Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 131 of 190
Found at i:21071522 original size:31 final size:31
Alignment explanation
Indices: 21071464--21071545 Score: 114
Period size: 31 Copynumber: 2.7 Consensus size: 31
21071454 TTTAAAACCC
*
21071464 CTAAAATCCAAAATCCCCTAAAATCCAAAATT
1 CTAAAATCCAAAAT-CCCTAAAATCCAAAACT
* *
21071496 CTAAAATCCAAAATCCCTTAAATCCAAACCT
1 CTAAAATCCAAAATCCCTAAAATCCAAAACT
21071527 CTAAAAT-CAAAA-CCCTAAA
1 CTAAAATCCAAAATCCCTAAA
21071546 CCTTTCATAC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 6 0.13
30 5 0.11
31 21 0.46
32 14 0.30
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (31 bp):
CTAAAATCCAAAATCCCTAAAATCCAAAACT
Found at i:21071604 original size:29 final size:30
Alignment explanation
Indices: 21071530--21071604 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 30
21071520 CAAACCTCTA
* * * *
21071530 AAATCAAAACCCT-AAACCTTTCATACCTT
1 AAATCCAAACCCTAAAACCTCTCAAAACTT
*
21071559 AAAACCAAACCCTAAAACC-CTCAAAACTT
1 AAATCCAAACCCTAAAACCTCTCAAAACTT
21071588 AAATCCAAACCCTAAAA
1 AAATCCAAACCCTAAAA
21071605 TCCGAATCTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 34 0.87
30 5 0.13
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.19
Consensus pattern (30 bp):
AAATCCAAACCCTAAAACCTCTCAAAACTT
Found at i:21072791 original size:64 final size:64
Alignment explanation
Indices: 21072723--21072868 Score: 141
Period size: 64 Copynumber: 2.3 Consensus size: 64
21072713 AGGACTGAGT
* * * *
21072723 CACAAGTTAGGAAAATGAGATGATCTAGATTGAGCCAAAATCAAACAAGTGA-CTGAGACTAAAC
1 CACAAGTTAGGAAAATGAAATAATCTAGACTGAACCAAAATCAAACAAGTGATC-GAGACTAAAC
* * ** * * * * * **
21072787 CACAAATCAAAAAAATAAAATAATCTAGACTGAACCGAGATCAAACAGGTGATCGGGACTAAGT
1 CACAAGTTAGGAAAATGAAATAATCTAGACTGAACCAAAATCAAACAAGTGATCGAGACTAAAC
21072851 CACAAGTTAGGAAAATGA
1 CACAAGTTAGGAAAATGA
21072869 TCTGGACTCA
Statistics
Matches: 61, Mismatches: 20, Indels: 2
0.73 0.24 0.02
Matches are distributed among these distances:
64 60 0.98
65 1 0.02
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.18
Consensus pattern (64 bp):
CACAAGTTAGGAAAATGAAATAATCTAGACTGAACCAAAATCAAACAAGTGATCGAGACTAAAC
Found at i:21072905 original size:49 final size:48
Alignment explanation
Indices: 21072827--21072922 Score: 138
Period size: 49 Copynumber: 2.0 Consensus size: 48
21072817 TGAACCGAGA
** * *
21072827 TCAAACAGGTGATCGGGACTAAGTCACAAGTTAGGAAAATGATCTGGAC
1 TCAAACAGGTGATCGAAACAAAATCACAAGTTAGG-AAATGATCTGGAC
*
21072876 TCAAACAGGTGATCGAAACAAAATTACAAGTTAGGAAATGATCTGGA
1 TCAAACAGGTGATCGAAACAAAATCACAAGTTAGGAAATGATCTGGA
21072923 TTGAGCTAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 12 0.29
49 30 0.71
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.21
Consensus pattern (48 bp):
TCAAACAGGTGATCGAAACAAAATCACAAGTTAGGAAATGATCTGGAC
Found at i:21072974 original size:55 final size:54
Alignment explanation
Indices: 21072900--21073213 Score: 190
Period size: 55 Copynumber: 5.8 Consensus size: 54
21072890 GAAACAAAAT
* * *
21072900 TACAAGT-TAGGAAATGATCTGGATTGAGCTAAGAT-TAGATGATCGAAATGAAAC
1 TACAAGTCTAGAAAATGATCTGGATTGAGCCAAGATCGA-ATGA-CGAAATGAAAC
* * * * * * *
21072954 TATAAGTCTAGAAAATGATCTAGACTAAGCCAAGATCGAATGACCAAGA-CAAAA
1 TACAAGTCTAGAAAATGATCTGGATTGAGCCAAGATCGAATGACGAA-ATGAAAC
* * * * *
21073008 TCATAAGTCTAGAAAATGATATGGATTGAGCCAATATCGAATGACTGAGATGTAAC
1 T-ACAAGTCTAGAAAATGATCTGGATTGAGCCAAGATCGAATGAC-GAAATGAAAC
* * * * * * **
21073064 CACAAGTCTGGCAAATGATTTGGATTGAGCTAAGAT-TAATGACGGGGATGAAA-
1 TACAAGTCTAGAAAATGATCTGGATTGAGCCAAGATCGAATGAC-GAAATGAAAC
* * * **
21073117 TCACAAGT-TAAAAAAATGATTTGGATTGAGCCAAAATCGAATGATCGGGATGAAAC
1 T-ACAAGTCT-AGAAAATGATCTGGATTGAGCCAAGATCGAATGA-CGAAATGAAAC
* * * * * * *
21073173 CATAAGTCAAGAAAATGATCTGAACTGAGTCAAGATTGAAT
1 TACAAGTCTAGAAAATGATCTGGATTGAGCCAAGATCGAAT
21073214 ATGGGTGATA
Statistics
Matches: 200, Mismatches: 48, Indels: 23
0.74 0.18 0.08
Matches are distributed among these distances:
53 1 0.00
54 54 0.27
55 140 0.70
56 5 0.03
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (54 bp):
TACAAGTCTAGAAAATGATCTGGATTGAGCCAAGATCGAATGACGAAATGAAAC
Found at i:21073606 original size:18 final size:19
Alignment explanation
Indices: 21073583--21073628 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
21073573 TTTATGAACA
21073583 TTGTCATTCATTTATTTG-
1 TTGTCATTCATTTATTTGC
21073601 TTGTCATTCATTTATTTGC
1 TTGTCATTCATTTATTTGC
21073620 TT-TCATTCA
1 TTGTCATTCA
21073629 GATTAGTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 25 0.93
19 2 0.07
ACGTcount: A:0.17, C:0.15, G:0.09, T:0.59
Consensus pattern (19 bp):
TTGTCATTCATTTATTTGC
Found at i:21073996 original size:18 final size:19
Alignment explanation
Indices: 21073975--21074020 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
21073965 CAGTTTAAGT
21073975 CTTTTTTTTTTC-TTTTTC
1 CTTTTTTTTTTCATTTTTC
* *
21073993 CTTTTTTTATTCATTTTTT
1 CTTTTTTTTTTCATTTTTC
*
21074012 ATTTTTTTT
1 CTTTTTTTT
21074021 GCACACCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.83
Consensus pattern (19 bp):
CTTTTTTTTTTCATTTTTC
Found at i:21074009 original size:19 final size:18
Alignment explanation
Indices: 21073975--21074010 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21073965 CAGTTTAAGT
*
21073975 CTTTTTTTTTTCTTTTTC
1 CTTTTTTTATTCTTTTTC
21073993 CTTTTTTTATTCATTTTT
1 CTTTTTTTATTC-TTTTT
21074011 TATTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.81
Consensus pattern (18 bp):
CTTTTTTTATTCTTTTTC
Found at i:21078095 original size:17 final size:18
Alignment explanation
Indices: 21078061--21078103 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
21078051 ATTGCTCAAC
*
21078061 AAAAAAAATCAACAAAAT
1 AAAATAAATCAACAAAAT
*
21078079 AAAATAAAT-AACTAAAT
1 AAAATAAATCAACAAAAT
*
21078096 GAAATAAA
1 AAAATAAA
21078104 AAAAACTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.16
Consensus pattern (18 bp):
AAAATAAATCAACAAAAT
Found at i:21078132 original size:10 final size:9
Alignment explanation
Indices: 21078128--21078167 Score: 64
Period size: 9 Copynumber: 4.4 Consensus size: 9
21078118 TAAAATGATA
21078128 AAAAAAAAT
1 AAAAAAAAT
21078137 AAAAAAAAT
1 AAAAAAAAT
21078146 -AAAAAAAT
1 AAAAAAAAT
21078154 AAAAAAAAT
1 AAAAAAAAT
21078163 GAAAA
1 -AAAA
21078168 CCTACGATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.28
9 17 0.59
10 4 0.14
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.10
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:21078167 original size:8 final size:8
Alignment explanation
Indices: 21078062--21078160 Score: 58
Period size: 8 Copynumber: 11.9 Consensus size: 8
21078052 TTGCTCAACA
21078062 AAAAAAAT
1 AAAAAAAT
*
21078070 CAACAAAAT
1 -AAAAAAAT
21078079 AAAATAAAT
1 AAAA-AAAT
**
21078088 AACTAAAT
1 AAAAAAAT
* *
21078096 GAAATAA-
1 AAAAAAAT
*
21078103 AAAAAACT
1 AAAAAAAT
* *
21078111 TAAAATAT
1 AAAAAAAT
21078119 AAAATGATAA-
1 AAAA--A-AAT
21078129 AAAAAAAT
1 AAAAAAAT
21078137 AAAAAAAAT
1 -AAAAAAAT
21078146 AAAAAAAT
1 AAAAAAAT
21078154 AAAAAAA
1 AAAAAAA
21078161 ATGAAAACCT
Statistics
Matches: 67, Mismatches: 16, Indels: 15
0.68 0.16 0.15
Matches are distributed among these distances:
7 6 0.09
8 34 0.51
9 21 0.31
10 5 0.07
11 1 0.01
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (8 bp):
AAAAAAAT
Found at i:21079120 original size:28 final size:28
Alignment explanation
Indices: 21079088--21079154 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
21079078 CTTTTTTCTT
21079088 TTTTTTTTATTTTTTGTTT-TGATTTTG
1 TTTTTTTTATTTTTTGTTTATGATTTTG
* *
21079115 ATTTTTTTGATTTTTTGTTTATGTTTTTG
1 -TTTTTTTTATTTTTTGTTTATGATTTTG
21079144 TTGTTTTTTAT
1 TT-TTTTTTAT
21079155 GATGTTATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 20 0.59
29 14 0.41
ACGTcount: A:0.09, C:0.00, G:0.12, T:0.79
Consensus pattern (28 bp):
TTTTTTTTATTTTTTGTTTATGATTTTG
Found at i:21079594 original size:13 final size:13
Alignment explanation
Indices: 21079554--21079602 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
21079544 GATTTATTTG
21079554 AATAATAAGAAAA-
1 AATAAT-AGAAAAT
*
21079567 AATGAT-GAAAAT
1 AATAATAGAAAAT
*
21079579 AATAATAGAAAGT
1 AATAATAGAAAAT
21079592 AATAATA-AAAA
1 AATAATAGAAAA
21079603 ACATAAACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
11 5 0.17
12 8 0.27
13 17 0.57
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.20
Consensus pattern (13 bp):
AATAATAGAAAAT
Found at i:21081297 original size:22 final size:22
Alignment explanation
Indices: 21081272--21081321 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 22
21081262 TATAAATTAG
21081272 ATAATTATAAATTTATTTAAA-T
1 ATAATTA-AAATTTATTTAAATT
21081294 AT-A--AAAA-TTATTTAAATT
1 ATAATTAAAATTTATTTAAATT
21081312 ATAATTAAAA
1 ATAATTAAAA
21081322 ATTAAATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
17 9 0.38
18 6 0.25
19 2 0.08
21 5 0.21
22 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAATTAAAATTTATTTAAATT
Found at i:21081314 original size:18 final size:18
Alignment explanation
Indices: 21081274--21081315 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
21081264 TAAATTAGAT
*
21081274 AATTAT-AAATTTATTTA
1 AATTATAAAAATTATTTA
21081291 AA-TATAAAAATTATTTA
1 AATTATAAAAATTATTTA
21081308 AATTATAA
1 AATTATAA
21081316 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 14 0.64
18 5 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTATAAAAATTATTTA
Found at i:21084010 original size:30 final size:30
Alignment explanation
Indices: 21083974--21084060 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
21083964 GTTTTAAGAG
21083974 ATTTATTTAAGTATAAATTAAAAATTAAAA
1 ATTTATTTAAGTATAAATTAAAAATTAAAA
* **
21084004 ATTTATTT--GGATGAAAGTTAAATGTTAAAA
1 ATTTATTTAAGTAT-AAA-TTAAAAATTAAAA
*
21084034 ACTTATTTCAA-TATAAATTAAAAATTA
1 ATTTATTT-AAGTATAAATTAAAAATTA
21084061 TTAACTTATT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
28 3 0.07
29 3 0.07
30 34 0.76
31 3 0.07
32 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (30 bp):
ATTTATTTAAGTATAAATTAAAAATTAAAA
Found at i:21084990 original size:13 final size:13
Alignment explanation
Indices: 21084935--21084979 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
21084925 TCAAATATAT
21084935 ATTAAAAATAAAA
1 ATTAAAAATAAAA
**
21084948 ATTATACATGTAAAA
1 ATTA-A-AAATAAAA
21084963 ATTAAAAATAAAA
1 ATTAAAAATAAAA
21084976 ATTA
1 ATTA
21084980 TATAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 14 0.54
14 2 0.08
15 10 0.38
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (13 bp):
ATTAAAAATAAAA
Found at i:21089744 original size:19 final size:19
Alignment explanation
Indices: 21089722--21089801 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
21089712 TAGTTAAGTG
21089722 TTTGGGATTTAGGTTAGGA
1 TTTGGGATTTAGGTTAGGA
** * *
21089741 TTTGGGACCTAGATTAAGA
1 TTTGGGATTTAGGTTAGGA
* *
21089760 TTTAGGATTTA-GTTAGGG
1 TTTGGGATTTAGGTTAGGA
21089778 TTTGGTG-TTTAGGTTAGGA
1 TTTGG-GATTTAGGTTAGGA
21089797 TTTGG
1 TTTGG
21089802 TTGGGTTTGG
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
18 12 0.26
19 35 0.74
ACGTcount: A:0.21, C:0.03, G:0.34, T:0.42
Consensus pattern (19 bp):
TTTGGGATTTAGGTTAGGA
Found at i:21089861 original size:19 final size:19
Alignment explanation
Indices: 21089800--21089866 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
21089790 GTTAGGATTT
*
21089800 GGTT-GGGTTTGGGGTCTA
1 GGTTAGGGTTTGGGGTTTA
*
21089818 -GTTAAGGGTTT-GAGTTT-
1 GGTT-AGGGTTTGGGGTTTA
*
21089835 GATGTAGGGTTTGGGGTTTA
1 GGT-TAGGGTTTGGGGTTTA
21089855 GGTTAGGGTTTG
1 GGTTAGGGTTTG
21089867 AAAGTTTAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 11
0.70 0.09 0.20
Matches are distributed among these distances:
17 3 0.08
18 12 0.32
19 21 0.55
20 2 0.05
ACGTcount: A:0.12, C:0.01, G:0.45, T:0.42
Consensus pattern (19 bp):
GGTTAGGGTTTGGGGTTTA
Found at i:21089972 original size:16 final size:17
Alignment explanation
Indices: 21089933--21089976 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
21089923 GTTTAGGTAT
*
21089933 GGTTTAGGGATGGCTTAG
1 GGTTT-GGGAAGGCTTAG
21089951 GGTTTGGGAAGGCTTA-
1 GGTTTGGGAAGGCTTAG
21089967 GGTTTGGGAA
1 GGTTTGGGAA
21089977 TGGTTTAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 10 0.40
17 10 0.40
18 5 0.20
ACGTcount: A:0.18, C:0.05, G:0.45, T:0.32
Consensus pattern (17 bp):
GGTTTGGGAAGGCTTAG
Found at i:21093587 original size:17 final size:17
Alignment explanation
Indices: 21093557--21093592 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21093547 TAGTAAAAAG
*
21093557 TTTTTCTTTGAATTTTT
1 TTTTTCTTTCAATTTTT
*
21093574 TTTTTTTTTCAATTTTT
1 TTTTTCTTTCAATTTTT
21093591 TT
1 TT
21093593 AGGTGCCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.06, G:0.03, T:0.81
Consensus pattern (17 bp):
TTTTTCTTTCAATTTTT
Found at i:21096979 original size:20 final size:20
Alignment explanation
Indices: 21096930--21096971 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
21096920 CAAATTTATC
21096930 TTTTCT-AAATCCCTAACAT
1 TTTTCTAAAATCCCTAACAT
21096949 TTTTCTAAAATCCCTAAC-T
1 TTTTCTAAAATCCCTAACAT
21096968 TTTT
1 TTTT
21096972 GTTGAAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTTCTAAAATCCCTAACAT
Found at i:21099887 original size:20 final size:21
Alignment explanation
Indices: 21099859--21099902 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
21099849 AGCAATGGAG
*
21099859 TTTTCCATCGCTAACT-TATT
1 TTTTCCATCGCTAAATATATT
*
21099879 TTTTTCATCGCTAAATATATT
1 TTTTCCATCGCTAAATATATT
21099900 TTT
1 TTT
21099903 GTCTATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.23, C:0.18, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTTCCATCGCTAAATATATT
Found at i:21100080 original size:21 final size:21
Alignment explanation
Indices: 21100056--21100095 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
21100046 TTCATTAAAA
*
21100056 GATGGAAGGAATGTTTTTAAC
1 GATGGAAGAAATGTTTTTAAC
21100077 GATGGAAGAAATGTTTTTA
1 GATGGAAGAAATGTTTTTA
21100096 GCAACGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.35
Consensus pattern (21 bp):
GATGGAAGAAATGTTTTTAAC
Found at i:21105014 original size:311 final size:312
Alignment explanation
Indices: 21104526--21105135 Score: 886
Period size: 311 Copynumber: 2.0 Consensus size: 312
21104516 TACAGAGGAA
*
21104526 TATTATGTCAAATTTTAAGAAATATTATGAGAATTCTAAGTGAAGGAATTTTGCCACAATTTCAC
1 TATTATGTCAAATTTTAAAAAATATTATGAGAATTCTAAGTGAAGGAATTTTGCCACAATTTCAC
** * * * * * *
21104591 CTAGATATTAGGGAATTTAGAAAGATTTTGAAACTAAATATTCTTATTTTATTTCTAAATAAAAT
66 CTAGATATTAGAAAATTTAAAAAGACTTTGAAACTAAAGATTATCATTTTATTCCTAAATAAAAT
*
21104656 GAATTAAATTTAAATATGTGTTAGGTAATTTTAATTGATTGTTTGCATTTAATTTACAATCATGT
131 GAATTAAATTTAAATATGTGTTAGATAATTTTAATTGATTGTTTGCATTTAATTTACAATCATGT
** * * *
21104721 CATACATTTGCGTTATATGATATTGGCTTGCATGTTATTGTTTTCAAAAAATTAATGAATGGC-A
196 CATACATTTGCACTATATAACATTGGCTTGCATGTTATCGTTTTCAAAAAATTAATGAATGGCTA
* *
21104785 GTTTTTGAGAAAACTATTTTTAATAA-T-AAAAAACTAATTCCGAAGTAAAAT
261 -ATTTTGAGAAAACTATTTTAAATAATTAAAAAAACTAATTCCGAAGTAAAAT
* * * *
21104836 TATTATGTCAAATTTTAAAAAATATTATGAGAATTCTAAGTGGAGGCAATTTT-TCATAATTTCG
1 TATTATGTCAAATTTTAAAAAATATTATGAGAATTCTAAGTGAAGG-AATTTTGCCACAATTTCA
*
21104900 CCTAGATATTAGAAAATTTAAAAAGTACTTTGAAACTAAGGATTATCATTTTATTCCTAAATAAA
65 CCTAGATATTAGAAAATTTAAAAAG-ACTTTGAAACTAAAGATTATCATTTTATTCCTAAATAAA
* * *
21104965 ATGAATTAAATTTAAATATGTGTTAGATAATTTTAATTGATTGTTTGCATTTAATTTATATTCGT
129 ATGAATTAAATTTAAATATGTGTTAGATAATTTTAATTGATTGTTTGCATTTAATTTACAATCAT
* * * * *
21105030 TTCATACATTTGCACTATATAACGTTGGCTTGCATTTTATCGTTTTCTAAATATTAATGAATGGC
194 GTCATACATTTGCACTATATAACATTGGCTTGCATGTTATCGTTTTCAAAAAATTAATGAATGGC
*
21105095 TAATTTTGGGAAAACTATTTTAAATAATTAAAAAAACTAAT
259 TAATTTTGAGAAAACTATTTTAAATAATTAAAAAAACTAAT
21105136 ACTCTCAAGT
Statistics
Matches: 264, Mismatches: 31, Indels: 7
0.87 0.10 0.02
Matches are distributed among these distances:
310 74 0.28
311 177 0.67
312 2 0.01
313 11 0.04
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.41
Consensus pattern (312 bp):
TATTATGTCAAATTTTAAAAAATATTATGAGAATTCTAAGTGAAGGAATTTTGCCACAATTTCAC
CTAGATATTAGAAAATTTAAAAAGACTTTGAAACTAAAGATTATCATTTTATTCCTAAATAAAAT
GAATTAAATTTAAATATGTGTTAGATAATTTTAATTGATTGTTTGCATTTAATTTACAATCATGT
CATACATTTGCACTATATAACATTGGCTTGCATGTTATCGTTTTCAAAAAATTAATGAATGGCTA
ATTTTGAGAAAACTATTTTAAATAATTAAAAAAACTAATTCCGAAGTAAAAT
Found at i:21105809 original size:15 final size:14
Alignment explanation
Indices: 21105789--21105838 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
21105779 GTGCAAGGCA
21105789 TCTTTTTAGCATTTT
1 TCTTTTT-GCATTTT
*
21105804 TCTTTTTCTCATTTT
1 TCTTTTT-GCATTTT
*
21105819 TCATTTTTGAATTTT
1 TC-TTTTTGCATTTT
21105834 TCTTT
1 TCTTT
21105839 AATATTTTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 3 0.10
15 22 0.73
16 5 0.17
ACGTcount: A:0.12, C:0.14, G:0.04, T:0.70
Consensus pattern (14 bp):
TCTTTTTGCATTTT
Found at i:21106714 original size:29 final size:27
Alignment explanation
Indices: 21106670--21106725 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
21106660 TAGTCTATCA
*
21106670 AAATTTAAAATTTAATATTTT-TATTAT
1 AAATTTAAAATATAAT-TTTTATATTAT
21106697 AAATTATATAAATATAATTTTTATATTAT
1 AAATT-TA-AAATATAATTTTTATATTAT
21106726 TTTAATTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 5 0.20
28 6 0.24
29 14 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
AAATTTAAAATATAATTTTTATATTAT
Found at i:21112450 original size:4 final size:4
Alignment explanation
Indices: 21112441--21112467 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
21112431 TTAAGCATTG
21112441 ATTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATT
21112468 TTAATTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:21112812 original size:13 final size:14
Alignment explanation
Indices: 21112794--21112822 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
21112784 ATAAAAAAAA
21112794 TTTAATTTTT-AAT
1 TTTAATTTTTGAAT
21112807 TTTAATTTTTGAAT
1 TTTAATTTTTGAAT
21112821 TT
1 TT
21112823 AAAAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTAATTTTTGAAT
Found at i:21115722 original size:31 final size:31
Alignment explanation
Indices: 21115661--21115724 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
21115651 ATTGCATATT
* * *
21115661 TTGCATGGTTTATATATTCTGATTTACATGA
1 TTGCATGATTTATATAATATGATTTACATGA
* *
21115692 TTGCATGATTTATATAATATTATTTGCATGA
1 TTGCATGATTTATATAATATGATTTACATGA
21115723 TT
1 TT
21115725 ATGTATTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.50
Consensus pattern (31 bp):
TTGCATGATTTATATAATATGATTTACATGA
Found at i:21115740 original size:20 final size:20
Alignment explanation
Indices: 21115691--21115880 Score: 70
Period size: 20 Copynumber: 9.7 Consensus size: 20
21115681 GATTTACATG
21115691 ATTGCATGATTTATATAATATTA
1 ATTGCATGA-TTATAT-AT-TTA
* *
21115714 TTTGCATGATTATGTATTTA
1 ATTGCATGATTATATATTTA
21115734 ATTGCATG--T-T-TA--T-
1 ATTGCATGATTATATATTTA
*
21115747 -TTGCATGATTTATGTATTATTA
1 ATTGCATGA-TTATATA-T-TTA
*
21115769 GTTGCATGATTATATATTTAA
1 ATTGCATGATTATATATTT-A
*
21115790 TTAGTTGCATGATTATTTATTTA
1 --A-TTGCATGATTATATATTTA
21115813 ATTGCAT-A-T-T-TATTT-
1 ATTGCATGATTATATATTTA
21115828 A---CATGATTTATATATTATTA
1 ATTGCATGA-TTATATA-T-TTA
* *
21115848 TTTGCATGATTATATGTTTA
1 ATTGCATGATTATATATTTA
* *
21115868 ACTGCATGTTTAT
1 ATTGCATGATTAT
21115881 TTGCATGATT
Statistics
Matches: 130, Mismatches: 11, Indels: 55
0.66 0.06 0.28
Matches are distributed among these distances:
12 10 0.08
13 1 0.01
14 1 0.01
15 3 0.02
16 9 0.07
17 6 0.05
18 3 0.02
19 3 0.02
20 31 0.24
21 7 0.05
22 17 0.13
23 22 0.17
24 17 0.13
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.53
Consensus pattern (20 bp):
ATTGCATGATTATATATTTA
Found at i:21115797 original size:24 final size:24
Alignment explanation
Indices: 21115747--21115815 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
21115737 GCATGTTTAT
*
21115747 TTGCATGATT-TATGTATT-ATTAG
1 TTGCATGATTATATAT-TTAATTAG
21115770 TTGCATGATTATATATTTAATTAG
1 TTGCATGATTATATATTTAATTAG
*
21115794 TTGCATGATTATTTATTTAATT
1 TTGCATGATTATATATTTAATT
21115816 GCATATTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
23 12 0.29
24 30 0.71
ACGTcount: A:0.29, C:0.04, G:0.13, T:0.54
Consensus pattern (24 bp):
TTGCATGATTATATATTTAATTAG
Found at i:21115800 original size:79 final size:79
Alignment explanation
Indices: 21115692--21115868 Score: 259
Period size: 79 Copynumber: 2.3 Consensus size: 79
21115682 ATTTACATGA
* * * *
21115692 TTGCATGATT-TATA-TAATATTATTTGCATGATTATGTATTTAATTGCATGTTTATTTGCATGA
1 TTGCATGATTATATATTTA-ATTAGTTGCATGATTATGTATTTAATTGCATATTTATTTACATGA
*
21115755 TTTATGTATTATTAG
65 TTTATATATTATTAG
*
21115770 TTGCATGATTATATATTTAATTAGTTGCATGATTATTTATTTAATTGCATATTTATTTACATGAT
1 TTGCATGATTATATATTTAATTAGTTGCATGATTATGTATTTAATTGCATATTTATTTACATGAT
*
21115835 TTATATATTATTAT
66 TTATATATTATTAG
*
21115849 TTGCATGATTATATGTTTAA
1 TTGCATGATTATATATTTAA
21115869 CTGCATGTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
78 10 0.11
79 77 0.87
80 2 0.02
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (79 bp):
TTGCATGATTATATATTTAATTAGTTGCATGATTATGTATTTAATTGCATATTTATTTACATGAT
TTATATATTATTAG
Found at i:21115859 original size:55 final size:55
Alignment explanation
Indices: 21115770--21115953 Score: 235
Period size: 55 Copynumber: 3.3 Consensus size: 55
21115760 GTATTATTAG
* * *
21115770 TTGCATGA-TTATATATTTAATTAGTTGCATGATTATTTATTTAATTGCATATTTAT
1 TTGCATGATTTATATA-TT-ATTATTTGCATGATTATATATTTAATTGCATGTTTAT
* * *
21115826 TTACATGATTTATATATTATTATTTGCATGATTATATGTTTAACTGCATGTTTAT
1 TTGCATGATTTATATATTATTATTTGCATGATTATATATTTAATTGCATGTTTAT
** * * *
21115881 TTGCATGATTTATGCATTTTTATTTGTATGATTATATATTTAATTGTATGTTTAT
1 TTGCATGATTTATATATTATTATTTGCATGATTATATATTTAATTGCATGTTTAT
*
21115936 TTGCATGGTTTATATATT
1 TTGCATGATTTATATATT
21115954 TAATTGTATG
Statistics
Matches: 110, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
55 94 0.85
56 9 0.08
57 7 0.06
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.55
Consensus pattern (55 bp):
TTGCATGATTTATATATTATTATTTGCATGATTATATATTTAATTGCATGTTTAT
Found at i:21115896 original size:23 final size:23
Alignment explanation
Indices: 21115870--21115913 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
21115860 TATGTTTAAC
21115870 TGCATGTTTATTTGCATGATTTA
1 TGCATGTTTATTTGCATGATTTA
* *
21115893 TGCATTTTTATTTGTATGATT
1 TGCATGTTTATTTGCATGATT
21115914 ATATATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.07, G:0.16, T:0.57
Consensus pattern (23 bp):
TGCATGTTTATTTGCATGATTTA
Found at i:21115921 original size:22 final size:22
Alignment explanation
Indices: 21115876--21115921 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
21115866 TAACTGCATG
21115876 TTTATTTGCATGATTTATGCATT
1 TTTATTTGCATGATTTAT-CATT
*
21115899 TTTATTTGTATGATTATAT-ATT
1 TTTATTTGCATGATT-TATCATT
21115921 T
1 T
21115922 AATTGTATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 14 0.67
24 3 0.14
ACGTcount: A:0.24, C:0.04, G:0.11, T:0.61
Consensus pattern (22 bp):
TTTATTTGCATGATTTATCATT
Found at i:21115952 original size:33 final size:32
Alignment explanation
Indices: 21115899--21115980 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 32
21115889 TTTATGCATT
*
21115899 TTTATTTGTATGATTATATATTTAATTGTATG
1 TTTATTTGCATGATTATATATTTAATTGTATG
*
21115931 TTTATTTGCATGGTTTATATATTTAATTGTATG
1 TTTATTTGCAT-GATTATATATTTAATTGTATG
* * *
21115964 TCTATTTGTATAATTAT
1 TTTATTTGCATGATTAT
21115981 TAATTTATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 14 0.33
33 29 0.67
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.59
Consensus pattern (32 bp):
TTTATTTGCATGATTATATATTTAATTGTATG
Found at i:21116098 original size:25 final size:24
Alignment explanation
Indices: 21116058--21116118 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
21116048 TTATTATTGC
*
21116058 ATGATTTTATATTTATTACATGAT
1 ATGATATTATATTTATTACATGAT
*
21116082 ATGATATTATATGTTATTGCATGAT
1 ATGATATTATAT-TTATTACATGAT
*
21116107 -TAATATT-TATTT
1 ATGATATTATATTT
21116119 GAATGATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 2 0.06
23 3 0.09
24 17 0.52
25 11 0.33
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (24 bp):
ATGATATTATATTTATTACATGAT
Found at i:21116355 original size:20 final size:18
Alignment explanation
Indices: 21116289--21116357 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
21116279 TTGTATGATG
21116289 ATATATTTGCATGATATT
1 ATATATTTGCATGATATT
* * *
21116307 TTATATTTACATGATTGTT
1 ATATATTTGCATGA-TATT
21116326 AT-TA-TTGCATGATAATT
1 ATATATTTGCATGAT-ATT
21116343 AATATATTTGCATGA
1 -ATATATTTGCATGA
21116358 CATTCTTACA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
16 1 0.03
17 9 0.22
18 16 0.40
19 6 0.15
20 8 0.20
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.49
Consensus pattern (18 bp):
ATATATTTGCATGATATT
Found at i:21118718 original size:140 final size:140
Alignment explanation
Indices: 21118466--21118724 Score: 353
Period size: 140 Copynumber: 1.9 Consensus size: 140
21118456 AAATAGTCCC
*
21118466 AAATAGACATAAACAATAACTTTTTCACACATATCATCTGTAGAAACCAAGTTTAATCAATTAGA
1 AAATAGACATAAACAATAACTTTTTCACACATATCATCTGTAGAAACCAAGTTCAATCAATTAGA
* * * *
21118531 CAAATTTAATATCAAGTATTGAAGCTATCCAAACTGTTAAAATAGAACAATAACAACAAATTTAT
66 CAAATTTAATATCAAGTATTGAAACTATCAAAACTATTAAAACAGAACAATAACAACAAATTTAT
21118596 ATTTTTACCT
131 ATTTTTACCT
* * * * *
21118606 AAATAGACATAAACAATAACTTTTTCATACATATCAAT-TGTGGCAACTAAGTTCAAT-ACTTTC
1 AAATAGACATAAACAATAACTTTTTCACACATATC-ATCTGTAGAAACCAAGTTCAATCA-ATT-
* * *
21118669 A-ATAAGTTTAATATCATGTATTGAAACTATCAAAACTATTAAAACAGAACAATAAC
63 AGACAAATTTAATATCAAGTATTGAAACTATCAAAACTATTAAAACAGAACAATAAC
21118725 TGTTAATTTG
Statistics
Matches: 103, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
139 1 0.01
140 99 0.96
141 3 0.03
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.31
Consensus pattern (140 bp):
AAATAGACATAAACAATAACTTTTTCACACATATCATCTGTAGAAACCAAGTTCAATCAATTAGA
CAAATTTAATATCAAGTATTGAAACTATCAAAACTATTAAAACAGAACAATAACAACAAATTTAT
ATTTTTACCT
Found at i:21121919 original size:12 final size:12
Alignment explanation
Indices: 21121873--21121920 Score: 60
Period size: 12 Copynumber: 3.7 Consensus size: 12
21121863 TTTAAATATT
21121873 ATGGTTTGTTGA
1 ATGGTTTGTTGA
21121885 ATGGTATTGTATGA
1 ATGGT-TTGT-TGA
21121899 TATTGGTTTGTTGA
1 -A-TGGTTTGTTGA
21121913 ATGGTTTG
1 ATGGTTTG
21121921 CTGTTTCTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 12 0.38
13 5 0.16
14 6 0.19
15 5 0.16
16 4 0.12
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (12 bp):
ATGGTTTGTTGA
Found at i:21123685 original size:31 final size:31
Alignment explanation
Indices: 21123647--21123705 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
21123637 GGACTCAGAG
* *
21123647 TATGACCCTTGCTCAGGCTACCATGGATAAC
1 TATGACCCTTACTCAAGCTACCATGGATAAC
* *
21123678 TATGACCCTTACTTAAGCTACTATGGAT
1 TATGACCCTTACTCAAGCTACCATGGAT
21123706 GACTTATCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (31 bp):
TATGACCCTTACTCAAGCTACCATGGATAAC
Found at i:21125176 original size:35 final size:35
Alignment explanation
Indices: 21125130--21125201 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
21125120 ATATATAAAC
* *
21125130 CAAATGTTTTCTGGGCATAAACCTACAATTGACTT
1 CAAATGTTTTCTGAGCATAAACCTACAACTGACTT
21125165 CAAATGTTTTCTGAGCATAAACCTACAACTGACTT
1 CAAATGTTTTCTGAGCATAAACCTACAACTGACTT
21125200 CA
1 CA
21125202 CATATATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.32
Consensus pattern (35 bp):
CAAATGTTTTCTGAGCATAAACCTACAACTGACTT
Found at i:21125437 original size:62 final size:61
Alignment explanation
Indices: 21125348--21125556 Score: 163
Period size: 62 Copynumber: 3.3 Consensus size: 61
21125338 ATTTATTATG
** * *
21125348 TAGATTATTAAAGGTATTTTGGGCCAAAAATACCTTCAAGAATCCGTTCTAACTTTTTTGTA
1 TAGATTATTAAAGGTATTTTTAGCCAAAAATACCTTCAAGAATCCATTATAA-TTTTTTGTA
* * * * *
21125410 TAGATTATTGAAGGTATTTTTAACC-AAAAT-CGTCTTCAATAATCCCTTATGAAAATTTATTG-
1 TAGATTATTAAAGGTATTTTTAGCCAAAAATAC--CTTCAAGAATCCATTAT---AATTTTTTGT
21125472 A
61 A
* * * * * * * *
21125473 GTGGATTATTGAAGGCACTTTCAGCTAAAAATATCTTCAAGAATCCATTTTATATTTTTTGTA
1 -TAGATTATTAAAGGTATTTTTAGCCAAAAATACCTTCAAGAATCCATTATA-ATTTTTTGTA
*
21125536 TGGATTATTAAAGGTATTTTT
1 TAGATTATTAAAGGTATTTTT
21125557 CTGTCGAAAA
Statistics
Matches: 114, Mismatches: 23, Indels: 20
0.73 0.15 0.13
Matches are distributed among these distances:
60 1 0.01
61 6 0.05
62 59 0.52
63 2 0.02
64 39 0.34
65 7 0.06
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (61 bp):
TAGATTATTAAAGGTATTTTTAGCCAAAAATACCTTCAAGAATCCATTATAATTTTTTGTA
Found at i:21132522 original size:23 final size:23
Alignment explanation
Indices: 21132495--21132540 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
21132485 GATGTTGATT
21132495 TTAAAAATTTTCTTGAATTTATA
1 TTAAAAATTTTCTTGAATTTATA
21132518 TTAAAAATTTTCTTGAATTTATA
1 TTAAAAATTTTCTTGAATTTATA
21132541 GAAGAAGGAG
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:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (23 bp):
TTAAAAATTTTCTTGAATTTATA
Found at i:21136949 original size:16 final size:18
Alignment explanation
Indices: 21136918--21136952 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
21136908 ATGTCTATAT
21136918 ATAAAAAATTAGTAAATA
1 ATAAAAAATTAGTAAATA
21136936 ATAAAAAA-TA-TAAATA
1 ATAAAAAATTAGTAAATA
21136952 A
1 A
21136953 ATGCACAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 2 0.12
18 8 0.47
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
ATAAAAAATTAGTAAATA
Found at i:21137259 original size:14 final size:14
Alignment explanation
Indices: 21137240--21137267 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21137230 TACTTTCTAT
21137240 GTAGCAAAAGCAAA
1 GTAGCAAAAGCAAA
21137254 GTAGCAAAAGCAAA
1 GTAGCAAAAGCAAA
21137268 TCTTAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.14, G:0.21, T:0.07
Consensus pattern (14 bp):
GTAGCAAAAGCAAA
Found at i:21141116 original size:6 final size:7
Alignment explanation
Indices: 21141099--21141126 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
21141089 ATGTGGTGTT
21141099 TTTTTTC
1 TTTTTTC
21141106 TTTTTTC
1 TTTTTTC
21141113 TTTTTTC
1 TTTTTTC
21141120 TTTTTTC
1 TTTTTTC
21141127 CCCTCCTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTC
Found at i:21143469 original size:22 final size:22
Alignment explanation
Indices: 21143422--21143481 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
21143412 AAAATATATA
21143422 AATTATCGAGAATTA-CTAAAG
1 AATTATCGAGAATTATCTAAAG
*
21143443 AATTATGCGAGAATTATC-AATG
1 AATTAT-CGAGAATTATCTAAAG
*
21143465 GATTATCGATGAATTAT
1 AATTATCGA-GAATTAT
21143482 TTTATAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 9 0.26
22 24 0.71
23 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (22 bp):
AATTATCGAGAATTATCTAAAG
Found at i:21147350 original size:28 final size:27
Alignment explanation
Indices: 21147319--21147378 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
21147309 TATATATATA
* *
21147319 ATATTATATTATATTATAATTGTTTCAT
1 ATATTATATTAAATTA-AATTGGTTCAT
* *
21147347 ATATTTCTATTAAATTAAATTGGTTCTT
1 ATA-TTATATTAAATTAAATTGGTTCAT
21147375 ATAT
1 ATAT
21147379 AAAAATTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
27 1 0.04
28 15 0.56
29 11 0.41
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (27 bp):
ATATTATATTAAATTAAATTGGTTCAT
Found at i:21149325 original size:17 final size:17
Alignment explanation
Indices: 21149303--21149338 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
21149293 ATTTTTTCAC
21149303 TATCAAAAGTTTATAAT
1 TATCAAAAGTTTATAAT
21149320 TATCAAAAGTTTATAAT
1 TATCAAAAGTTTATAAT
21149337 TA
1 TA
21149339 AATAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (17 bp):
TATCAAAAGTTTATAAT
Found at i:21149760 original size:42 final size:42
Alignment explanation
Indices: 21149703--21149788 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
21149693 AGAACACCCC
* * *
21149703 TAAAAAATTCTTTGTAACATTTGATGATTAAATAATTATTTT
1 TAAAAAAATCATTGTAACATTTGATGATTAAATAATCATTTT
*
21149745 TAAAAAAATCATTGTAATATTTGATGATTAAATAATCATTTT
1 TAAAAAAATCATTGTAACATTTGATGATTAAATAATCATTTT
21149787 TA
1 TA
21149789 TAATTAGAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (42 bp):
TAAAAAAATCATTGTAACATTTGATGATTAAATAATCATTTT
Found at i:21150680 original size:2 final size:2
Alignment explanation
Indices: 21150673--21150711 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
21150663 TTATCTTCTA
21150673 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21150712 AAACTGACTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21153231 original size:15 final size:16
Alignment explanation
Indices: 21153206--21153238 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
21153196 AAAGATACCT
21153206 TCATATATCATCATCA
1 TCATATATCATCATCA
21153222 TCAT-TATCATCATCA
1 TCATATATCATCATCA
21153237 TC
1 TC
21153239 TACGAGAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.39
Consensus pattern (16 bp):
TCATATATCATCATCA
Found at i:21153296 original size:3 final size:3
Alignment explanation
Indices: 21153288--21153324 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
21153278 AAACTTTTAC
21153288 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
21153325 TACTGCAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:21155261 original size:2 final size:2
Alignment explanation
Indices: 21155249--21155278 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
21155239 GTTTGCAAAA
21155249 AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
21155279 CTTCAGGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21155499 original size:3 final size:3
Alignment explanation
Indices: 21155491--21155574 Score: 53
Period size: 3 Copynumber: 28.0 Consensus size: 3
21155481 GAAGTTAACA
* * * * * * * *
21155491 TAT TAT TAT TTT TAT TGT AAT TAT TAT TTT TGT TAT TGT AAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
21155539 T-T TTT TAT TAT TTT TAT TAT TAT AATT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
21155575 CATCATCATC
Statistics
Matches: 60, Mismatches: 19, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
2 2 0.03
3 56 0.93
4 2 0.03
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:21155517 original size:21 final size:20
Alignment explanation
Indices: 21155491--21155547 Score: 87
Period size: 21 Copynumber: 2.8 Consensus size: 20
21155481 GAAGTTAACA
21155491 TATTATTATTTTTATTGTAAT
1 TATTATT-TTTTTATTGTAAT
21155512 TATTATTTTTGTTATTGTAAT
1 TATTATTTTT-TTATTGTAAT
*
21155533 CATTATTTTTTTATT
1 TATTATTTTTTTATT
21155548 ATTTTTATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 8 0.24
21 26 0.76
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (20 bp):
TATTATTTTTTTATTGTAAT
Found at i:21155992 original size:16 final size:15
Alignment explanation
Indices: 21155967--21156030 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 15
21155957 TACTGTTACC
*
21155967 TTTTTTATTTTTTAT
1 TTTTTTATTTTTAAT
21155982 TTTTTTAATTTTTAAT
1 TTTTTT-ATTTTTAAT
** *
21155998 TTTCCTATTTTGAGAT
1 TTTTTTATTTTTA-AT
*
21156014 TTTTTT-TTGTTAAT
1 TTTTTTATTTTTAAT
21156028 TTT
1 TTT
21156031 ACCTTCAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
14 5 0.13
15 16 0.41
16 18 0.46
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (15 bp):
TTTTTTATTTTTAAT
Found at i:21157307 original size:24 final size:24
Alignment explanation
Indices: 21157280--21157327 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
21157270 GACTAATAGG
21157280 AAATCAAGTG-CTTCTAAGCACACA
1 AAATCAAGTGTC-TCTAAGCACACA
*
21157304 AAATCAGGTGTCTCTAAGCACACA
1 AAATCAAGTGTCTCTAAGCACACA
21157328 CCACCAACGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.21
Consensus pattern (24 bp):
AAATCAAGTGTCTCTAAGCACACA
Found at i:21157725 original size:25 final size:25
Alignment explanation
Indices: 21157697--21157773 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
21157687 GGAGTGTAAC
21157697 GATGCTTGAAGCAAGGATTTTTAGT
1 GATGCTTGAAGCAAGGATTTTTAGT
* * * **
21157722 GATGC-T-ATTG--AGGA-GTGTAAC
1 GATGCTTGA-AGCAAGGATTTTTAGT
21157743 GATGCTTGAAGCAAGGATTTTTAGT
1 GATGCTTGAAGCAAGGATTTTTAGT
21157768 GATGCT
1 GATGCT
21157774 ATCATAAAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 12
0.62 0.17 0.21
Matches are distributed among these distances:
21 8 0.22
22 6 0.17
23 2 0.06
24 6 0.17
25 14 0.39
ACGTcount: A:0.27, C:0.09, G:0.30, T:0.34
Consensus pattern (25 bp):
GATGCTTGAAGCAAGGATTTTTAGT
Found at i:21157733 original size:46 final size:46
Alignment explanation
Indices: 21157680--21157775 Score: 192
Period size: 46 Copynumber: 2.1 Consensus size: 46
21157670 AAGTTGAAAA
21157680 CTATTGAGGAGTGTAACGATGCTTGAAGCAAGGATTTTTAGTGATG
1 CTATTGAGGAGTGTAACGATGCTTGAAGCAAGGATTTTTAGTGATG
21157726 CTATTGAGGAGTGTAACGATGCTTGAAGCAAGGATTTTTAGTGATG
1 CTATTGAGGAGTGTAACGATGCTTGAAGCAAGGATTTTTAGTGATG
21157772 CTAT
1 CTAT
21157776 CATAAAATTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.28, C:0.09, G:0.29, T:0.33
Consensus pattern (46 bp):
CTATTGAGGAGTGTAACGATGCTTGAAGCAAGGATTTTTAGTGATG
Found at i:21159046 original size:11 final size:11
Alignment explanation
Indices: 21158993--21159046 Score: 56
Period size: 11 Copynumber: 4.7 Consensus size: 11
21158983 TATTTTCTTG
21158993 TTTCATTTGA-
1 TTTCATTTGAT
*
21159003 TTTGATTTGAT
1 TTTCATTTGAT
*
21159014 TTTAATTTGATTT
1 TTTCATTTGA--T
21159027 TTTCTATTTGAT
1 TTTC-ATTTGAT
21159039 TTTCATTT
1 TTTCATTT
21159047 TATTATATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 9 0.24
11 13 0.35
12 5 0.14
13 4 0.11
14 6 0.16
ACGTcount: A:0.19, C:0.06, G:0.09, T:0.67
Consensus pattern (11 bp):
TTTCATTTGAT
Found at i:21159059 original size:25 final size:25
Alignment explanation
Indices: 21159007--21159060 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
21158997 ATTTGATTTG
* * *
21159007 ATTTGATTTTAATTTGATTTTTTCT
1 ATTTGATTTTAATTTGATTATATAT
* *
21159032 ATTTGATTTTCATTTTATTATATAT
1 ATTTGATTTTAATTTGATTATATAT
21159057 ATTT
1 ATTT
21159061 TTTACTATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.67
Consensus pattern (25 bp):
ATTTGATTTTAATTTGATTATATAT
Found at i:21159080 original size:11 final size:12
Alignment explanation
Indices: 21159043--21159085 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
21159033 TTTGATTTTC
21159043 ATTTTATTATATAT
1 ATTTT-TTATAT-T
21159057 ATTTTTTACTATT
1 ATTTTTTA-TATT
21159070 ATTTTTT-TATT
1 ATTTTTTATATT
21159081 ATTTT
1 ATTTT
21159086 CAATTGAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 9 0.32
13 11 0.39
14 8 0.29
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTTTTATATT
Found at i:21162893 original size:9 final size:9
Alignment explanation
Indices: 21162881--21162905 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
21162871 AAAATAATTA
21162881 AAAAAAAAG
1 AAAAAAAAG
21162890 AAAAAAAAG
1 AAAAAAAAG
21162899 AAAAAAA
1 AAAAAAA
21162906 TAAAAGAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:21164338 original size:44 final size:45
Alignment explanation
Indices: 21164268--21164422 Score: 156
Period size: 44 Copynumber: 3.5 Consensus size: 45
21164258 GATACGAAAC
* ** *
21164268 CCCAAAATTTTTTGAATGTGAATCTTTGAAATTTCGAATGTGTAT
1 CCCAAAATTTTTTCAATGAAAATCTTTGAAATTTCGAATGTGAAT
* *
21164313 CCCAAAA-TTTTTCAATGAAAATCTTT-AACTTTC-ATATGAGAAT
1 CCCAAAATTTTTTCAATGAAAATCTTTGAAATTTCGA-ATGTGAAT
* * * * *
21164356 CCCAAAATTTTTTGAATGAGAATCTTTGAAATTTTGGAGGTGAAT
1 CCCAAAATTTTTTCAATGAAAATCTTTGAAATTTCGAATGTGAAT
* *
21164401 CCTAAAA-TTTTTCATTGAAAAT
1 CCCAAAATTTTTTCAATGAAAAT
21164423 ATTTAACTTT
Statistics
Matches: 89, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
42 1 0.01
43 19 0.21
44 45 0.51
45 24 0.27
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.39
Consensus pattern (45 bp):
CCCAAAATTTTTTCAATGAAAATCTTTGAAATTTCGAATGTGAAT
Found at i:21164381 original size:88 final size:88
Alignment explanation
Indices: 21164268--21164432 Score: 258
Period size: 88 Copynumber: 1.9 Consensus size: 88
21164258 GATACGAAAC
* * *
21164268 CCCAAAATTTTTTGAATGTGAATCTTTGAAATTTCGAATGTGTATCCCAAAATTTTTCAATGAAA
1 CCCAAAATTTTTTGAATGAGAATCTTTGAAATTTCGAAGGTGAATCCCAAAATTTTTCAATGAAA
*
21164333 ATCTTTAACTTTCATATGAGAAT
66 ATATTTAACTTTCATATGAGAAT
* * * *
21164356 CCCAAAATTTTTTGAATGAGAATCTTTGAAATTTTGGAGGTGAATCCTAAAATTTTTCATTGAAA
1 CCCAAAATTTTTTGAATGAGAATCTTTGAAATTTCGAAGGTGAATCCCAAAATTTTTCAATGAAA
21164421 ATATTTAACTTT
66 ATATTTAACTTT
21164433 TAAATGTGAG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 69 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (88 bp):
CCCAAAATTTTTTGAATGAGAATCTTTGAAATTTCGAAGGTGAATCCCAAAATTTTTCAATGAAA
ATATTTAACTTTCATATGAGAAT
Found at i:21164456 original size:88 final size:89
Alignment explanation
Indices: 21164287--21164571 Score: 279
Period size: 97 Copynumber: 3.1 Consensus size: 89
21164277 TTTTGAATGT
* * * * * * * *
21164287 GAATCTTTGAAATTTCGAATGTGTATCCCAAAATTTTTCAATGAAAATCTTTAACTTTCATATGA
1 GAATCTTTGAAATTTTGAATGTGAATCCTAAAATTTTTCATTGAAAATATTTAACTTTTAAATGT
* **
21164352 GA-ATCCC-AAAATTTTTTGAA-TGA
66 GAGA-CCCTGAAA-TTTTTGAACCAA
* *
21164375 GAATCTTTGAAATTTTGGAGGTGAATCCTAAAATTTTTCATTGAAAATATTTAACTTTTAAATGT
1 GAATCTTTGAAATTTTGAATGTGAATCCTAAAATTTTTCATTGAAAATATTTAACTTTTAAATGT
*
21164440 GAGACCCTGAAATTTTTTAACCAA
66 GAGACCCTGAAATTTTTGAACCAA
** * **
21164464 GAATCTTTGAACCTTTAAATTTTTTATTTGCCTCCCTAAAATTTTTCATTGAAAATATTTAACTT
1 GAATCTTTG-------AAATTTTGAATGTGAAT-CCTAAAATTTTTCATTGAAAATATTTAACTT
*
21164529 TTAAATGTGAGACCCTGAAATTTTTTAACCAA
58 TTAAATGTGAGACCCTGAAATTTTTGAACCAA
21164561 GAATCTTTGAA
1 GAATCTTTGAA
21164572 CCTTTAAATT
Statistics
Matches: 166, Mismatches: 20, Indels: 20
0.81 0.10 0.10
Matches are distributed among these distances:
88 67 0.40
89 14 0.08
90 2 0.01
96 11 0.07
97 72 0.43
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.40
Consensus pattern (89 bp):
GAATCTTTGAAATTTTGAATGTGAATCCTAAAATTTTTCATTGAAAATATTTAACTTTTAAATGT
GAGACCCTGAAATTTTTGAACCAA
Found at i:21164512 original size:97 final size:97
Alignment explanation
Indices: 21164401--21164607 Score: 407
Period size: 97 Copynumber: 2.1 Consensus size: 97
21164391 GGAGGTGAAT
21164401 CCTAAAATTTTTCATTGAAAATATTTAACTTTTAAATGTGAGACCCTGAAATTTTTTAACCAAGA
1 CCTAAAATTTTTCATTGAAAATATTTAACTTTTAAATGTGAGACCCTGAAATTTTTTAACCAAGA
21164466 ATCTTTGAACCTTTAAATTTTTTATTTGCCTC
66 ATCTTTGAACCTTTAAATTTTTTATTTGCCTC
21164498 CCTAAAATTTTTCATTGAAAATATTTAACTTTTAAATGTGAGACCCTGAAATTTTTTAACCAAGA
1 CCTAAAATTTTTCATTGAAAATATTTAACTTTTAAATGTGAGACCCTGAAATTTTTTAACCAAGA
21164563 ATCTTTGAACCTTTAAATTTTTTATTTGCCTC
66 ATCTTTGAACCTTTAAATTTTTTATTTGCCTC
21164595 CCT-AAATTTTTCA
1 CCTAAAATTTTTCA
21164608 AACATAAAGC
Statistics
Matches: 110, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
96 10 0.09
97 100 0.91
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (97 bp):
CCTAAAATTTTTCATTGAAAATATTTAACTTTTAAATGTGAGACCCTGAAATTTTTTAACCAAGA
ATCTTTGAACCTTTAAATTTTTTATTTGCCTC
Found at i:21164673 original size:19 final size:19
Alignment explanation
Indices: 21164640--21164709 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
21164630 ATCTCTTGCA
* *
21164640 AATCTTTGGAGTTCTTATG
1 AATCTTTGAATTTCTTATG
* *
21164659 AATCTTTAAATTTCTTACG
1 AATCTTTGAATTTCTTATG
* *
21164678 AA--TATGAATTTCTTATA
1 AATCTTTGAATTTCTTATG
21164695 AATCTTTGAATTTCT
1 AATCTTTGAATTTCT
21164710 CGCGAACCTG
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
17 13 0.32
19 27 0.68
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (19 bp):
AATCTTTGAATTTCTTATG
Found at i:21164699 original size:36 final size:36
Alignment explanation
Indices: 21164651--21164736 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
21164641 ATCTTTGGAG
* *
21164651 TTCTTATGAATCTTTAAATTTCTTACGAATATGAAT
1 TTCTTATGAATCTTTAAATTTCTCACGAACATGAAT
* * * *
21164687 TTCTTATAAATCTTTGAATTTCTCGCGAACCTGAAT
1 TTCTTATGAATCTTTAAATTTCTCACGAACATGAAT
*
21164723 CTCTTATGAATCTT
1 TTCTTATGAATCTT
21164737 ATTTCTTGTG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.45
Consensus pattern (36 bp):
TTCTTATGAATCTTTAAATTTCTCACGAACATGAAT
Found at i:21164864 original size:17 final size:17
Alignment explanation
Indices: 21164846--21165112 Score: 119
Period size: 17 Copynumber: 15.0 Consensus size: 17
21164836 GCAAACCTTA
*
21164846 CGAACTTGAATTTCTTA
1 CGAACTTGAATTTCTTG
*
21164863 CGAATCTTTAAATTTCTTG
1 CGAA-C-TTGAATTTCTTG
21164882 CGAA-TATGAATTTCTTG
1 CGAACT-TGAATTTCTTG
*
21164899 TGAATCTTTGAATTTCTCT-
1 CGAA-C-TTGAATTTCT-TG
* * *
21164918 CAAACTTGAATCTCTTA
1 CGAACTTGAATTTCTTG
* *
21164935 TGAATATTTGAATTTCTTG
1 CG-A-ACTTGAATTTCTTG
* *
21164954 TGAATCTTTGAAGTTT-TTA
1 CGAA-C-TTGAA-TTTCTTG
*
21164973 C-AAATCTGAATTTCTTG
1 CGAACT-TGAATTTCTTG
* *
21164990 CGAATCTTTAAAATTCTTG
1 CGAA-C-TTGAATTTCTTG
* * *
21165009 TGAACCTAAATTTCTTG
1 CGAACTTGAATTTCTTG
*
21165026 CGAATTTGAATTTCTTG
1 CGAACTTGAATTTCTTG
* *
21165043 CAAATCTTTGAATTTCTAG
1 CGAA-C-TTGAATTTCTTG
** * *
21165062 TAAACCTGAATTTCTTA
1 CGAACTTGAATTTCTTG
* *
21165079 CGAACTTAAATTTTTTG
1 CGAACTTGAATTTCTTG
* *
21165096 TGAACTTGAATCTCTTG
1 CGAACTTGAATTTCTTG
21165113 TAAATCTTTG
Statistics
Matches: 186, Mismatches: 44, Indels: 40
0.69 0.16 0.15
Matches are distributed among these distances:
16 6 0.03
17 93 0.50
18 10 0.05
19 71 0.38
20 6 0.03
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (17 bp):
CGAACTTGAATTTCTTG
Found at i:21164904 original size:36 final size:37
Alignment explanation
Indices: 21164846--21165111 Score: 155
Period size: 36 Copynumber: 7.5 Consensus size: 37
21164836 GCAAACCTTA
21164846 CGAAC-TTGAATTTCTTACGAATCTTTAAATTTCTTG
1 CGAACTTTGAATTTCTTACGAATCTTTAAATTTCTTG
* ** *
21164882 CGAA-TATGAATTTCTTGTGAATCTTTGAATTTCTCT-
1 CGAACTTTGAATTTCTTACGAATCTTTAAATTTCT-TG
* * * * *
21164918 CAAAC-TTGAATCTCTTATGAATATTTGAATTTCTTG
1 CGAACTTTGAATTTCTTACGAATCTTTAAATTTCTTG
* * *
21164954 TGAATCTTTGAAGTTT-TTACAAATC--TGAATTTCTTG
1 CGAA-CTTTGAA-TTTCTTACGAATCTTTAAATTTCTTG
* * ** *
21164990 CGAATCTTTAAAATTCTTGTGAA-C-CTAAATTTCTTG
1 CGAA-CTTTGAATTTCTTACGAATCTTTAAATTTCTTG
* * * *
21165026 CGAA-TTTGAATTTCTTGCAAATCTTTGAATTTCTAG
1 CGAACTTTGAATTTCTTACGAATCTTTAAATTTCTTG
** * *
21165062 TAAAC-CTGAATTTCTTACGAA-C-TTAAATTTTTTG
1 CGAACTTTGAATTTCTTACGAATCTTTAAATTTCTTG
* *
21165096 TGAAC-TTGAATCTCTT
1 CGAACTTTGAATTTCTT
21165112 GTAAATCTTT
Statistics
Matches: 178, Mismatches: 40, Indels: 26
0.73 0.16 0.11
Matches are distributed among these distances:
34 35 0.20
35 6 0.03
36 122 0.69
37 2 0.01
38 11 0.06
39 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.45
Consensus pattern (37 bp):
CGAACTTTGAATTTCTTACGAATCTTTAAATTTCTTG
Found at i:21164983 original size:55 final size:55
Alignment explanation
Indices: 21164888--21165012 Score: 148
Period size: 55 Copynumber: 2.3 Consensus size: 55
21164878 CTTGCGAATA
*
21164888 TGAATTTCTTGTGAATCTTTGAATTTCTCTCAAACTTGAATCTCTTATGAATATT
1 TGAATTTCTTGTGAATCTTTGAATTTCTCTCAAACTTGAATCTCTTACGAATATT
* * *
21164943 TGAATTTCTTGTGAATCTTTGAAGTTT-T-TACAAA-TCTGAATTTCTTGCGAATCTT
1 TGAATTTCTTGTGAATCTTTGAA-TTTCTCT-CAAACT-TGAATCTCTTACGAATATT
* *
21164998 TAAAATTCTTGTGAA
1 TGAATTTCTTGTGAA
21165013 CCTAAATTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
54 2 0.03
55 56 0.92
56 3 0.05
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (55 bp):
TGAATTTCTTGTGAATCTTTGAATTTCTCTCAAACTTGAATCTCTTACGAATATT
Found at i:21165038 original size:206 final size:204
Alignment explanation
Indices: 21164651--21165046 Score: 530
Period size: 206 Copynumber: 1.9 Consensus size: 204
21164641 ATCTTTGGAG
* *
21164651 TTCTTATGAATCTTTAAATTTCTTACGAATATGAATTTCTTATAAATCTTTGAATTTCTCGCGAA
1 TTCTTACGAATCTTTAAATTTCTTACGAATATGAATTTCTTATAAATCTTTGAATTTCTCGCAAA
* *
21164716 CCTGAATCTCTTATGAATCTTATTTCTTGTGAATCTTTTAAGTTCACGTAAATTTGAATTTCTTG
66 CCTGAATCTCTTATGAATCTTATTTCTTGTGAATCTTTGAAGTTCACG-AAATCTGAATTTCTTG
* * *
21164781 CAAATTTGAAAATTTTCTTATGAACTTGAATTTCTTGCGAGTCTATGAATTTCTCGCAAACCTTA
130 CAAATTTGAAAA-TTTCTTATGAACCTAAATTTCTTGCGAATCTATGAATTTCTCGCAAACCTTA
21164846 CGAACTTGAAT
194 CGAACTTGAAT
* * * *
21164857 TTCTTACGAATCTTTAAATTTCTTGCGAATATGAATTTCTTGTGAATCTTTGAATTTCTCTCAAA
1 TTCTTACGAATCTTTAAATTTCTTACGAATATGAATTTCTTATAAATCTTTGAATTTCTCGCAAA
* * *
21164922 CTTGAATCTCTTATGAATATTTGAATTTCTTGTGAATCTTTGAAGTTTTTAC-AAATCTGAATTT
66 CCTGAATCTCTTATGAAT-CTT--ATTTCTTGTGAATCTTTGAAG--TTCACGAAATCTGAATTT
* * * *
21164986 CTTGCGAATCTTTAAAA-TTCTTGTGAACCTAAATTTCTTGCGAAT-T-TGAATTTCTTGCAAA
126 CTTGCAAAT-TTGAAAATTTCTTATGAACCTAAATTTCTTGCGAATCTATGAATTTCTCGCAAA
21165047 TCTTTGAATT
Statistics
Matches: 166, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
206 90 0.54
207 3 0.02
208 24 0.14
209 39 0.23
210 6 0.04
211 4 0.02
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (204 bp):
TTCTTACGAATCTTTAAATTTCTTACGAATATGAATTTCTTATAAATCTTTGAATTTCTCGCAAA
CCTGAATCTCTTATGAATCTTATTTCTTGTGAATCTTTGAAGTTCACGAAATCTGAATTTCTTGC
AAATTTGAAAATTTCTTATGAACCTAAATTTCTTGCGAATCTATGAATTTCTCGCAAACCTTACG
AACTTGAAT
Found at i:21165041 original size:53 final size:53
Alignment explanation
Indices: 21164979--21165091 Score: 145
Period size: 53 Copynumber: 2.1 Consensus size: 53
21164969 TTTACAAATC
* * * * *
21164979 TGAATTTCTTGCGAATCTTTAAAATTCTTGTGAACCTAAATTTCTTGCGAATT
1 TGAATTTCTTGCAAATCTTTAAAATTCTAGTAAACCTAAATTTCTTACGAACT
* * *
21165032 TGAATTTCTTGCAAATCTTTGAATTTCTAGTAAACCTGAATTTCTTACGAACT
1 TGAATTTCTTGCAAATCTTTAAAATTCTAGTAAACCTAAATTTCTTACGAACT
*
21165085 TAAATTT
1 TGAATTT
21165092 TTTGTGAACT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (53 bp):
TGAATTTCTTGCAAATCTTTAAAATTCTAGTAAACCTAAATTTCTTACGAACT
Found at i:21165548 original size:21 final size:23
Alignment explanation
Indices: 21165524--21165568 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
21165514 TTGCCAATCT
* *
21165524 TGGAGCCTTG-GAAT-TTTTCAA
1 TGGAACCTTGTGAATCTTTGCAA
21165545 TGGAACCTTGTGAATCTTTGCAA
1 TGGAACCTTGTGAATCTTTGCAA
21165568 T
1 T
21165569 TGTGTACCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 4 0.20
23 7 0.35
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (23 bp):
TGGAACCTTGTGAATCTTTGCAA
Found at i:21165823 original size:3 final size:3
Alignment explanation
Indices: 21165815--21165845 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
21165805 TTTAATTTAG
21165815 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
21165846 GTAGACACCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:21167956 original size:57 final size:57
Alignment explanation
Indices: 21167809--21167964 Score: 224
Period size: 58 Copynumber: 2.7 Consensus size: 57
21167799 ATTTCAAGAA
* * * *
21167809 AAAAAATATTCTCGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAATTTTCT
1 AAAAAATATTTTAGATGAAAAGTTGAAAGTATCAATTTT-TTTGAAAATAAAGTTTCT
* *
21167867 AAAAAATATTTTTGATGAAAAGTTGAAAGTATCAATTTTTTTCGAAATTAAAGTTTCT
1 AAAAAATATTTTAGATGAAAAGTTGAAAGTATCAATTTTTTT-GAAAATAAAGTTTCT
*
21167925 AAAAAGTATTTTAGA-GAAAAGTTGAAAGTATCAATTTTTT
1 AAAAAATATTTTAGATGAAAAGTTGAAAGTATCAATTTTTT
21167965 CTGTACAAAA
Statistics
Matches: 90, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
57 28 0.31
58 62 0.69
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (57 bp):
AAAAAATATTTTAGATGAAAAGTTGAAAGTATCAATTTTTTTGAAAATAAAGTTTCT
Found at i:21171944 original size:34 final size:34
Alignment explanation
Indices: 21171904--21171968 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
21171894 ATCAACAATG
21171904 GATGAAAAATGAGAAAAA-AAAAAAAAAAGAAGAT
1 GATGAAAAATGA-AAAAATAAAAAAAAAAGAAGAT
*
21171938 GATGAAAAATGAAAAAATGAAAAAAAAAGAA
1 GATGAAAAATGAAAAAATAAAAAAAAAAGAA
21171969 AGAAAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.17
34 24 0.83
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (34 bp):
GATGAAAAATGAAAAAATAAAAAAAAAAGAAGAT
Found at i:21171950 original size:41 final size:40
Alignment explanation
Indices: 21171905--21172004 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 40
21171895 TCAACAATGG
* * *
21171905 ATGAAAAATGAGAAAAAAAA-AAA-AAAAGAAGATGATGAAAA
1 ATGAAAAATGA-AAAAAAAAGAAAGAAAA-AAAAAGA-AAAAA
21171946 ATGAAAAAATGAAAAAAAAAGAAAGAAAAAAAAAGAAAAAA
1 ATG-AAAAATGAAAAAAAAAGAAAGAAAAAAAAAGAAAAAA
21171987 ATGAGAAAATGAAAAAAA
1 ATGA-AAAATGAAAAAAA
21172005 GATTCAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
40 1 0.02
41 31 0.60
42 16 0.31
43 4 0.08
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (40 bp):
ATGAAAAATGAAAAAAAAAGAAAGAAAAAAAAAGAAAAAA
Found at i:21171957 original size:15 final size:14
Alignment explanation
Indices: 21171939--21171982 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
21171929 AAAGAAGATG
21171939 ATGAAAAATGAAAA-A
1 ATGAAAAA--AAAAGA
21171954 ATGAAAAAAAAAGA
1 ATGAAAAAAAAAGA
*
21171968 AAGAAAAAAAAAGA
1 ATGAAAAAAAAAGA
21171982 A
1 A
21171983 AAAAATGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 4 0.15
14 15 0.56
15 8 0.30
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07
Consensus pattern (14 bp):
ATGAAAAAAAAAGA
Found at i:21171973 original size:14 final size:14
Alignment explanation
Indices: 21171956--21171987 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
21171946 ATGAAAAAAT
21171956 GAAAAAAAAAGAAA
1 GAAAAAAAAAGAAA
21171970 GAAAAAAAAAGAAA
1 GAAAAAAAAAGAAA
21171984 -AAAA
1 GAAAA
21171988 TGAGAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAAGAAA
Found at i:21173956 original size:45 final size:42
Alignment explanation
Indices: 21173843--21173963 Score: 158
Period size: 41 Copynumber: 2.9 Consensus size: 42
21173833 ACATTCGTCA
*
21173843 AGGAGCCATTTA-TTTTC-AAAGTTGTTGAGCCTTTGATTAG
1 AGGAGCCATTTATTTTTCTAAAGTTGTTGAGCCTCTGATTAG
*
21173883 AGGAGCCATTTATTTTT-TAAAGTTGTTGAGCCTCTGCTTAG
1 AGGAGCCATTTATTTTTCTAAAGTTGTTGAGCCTCTGATTAG
* *
21173924 AGGAGCCGTTGTTTATTTTTCTAAAGTTGTTGAGTCTCTG
1 AGGAGCC---ATTTATTTTTCTAAAGTTGTTGAGCCTCTG
21173964 TCATTGAGTC
Statistics
Matches: 71, Mismatches: 4, Indels: 7
0.87 0.05 0.09
Matches are distributed among these distances:
40 12 0.17
41 32 0.45
44 9 0.13
45 18 0.25
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.42
Consensus pattern (42 bp):
AGGAGCCATTTATTTTTCTAAAGTTGTTGAGCCTCTGATTAG
Found at i:21176156 original size:59 final size:57
Alignment explanation
Indices: 21176093--21176366 Score: 286
Period size: 61 Copynumber: 4.7 Consensus size: 57
21176083 ATTTTAAGAA
* * ** *
21176093 AAAAAATATTCTCGAGAAAAAGTTGAAAGTATTAATTTTTTTTTTAAAATAAATTTTCT
1 AAAAAATATT-TTGAGAAAAAGTTGAAAGTATCAA-TTTTCCTTGAAAATAAATTTTCT
* **
21176152 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCT
1 AAAAAATA-TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTCT
* * *
21176210 AAAAAAAATATTTTTGGGAAAAAAGTTGAAAATATCAATTTTCCTTAAAAATAAATTTTC-
1 --AAAAAATA-TTTTGAG-AAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTCT
* * * * *
21176270 AAAAGTGAAT-TTTTGAGGAAAAGTT--AAGTATCAATTTTTCTCGAAATTAAAGTTTCT
1 AAAA---AATATTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTCT
21176327 AAAAAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTCC
21176367 CTATACAAAA
Statistics
Matches: 180, Mismatches: 24, Indels: 24
0.79 0.11 0.11
Matches are distributed among these distances:
54 3 0.02
55 14 0.08
56 25 0.14
57 18 0.10
58 29 0.16
59 35 0.19
60 17 0.09
61 39 0.22
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (57 bp):
AAAAAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTCT
Found at i:21176261 original size:119 final size:115
Alignment explanation
Indices: 21176091--21176366 Score: 337
Period size: 119 Copynumber: 2.4 Consensus size: 115
21176081 TAATTTTAAG
* * * ** *
21176091 AAAAAAAATATTCTCGAGAAAAAGTTGAAAGTATTAATTTTTTTTTTAAAATAAATTTTCTAAAA
1 AAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAA-TTTTCCTTAAAAATAAATTTTC-AAAA
*
21176156 A-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAGCTTTCT
64 ATA-ATTTTTGAGGAAAAGTT--AAGTATCAATTTTCCTCGAAAATAAAG-TTTCT
* * *
21176210 AAAAAAAATATTTTTGGGAAAAAAGTTGAAAATATCAATTTTCCTTAAAAATAAATTTTCAAAAG
1 AAAAAAAATATTTTTGAG-AAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAA
* *
21176275 TGAATTTTTGAGGAAAAGTTAAGTATCAATTTTTCTCGAAATTAAAGTTTCT
65 T-AATTTTTGAGGAAAAGTTAAGTATCAATTTTCCTCGAAAATAAAGTTTCT
21176327 --AAAAAATA-TTTTGAGAAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCC
21176367 CTATACAAAA
Statistics
Matches: 139, Mismatches: 14, Indels: 14
0.83 0.08 0.08
Matches are distributed among these distances:
113 24 0.17
114 6 0.04
115 8 0.06
117 25 0.18
118 7 0.05
119 51 0.37
120 18 0.13
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.37
Consensus pattern (115 bp):
AAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAT
AATTTTTGAGGAAAAGTTAAGTATCAATTTTCCTCGAAAATAAAGTTTCT
Found at i:21177313 original size:19 final size:20
Alignment explanation
Indices: 21177270--21177313 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
21177260 TGGCTGGGTT
21177270 TTTTTGGGTTTGTGTATGAA
1 TTTTTGGGTTTGTGTATGAA
* *
21177290 GTTTTGGGTTT-TTTATGAA
1 TTTTTGGGTTTGTGTATGAA
21177309 TTTTT
1 TTTTT
21177314 TGGTAAGGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.14, C:0.00, G:0.25, T:0.61
Consensus pattern (20 bp):
TTTTTGGGTTTGTGTATGAA
Found at i:21177314 original size:20 final size:21
Alignment explanation
Indices: 21177269--21177316 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
21177259 ATGGCTGGGT
21177269 TTTTTTGGGTTTGTGTATGAA
1 TTTTTTGGGTTTGTGTATGAA
* *
21177290 -GTTTTGGGTTT-TTTATGAA
1 TTTTTTGGGTTTGTGTATGAA
21177309 TTTTTTGG
1 TTTTTTGG
21177317 TAAGGATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.12, C:0.00, G:0.27, T:0.60
Consensus pattern (21 bp):
TTTTTTGGGTTTGTGTATGAA
Found at i:21177685 original size:14 final size:15
Alignment explanation
Indices: 21177654--21177693 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
21177644 TTTAGTTTGA
21177654 TTTTATTATATATATT
1 TTTTATTAT-TATATT
*
21177670 TTTTACTATTAT-TT
1 TTTTATTATTATATT
21177684 TTTTATTATT
1 TTTTATTATT
21177694 TTCAATTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 11 0.50
15 3 0.14
16 8 0.36
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTATTATTATATT
Found at i:21177690 original size:11 final size:12
Alignment explanation
Indices: 21177653--21177695 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
21177643 TTTTAGTTTG
21177653 ATTTTATTATATAT
1 ATTTT-TTATAT-T
21177667 ATTTTTTACTATT
1 ATTTTTTA-TATT
21177680 ATTTTTT-TATT
1 ATTTTTTATATT
21177691 ATTTT
1 ATTTT
21177696 CAATTGAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 9 0.32
13 11 0.39
14 8 0.29
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTTTTATATT
Found at i:21179296 original size:16 final size:16
Alignment explanation
Indices: 21179275--21179305 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21179265 TTAGGGTTTT
21179275 GATTTTAGAGTTTGGA
1 GATTTTAGAGTTTGGA
*
21179291 GATTTTAGGGTTTGG
1 GATTTTAGAGTTTGG
21179306 GTTTTGGGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.45
Consensus pattern (16 bp):
GATTTTAGAGTTTGGA
Found at i:21179370 original size:31 final size:31
Alignment explanation
Indices: 21179322--21179433 Score: 131
Period size: 32 Copynumber: 3.6 Consensus size: 31
21179312 GGGTTTGGGG
21179322 TTTTGA-TTTA-AGGGTTTGGATTTTAGGGA
1 TTTTGATTTTAGAGGGTTTGGATTTTAGGGA
** *
21179351 TTTTGATTTTTTAGGGTTTGGATTTTAGGGG
1 TTTTGATTTTAGAGGGTTTGGATTTTAGGGA
* *
21179382 TTTCGGATTTTAGAGGGTTTGAATTTTAGGGGA
1 TTT-TGATTTTAGAGGGTTTGGATTTTA-GGGA
21179415 TTTTGGATTTTAG-GGGTTT
1 TTTT-GATTTTAGAGGGTTT
21179434 TAGAAACCTA
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
29 6 0.09
30 3 0.04
31 21 0.30
32 26 0.37
33 14 0.20
ACGTcount: A:0.17, C:0.01, G:0.32, T:0.50
Consensus pattern (31 bp):
TTTTGATTTTAGAGGGTTTGGATTTTAGGGA
Found at i:21179378 original size:14 final size:14
Alignment explanation
Indices: 21179264--21179429 Score: 103
Period size: 14 Copynumber: 11.5 Consensus size: 14
21179254 ATATAGAAGG
*
21179264 TTTAGGGTTTTGAT
1 TTTAGGGTTTGGAT
*
21179278 TTTAGAGTTTGGAGAT
1 TTTAGGGTTT-G-GAT
*
21179294 TTTAGGGTTTGGGT
1 TTTAGGGTTTGGAT
21179308 TTT--GG---GG--
1 TTTAGGGTTTGGAT
* *
21179315 TTTGGGGTTTTGAT
1 TTTAGGGTTTGGAT
*
21179329 TTAAGGGTTTGGAT
1 TTTAGGGTTTGGAT
*
21179343 TTTAGGGATTTTGATTT
1 TTTAGGG-TTTGGA--T
21179360 TTTAGGGTTTGGAT
1 TTTAGGGTTTGGAT
21179374 TTTAGGGGTTTCGGAT
1 TTTA-GGGTTT-GGAT
*
21179390 TTTAGAGGGTTTGAAT
1 TTT--AGGGTTTGGAT
21179406 TTTAGGGGATTTTGGAT
1 TTTA-GGG--TTTGGAT
21179423 TTTAGGG
1 TTTAGGG
21179430 GTTTTAGAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 36
0.71 0.08 0.21
Matches are distributed among these distances:
7 3 0.03
9 4 0.03
12 3 0.03
14 37 0.31
15 15 0.12
16 33 0.28
17 24 0.20
18 1 0.01
ACGTcount: A:0.16, C:0.01, G:0.35, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTGGAT
Found at i:21179419 original size:17 final size:16
Alignment explanation
Indices: 21179304--21179434 Score: 116
Period size: 16 Copynumber: 8.4 Consensus size: 16
21179294 TTTAGGGTTT
**
21179304 GGGTTTTGGGGTTT-G
1 GGGTTTTGGATTTTAG
*
21179319 GGGTTTT-GA-TTTAA
1 GGGTTTTGGATTTTAG
21179333 GGG-TTTGGATTTTAG
1 GGGTTTTGGATTTTAG
*
21179348 GGATTTT-GATTTTTTA-
1 GGGTTTTGGA--TTTTAG
21179364 GGG-TTTGGATTTTAG
1 GGGTTTTGGATTTTAG
*
21179379 GGGTTTCGGATTTTAG
1 GGGTTTTGGATTTTAG
*
21179395 AGGG-TTTGAATTTTAG
1 -GGGTTTTGGATTTTAG
21179411 GGGATTTTGGATTTTAG
1 GGG-TTTTGGATTTTAG
21179428 GGGTTTT
1 GGGTTTT
21179435 AGAAACCTAG
Statistics
Matches: 95, Mismatches: 9, Indels: 23
0.75 0.07 0.18
Matches are distributed among these distances:
13 6 0.06
14 11 0.12
15 24 0.25
16 32 0.34
17 22 0.23
ACGTcount: A:0.15, C:0.01, G:0.36, T:0.49
Consensus pattern (16 bp):
GGGTTTTGGATTTTAG
Found at i:21180930 original size:23 final size:22
Alignment explanation
Indices: 21180900--21180949 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
21180890 TTGTTTTTAT
*
21180900 TTATTTATTTATATAATTAATAA
1 TTATTTATTTATAAAATTAAT-A
*
21180923 TTATTTATTTTTAAAATTAATA
1 TTATTTATTTATAAAATTAATA
21180945 TTATT
1 TTATT
21180950 ATTATTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATTTATTTATAAAATTAATA
Found at i:21180951 original size:3 final size:3
Alignment explanation
Indices: 21180938--21180981 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
21180928 TATTTTTAAA
* ** *
21180938 ATT AAT ATT ATT ATT ATT ATT ATT ATT AAA ATT ATT AAT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
21180982 ACTAAAATGA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:21180956 original size:15 final size:15
Alignment explanation
Indices: 21180915--21180980 Score: 69
Period size: 15 Copynumber: 4.3 Consensus size: 15
21180905 TATTTATATA
21180915 ATTAATAATTATTTATT
1 ATTAA-AATTA-TTATT
* *
21180932 TTTAAAATTAATATT
1 ATTAAAATTATTATT
**
21180947 ATTATTATTATTATT
1 ATTAAAATTATTATT
*
21180962 ATTAAAATTATTAAT
1 ATTAAAATTATTATT
21180977 ATTA
1 ATTA
21180981 TACTAAAATG
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
15 31 0.77
16 5 0.12
17 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTAAAATTATTATT
Found at i:21187849 original size:58 final size:58
Alignment explanation
Indices: 21187778--21187889 Score: 188
Period size: 58 Copynumber: 1.9 Consensus size: 58
21187768 ATGTGAATTG
* * * *
21187778 ATTTAAATGATGTTAGGTTAATGTTTAGCATGCGTTTGCTAAAATACCTTTAAACGTA
1 ATTTAAATAATGTTAAGTTAATGTTTAGCATACGTTTGCTAAAATAACTTTAAACGTA
21187836 ATTTAAATAATGTTAAGTTAATGTTTAGCATACGTTTGCTAAAATAACTTTAAA
1 ATTTAAATAATGTTAAGTTAATGTTTAGCATACGTTTGCTAAAATAACTTTAAA
21187890 GGAGGTACTT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (58 bp):
ATTTAAATAATGTTAAGTTAATGTTTAGCATACGTTTGCTAAAATAACTTTAAACGTA
Found at i:21188473 original size:16 final size:16
Alignment explanation
Indices: 21188448--21188485 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
21188438 AAGCCCTAAG
*
21188448 CACCAAGACCAAAGAA
1 CACCAGGACCAAAGAA
21188464 CACCAGGACCAAAGAA
1 CACCAGGACCAAAGAA
21188480 CACCAG
1 CACCAG
21188486 CCCGGTTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.34, G:0.16, T:0.00
Consensus pattern (16 bp):
CACCAGGACCAAAGAA
Found at i:21191778 original size:3 final size:3
Alignment explanation
Indices: 21191770--21191804 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
21191760 TTTTGTCTAA
21191770 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
21191805 GTAAAAAAGA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:21192109 original size:2 final size:2
Alignment explanation
Indices: 21192102--21192135 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
21192092 AGGTCATAAT
*
21192102 TA TA TA TA TA TA TA TG 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
21192136 ACACCATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21192793 original size:20 final size:19
Alignment explanation
Indices: 21192770--21192816 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
21192760 TTAGGCAAAA
21192770 AAATTTTTTT-TTAAATTTTG
1 AAATTTTTTTATT--ATTTTG
21192790 AAATTATTTTTATTATTTTG
1 AAATT-TTTTTATTATTTTG
21192810 -AATTTTT
1 AAATTTTT
21192817 ATCATTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.12
19 4 0.16
20 11 0.44
21 5 0.20
22 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (19 bp):
AAATTTTTTTATTATTTTG
Found at i:21194235 original size:7 final size:7
Alignment explanation
Indices: 21194223--21194261 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
21194213 ATTCCTTTTC
21194223 AATAAAA
1 AATAAAA
21194230 AATAAAA
1 AATAAAA
21194237 AA-AAAA
1 AATAAAA
*
21194243 TA-AAAA
1 AATAAAA
21194249 AATAAAA
1 AATAAAA
21194256 AATAAA
1 AATAAA
21194262 TTAAAAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 10 0.34
7 19 0.66
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AATAAAA
Found at i:21194242 original size:11 final size:11
Alignment explanation
Indices: 21194226--21194279 Score: 51
Period size: 12 Copynumber: 5.0 Consensus size: 11
21194216 CCTTTTCAAT
21194226 AAAAAATAAAA
1 AAAAAATAAAA
21194237 AAAAAAT---A
1 AAAAAATAAAA
21194245 AAAAAATAAAA
1 AAAAAATAAAA
*
21194256 AATAAATTAAAA
1 AA-AAAATAAAA
*
21194268 ACAAAAAGAAAA
1 A-AAAAATAAAA
21194280 TTTCACATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
8 8 0.23
11 10 0.29
12 16 0.46
13 1 0.03
ACGTcount: A:0.85, C:0.02, G:0.02, T:0.11
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:21194246 original size:18 final size:18
Alignment explanation
Indices: 21194223--21194280 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
21194213 ATTCCTTTTC
21194223 AATAAAAAATAAAAAAAA
1 AATAAAAAATAAAAAAAA
*
21194241 AATAAAAAAATAAAAAATA
1 AAT-AAAAAATAAAAAAAA
* * *
21194260 AATTAAAAACAAAAAGAA
1 AATAAAAAATAAAAAAAA
21194278 AAT
1 AAT
21194281 TTCACATGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 17 0.50
19 17 0.50
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.14
Consensus pattern (18 bp):
AATAAAAAATAAAAAAAA
Found at i:21194250 original size:19 final size:20
Alignment explanation
Indices: 21194226--21194268 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
21194216 CCTTTTCAAT
21194226 AAAAAATAAAAAA-AAAATA
1 AAAAAATAAAAAATAAAATA
*
21194245 AAAAAATAAAAAATAAATTA
1 AAAAAATAAAAAATAAAATA
21194265 AAAA
1 AAAA
21194269 CAAAAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (20 bp):
AAAAAATAAAAAATAAAATA
Found at i:21194267 original size:26 final size:26
Alignment explanation
Indices: 21194223--21194274 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
21194213 ATTCCTTTTC
*
21194223 AATAAAAAATAAAAAAAAAATAAAAA
1 AATAAAAAATAAAAAAAAAACAAAAA
**
21194249 AATAAAAAATAAATTAAAAACAAAAA
1 AATAAAAAATAAAAAAAAAACAAAAA
21194275 GAAAATTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.85, C:0.02, G:0.00, T:0.13
Consensus pattern (26 bp):
AATAAAAAATAAAAAAAAAACAAAAA
Found at i:21200570 original size:23 final size:23
Alignment explanation
Indices: 21200541--21200584 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
21200531 TTTAAGCTAT
21200541 TTTTAGTAAATGACGCACAAGGA
1 TTTTAGTAAATGACGCACAAGGA
**
21200564 TTTTAGTAAATGGTGCACAAG
1 TTTTAGTAAATGACGCACAAG
21200585 AGAGATAGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (23 bp):
TTTTAGTAAATGACGCACAAGGA
Found at i:21201804 original size:63 final size:62
Alignment explanation
Indices: 21201706--21201880 Score: 280
Period size: 62 Copynumber: 2.8 Consensus size: 62
21201696 CATAAATGCC
* * * *
21201706 TTGAATAATCCCCTTAAATTTTTATGAGTA-GATTATTGAAGGCATTTTTGACTAAAACCACT
1 TTGAATAATCCCCTTCAATTTTT-TAAATAGGATTATTGAAGGTATTTTTGACTAAAACCACT
*
21201768 TTGAATAATCCCCCTCCAATTTTTTAAATAGGATTATTGAAGGTATTTTTGACTAAAACCACT
1 TTGAATAAT-CCCCTTCAATTTTTTAAATAGGATTATTGAAGGTATTTTTGACTAAAACCACT
21201831 TTGAATAATCCCCTTCAATTTTTTAAATAGGATTATTGAAGGTATTTTTG
1 TTGAATAATCCCCTTCAATTTTTTAAATAGGATTATTGAAGGTATTTTTG
21201881 GCCAAAAATG
Statistics
Matches: 105, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
62 53 0.50
63 52 0.50
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41
Consensus pattern (62 bp):
TTGAATAATCCCCTTCAATTTTTTAAATAGGATTATTGAAGGTATTTTTGACTAAAACCACT
Found at i:21201900 original size:62 final size:62
Alignment explanation
Indices: 21201704--21201916 Score: 259
Period size: 62 Copynumber: 3.4 Consensus size: 62
21201694 ACCATAAATG
* * * * *
21201704 CCTTGAATAATCCCCTTAAATTTTTATGAGTA-GATTATTGAAGGCATTTTTGACTAAAACCA
1 CCTTGAATAATCCCCTTCAATTTTT-TAAATAGGATTATTGAAGGTATTTTTGACTAAAAACA
* * *
21201766 CTTTGAATAATCCCCCTCCAATTTTTTAAATAGGATTATTGAAGGTATTTTTGACTAAAACCA
1 CCTTGAATAAT-CCCCTTCAATTTTTTAAATAGGATTATTGAAGGTATTTTTGACTAAAAACA
* * * **
21201829 CTTTGAATAATCCCCTTCAATTTTTTAAATAGGATTATTGAAGGTATTTTTGGCCAAAAATG
1 CCTTGAATAATCCCCTTCAATTTTTTAAATAGGATTATTGAAGGTATTTTTGACTAAAAACA
*
21201891 CCTTCAATAATCCCC-TCATATTTTTT
1 CCTTGAATAATCCCCTTCA-ATTTTTT
21201917 TTGGAATTAT
Statistics
Matches: 134, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
61 3 0.02
62 79 0.59
63 52 0.39
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.39
Consensus pattern (62 bp):
CCTTGAATAATCCCCTTCAATTTTTTAAATAGGATTATTGAAGGTATTTTTGACTAAAAACA
Found at i:21202119 original size:46 final size:47
Alignment explanation
Indices: 21202045--21202133 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 47
21202035 TTTTATAAGG
** *
21202045 GGATTATTAAAGGCATTTCTAG-TTAAAAATGCCTTGAATAATTTGT
1 GGATTATTAAAGGCATTTCTAGCAAAAAAATGCCTTCAATAATTTGT
* * *
21202091 GGATTATTGAAGGCATTTTTGGCAAAAAAATGCCTTCAATAAT
1 GGATTATTAAAGGCATTTCTAGCAAAAAAATGCCTTCAATAAT
21202134 CTCAATGTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 19 0.53
47 17 0.47
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (47 bp):
GGATTATTAAAGGCATTTCTAGCAAAAAAATGCCTTCAATAATTTGT
Found at i:21209516 original size:13 final size:13
Alignment explanation
Indices: 21209498--21209522 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21209488 TCTTGAAAAC
21209498 TTTTTTATGTTTT
1 TTTTTTATGTTTT
21209511 TTTTTTATGTTT
1 TTTTTTATGTTT
21209523 CTCTAAAAAA
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:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (13 bp):
TTTTTTATGTTTT
Found at i:21209625 original size:26 final size:24
Alignment explanation
Indices: 21209590--21209656 Score: 71
Period size: 26 Copynumber: 2.7 Consensus size: 24
21209580 TAAAGACCAG
*
21209590 TAAAATAAAATAGAAAAAATTTAAAA
1 TAAAATAAAAT-GAAAAAA-TGAAAA
* *
21209616 TAAAATAAAATTTAAAATATGAAAA
1 TAAAATAAAA-TGAAAAAATGAAAA
*
21209641 AAAAATAAAATGAAAA
1 TAAAATAAAATGAAAA
21209657 TGGAAAAGGG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 5 0.14
25 14 0.40
26 15 0.43
27 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (24 bp):
TAAAATAAAATGAAAAAATGAAAA
Found at i:21209642 original size:17 final size:16
Alignment explanation
Indices: 21209595--21209642 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
21209585 ACCAGTAAAA
21209595 TAAAATAGAAAAAATT
1 TAAAATAGAAAAAATT
*
21209611 TAAAATAAAATAAAATT
1 TAAAATAGAA-AAAATT
21209628 TAAAATATGAAAAAA
1 TAAAATA-GAAAAAA
21209643 AAATAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 9 0.32
17 17 0.61
18 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (16 bp):
TAAAATAGAAAAAATT
Found at i:21210587 original size:3 final size:3
Alignment explanation
Indices: 21210572--21210607 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
21210562 AAAAATAAAA
*
21210572 AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
21210608 CTATACAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:21210975 original size:87 final size:87
Alignment explanation
Indices: 21210829--21211006 Score: 268
Period size: 87 Copynumber: 2.0 Consensus size: 87
21210819 TGGAGATGAA
* *** *
21210829 GTGACCAGGACTGAGTCGAAGTTAAAAATAAATGATTGGGATGAAACCACGAGTCATAAGAAATG
1 GTGACCAGGACTGAGTCGAAGTAAAAAATAAATGACCAGGATAAAACCACGAGTCATAAGAAATG
21210894 ATCTAAAATGAGCCAAGATCAG
66 ATCTAAAATGAGCCAAGATCAG
21210916 GTGACCAGGACTGAGTCG-AGATAAAAAATAAATGACCAGGATAAAACCACGAGTCATAAGAAAT
1 GTGACCAGGACTGAGTCGAAG-TAAAAAATAAATGACCAGGATAAAACCACGAGTCATAAGAAAT
* * *
21210980 GATTTGAACTGAGCCAAGATCAG
65 GATCTAAAATGAGCCAAGATCAG
21211003 GTGA
1 GTGA
21211007 TTGGGATGAA
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
86 2 0.02
87 80 0.98
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.19
Consensus pattern (87 bp):
GTGACCAGGACTGAGTCGAAGTAAAAAATAAATGACCAGGATAAAACCACGAGTCATAAGAAATG
ATCTAAAATGAGCCAAGATCAG
Found at i:21211384 original size:238 final size:238
Alignment explanation
Indices: 21211140--21211667 Score: 562
Period size: 238 Copynumber: 2.2 Consensus size: 238
21211130 TGAAATTATG
* * *
21211140 AGTCAAATAATAAAATGACCAGGATCGAATCGAGGTCAAAGATGACTGACC-AGGATGAAACTGT
1 AGTCAAAAAATAAAATGACCAAGATCGAATCGAGGTCAAAGATGACTGACCGA-GATGAAACTGC
* *
21211204 AAGTTAGAAGATGATTTGGAT-GAAATCGAGATCGAATGACCAG-GATGAAACCACAAGTAAAAA
65 AAGTCAGAAGATGATCTGGATAGAAAT-GAGATCGAATGA-CAGAGATGAAACCACAAGTAAAAA
** * * * *
21211267 AATAAAGTGACTAGAATCGAGTTAAGGTTGAA-AATGACTGATTGAGACGATGCCACGGGTCAAG
128 AATAAAACGACTAGAACCGAGTCAAGG-TCAATAATGACTGATCGAGACGATGCCACGGGTCAAG
* ** * * * *
21211331 AGATGATCTGGATGGAACAAAGATCGAATGATCGAGATGAAACTACA
192 AGATGATCTGCACAGAACAAAGATCAAATGACCGAGATAAAACCACA
** * * * * *
21211378 AGTCAAAAAATAAAACAACCAAGTTCGAGTCGAGGTTAAAGATGACTGACCGAGATGGAACTGCG
1 AGTCAAAAAATAAAATGACCAAGATCGAATCGAGGTCAAAGATGACTGACCGAGATGAAACTGCA
* * * * * * ** *
21211443 GGTCAGGAGATGATCTGGATAGAACTGAGATTGAATGACTGAGATGAAATCATGAGTCAAAAAAT
66 AGTCAGAAGATGATCTGGATAGAAATGAGATCGAATGACAGAGATGAAACCACAAGTAAAAAAAT
* * * * *
21211508 AAAACGACTAGGACCGAGTCAAGGTCAATAATGACTGATCGAGATGATGTCATGGGTCAGGAGAT
131 AAAACGACTAGAACCGAGTCAAGGTCAATAATGACTGATCGAGACGATGCCACGGGTCAAGAGAT
* *
21211573 GATCTGCACAGAACCAAGATCAAATGACCGAGATAAAACCACG
196 GATCTGCACAGAACAAAGATCAAATGACCGAGATAAAACCACA
* * * **
21211616 AGTCAAAAAATAAAGTGACCAAGA-CTGAACCGAAGTTGAAGATGACTGACCG
1 AGTCAAAAAATAAAATGACCAAGATC-GAATCGAGGTCAAAGATGACTGACCG
21211668 GGACAGAGTG
Statistics
Matches: 236, Mismatches: 49, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
237 6 0.03
238 225 0.95
239 5 0.02
ACGTcount: A:0.41, C:0.15, G:0.25, T:0.19
Consensus pattern (238 bp):
AGTCAAAAAATAAAATGACCAAGATCGAATCGAGGTCAAAGATGACTGACCGAGATGAAACTGCA
AGTCAGAAGATGATCTGGATAGAAATGAGATCGAATGACAGAGATGAAACCACAAGTAAAAAAAT
AAAACGACTAGAACCGAGTCAAGGTCAATAATGACTGATCGAGACGATGCCACGGGTCAAGAGAT
GATCTGCACAGAACAAAGATCAAATGACCGAGATAAAACCACA
Found at i:21211661 original size:119 final size:117
Alignment explanation
Indices: 21211232--21211664 Score: 349
Period size: 119 Copynumber: 3.6 Consensus size: 117
21211222 GATGAAATCG
* * ** * * *
21211232 AGATCGAATGACC-AGGATGAAACCACAAGTAAAAAAATAAAGTGA-CTAGAATCGAGT-TAAGG
1 AGATCGAATGACCGA-GATGAAACCACGAGTCAAAAAATAAAACGACCAAGACT-GAGTCGAA-G
* * * *
21211294 TTGAAAATGACTGATTGAGACGATGCCACGGGTCAAGAGATGATCTGGATGGAACAA
63 TTGAAAATGACTGATCGAGATGATG-CA-GGGTCAGGAGATGATCTGGATAGAACAA
* * * * * *
21211351 AGATCGAATGATCGAGATGAAACTACAAGTCAAAAAATAAAACAACCAAG-TTCGAGTCGAGGTT
1 AGATCGAATGACCGAGATGAAACCACGAGTCAAAAAATAAAACGACCAAGACT-GAGTCGAAGTT
* **
21211415 -AAAGATGACTGACCGAGATGGAACTGC-GGGTCAGGAGATGATCTGGATAGAACTG
65 GAAA-ATGACTGATCGAGAT-G-A-TGCAGGGTCAGGAGATGATCTGGATAGAACAA
* * * * * * * * *
21211470 AGATTGAATGACTGAGATGAAATCATGAGTCAAAAAATAAAACGACTAGGACCGAGTC-AAGGTC
1 AGATCGAATGACCGAGATGAAACCACGAGTCAAAAAATAAAACGACCAAGACTGAGTCGAAGTTG
* * *
21211534 AATAATGACTGATCGAGATGATGTCATGGGTCAGGAGATGATCTGCACAGAACCA
66 AA-AATGACTGATCGAGATGATG-CA-GGGTCAGGAGATGATCTGGATAGAACAA
* * ** **
21211589 AGATCAAATGACCGAGATAAAACCACGAGTCAAAAAATAAAGTGACCAAGACTGAACCGAAGTTG
1 AGATCGAATGACCGAGATGAAACCACGAGTCAAAAAATAAAACGACCAAGACTGAGTCGAAGTTG
*
21211654 AAGATGACTGA
66 AAAATGACTGA
21211665 CCGGGACAGA
Statistics
Matches: 248, Mismatches: 52, Indels: 28
0.76 0.16 0.09
Matches are distributed among these distances:
116 2 0.01
117 2 0.01
118 7 0.03
119 220 0.89
120 13 0.05
121 2 0.01
122 2 0.01
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.18
Consensus pattern (117 bp):
AGATCGAATGACCGAGATGAAACCACGAGTCAAAAAATAAAACGACCAAGACTGAGTCGAAGTTG
AAAATGACTGATCGAGATGATGCAGGGTCAGGAGATGATCTGGATAGAACAA
Found at i:21212955 original size:6 final size:7
Alignment explanation
Indices: 21212938--21213006 Score: 61
Period size: 7 Copynumber: 9.6 Consensus size: 7
21212928 TAACTCTTTT
21212938 TTTTTCC
1 TTTTTCC
21212945 TTTTTCC
1 TTTTTCC
21212952 TTTTT-C
1 TTTTTCC
*
21212958 TTCTTTCG
1 TT-TTTCC
*
21212966 TTTTTGC
1 TTTTTCC
21212973 TTTTTACTC
1 TTTTT-C-C
21212982 TTTTT-C
1 TTTTTCC
*
21212988 TTTTTTC
1 TTTTTCC
21212995 TTTTTCTC
1 TTTTTC-C
21213003 TTTT
1 TTTT
21213007 GTTAACACTT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
6 9 0.18
7 29 0.57
8 7 0.14
9 6 0.12
ACGTcount: A:0.01, C:0.20, G:0.03, T:0.75
Consensus pattern (7 bp):
TTTTTCC
Done.