATTTTGCAGT
* * *
19371476 ATCTAAAGCATCACAAACTTCTCCAAGTTTCT-TCCTGGAA-TCACCTTCCATTTGCAAAGCTTT
65 ATCTAAAGCATCACAAACTTCTCCAAGTTTCTCTCC--AAATTCACCTTCCATATGCAAAGCTTG
* * * * * *
19371539 CTCTTCGAAGTG-TGTTTGA-TACCTAGATGCTTCCTCGATCCTTTCTTTATACCTCTCAAGCTC
128 CTCTTCGAACTGACG-TTGACT-CCTAGATGCTTCCTCAAGCATTTCCTTATACCTCTCAAGCTC
** *
19371602 TTCCTGC-ATCTGGAGCCGTTG-TCCTGCAATAAGATCCAAG
191 TTCCT-CTATCTGGAGCCACTGCT-CTGCAATAAGATCCAAA
* * * * * * * *
19371642 GACTCAACTCTCCTT-AACAAAGATGCTGCCTTCTC-CCGTTCTTTTA-CCACTTCAGAATTTGC
1 GATTCAACCCT-CTTCATCAAAGAAGCTG--TTCTCTCCGTTC-TTCAGTCAGTTCAGATTTTG-
*
19371704 CA-CATCTAAAGCATCACAAACTTCTC
61 CAGTATCTAAAGCATCACAAACTTCTC
19371730 TTATTTTTTC
Statistics
Matches: 264, Mismatches: 43, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
230 6 0.02
231 241 0.91
232 12 0.05
233 5 0.02
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.35
Consensus pattern (230 bp):
GATTCAACCCTCTTCATCAAAGAAGCTGTTCTCTCCGTTCTTCAGTCAGTTCAGATTTTGCAGTA
TCTAAAGCATCACAAACTTCTCCAAGTTTCTCTCCAAATTCACCTTCCATATGCAAAGCTTGCTC
TTCGAACTGACGTTGACTCCTAGATGCTTCCTCAAGCATTTCCTTATACCTCTCAAGCTCTTCCT
CTATCTGGAGCCACTGCTCTGCAATAAGATCCAAA
Found at i:19372360 original size:15 final size:16
Alignment explanation
Indices: 19372340--19372370 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
19372330 AAGAACTTCC
19372340 AGCTTCCTGAA-TTCT
1 AGCTTCCTGAAGTTCT
19372355 AGCTTCCTGAAGTTCT
1 AGCTTCCTGAAGTTCT
19372371 TTGAGTGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.39
Consensus pattern (16 bp):
AGCTTCCTGAAGTTCT
Found at i:19374060 original size:14 final size:16
Alignment explanation
Indices: 19374041--19374072 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19374031 TTACCAAGAG
19374041 AAAAGG-AG-AAGAAA
1 AAAAGGAAGAAAGAAA
19374055 AAAAGGAAGAAAGAAA
1 AAAAGGAAGAAAGAAA
19374071 AA
1 AA
19374073 GAAATGACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 2 0.12
16 8 0.50
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (16 bp):
AAAAGGAAGAAAGAAA
Found at i:19375822 original size:31 final size:31
Alignment explanation
Indices: 19375787--19375893 Score: 78
Period size: 31 Copynumber: 3.3 Consensus size: 31
19375777 ATAATTTGTC
19375787 TATTTATATTATTTAAAATATTAAAAATATA
1 TATTTATATTATTTAAAATATTAAAAATATA
* *
19375818 TATTTACATCATATTT--TATA-TAAAAATTATA
1 TATTTATAT--TATTTAAAATATTAAAAA-TATA
*
19375849 TATTATAATTTTATTAATACAAA-ATTAAAAATATA
1 TATT-T-ATATTATT--TA-AAATATTAAAAATATA
*
19375884 TATTTTTATT
1 TATTTATATT
19375894 TTATTAAATT
Statistics
Matches: 58, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
30 6 0.10
31 23 0.40
32 1 0.02
33 11 0.19
34 1 0.02
35 9 0.16
36 7 0.12
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.50
Consensus pattern (31 bp):
TATTTATATTATTTAAAATATTAAAAATATA
Found at i:19376925 original size:2 final size:2
Alignment explanation
Indices: 19376918--19376947 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19376908 CACTTTACCG
19376918 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19376948 AAAAGAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19377589 original size:27 final size:28
Alignment explanation
Indices: 19377551--19377610 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 28
19377541 TTAAATTATA
19377551 ATAAAATATTTAATATAATA-TTAAATT
1 ATAAAATATTTAATATAATATTTAAATT
* *
19377578 TTAAAATTTTTAATATAATATTTAAATT
1 ATAAAATATTTAATATAATATTTAAATT
19377606 ATAAA
1 ATAAA
19377611 TCTATTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
ATAAAATATTTAATATAATATTTAAATT
Found at i:19377618 original size:28 final size:27
Alignment explanation
Indices: 19377541--19377627 Score: 79
Period size: 27 Copynumber: 3.1 Consensus size: 27
19377531 TGAATCATTT
*
19377541 TTAAATTATAATAAAATATTTAATATAATA
1 TTAAATTAT-A-AAATTA-TTAATATAATA
* *
19377571 TTAAATTTTAAAATTTTTAATATAATA
1 TTAAATTATAAAATTATTAATATAATA
*
19377598 TTTAAATTAT-AAATCTATTAAT-TACTA
1 -TTAAATTATAAAAT-TATTAATATAATA
19377625 TTA
1 TTA
19377628 TACTTTAAGG
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
26 3 0.06
27 19 0.39
28 18 0.37
29 1 0.02
30 8 0.16
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
TTAAATTATAAAATTATTAATATAATA
Found at i:19381280 original size:18 final size:18
Alignment explanation
Indices: 19381257--19381291 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19381247 CTAGACTATC
*
19381257 ATAATTCATATCTTTATG
1 ATAATTCATATATTTATG
*
19381275 ATAATTGATATATTTAT
1 ATAATTCATATATTTAT
19381292 ATTATGTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (18 bp):
ATAATTCATATATTTATG
Found at i:19381395 original size:37 final size:38
Alignment explanation
Indices: 19381313--19381402 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 38
19381303 TATTAAAAAT
* *
19381313 TTATATATTTATATT-ATATTTTATATAAAAATTATGTG
1 TTATA-ATTTATATTAATATATAATATAAAAATTATGTG
*
19381351 TTATAATTTATATTAATATAATAATATAAAATTTAT-T-
1 TTATAATTTATATTAATAT-ATAATATAAAAATTATGTG
*
19381388 TTTTAATTT-TATTAA
1 TTATAATTTATATTAA
19381403 ATTTATTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
36 6 0.13
37 17 0.37
38 10 0.22
39 13 0.28
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (38 bp):
TTATAATTTATATTAATATATAATATAAAAATTATGTG
Found at i:19382737 original size:20 final size:19
Alignment explanation
Indices: 19382701--19382744 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
19382691 TTTTAGATTA
*
19382701 TTTTTAATTTTTAATTTTC
1 TTTTTAATTTTTAATTTAC
19382720 TTTTTAATTAATTT-ATTTAC
1 TTTTTAATT--TTTAATTTAC
19382740 TTTTT
1 TTTTT
19382745 TTTCTCTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 10 0.45
21 3 0.14
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTAATTTTTAATTTAC
Found at i:19383538 original size:27 final size:29
Alignment explanation
Indices: 19383451--19383538 Score: 72
Period size: 29 Copynumber: 3.0 Consensus size: 29
19383441 ATGAATAGTT
* * **
19383451 TTTAAATTATATTAAAATATTTAATTTGGTA
1 TTTAAATTATA--AAAATTTTTAATATAATA
* * *
19383482 TTTAAATTTTAAAAATTTTTGATATGATA
1 TTTAAATTATAAAAATTTTTAATATAATA
*
19383511 TTTAAATTAT-AAATTTTTTAAT-TAATA
1 TTTAAATTATAAAAATTTTTAATATAATA
19383538 T
1 T
19383539 GATACTTAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
27 5 0.10
28 10 0.21
29 23 0.48
31 10 0.21
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (29 bp):
TTTAAATTATAAAAATTTTTAATATAATA
Found at i:19383673 original size:17 final size:17
Alignment explanation
Indices: 19383651--19383685 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
19383641 ATTCAAATTT
19383651 TTTTAAAT-TATTTACTA
1 TTTTAAATAT-TTTACTA
19383668 TTTTAAATATTTTACTA
1 TTTTAAATATTTTACTA
19383685 T
1 T
19383686 AATTTATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.94
18 1 0.06
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTAAATATTTTACTA
Found at i:19393691 original size:24 final size:24
Alignment explanation
Indices: 19393658--19393715 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
19393648 CAAAGGGAAG
*
19393658 GGATGCGAAATTAGAAGGGAGGGA
1 GGATGCGAAATTAGAAGAGAGGGA
* *
19393682 GGATGTGAAATTGGAAGAGAGGGA
1 GGATGCGAAATTAGAAGAGAGGGA
19393706 GGATGCGAAA
1 GGATGCGAAA
19393716 GCACGTGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.03, G:0.45, T:0.14
Consensus pattern (24 bp):
GGATGCGAAATTAGAAGAGAGGGA
Found at i:19393912 original size:27 final size:27
Alignment explanation
Indices: 19393874--19393926 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
19393864 ATGAGAGAGG
19393874 GCAAGAGGATGAGCCAGATTGGAAGCT
1 GCAAGAGGATGAGCCAGATTGGAAGCT
19393901 GCAAGAGGATGAGCCAGATTGGAAGC
1 GCAAGAGGATGAGCCAGATTGGAAGC
19393927 AGTTGTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.15, G:0.38, T:0.13
Consensus pattern (27 bp):
GCAAGAGGATGAGCCAGATTGGAAGCT
Found at i:19399348 original size:49 final size:46
Alignment explanation
Indices: 19399293--19399391 Score: 112
Period size: 46 Copynumber: 2.1 Consensus size: 46
19399283 AATTATTTAT
*
19399293 TATATATCGTATGTAATAATTAATTAATGAATTTTTT-TTAATA-AATTCA
1 TATATAT-G-ATGT-ATAATAAATT-ATGAATTTTTTATTAATATAATT-A
* *
19399342 TATATATGATGTGTAATAAATTATTAATTTTTTATTAATATAATTA
1 TATATATGATGTATAATAAATTATGAATTTTTTATTAATATAATTA
19399388 TATA
1 TATA
19399392 AAATGATTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
45 10 0.22
46 19 0.42
47 8 0.18
48 1 0.02
49 7 0.16
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (46 bp):
TATATATGATGTATAATAAATTATGAATTTTTTATTAATATAATTA
Found at i:19404031 original size:17 final size:17
Alignment explanation
Indices: 19404009--19404042 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
19403999 AAAATTACAC
19404009 CAATTGAAC-AAAATGAA
1 CAATTG-ACTAAAATGAA
19404026 CAATTGACTAAAATGAA
1 CAATTGACTAAAATGAA
19404043 ACATAAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.21
Consensus pattern (17 bp):
CAATTGACTAAAATGAA
Found at i:19405872 original size:22 final size:22
Alignment explanation
Indices: 19405842--19405884 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
19405832 TATTCCTTTA
* * *
19405842 AGAGTTTAATTGATTATATTTC
1 AGAGATTAATTAATTAAATTTC
19405864 AGAGATTAATTAATTAAATTT
1 AGAGATTAATTAATTAAATTT
19405885 TATCACATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47
Consensus pattern (22 bp):
AGAGATTAATTAATTAAATTTC
Found at i:19410378 original size:21 final size:21
Alignment explanation
Indices: 19410349--19410388 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19410339 TAACTTAAGA
19410349 GAAAATT-AATTTATAAATATT
1 GAAAATTAAATTT-TAAATATT
*
19410370 GAAATTTAAATTTTAAATA
1 GAAAATTAAATTTTAAATA
19410389 AATTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (21 bp):
GAAAATTAAATTTTAAATATT
Found at i:19414565 original size:12 final size:12
Alignment explanation
Indices: 19414546--19414575 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
19414536 AAAACTGGGT
19414546 TAAATGGGAATG
1 TAAATGGGAATG
*
19414558 TGAATGGGAATG
1 TAAATGGGAATG
19414570 TAAATG
1 TAAATG
19414576 TGGTGGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.27
Consensus pattern (12 bp):
TAAATGGGAATG
Found at i:19425153 original size:18 final size:18
Alignment explanation
Indices: 19425130--19425164 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
19425120 GTAAAAATAC
19425130 TATTTAA-TATATTATTAT
1 TATTTAATTAT-TTATTAT
19425148 TATTTAATTATTTATTA
1 TATTTAATTATTTATTA
19425165 ACATAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTAATTATTTATTAT
Found at i:19425253 original size:27 final size:27
Alignment explanation
Indices: 19425223--19425274 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
19425213 TTATTAATTT
19425223 TATAACTATTAATAAT-ATAAATTTTAA
1 TATAA-TATTAATAATAATAAATTTTAA
**
19425250 TATAATATTCTTAATAATAAATTTT
1 TATAATATTAATAATAATAAATTTT
19425275 TTTTCTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (27 bp):
TATAATATTAATAATAATAAATTTTAA
Found at i:19425265 original size:14 final size:12
Alignment explanation
Indices: 19425235--19425274 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 12
19425225 TAACTATTAA
19425235 TAATATAAATTT
1 TAATATAAATTT
19425247 TAATATAATATTCT
1 TAATATAA-ATT-T
19425261 TAATAATAAATTT
1 TAAT-ATAAATTT
19425274 T
1 T
19425275 TTTTCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 8 0.32
13 5 0.20
14 8 0.32
15 4 0.16
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATATAAATTT
Found at i:19426139 original size:125 final size:125
Alignment explanation
Indices: 19425978--19426268 Score: 297
Period size: 125 Copynumber: 2.3 Consensus size: 125
19425968 TTTAAAAGAG
* * * *
19425978 ATTATTTAAGATATTTTTTATTCAAAATTACCTTAAATAAT-TATTTTTAAAATATATTAA-GAG
1 ATTAATTAAGGTATTTTTT-GTCAAAAATACCTTAAATAATCTA-TTTTAAAATATA-TAAGGAG
* * * ** *
19426041 ATTATTTTAGGTATTTTTTATTTAAAAATACCA-TAAATAATACCCTTT-AAAAA-TATAATG-G
63 ATTATTTAAAGCATTTTTTATCAAAAAATA-CATTAAATAAT--CCTTTAAAAAATTATAAAGTG
19426102 C
125 C
* * * * *
19426103 ATTAATTGATGTATTTTTTGTCAACAAATACCTTAAATAGTCTATTTTAAAATGTATAAGGGGAT
1 ATTAATTAAGGTATTTTTTGTCAA-AAATACCTTAAATAATCTATTTTAAAATATATAAGGAGAT
* *
19426168 TATTTAAAGCATTTTTTATCAAAAAATACATTAAATAATCTTTTAAAAAATTTTAAAGTGC
65 TATTTAAAGCATTTTTTATCAAAAAATACATTAAATAATCCTTTAAAAAATTATAAAGTGC
* * *
19426229 ATTATTTAAGGTATTTTTGGTAAAAAATACCTTAAATAAT
1 ATTAATTAAGGTATTTTTTGTCAAAAATACCTTAAATAAT
19426269 ACATTTAATT
Statistics
Matches: 136, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
123 4 0.03
124 14 0.10
125 95 0.70
126 23 0.17
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (125 bp):
ATTAATTAAGGTATTTTTTGTCAAAAATACCTTAAATAATCTATTTTAAAATATATAAGGAGATT
ATTTAAAGCATTTTTTATCAAAAAATACATTAAATAATCCTTTAAAAAATTATAAAGTGC
Found at i:19426196 original size:63 final size:63
Alignment explanation
Indices: 19425977--19426268 Score: 215
Period size: 63 Copynumber: 4.7 Consensus size: 63
19425967 TTTTAAAAGA
*
19425977 GATTATTT-AAGATATTTTTTATTC-AAAATTACCTTAAATAAT-TATTTTTAAAATATATTAA-
1 GATTATTTAAAG-TATTTTTTA-TCAAAAAATACCTTAAATAATCTA-TTTTAAAATATA-TAAG
*
19426038 GA
62 GG
* * ** * ** *
19426040 GATTATTTTAGGTATTTTTTATTTAAAAATACCATAAATAATAC-CCTTTAAAA-ATATAATGG
1 GATTATTTAAAGTATTTTTTATCAAAAAATACCTTAAATAAT-CTATTTTAAAATATATAAGGG
* * * * * * * *
19426102 CATTAATTGATGTATTTTTTGTCAACAAATACCTTAAATAGTCTATTTTAAAATGTATAAGGG
1 GATTATTTAAAGTATTTTTTATCAAAAAATACCTTAAATAATCTATTTTAAAATATATAAGGG
* * * * *
19426165 GATTATTTAAAGCATTTTTTATCAAAAAATACATTAAATAATC--TTTTAAAAAATTTTAAAGTG
1 GATTATTTAAAGTATTTTTTATCAAAAAATACCTTAAATAATCTATTTTAAAATA-TAT-AAGGG
* * **
19426228 CATTATTTAAGGTATTTTTGGT-AAAAAATACCTTAAATAAT
1 GATTATTTAAAGTATTTTTTATCAAAAAATACCTTAAATAAT
19426269 ACATTTAATT
Statistics
Matches: 180, Mismatches: 40, Indels: 19
0.75 0.17 0.08
Matches are distributed among these distances:
61 12 0.07
62 64 0.36
63 102 0.57
64 2 0.01
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (63 bp):
GATTATTTAAAGTATTTTTTATCAAAAAATACCTTAAATAATCTATTTTAAAATATATAAGGG
Found at i:19427063 original size:13 final size:12
Alignment explanation
Indices: 19427040--19427089 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
19427030 TCAAATTACC
*
19427040 TTAAATTAAATA
1 TTAAAATAAATA
19427052 TTAAAATCAAATA
1 TTAAAAT-AAATA
19427065 TCTAATAATAAA-A
1 T-TAA-AATAAATA
19427078 TTAAAA-AAATA
1 TTAAAATAAATA
19427089 T
1 T
19427090 AAATTCTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
10 3 0.09
11 4 0.12
12 9 0.27
13 8 0.24
14 6 0.18
15 3 0.09
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (12 bp):
TTAAAATAAATA
Found at i:19427485 original size:13 final size:13
Alignment explanation
Indices: 19427467--19427491 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19427457 TGGTTTTTCT
19427467 TTCTCTTTCTCTG
1 TTCTCTTTCTCTG
19427480 TTCTCTTTCTCT
1 TTCTCTTTCTCT
19427492 CCCTTTAAAA
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:0.00, C:0.32, G:0.04, T:0.64
Consensus pattern (13 bp):
TTCTCTTTCTCTG
Found at i:19432939 original size:47 final size:47
Alignment explanation
Indices: 19432868--19433022 Score: 154
Period size: 55 Copynumber: 3.2 Consensus size: 47
19432858 AATAAATTAA
* * *
19432868 AAATTT-TTACGTGACATAAATAATATATGTAAAAATTAAATAAAAT
1 AAATTTATCACGTGACGTAAGTAATATATGTAAAAATTAAATAAAAT
* *
19432914 AAATTTATCATGTGACGTAAGTAATATAT-TAAAATAAATAAAATAAAATAAATT
1 AAATTTATCACGTGACGTAAGTAATATATGT--AA-AAAT----T-AAATAAAAT
*
19432968 AAAATTTATCACGTGATGTAAGTAATATATGT-AAAATTAAATAAAAT
1 -AAATTTATCACGTGACGTAAGTAATATATGTAAAAATTAAATAAAAT
19433015 AAATTTAT
1 AAATTTAT
19433023 TTTTTTTTAT
Statistics
Matches: 90, Mismatches: 8, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
46 15 0.17
47 26 0.29
48 3 0.03
49 4 0.04
52 4 0.04
53 2 0.02
54 8 0.09
55 27 0.30
56 1 0.01
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.35
Consensus pattern (47 bp):
AAATTTATCACGTGACGTAAGTAATATATGTAAAAATTAAATAAAAT
Done.