Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 132 of 163
Found at i:35996127 original size:60 final size:60
Alignment explanation
Indices: 35996044--35996213 Score: 222
Period size: 60 Copynumber: 2.9 Consensus size: 60
35996034 AATTATTTTA
*
35996044 TGACCCCTAAACTTTCTAGAAATTTGAATTTGACACTTGAAC-TTTCTAAAAATTCAAATT
1 TGACCCCTAAACTTTCTAAAAATTTGAATTTGACACTTGAACTTTTC-AAAAATTCAAATT
* * *
35996104 TGACCCCTAAACTTTCTAAAAATTTGAATTTGACCCCTAAACTTTTCAAAAATTCAAATT
1 TGACCCCTAAACTTTCTAAAAATTTGAATTTGACACTTGAACTTTTCAAAAATTCAAATT
* * *
35996164 TGA-CCCTAAATTTTCCAAAAATTCTG-ATTTGA-ACCTTGAATTTTTCAAAA
1 TGACCCCTAAACTTTCTAAAAATT-TGAATTTGACA-CTTGAACTTTTCAAAA
35996214 TTTTGATTTG
Statistics
Matches: 97, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
59 37 0.38
60 56 0.58
61 4 0.04
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.36
Consensus pattern (60 bp):
TGACCCCTAAACTTTCTAAAAATTTGAATTTGACACTTGAACTTTTCAAAAATTCAAATT
Found at i:35996253 original size:30 final size:30
Alignment explanation
Indices: 35996044--35996258 Score: 182
Period size: 30 Copynumber: 7.2 Consensus size: 30
35996034 AATTATTTTA
* * * **
35996044 TGACCCCTAAACTTTCTAGAAATTTGAATT
1 TGACCCTTAAACTTTCCAAAAATTCAAATT
* * *
35996074 TGACACTTGAACTTTCTAAAAATTCAAATT
1 TGACCCTTAAACTTTCCAAAAATTCAAATT
* * **
35996104 TGACCCCTAAACTTTCTAAAAATTTGAATT
1 TGACCCTTAAACTTTCCAAAAATTCAAATT
* *
35996134 TGACCCCTAAACTTTTCAAAAATTCAAATT
1 TGACCCTTAAACTTTCCAAAAATTCAAATT
* **
35996164 TGACCC-TAAATTTTCCAAAAATTCTGATT
1 TGACCCTTAAACTTTCCAAAAATTCAAATT
* * * * ***
35996193 TGAACCTTGAATTTTTC-AAAATTTTGATT
1 TGACCCTTAAACTTTCCAAAAATTCAAATT
* *
35996222 TGACCCTTGAAGTTTCCAAAAATTCAAATT
1 TGACCCTTAAACTTTCCAAAAATTCAAATT
35996252 TGACCCT
1 TGACCCT
35996259 GTTTTAATGC
Statistics
Matches: 154, Mismatches: 29, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
29 49 0.32
30 105 0.68
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (30 bp):
TGACCCTTAAACTTTCCAAAAATTCAAATT
Found at i:36005565 original size:12 final size:12
Alignment explanation
Indices: 36005548--36005572 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36005538 TAACTCAAAA
36005548 ACAATGTGTGTT
1 ACAATGTGTGTT
36005560 ACAATGTGTGTT
1 ACAATGTGTGTT
36005572 A
1 A
36005573 TTTTCCATCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (12 bp):
ACAATGTGTGTT
Found at i:36019715 original size:19 final size:20
Alignment explanation
Indices: 36019675--36019715 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
36019665 TTTATATTTG
*
36019675 AATTCATTAAAAATTTACAA
1 AATTCATTAAAAATATACAA
*
36019695 AATT-ATTAAAAATATATAA
1 AATTCATTAAAAATATACAA
36019714 AA
1 AA
36019716 GGTAAGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
AATTCATTAAAAATATACAA
Found at i:36020032 original size:28 final size:28
Alignment explanation
Indices: 36019993--36020046 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
36019983 TATGCTTTTT
36019993 TTAATAATA-TTTTATAATATTTTTTAAA
1 TTAATAATATTTTTA-AATATTTTTTAAA
36020021 TTAACTAA-ATTTTTAAATATTTTTTA
1 TTAA-TAATATTTTTAAATATTTTTTA
36020047 TATTTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (28 bp):
TTAATAATATTTTTAAATATTTTTTAAA
Found at i:36020175 original size:28 final size:28
Alignment explanation
Indices: 36019999--36020178 Score: 71
Period size: 28 Copynumber: 6.4 Consensus size: 28
36019989 TTTTTTAATA
* * *
36019999 ATATTTTATAATATTTTTTA-AATTAACT
1 ATATTTTTTAATAATTTTTATAATTTA-T
* * * *
36020027 AAATTTTTAAATATTTTTTATATTTTA-
1 ATATTTTTTAATAATTTTTATAATTTAT
** * * *
36020054 ATACATTTTCATAATTTTTACAATTTTT
1 ATATTTTTTAATAATTTTTATAATTTAT
** * *
36020082 CATAATAATATAAT-TTTTTTATAATTTAT
1 -AT-ATTTTTTAATAATTTTTATAATTTAT
** * * *
36020111 ATA-AATTAAAAAATTATTTTAATAATTTTT
1 ATATTTTTTAATAA-T-TTTT-ATAATTTAT
* *
36020141 GTGTTTTTTAATAATTTTTATAATTTAT
1 ATATTTTTTAATAATTTTTATAATTTAT
36020169 ATATTTTTTA
1 ATATTTTTTA
36020179 GGCATTTATA
Statistics
Matches: 108, Mismatches: 35, Indels: 18
0.67 0.22 0.11
Matches are distributed among these distances:
26 5 0.05
27 19 0.18
28 36 0.33
29 26 0.24
30 16 0.15
31 6 0.06
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (28 bp):
ATATTTTTTAATAATTTTTATAATTTAT
Found at i:36020206 original size:9 final size:9
Alignment explanation
Indices: 36020041--36020218 Score: 72
Period size: 9 Copynumber: 18.9 Consensus size: 9
36020031 TTTTAAATAT
36020041 TTTTTAT-A
1 TTTTTATAA
*
36020049 TTTTAATACA
1 TTTTTATA-A
*
36020059 TTTTCATAA
1 TTTTTATAA
*
36020068 TTTTTACAA
1 TTTTTATAA
36020077 TTTTTCATAA
1 TTTTT-ATAA
**
36020087 -TAATATAA
1 TTTTTATAA
36020095 TTTTTTTATAA
1 --TTTTTATAA
*
36020106 TTTATATAA
1 TTTTTATAA
* ** *
36020115 ATTAAAAAA
1 TTTTTATAA
36020124 TTATTTTAATAA
1 -T-TTTT-ATAA
* **
36020136 TTTTTGTGT
1 TTTTTATAA
36020145 TTTTTAATAA
1 TTTTT-ATAA
36020155 TTTTTATAA
1 TTTTTATAA
* *
36020164 TTTATATAT
1 TTTTTATAA
**
36020173 TTTTTAGGCA
1 TTTTTA-TAA
*
36020183 TTTATAATAA
1 TTT-TTATAA
36020193 TTTTTATAA
1 TTTTTATAA
* *
36020202 GTTTTGTAA
1 TTTTTATAA
36020211 TTTTTATA
1 TTTTTATA
36020219 TTGTTGCACT
Statistics
Matches: 121, Mismatches: 37, Indels: 23
0.67 0.20 0.13
Matches are distributed among these distances:
8 10 0.08
9 69 0.57
10 28 0.23
11 11 0.09
12 3 0.02
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (9 bp):
TTTTTATAA
Found at i:36022971 original size:27 final size:28
Alignment explanation
Indices: 36022932--36022985 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
36022922 AGAGTTGTAC
*
36022932 TTCTTATCAACAAGTAAATTTACCAAAA
1 TTCTTATCAACAAGTAAATTGACCAAAA
36022960 TTCTT-TCAACAAGTAAATTGACCAAA
1 TTCTTATCAACAAGTAAATTGACCAAA
36022986 TTGAGTTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (28 bp):
TTCTTATCAACAAGTAAATTGACCAAAA
Found at i:36026911 original size:13 final size:15
Alignment explanation
Indices: 36026886--36026923 Score: 53
Period size: 13 Copynumber: 2.6 Consensus size: 15
36026876 GTTTTAATCT
36026886 TATTAAGTTTAATAA-
1 TATTAA-TTTAATAAC
36026901 T-TTAATTTAATAAC
1 TATTAATTTAATAAC
36026915 TATTAATTT
1 TATTAATTT
36026924 TAGAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 8 0.38
14 5 0.24
15 8 0.38
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (15 bp):
TATTAATTTAATAAC
Found at i:36041497 original size:2 final size:2
Alignment explanation
Indices: 36041490--36041541 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
36041480 AAATTAATAA
36041490 AT AT AT AT AT AT 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 AT AT AT
36041532 AT AT AT AT AT
1 AT AT AT AT AT
36041542 CTAGAATAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36041625 original size:9 final size:9
Alignment explanation
Indices: 36041613--36041706 Score: 84
Period size: 10 Copynumber: 10.2 Consensus size: 9
36041603 AATTTTCTAA
36041613 AAAAATTAT
1 AAAAATTAT
*
36041622 AAAATTTATT
1 AAAAATTA-T
36041632 AAAAATTACT
1 AAAAATTA-T
*
36041642 AAAATTTGAT
1 AAAAATT-AT
*
36041652 AAATATTAT
1 AAAAATTAT
*
36041661 -AAAATTTT
1 AAAAATTAT
*
36041669 AAACA-TAT
1 AAAAATTAT
36041677 AAAAATTAT
1 AAAAATTAT
*
36041686 TAAAATTACT
1 AAAAATTA-T
36041696 AAAAATTAT
1 AAAAATTAT
36041705 AA
1 AA
36041707 TCTATAAAAA
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
8 12 0.18
9 25 0.37
10 29 0.43
11 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (9 bp):
AAAAATTAT
Found at i:36041637 original size:19 final size:19
Alignment explanation
Indices: 36041613--36041704 Score: 86
Period size: 19 Copynumber: 4.9 Consensus size: 19
36041603 AATTTTCTAA
*
36041613 AAAAATTATAAAATTTATT
1 AAAAATTATAAAAATTATT
*
36041632 AAAAATTACTAAAATTTGA-T
1 AAAAATTA-TAAAAATT-ATT
*
36041652 AAATATTAT-AAAATT-TT
1 AAAAATTATAAAAATTATT
*
36041669 AAACA-TATAAAAATTATT
1 AAAAATTATAAAAATTATT
36041687 -AAAATTACTAAAAATTAT
1 AAAAATTA-TAAAAATTAT
36041705 AATCTATAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 14
0.77 0.05 0.17
Matches are distributed among these distances:
16 3 0.05
17 14 0.23
18 9 0.15
19 19 0.31
20 16 0.26
21 1 0.02
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (19 bp):
AAAAATTATAAAAATTATT
Found at i:36041699 original size:35 final size:35
Alignment explanation
Indices: 36041651--36041717 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
36041641 TAAAATTTGA
*
36041651 TAAATATTAT-AAAATTTTAAACATATAAAAATTAT
1 TAAATATTATAAAAATTATAAAC-TATAAAAATTAT
*
36041686 TAAA-ATTACTAAAAATTATAATCTATAAAAAT
1 TAAATATTA-TAAAAATTATAAACTATAAAAAT
36041718 AGGGTAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 4 0.14
35 14 0.50
36 10 0.36
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.37
Consensus pattern (35 bp):
TAAATATTATAAAAATTATAAACTATAAAAATTAT
Found at i:36042500 original size:22 final size:21
Alignment explanation
Indices: 36042475--36042525 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
36042465 TTTTTATAAA
36042475 TTATAATA-TTTTTTGAAATTTT
1 TTATAATACTTTTTTG-AA-TTT
**
36042497 TTATTTTACTTTTTTTGAATTT
1 TTATAATAC-TTTTTTGAATTT
36042519 TTATAAT
1 TTATAAT
36042526 TCTTAATATC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
22 14 0.61
23 2 0.09
24 7 0.30
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (21 bp):
TTATAATACTTTTTTGAATTT
Found at i:36049782 original size:23 final size:23
Alignment explanation
Indices: 36049740--36049783 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
36049730 TTTATATTTT
* * *
36049740 TTTATTTATATAACTGTTTATTG
1 TTTATTTAAATAAATATTTATTG
36049763 TTTATTTAAATAAATATTTAT
1 TTTATTTAAATAAATATTTAT
36049784 ATTAATGCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (23 bp):
TTTATTTAAATAAATATTTATTG
Found at i:36050883 original size:22 final size:23
Alignment explanation
Indices: 36050825--36050886 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
36050815 AATACAATCC
*
36050825 TATAAAAATATAAAT-AATATGA
1 TATAAAATTATAAATAAATATGA
* *
36050847 T-TAAAATCAGT-AATAAAT-TTA
1 TATAAAATTA-TAAATAAATATGA
36050868 TATAAAATTATAAATAAAT
1 TATAAAATTATAAATAAAT
36050887 CATGTAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
21 13 0.41
22 19 0.59
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (23 bp):
TATAAAATTATAAATAAATATGA
Found at i:36051602 original size:16 final size:16
Alignment explanation
Indices: 36051581--36051613 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
36051571 ATACTATATC
36051581 ATCATAC-ATAAGAATT
1 ATCATACAAT-AGAATT
36051597 ATCATACAATAGAATT
1 ATCATACAATAGAATT
36051613 A
1 A
36051614 CACATTAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (16 bp):
ATCATACAATAGAATT
Found at i:36055747 original size:41 final size:41
Alignment explanation
Indices: 36055680--36055858 Score: 247
Period size: 41 Copynumber: 4.3 Consensus size: 41
36055670 AATGGTGCTA
* *
36055680 TTTTAAGGCACACG-GTCGTGTGTCAAGGTGTGTGTATACTG
1 TTTTGAGGCACACGAG-CATGTGTCAAGGTGTGTGTATACTG
36055721 TTTTGAGGCACAC-AG-ATGTGTATCAAGGTGTGTGTATACTG
1 TTTTGAGGCACACGAGCATGTG--TCAAGGTGTGTGTATACTG
* *
36055762 TTTTGAGGCACACGGGCATGTGTCAAGGTGTGTGTATATTG
1 TTTTGAGGCACACGAGCATGTGTCAAGGTGTGTGTATACTG
36055803 TTTTGAGGCACACGAGCATGTGTCAAGGGTGTGTGTGTATACTG
1 TTTTGAGGCACACGAGCATGTGTCAA--G-GTGTGTGTATACTG
36055847 TTTTGAGGCACA
1 TTTTGAGGCACA
36055859 TGGGCTAGCA
Statistics
Matches: 124, Mismatches: 6, Indels: 13
0.87 0.04 0.09
Matches are distributed among these distances:
39 4 0.03
41 88 0.71
42 1 0.01
43 6 0.05
44 25 0.20
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.34
Consensus pattern (41 bp):
TTTTGAGGCACACGAGCATGTGTCAAGGTGTGTGTATACTG
Found at i:36055881 original size:85 final size:81
Alignment explanation
Indices: 36055709--36055881 Score: 199
Period size: 85 Copynumber: 2.1 Consensus size: 81
36055699 GTGTCAAGGT
36055709 GTGTGTATACTGTTTTGAGGCACACAGATGTGTATCAAGGTGTGTGTATACTGTTTTGAGGCACA
1 GTGTGTATACTGTTTTGAGGCACACAGATGTG-ATCAAGGTGTGTGTATACTGTTTTGAGGCACA
** * *
36055774 CGGGCATGTGTCAAGGT
65 CGGGCATGTCACAAAGC
*
36055791 GTGTGTATATTGTTTTGAGGCACACGAGCATGTG-TCAAGGGTGTGTGTGTATACTGTTTTGAGG
1 GTGTGTATACTGTTTTGAGGCACAC-AG-ATGTGATCAA--G-GTGTGTGTATACTGTTTTGAGG
*
36055855 CACATGGGC-TAG-CACACAAGC
61 CACACGGGCAT-GTCACA-AAGC
36055876 GTGTGT
1 GTGTGT
36055882 CAGGGTGTGT
Statistics
Matches: 78, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
82 28 0.36
83 2 0.03
84 9 0.12
85 39 0.50
ACGTcount: A:0.21, C:0.14, G:0.32, T:0.32
Consensus pattern (81 bp):
GTGTGTATACTGTTTTGAGGCACACAGATGTGATCAAGGTGTGTGTATACTGTTTTGAGGCACAC
GGGCATGTCACAAAGC
Found at i:36055898 original size:53 final size:52
Alignment explanation
Indices: 36055810--36055967 Score: 199
Period size: 53 Copynumber: 2.9 Consensus size: 52
36055800 TTGTTTTGAG
* *
36055810 GCACACGAGCATGTGTCAAGGGTGTGTGTGTATACTGTTTTGAGGCACATGGGCT
1 GCACACGAGCGTGTGTC-A-GG-GTGTGTGTATACTGTTTTGAGGCACATGGGAT
* * * *
36055865 AGCACACAAGCGTGTGTCAGGGTGTGTGTATACTGTTCTGAAGCACACGGGAT
1 -GCACACGAGCGTGTGTCAGGGTGTGTGTATACTGTTTTGAGGCACATGGGAT
* *
36055918 GACACACGAGTGTGTGTCAGGGTGTGTGTATACTGTTTTAAGGCACATGG
1 G-CACACGAGCGTGTGTCAGGGTGTGTGTATACTGTTTTGAGGCACATGG
36055968 TCTGCAATAA
Statistics
Matches: 89, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
52 1 0.01
53 70 0.79
54 2 0.02
55 1 0.01
56 15 0.17
ACGTcount: A:0.22, C:0.16, G:0.34, T:0.28
Consensus pattern (52 bp):
GCACACGAGCGTGTGTCAGGGTGTGTGTATACTGTTTTGAGGCACATGGGAT
Found at i:36066989 original size:21 final size:21
Alignment explanation
Indices: 36066963--36067010 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
36066953 AGTAATGTTT
36066963 TACCGAAACAACACT-TCTAAC
1 TACCGAAACAACA-TATCTAAC
* *
36066984 TACCGATACAATATATCTAAC
1 TACCGAAACAACATATCTAAC
36067005 TACCGA
1 TACCGA
36067011 TAGTATAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.42, C:0.29, G:0.06, T:0.23
Consensus pattern (21 bp):
TACCGAAACAACATATCTAAC
Found at i:36069443 original size:21 final size:22
Alignment explanation
Indices: 36069397--36069444 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
36069387 CTCTTGAATT
* *
36069397 TGTTGTATTGGTAGAAGGTTAG
1 TGTTGTATTGGTAGAAGCTCAG
36069419 -GTTGTATTGGTAGAA-CTCAG
1 TGTTGTATTGGTAGAAGCTCAG
36069439 TGTTGT
1 TGTTGT
36069445 GTCAGTAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.21, C:0.04, G:0.33, T:0.42
Consensus pattern (22 bp):
TGTTGTATTGGTAGAAGCTCAG
Found at i:36079401 original size:29 final size:29
Alignment explanation
Indices: 36079343--36079400 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
36079333 AAATATGATA
*
36079343 AATTATATTTTTAAAAAAGAATCTATTTT
1 AATTATATTTTTAAAAAACAATCTATTTT
* *
36079372 AATTATATATTTTAAAATACCATCTATTT
1 AATTATAT-TTTTAAAAAACAATCTATTT
36079401 ACTTCTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (29 bp):
AATTATATTTTTAAAAAACAATCTATTTT
Found at i:36086479 original size:21 final size:21
Alignment explanation
Indices: 36086455--36086494 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
36086445 CCCCCGTTGG
*
36086455 TACAAATCTATAA-GAAAATAA
1 TACAAA-CTAAAATGAAAATAA
36086476 TACAAACTAAAATGAAAAT
1 TACAAACTAAAATGAAAAT
36086495 TGATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.23
Consensus pattern (21 bp):
TACAAACTAAAATGAAAATAA
Found at i:36090220 original size:26 final size:26
Alignment explanation
Indices: 36090189--36090248 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
36090179 TTTTACCTAG
* * *
36090189 TAAAATTTTGATAACTTTACCCTCGA
1 TAAAATTTTAACAACTTTACCCTCAA
* *
36090215 TAAAATTTTAACAATTTTACCCTTAA
1 TAAAATTTTAACAACTTTACCCTCAA
36090241 TAAAATTT
1 TAAAATTT
36090249 CGAGAAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (26 bp):
TAAAATTTTAACAACTTTACCCTCAA
Found at i:36095847 original size:19 final size:19
Alignment explanation
Indices: 36095823--36095900 Score: 54
Period size: 20 Copynumber: 4.0 Consensus size: 19
36095813 ACAACAATAT
*
36095823 TTTTCTTTAATTTTTATAA
1 TTTTCTATAATTTTTATAA
*
36095842 TTTTCTATAATATTTCAATAA
1 TTTTCTATAAT-TTT-TATAA
*
36095863 -TTTC-AGTAAATTTTATACA
1 TTTTCTA-TAATTTTTATA-A
*
36095882 TTTTTCTA-ATTTTTTATAA
1 -TTTTCTATAATTTTTATAA
36095901 CATTTAATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
18 3 0.07
19 16 0.35
20 18 0.39
21 8 0.17
22 1 0.02
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.59
Consensus pattern (19 bp):
TTTTCTATAATTTTTATAA
Found at i:36095850 original size:10 final size:10
Alignment explanation
Indices: 36095823--36095865 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
36095813 ACAACAATAT
*
36095823 TTTTCTTTAA
1 TTTTCTATAA
36095833 TTTT-TATAA
1 TTTTCTATAA
36095842 TTTTCTATAA
1 TTTTCTATAA
*
36095852 TATTTCAATAA
1 T-TTTCTATAA
36095863 TTT
1 TTT
36095866 CAGTAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 8 0.28
10 12 0.41
11 9 0.31
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTCTATAA
Found at i:36095862 original size:21 final size:20
Alignment explanation
Indices: 36095817--36095865 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
36095807 AAATTCACAA
* *
36095817 CAATATTTTTCTTTAATTTT
1 CAATAATTTTCTATAATTTT
*
36095837 -TATAATTTTCTATAATATTT
1 CAATAATTTTCTATAAT-TTT
36095857 CAATAATTT
1 CAATAATTT
36095866 CAGTAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 13 0.57
20 3 0.13
21 7 0.30
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (20 bp):
CAATAATTTTCTATAATTTT
Found at i:36095921 original size:11 final size:11
Alignment explanation
Indices: 36095905--36095959 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
36095895 TTATAACATT
36095905 TAATTTATATA
1 TAATTTATATA
*
36095916 TAATTTTTA-A
1 TAATTTATATA
36095926 TAATTT-TATAA
1 TAATTTATAT-A
*
36095937 TAATTTTATCTA
1 TAA-TTTATATA
*
36095949 TAATATATATA
1 TAATTTATATA
36095960 AAAGTACGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
9 2 0.06
10 7 0.19
11 18 0.50
12 7 0.19
13 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
TAATTTATATA
Found at i:36097646 original size:360 final size:360
Alignment explanation
Indices: 36096985--36098369 Score: 2671
Period size: 360 Copynumber: 3.8 Consensus size: 360
36096975 AAAGAGATAT
36096985 TAAAAATGTACGCTCTCATGTCAAGAAAAAAAAGTTCCCATCGTGGAAGGCTTAGGAATTTCCTT
1 TAAAAATGTACGCTCTCATGTCAAGAAAAAAAAGTTCCCATCGTGGAAGGCTTAGGAATTTCCTT
* * *
36097050 CTATATGGTGTTCGTTCTCTCTTGGATTGAACGGTGGTGTAAGATTATGTCTGTCGTGGTTAAGG
66 CTATATGGTGTTCGTTCTCTCTTGGATTGAACGATGGTATAAGATTGTGTCTGTCGTGGTTAAGG
* *
36097115 TAGATTGAAATTTCGCTTCTAGTATTCTGTTCTTTTGTTTTCTTTTCTATTTCTATTTTAGCTCT
131 TAGATTGAAATTTCGCTTCTAGTATTCTGTTCTTTTGTTTTCTTTTCTGTTTCTGTTTTAGCTCT
*
36097180 CTTTGTGCCTGTTTCCCCGTCCTCTCGGATGTCTGGTTTATCCCTGTAGGTTTTCGCAAAGCTGG
196 CTTTGTGCCTATTTCCCCGTCCTCTCGGATGTCTGGTTTATCCCTGTAGGTTTTCGCAAAGCTGG
36097245 GGGGTCGGTTTTCTTCCCTTTGCTTTTGGTGTTGTTTTTTCCTTTTCAATTACTTAATTTTTACT
261 GGGGTCGGTTTTCTTCCCTTTGCTTTTGGTGTTGTTTTTTCCTTTTCAATTACTTAATTTTTACT
36097310 ATTTGTTATTCCCCTTTTTATTATTTTTAATACTA
326 ATTTGTTATTCCCCTTTTTATTATTTTTAATACTA
36097345 TAAAAATGTACGCTCTCATGTCAAGAAAAAAAAGTTCCCATCGTGGAAGGCTTAGGAATTTCCTT
1 TAAAAATGTACGCTCTCATGTCAAGAAAAAAAAGTTCCCATCGTGGAAGGCTTAGGAATTTCCTT
36097410 CTATATGGTGTTCGTTCTCTCTTGGATTGAACGATGGTATAAGATTGTGTCTGTCGTGGTTAAGG
66 CTATATGGTGTTCGTTCTCTCTTGGATTGAACGATGGTATAAGATTGTGTCTGTCGTGGTTAAGG
36097475 TAGATTGAAATTTCGCTTCTAGTATTCTGTTCTTTTGTTTTCTTTTCTGTTTCTGTTTTAGCTCT
131 TAGATTGAAATTTCGCTTCTAGTATTCTGTTCTTTTGTTTTCTTTTCTGTTTCTGTTTTAGCTCT
*
36097540 CTTTGTGCCTGTTTCCCCGTCCTCTCGGATGTCTGGTTTATCCCTGTAGGTTTTCGCAAAGCTGG
196 CTTTGTGCCTATTTCCCCGTCCTCTCGGATGTCTGGTTTATCCCTGTAGGTTTTCGCAAAGCTGG
36097605 GGGGTCGGTTTTCTTCCCTTTGCTTTTGGTGTTGTTTTTTCCTTTTCAATTACTTAATTTTTACT
261 GGGGTCGGTTTTCTTCCCTTTGCTTTTGGTGTTGTTTTTTCCTTTTCAATTACTTAATTTTTACT
36097670 ATTTGTTATTCCCCTTTTTATTATTTTTAATACTA
326 ATTTGTTATTCCCCTTTTTATTATTTTTAATACTA
36097705 TAAAAATGTACGCTCTCATGTCAAGAAAAAAAAGTTCCCATCGTGGAAGGCTTAGGAATTTCCTT
1 TAAAAATGTACGCTCTCATGTCAAGAAAAAAAAGTTCCCATCGTGGAAGGCTTAGGAATTTCCTT
36097770 CTATATGGTGTTCGTTCTCTCTTGGATTGAACGATGGTATAAGATTGTGTCTGTCGTGGTTAAGG
66 CTATATGGTGTTCGTTCTCTCTTGGATTGAACGATGGTATAAGATTGTGTCTGTCGTGGTTAAGG
*
36097835 TAGATTGAAATTTTGCTTCTAGTATTCTGTTCTTTTGTTTTCTTTTCTGTTTCTGTTTTAGCTCT
131 TAGATTGAAATTTCGCTTCTAGTATTCTGTTCTTTTGTTTTCTTTTCTGTTTCTGTTTTAGCTCT
36097900 CTTTGTGCCTATTTCCCCGTCCTCTCGGATGTCTGGTTTATCCCTGTAGGTTTTCGCAAAGCTGG
196 CTTTGTGCCTATTTCCCCGTCCTCTCGGATGTCTGGTTTATCCCTGTAGGTTTTCGCAAAGCTGG
36097965 GGGGTCGGTTTTCTTCCCTTTGCTTTTGGTGTTGTTTTTTCCTTTTCAATTACTTAATTTTTACT
261 GGGGTCGGTTTTCTTCCCTTTGCTTTTGGTGTTGTTTTTTCCTTTTCAATTACTTAATTTTTACT
36098030 ATTTGTTATTCCCCTTTTTATTATTTTTAATACTA
326 ATTTGTTATTCCCCTTTTTATTATTTTTAATACTA
36098065 TAAAAATGTACGCTCTCATGTCAAGAAAAAAAAGTTCCCATCGTGGAAGGCTTAGGAATTTCCTT
1 TAAAAATGTACGCTCTCATGTCAAGAAAAAAAAGTTCCCATCGTGGAAGGCTTAGGAATTTCCTT
*
36098130 CTATATGGTGTTCGTTCTCTCTTGGATTGAACGATGGTATAAGATTGTGTCTATCGTGGTTAAGG
66 CTATATGGTGTTCGTTCTCTCTTGGATTGAACGATGGTATAAGATTGTGTCTGTCGTGGTTAAGG
*
36098195 TAGATTAAAATTTCGCTTCTAGTATTCTGTTCTTTTGTTTTCTTTTCTGTTTCTGTTTTAGCTCT
131 TAGATTGAAATTTCGCTTCTAGTATTCTGTTCTTTTGTTTTCTTTTCTGTTTCTGTTTTAGCTCT
*
36098260 CTTTGTGCCTATTTCCCCGTCCTCTCGGATGTCTGGTTTATCCCTGTAGGTTTTCGCAAAGCTAG
196 CTTTGTGCCTATTTCCCCGTCCTCTCGGATGTCTGGTTTATCCCTGTAGGTTTTCGCAAAGCTGG
36098325 GGGGTCGGTTTTCTTCCCTTTGCTTTTGGTGTTGTTTTTTCCTTT
261 GGGGTCGGTTTTCTTCCCTTTGCTTTTGGTGTTGTTTTTTCCTTT
36098370 CTTGTGGTTC
Statistics
Matches: 1014, Mismatches: 11, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
360 1014 1.00
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.45
Consensus pattern (360 bp):
TAAAAATGTACGCTCTCATGTCAAGAAAAAAAAGTTCCCATCGTGGAAGGCTTAGGAATTTCCTT
CTATATGGTGTTCGTTCTCTCTTGGATTGAACGATGGTATAAGATTGTGTCTGTCGTGGTTAAGG
TAGATTGAAATTTCGCTTCTAGTATTCTGTTCTTTTGTTTTCTTTTCTGTTTCTGTTTTAGCTCT
CTTTGTGCCTATTTCCCCGTCCTCTCGGATGTCTGGTTTATCCCTGTAGGTTTTCGCAAAGCTGG
GGGGTCGGTTTTCTTCCCTTTGCTTTTGGTGTTGTTTTTTCCTTTTCAATTACTTAATTTTTACT
ATTTGTTATTCCCCTTTTTATTATTTTTAATACTA
Found at i:36104433 original size:24 final size:24
Alignment explanation
Indices: 36104390--36104440 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
36104380 TTTAATTAGC
*
36104390 AAATATATTTTTAAAAAAATTATA
1 AAATATATTTTTAAAAAAATTAAA
*
36104414 AAATATATTATTT-AATAAATTAAA
1 AAATATATT-TTTAAAAAAATTAAA
36104438 AAA
1 AAA
36104441 ATAAACACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AAATATATTTTTAAAAAAATTAAA
Found at i:36119545 original size:22 final size:21
Alignment explanation
Indices: 36119501--36119551 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
36119491 TTTCTATTTG
*
36119501 AAATCATAAAAAATTATACAAA
1 AAAT-ATAGAAAATTATACAAA
**
36119523 AATATATAGAAAATTATTTAAA
1 AA-ATATAGAAAATTATACAAA
36119545 AAATATA
1 AAATATA
36119552 AAATACAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 5 0.20
22 18 0.72
23 2 0.08
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (21 bp):
AAATATAGAAAATTATACAAA
Found at i:36120340 original size:35 final size:34
Alignment explanation
Indices: 36120283--36120350 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 34
36120273 ATTTTTCAAA
* * *
36120283 TTTTTCAAATTTTTATAGTTTTTAAATACTTTTT
1 TTTTTCAAATTTTAACAATTTTTAAATACTTTTT
* *
36120317 TTTTTCATAATTTTAACAATTTTTTAATTCTTTT
1 TTTTTCA-AATTTTAACAATTTTTAAATACTTTT
36120351 CATAATTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 7 0.25
35 21 0.75
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.65
Consensus pattern (34 bp):
TTTTTCAAATTTTAACAATTTTTAAATACTTTTT
Found at i:36120526 original size:21 final size:21
Alignment explanation
Indices: 36120502--36120543 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
36120492 TATTGTTTGC
* *
36120502 ATTTTTTTATGTTTTGATAAT
1 ATTTTTATATATTTTGATAAT
*
36120523 ATTTTTATATATTTTTATAAT
1 ATTTTTATATATTTTGATAAT
36120544 TTATTATGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
ATTTTTATATATTTTGATAAT
Found at i:36120534 original size:10 final size:10
Alignment explanation
Indices: 36120425--36120550 Score: 54
Period size: 9 Copynumber: 12.9 Consensus size: 10
36120415 CAGTTTTCTT
36120425 TATTTTTATTA
1 TATTTTTA-TA
36120436 TAATTTTTATA
1 T-ATTTTTATA
*
36120447 -GTTTTTA-A
1 TATTTTTATA
36120455 TATTTTT-TA
1 TATTTTTATA
**
36120464 TCATTCATA-A
1 T-ATTTTTATA
*
36120474 TAGTTTTATA
1 TATTTTTATA
36120484 -ATTTTCTATA
1 TATTTT-TATA
* **
36120494 T-TGTTTGCA
1 TATTTTTATA
36120503 T-TTTTT-TA
1 TATTTTTATA
* *
36120511 TGTTTTGATAA
1 TATTTTTAT-A
36120522 TATTTTTATA
1 TATTTTTATA
36120532 TATTTTTATA
1 TATTTTTATA
36120542 -ATTTATTAT
1 TATTT-TTAT
36120551 GATTTTTAAT
Statistics
Matches: 87, Mismatches: 16, Indels: 25
0.68 0.12 0.20
Matches are distributed among these distances:
8 3 0.03
9 36 0.41
10 30 0.34
11 11 0.13
12 7 0.08
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (10 bp):
TATTTTTATA
Found at i:36120545 original size:19 final size:19
Alignment explanation
Indices: 36120426--36120550 Score: 60
Period size: 19 Copynumber: 6.4 Consensus size: 19
36120416 AGTTTTCTTT
36120426 ATTTTTATTATAATTTTTATA
1 ATTTTTA-TAT-ATTTTTATA
* *
36120447 GTTTTTA-ATATTTTTTATC
1 ATTTTTATATA-TTTTTATA
** *
36120466 ATTCATA-ATAGTTTTATA
1 ATTTTTATATATTTTTATA
* **
36120484 ATTTTCTATAT-TGTTT-GC
1 ATTTT-TATATATTTTTATA
* * *
36120502 ATTTTTTTATGTTTTGATAA
1 ATTTTTATATATTTTTAT-A
36120522 TATTTTTATATATTTTTATA
1 -ATTTTTATATATTTTTATA
36120542 ATTTATTAT
1 ATTT-TTAT
36120551 GATTTTTAAT
Statistics
Matches: 75, Mismatches: 21, Indels: 17
0.66 0.19 0.15
Matches are distributed among these distances:
17 4 0.05
18 18 0.24
19 25 0.33
20 7 0.09
21 21 0.28
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (19 bp):
ATTTTTATATATTTTTATA
Found at i:36128025 original size:21 final size:20
Alignment explanation
Indices: 36128001--36128047 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
36127991 TATGGCTGAG
36128001 TCTGATTCTGGTGTGGATGCA
1 TCTGATT-TGGTGTGGATGCA
* *
36128022 TCTGGCTTTGTTGTGGATGCA
1 TCT-GATTTGGTGTGGATGCA
36128043 TCTGA
1 TCTGA
36128048 GTGTGCTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 1 0.05
21 18 0.82
22 3 0.14
ACGTcount: A:0.13, C:0.15, G:0.32, T:0.40
Consensus pattern (20 bp):
TCTGATTTGGTGTGGATGCA
Found at i:36133607 original size:10 final size:10
Alignment explanation
Indices: 36133589--36133768 Score: 65
Period size: 10 Copynumber: 18.3 Consensus size: 10
36133579 TTTCTATTTG
*
36133589 AAATCATAAA
1 AAATTATAAA
36133599 AAATTATAAA
1 AAATTATAAA
* *
36133609 GAATGTATAGA
1 AAAT-TATAAA
36133620 AAATTATTTAAA
1 AAATTA--TAAA
36133632 AAA-TAT--A
1 AAATTATAAA
*
36133639 AAA-TACAAA
1 AAATTATAAA
*
36133648 AAAGTATAAA
1 AAATTATAAA
*
36133658 ATAA-T-TACA
1 A-AATTATAAA
36133667 AAA-TA-AAA
1 AAATTATAAA
* *
36133675 AAATTATTTAG
1 AAATTA-TAAA
* *
36133686 AAACTAT-GA
1 AAATTATAAA
36133695 AAATTATGAAA
1 AAATTAT-AAA
**
36133706 AAATTATTGA
1 AAATTATAAA
* *
36133716 AAGTTATAGA
1 AAATTATAAA
36133726 AAA-TATAAA
1 AAATTATAAA
*
36133735 AAATTATTCAA
1 AAATTA-TAAA
* *
36133746 AAATAATATA
1 AAATTATAAA
*
36133756 AAATTACAAA
1 AAATTATAAA
36133766 AAA
1 AAA
36133769 AACTTTATAA
Statistics
Matches: 126, Mismatches: 29, Indels: 30
0.68 0.16 0.16
Matches are distributed among these distances:
7 6 0.05
8 8 0.06
9 25 0.20
10 47 0.37
11 34 0.27
12 6 0.05
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.28
Consensus pattern (10 bp):
AAATTATAAA
Found at i:36133655 original size:17 final size:16
Alignment explanation
Indices: 36133629--36133660 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
36133619 AAAATTATTT
36133629 AAAAAATATAAAATAC
1 AAAAAATATAAAATAC
36133645 AAAAAAGTATAAAATA
1 AAAAAA-TATAAAATA
36133661 ATTACAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAAAATATAAAATAC
Found at i:36133707 original size:31 final size:30
Alignment explanation
Indices: 36133666--36133742 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
36133656 AAATAATTAC
36133666 AAAATA-AAAAAATTATTTAGAAA-CTAT-G
1 AAAATATAAAAAATTATTT-GAAAGCTATAG
*
36133694 AAAATTATGAAAAAATTA-TTGAAAGTTATAG
1 AAAA-TAT-AAAAAATTATTTGAAAGCTATAG
36133725 AAAATATAAAAAATTATT
1 AAAATATAAAAAATTATT
36133743 CAAAAATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
28 4 0.10
29 15 0.36
30 9 0.21
31 14 0.33
ACGTcount: A:0.60, C:0.01, G:0.08, T:0.31
Consensus pattern (30 bp):
AAAATATAAAAAATTATTTGAAAGCTATAG
Found at i:36134586 original size:21 final size:22
Alignment explanation
Indices: 36134557--36134597 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
36134547 TTGTTTGCAC
36134557 TTTTCTATG-TTTTGATAATAT
1 TTTTCTATGATTTTGATAATAT
* *
36134578 TTTTGTATGATTTTTATAAT
1 TTTTCTATGATTTTGATAAT
36134598 TTATTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.63
Consensus pattern (22 bp):
TTTTCTATGATTTTGATAATAT
Found at i:36137220 original size:31 final size:31
Alignment explanation
Indices: 36137153--36137220 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
36137143 TCTCAATCTG
* * ** * *
36137153 ATTTTATTCTAATTAAATTGATTTTGATTTG
1 ATTTAATTCTAATCAAATTGATTTAAATGTC
36137184 ATTTAATTCTAATCAAATTGATTTAAATGTC
1 ATTTAATTCTAATCAAATTGATTTAAATGTC
*
36137215 CTTTAA
1 ATTTAA
36137221 ATCAGATTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51
Consensus pattern (31 bp):
ATTTAATTCTAATCAAATTGATTTAAATGTC
Found at i:36139636 original size:3 final size:3
Alignment explanation
Indices: 36139628--36139652 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
36139618 CTCATTACTC
36139628 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
36139653 CTATTGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:36140422 original size:183 final size:183
Alignment explanation
Indices: 36140113--36140443 Score: 511
Period size: 183 Copynumber: 1.8 Consensus size: 183
36140103 CTTGGCAGCT
* * *
36140113 GATCATCATCCCTAATTATATCTCTCCACTCATCTCTCTTAGAGACAAGTTTCAATAGAGGGTTT
1 GATCATCATCCCTAATTAAATCTCTCCACTCATCCCTATTAGAGACAAGTTTCAATAGAGGGTTT
* *
36140178 TCTTGGATTTTCAAAGCTTTCCATTCACTAGGGTTGGAAATCGGATTTCTCAAACGGTTGAGATA
66 TCTTGAATCTTCAAAGCTTTCCATTCACTAGGGTTGGAAATCGGATTTCTCAAACGGTTGAGATA
*
36140243 ACCCTTTCTCTTTCGATTGAGGAGTGAATTTGATTCCATCTCCAACAAAATCC
131 ACCCTTTCTCCTTCGATTGAGGAGTGAATTTGATTCCATCTCCAACAAAATCC
* ** **
36140296 GATCATCATCCCTGATTAAATCTCTCCTTTCATCCCTATTAGAGACTGGTTTCAATAGAGGGTTT
1 GATCATCATCCCTAATTAAATCTCTCCACTCATCCCTATTAGAGACAAGTTTCAATAGAGGGTTT
* * * *
36140361 TCTTGAATCTTCAAAGCTTTCCATTTA-TCGGAGTTGGAAATCGGATTTCTCGAAGGGTTGAGAT
66 TCTTGAATCTTCAAAGCTTTCCATTCACTAGG-GTTGGAAATCGGATTTCTCAAACGGTTGAGAT
36140425 AACCCTTTCTCCTTCGATT
130 AACCCTTTCTCCTTCGATT
36140444 AATAATCAAA
Statistics
Matches: 132, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
182 3 0.02
183 129 0.98
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (183 bp):
GATCATCATCCCTAATTAAATCTCTCCACTCATCCCTATTAGAGACAAGTTTCAATAGAGGGTTT
TCTTGAATCTTCAAAGCTTTCCATTCACTAGGGTTGGAAATCGGATTTCTCAAACGGTTGAGATA
ACCCTTTCTCCTTCGATTGAGGAGTGAATTTGATTCCATCTCCAACAAAATCC
Found at i:36142477 original size:110 final size:110
Alignment explanation
Indices: 36142269--36142580 Score: 337
Period size: 112 Copynumber: 2.8 Consensus size: 110
36142259 AATTCCCGTA
* *
36142269 TAAGACGCGTTTTTTTGAAGATTTACCAATCTATATTATTATTGGAGAGA-AAAA-AAAATGCGT
1 TAAGACGCGTATTTTTGAAGATTTACCAATCTACATTATTATTGGAGAGAGAAAAGAAAATGCGT
* * * *
36142332 CCTACAGAGAGCGTTTTCATTGATCTAACCAAGAAAGCAAGTAC-TG
66 CCTACAGAAAACATTTTCATTAATCT-ACCAAGAAAGCAAG-ACTTG
* * * *
36142378 TAAGATGCG-ATTTTTAAAGATTTACCAATCTACATTGTTATTGGAGAGAGAAAAGAAAACGCGT
1 TAAGACGCGTATTTTTGAAGATTTACCAATCTACATTATTATTGGAGAGAGAAAAGAAAATGCGT
* * * ** * * *
36142442 CTTACAGAAAATATTTTCATTTATCTAGTAGAGAAAGTATGCCTTG
66 CCTACAGAAAACATTTTCATTAATCTACCA-AGAAAGCAAGACTTG
* * * * *
36142488 TAAGACGTGTTTCTTTTGAAGATTTACCAATTTACATTATTATTGGAGATAGAAAAGAAAATGCA
1 TAAGACGCGTAT-TTTTGAAGATTTACCAATCTACATTATTATTGGAGAGAGAAAAGAAAATGCG
36142553 TCCTACA-AAAAGCATTTTCATTAATCTA
65 TCCTACAGAAAA-CATTTTCATTAATCTA
36142581 ATAAATAAAG
Statistics
Matches: 167, Mismatches: 29, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
108 36 0.22
109 15 0.09
110 45 0.27
111 5 0.03
112 66 0.40
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.33
Consensus pattern (110 bp):
TAAGACGCGTATTTTTGAAGATTTACCAATCTACATTATTATTGGAGAGAGAAAAGAAAATGCGT
CCTACAGAAAACATTTTCATTAATCTACCAAGAAAGCAAGACTTG
Found at i:36143876 original size:22 final size:23
Alignment explanation
Indices: 36143850--36143892 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
36143840 AGTTTAAAAA
*
36143850 CCCAAAACA-ATAAAGAAAACGG
1 CCCAAAACATAAAAAGAAAACGG
36143872 CCCAAAACATAAAAAGAAAAC
1 CCCAAAACATAAAAAGAAAAC
36143893 AAAGCCTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.63, C:0.23, G:0.09, T:0.05
Consensus pattern (23 bp):
CCCAAAACATAAAAAGAAAACGG
Found at i:36146799 original size:16 final size:16
Alignment explanation
Indices: 36146744--36146792 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
36146734 CATATAAAAT
*
36146744 AAATAAAATATAAATAA
1 AAATATAATA-AAATAA
* *
36146761 TAATTATAATACAATAA
1 -AAATATAATAAAATAA
36146778 AAATATAATAAAATA
1 AAATATAATAAAATA
36146793 TGAATATTGG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 13 0.50
17 5 0.19
18 8 0.31
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATATAATAAAATAA
Found at i:36148502 original size:16 final size:17
Alignment explanation
Indices: 36148481--36148514 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
36148471 TTTCATAGAG
36148481 AAAAGGA-TATAAAATA
1 AAAAGGATTATAAAATA
*
36148497 AAAAGGATTATATAATA
1 AAAAGGATTATAAAATA
36148514 A
1 A
36148515 TAGTTGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (17 bp):
AAAAGGATTATAAAATA
Found at i:36150435 original size:15 final size:16
Alignment explanation
Indices: 36150409--36150441 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
36150399 TAAAGGAGGA
36150409 ATATTGCAAATAATTT
1 ATATTGCAAATAATTT
36150425 ATATT-CAAATAATTT
1 ATATTGCAAATAATTT
36150440 AT
1 AT
36150442 TAAATATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (16 bp):
ATATTGCAAATAATTT
Found at i:36151108 original size:30 final size:31
Alignment explanation
Indices: 36151073--36151133 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
36151063 ATAAAAATGC
*
36151073 AAAATTTAGATATATTA-TTTTGAATTTTTA
1 AAAATTTAGATATATTAGTTTTGAAATTTTA
*
36151103 AAAATTTAGATATTTTAGTTTTGAAATTTTA
1 AAAATTTAGATATATTAGTTTTGAAATTTTA
36151134 TATTTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.52
Consensus pattern (31 bp):
AAAATTTAGATATATTAGTTTTGAAATTTTA
Found at i:36151133 original size:23 final size:21
Alignment explanation
Indices: 36151098--36151140 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
36151088 TATTTTGAAT
36151098 TTTTAAAAATTTAGATATTTTAG
1 TTTTAAAAATTT--ATATTTTAG
* *
36151121 TTTTGAAATTTTATATTTTA
1 TTTTAAAAATTTATATTTTA
36151141 AATATTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
23 10 0.56
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
TTTTAAAAATTTATATTTTAG
Found at i:36151602 original size:25 final size:25
Alignment explanation
Indices: 36151572--36151621 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
36151562 CCCTTGTTTT
*
36151572 AAACCTAATTTTTATCCAAAATAAA
1 AAACCTAATTTTTATACAAAATAAA
* *
36151597 AAACCTATTTTTTATATAAAATAAA
1 AAACCTAATTTTTATACAAAATAAA
36151622 TAAAATCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (25 bp):
AAACCTAATTTTTATACAAAATAAA
Found at i:36152301 original size:12 final size:13
Alignment explanation
Indices: 36152284--36152312 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
36152274 GAGTAAGCTT
36152284 TTTTTTAAAAA-A
1 TTTTTTAAAAAGA
36152296 TTTTTTAAAAAGA
1 TTTTTTAAAAAGA
36152309 TTTT
1 TTTT
36152313 GATTGTTTTT
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:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (13 bp):
TTTTTTAAAAAGA
Found at i:36154573 original size:36 final size:36
Alignment explanation
Indices: 36154521--36154608 Score: 90
Period size: 36 Copynumber: 2.4 Consensus size: 36
36154511 AATTAGTCTA
* * *
36154521 ATGGTATGAAGAACATACCT-ACATATTCTCTGTCAC
1 ATGGAATGAAAAACATA-CTGACATATTCTCTATCAC
* *
36154557 ATGGAATGAAAAACATATTGACATATTTTCTATCAC
1 ATGGAATGAAAAACATACTGACATATTCTCTATCAC
*
36154593 AT-GACATAAAAAACAT
1 ATGGA-ATGAAAAACAT
36154609 GCTCTCATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
35 3 0.07
36 41 0.93
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (36 bp):
ATGGAATGAAAAACATACTGACATATTCTCTATCAC
Found at i:36154734 original size:23 final size:23
Alignment explanation
Indices: 36154705--36155134 Score: 482
Period size: 23 Copynumber: 19.1 Consensus size: 23
36154695 ATTCTTTACA
*
36154705 CACAAATCACATTAATATTTAAT
1 CACAAATCACATTAATATTTAAG
* * *
36154728 CATAAATCATATTAATATCTAAG
1 CACAAATCACATTAATATTTAAG
*
36154751 CACAAATCACATTAAAATTTAAG
1 CACAAATCACATTAATATTTAAG
*
36154774 CACAAATCACATTAATATTTGAG
1 CACAAATCACATTAATATTTAAG
*
36154797 CACAAATCATATTAATATTTAAG
1 CACAAATCACATTAATATTTAAG
* *
36154820 CACAAATCAAATTAATATTTGAG
1 CACAAATCACATTAATATTTAAG
* * *
36154843 CACAAATTATATTAATATTTAAA
1 CACAAATCACATTAATATTTAAG
*
36154866 CACAAATCACATTAATATTTAAT
1 CACAAATCACATTAATATTTAAG
* * *
36154889 CATAAACCACATTAATATTTGAG
1 CACAAATCACATTAATATTTAAG
* *
36154912 CAAAAATCATATTAATATTTAAG
1 CACAAATCACATTAATATTTAAG
* *
36154935 CACAAATCACATTAATACTTGAG
1 CACAAATCACATTAATATTTAAG
* * *
36154958 AATAAATCATATTAATATTTAAG
1 CACAAATCACATTAATATTTAAG
36154981 CACAAATCACATTAATATTTAAG
1 CACAAATCACATTAATATTTAAG
* *
36155004 CATAAATCACATTAATA---CA-
1 CACAAATCACATTAATATTTAAG
*
36155023 TACAAATCACATTAATATTTAAG
1 CACAAATCACATTAATATTTAAG
* *
36155046 CATAAATCACATTAATACTT---
1 CACAAATCACATTAATATTTAAG
*
36155066 -ACAAATCACATTAATATTTAAT
1 CACAAATCACATTAATATTTAAG
* * *
36155088 CATAAATCATATTAAGATTTAAG
1 CACAAATCACATTAATATTTAAG
* * *
36155111 CACACATTACATTAAT-GTTAAG
1 CACAAATCACATTAATATTTAAG
36155133 CA
1 CA
36155135 TAGATATAAG
Statistics
Matches: 338, Mismatches: 61, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
19 32 0.09
20 1 0.00
22 8 0.02
23 297 0.88
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (23 bp):
CACAAATCACATTAATATTTAAG
Found at i:36159666 original size:22 final size:22
Alignment explanation
Indices: 36159624--36159693 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
36159614 GCTCTCCGTT
* *
36159624 ATTTAGCACGTATCGTGCTCTCC
1 ATTTAGCACAT-TGGTGCTCTCC
* * *
36159647 GTTTAGCATATTTGTGCTCTCC
1 ATTTAGCACATTGGTGCTCTCC
*
36159669 ATTTAGCACCTTGGTGCTCTCC
1 ATTTAGCACATTGGTGCTCTCC
36159691 ATT
1 ATT
36159694 CATTAGTACA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 31 0.79
23 8 0.21
ACGTcount: A:0.16, C:0.27, G:0.17, T:0.40
Consensus pattern (22 bp):
ATTTAGCACATTGGTGCTCTCC
Found at i:36166043 original size:4 final size:4
Alignment explanation
Indices: 36166015--36166078 Score: 55
Period size: 4 Copynumber: 16.8 Consensus size: 4
36166005 TTCAGTCCCT
* * *
36166015 TTTA TTT- TTT- TGTA TTTA TTCA TTTA TTTTA GTT- TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA
*
36166061 TTTA TTT- GTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTT
36166079 TTATGTCATT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
3 9 0.19
4 35 0.73
5 4 0.08
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:36166063 original size:24 final size:22
Alignment explanation
Indices: 36166015--36166067 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 22
36166005 TTCAGTCCCT
36166015 TTTATTTTTTTGTATTTATTCA
1 TTTATTTTTTTGTATTTATTCA
* *
36166037 TTTATTTTAGTTTTTATTTATTTA
1 TTTATTTT--TTTGTATTTATTCA
36166061 TTTATTT
1 TTTATTT
36166068 GTTATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 8 0.30
24 19 0.70
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.75
Consensus pattern (22 bp):
TTTATTTTTTTGTATTTATTCA
Found at i:36166089 original size:15 final size:15
Alignment explanation
Indices: 36166042--36166089 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
36166032 ATTCATTTAT
36166042 TTTAGTTTTTAT-TTA
1 TTTA-TTTTTATGTTA
36166057 TTTATTTATT-TGTTA
1 TTTATTT-TTATGTTA
*
36166072 TTTATTTTTATGTCA
1 TTTATTTTTATGTTA
36166087 TTT
1 TTT
36166090 TATATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 6 0.21
15 23 0.79
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (15 bp):
TTTATTTTTATGTTA
Found at i:36168216 original size:12 final size:13
Alignment explanation
Indices: 36168192--36168220 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
36168182 ATTTGGGGTC
36168192 CCTTTTATTTTTT
1 CCTTTTATTTTTT
36168205 CCTTTT-TTTTTT
1 CCTTTTATTTTTT
36168217 CCTT
1 CCTT
36168221 AGGGCCTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (13 bp):
CCTTTTATTTTTT
Found at i:36172311 original size:22 final size:22
Alignment explanation
Indices: 36172269--36172338 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
36172259 GCTCTCCGTT
* *
36172269 ATTTAGCACGTATCGTGCTCTCC
1 ATTTAGCACAT-TGGTGCTCTCC
* * *
36172292 GTTTAGCATATTTGTGCTCTCC
1 ATTTAGCACATTGGTGCTCTCC
*
36172314 ATTTAGCACCTTGGTGCTCTCC
1 ATTTAGCACATTGGTGCTCTCC
36172336 ATT
1 ATT
36172339 CATTAGTACA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 31 0.79
23 8 0.21
ACGTcount: A:0.16, C:0.27, G:0.17, T:0.40
Consensus pattern (22 bp):
ATTTAGCACATTGGTGCTCTCC
Found at i:36178693 original size:4 final size:4
Alignment explanation
Indices: 36178665--36178728 Score: 55
Period size: 4 Copynumber: 16.8 Consensus size: 4
36178655 TTCAGTCCTT
* * *
36178665 TTTA TTT- TTT- TGTA TTTA TTCA TTTA TTTTA GTT- TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA
*
36178711 TTTA TTT- GTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTT
36178729 TTATGTCATT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
3 9 0.19
4 35 0.73
5 4 0.08
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:36178713 original size:24 final size:22
Alignment explanation
Indices: 36178665--36178717 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 22
36178655 TTCAGTCCTT
36178665 TTTATTTTTTTGTATTTATTCA
1 TTTATTTTTTTGTATTTATTCA
* *
36178687 TTTATTTTAGTTTTTATTTATTTA
1 TTTATTTT--TTTGTATTTATTCA
36178711 TTTATTT
1 TTTATTT
36178718 GTTATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 8 0.30
24 19 0.70
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.75
Consensus pattern (22 bp):
TTTATTTTTTTGTATTTATTCA
Found at i:36178739 original size:15 final size:15
Alignment explanation
Indices: 36178692--36178739 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
36178682 ATTCATTTAT
36178692 TTTAGTTTTTAT-TTA
1 TTTA-TTTTTATGTTA
36178707 TTTATTTATT-TGTTA
1 TTTATTT-TTATGTTA
*
36178722 TTTATTTTTATGTCA
1 TTTATTTTTATGTTA
36178737 TTT
1 TTT
36178740 TATATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 6 0.21
15 23 0.79
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (15 bp):
TTTATTTTTATGTTA
Found at i:36184474 original size:25 final size:25
Alignment explanation
Indices: 36184429--36184535 Score: 117
Period size: 25 Copynumber: 4.2 Consensus size: 25
36184419 TGACTCAAAT
*
36184429 GAGCCTAGACAGAA-TATCACTCATAC
1 GAGCC-AGACAGAATTA-CACTCTTAC
* *
36184455 GATCCAGAAAGAATTACACTCTTAC
1 GAGCCAGACAGAATTACACTCTTAC
* *
36184480 GAGCCAGACAGAATTTCGCTCTTAC
1 GAGCCAGACAGAATTACACTCTTAC
* * *
36184505 AAGCCAGACAGAATTACGCTCTTGC
1 GAGCCAGACAGAATTACACTCTTAC
36184530 GAGCCA
1 GAGCCA
36184536 AAATTAGAAT
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
25 63 0.91
26 6 0.09
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.21
Consensus pattern (25 bp):
GAGCCAGACAGAATTACACTCTTAC
Found at i:36184512 original size:50 final size:50
Alignment explanation
Indices: 36184429--36184535 Score: 133
Period size: 50 Copynumber: 2.1 Consensus size: 50
36184419 TGACTCAAAT
* *
36184429 GAGCCTAGACAGAATATCACTCATACGATCCAGAAAGAATTACACTCTTAC
1 GAGCC-AGACAGAATATCACTCATACAAGCCAGAAAGAATTACACTCTTAC
* * * * * *
36184480 GAGCCAGACAGAATTTCGCTCTTACAAGCCAGACAGAATTACGCTCTTGC
1 GAGCCAGACAGAATATCACTCATACAAGCCAGAAAGAATTACACTCTTAC
36184530 GAGCCA
1 GAGCCA
36184536 AAATTAGAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
50 43 0.90
51 5 0.10
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.21
Consensus pattern (50 bp):
GAGCCAGACAGAATATCACTCATACAAGCCAGAAAGAATTACACTCTTAC
Found at i:36186612 original size:57 final size:58
Alignment explanation
Indices: 36186543--36186655 Score: 165
Period size: 58 Copynumber: 2.0 Consensus size: 58
36186533 TGGATCTCTA
* ** * *
36186543 TCAGAGATAATAGATACTGGTA-CCTGTTCAGTTGTACGATCTTAGATACATACAATG
1 TCAGAGATAATAGATACTAGTACCCCATTCAGTCGTACGATCTCAGATACATACAATG
*
36186600 TCAGAGATAATAGATATTAGTACCCCATTCAGTCGTACGATCTCAGATACATACAA
1 TCAGAGATAATAGATACTAGTACCCCATTCAGTCGTACGATCTCAGATACATACAA
36186656 CTCATCCAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
57 20 0.41
58 29 0.59
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (58 bp):
TCAGAGATAATAGATACTAGTACCCCATTCAGTCGTACGATCTCAGATACATACAATG
Found at i:36187972 original size:21 final size:21
Alignment explanation
Indices: 36187948--36187989 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
36187938 ACTGTGTATG
*
36187948 ATCATTCTCCAACTTGGAATA
1 ATCATTCTCCAACTTAGAATA
36187969 ATCATTCTCCAACTTAGAATA
1 ATCATTCTCCAACTTAGAATA
36187990 GATTAGTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (21 bp):
ATCATTCTCCAACTTAGAATA
Found at i:36190799 original size:21 final size:21
Alignment explanation
Indices: 36190787--36190855 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
36190777 TTTTATCGAT
*
36190787 ACAAGTGACAATTCTACCGAT
1 ACAAGTGACAATTCTACCGAA
* *
36190808 ACAAGTCACTATTCTACCGAA
1 ACAAGTGACAATTCTACCGAA
* * *
36190829 ACAAGTGACTATTTTATCGAA
1 ACAAGTGACAATTCTACCGAA
36190850 ACAAGT
1 ACAAGT
36190856 CTTACTTCTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (21 bp):
ACAAGTGACAATTCTACCGAA
Found at i:36191611 original size:50 final size:49
Alignment explanation
Indices: 36191552--36191706 Score: 157
Period size: 50 Copynumber: 3.1 Consensus size: 49
36191542 TCAAACTTTC
* **
36191552 CCAGACAGAATATTGCTCATACGAGCTAAACAAAATTATTCTCTTATGAG
1 CCAGACAGAAT-TTGCTCATACGAGCCAAACAAAATTACCCTCTTATGAG
* * *
36191602 CCAGACAGAATTTCGCTCTTACGAGCCAGACAAAATTGCCCTCTTATGAG
1 CCAGACAGAATTT-GCTCATACGAGCCAAACAAAATTACCCTCTTATGAG
* * * * * * * *
36191652 CCAAACTGAATTTTGCCCCTACGAGCCAAATAGAATTACGCTCTTACGAG
1 CCAGACAGAA-TTTGCTCATACGAGCCAAACAAAATTACCCTCTTATGAG
36191702 CCAGA
1 CCAGA
36191707 ATCAAAATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
49 2 0.02
50 81 0.94
51 3 0.03
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.25
Consensus pattern (49 bp):
CCAGACAGAATTTGCTCATACGAGCCAAACAAAATTACCCTCTTATGAG
Found at i:36191613 original size:25 final size:25
Alignment explanation
Indices: 36191552--36191706 Score: 91
Period size: 25 Copynumber: 6.2 Consensus size: 25
36191542 TCAAACTTTC
*
36191552 CCAGACAGAA-TATTGCTCATACGAG
1 CCAGACAGAATTATT-CTCTTACGAG
* * * *
36191577 CTAAACAAAATTATTCTCTTATGAG
1 CCAGACAGAATTATTCTCTTACGAG
*
36191602 CCAGACAGAATT-TCGCTCTTACGAG
1 CCAGACAGAATTAT-TCTCTTACGAG
* *** *
36191627 CCAGACAAAATTGCCCTCTTATGAG
1 CCAGACAGAATTATTCTCTTACGAG
* * * *
36191652 CCAAACTGAATT-TTGCCCCTACGAG
1 CCAGACAGAATTATT-CTCTTACGAG
* * **
36191677 CCAAATAGAATTACGCTCTTACGAG
1 CCAGACAGAATTATTCTCTTACGAG
36191702 CCAGA
1 CCAGA
36191707 ATCAAAATTT
Statistics
Matches: 96, Mismatches: 29, Indels: 10
0.71 0.21 0.07
Matches are distributed among these distances:
24 1 0.01
25 91 0.95
26 4 0.04
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.25
Consensus pattern (25 bp):
CCAGACAGAATTATTCTCTTACGAG
Found at i:36193941 original size:18 final size:18
Alignment explanation
Indices: 36193918--36193963 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
36193908 ATGTTATTTT
*
36193918 AAATTTAAATATTATAAA
1 AAATTTAAATATTAAAAA
*
36193936 ACATTTAAA-ATTAAAAA
1 AAATTTAAATATTAAAAA
36193953 AAATTATAAAT
1 AAATT-TAAAT
36193964 TATAAACAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATTTAAATATTAAAAA
Found at i:36193964 original size:17 final size:18
Alignment explanation
Indices: 36193928--36193979 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
36193918 AAATTTAAAT
* *
36193928 ATTATAAAACATTTA-AA
1 ATTATAAAAAAATTATAA
36193945 ATTA-AAAAAAATTATAA
1 ATTATAAAAAAATTATAA
* *
36193962 ATTATAAACAATTTATAA
1 ATTATAAAAAAATTATAA
36193980 GAAATTATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 8 0.28
17 10 0.34
18 11 0.38
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTATAAAAAAATTATAA
Found at i:36193979 original size:18 final size:16
Alignment explanation
Indices: 36193918--36193976 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 16
36193908 ATGTTATTTT
36193918 AAATTTAAATATTATAA
1 AAATTTAAA-ATTATAA
*
36193935 AACATTTAAAATTAAAA
1 AA-ATTTAAAATTATAA
*
36193952 AAAATTATAAATTATAA
1 AAATTTA-AAATTATAA
36193969 ACAATTTA
1 A-AATTTA
36193977 TAAGAAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 4 0.11
17 19 0.54
18 12 0.34
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATTTAAAATTATAA
Found at i:36197021 original size:39 final size:40
Alignment explanation
Indices: 36196974--36197049 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
36196964 ACTATACTGT
*
36196974 ATCGGGCCTT-TGCCTACCAGGCTTCGTGCCAGTGTATTA
1 ATCGGGCCTTGTGCCTACCAGGCCTCGTGCCAGTGTATTA
* ** *
36197013 ATCGGGCCTTGTTCCTAGTAGGCCTCGTGCCGGTGTA
1 ATCGGGCCTTGTGCCTACCAGGCCTCGTGCCAGTGTA
36197050 ACATTTTGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 10 0.32
40 21 0.68
ACGTcount: A:0.13, C:0.28, G:0.29, T:0.30
Consensus pattern (40 bp):
ATCGGGCCTTGTGCCTACCAGGCCTCGTGCCAGTGTATTA
Found at i:36203759 original size:4 final size:4
Alignment explanation
Indices: 36203750--36203774 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
36203740 GTTGTACCAA
36203750 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
36203775 GACTAAGCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:36204384 original size:43 final size:43
Alignment explanation
Indices: 36204292--36204374 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
36204282 AGAAAAATGT
* * *
36204292 CGCTATAGAACATGGTCTTTAGCGACGTTTTTCTCACAAACAC
1 CGCTAAAGAACATGATCTTTAGCAACGTTTTTCTCACAAACAC
36204335 CGCTAAAGAACATGATCTTTAGCAACGTTTTTCTCACAAA
1 CGCTAAAGAACATGATCTTTAGCAACGTTTTTCTCACAAA
36204375 TGCTGCTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (43 bp):
CGCTAAAGAACATGATCTTTAGCAACGTTTTTCTCACAAACAC
Found at i:36205052 original size:490 final size:490
Alignment explanation
Indices: 36204132--36205603 Score: 2818
Period size: 490 Copynumber: 3.0 Consensus size: 490
36204122 GTATACCAGT
36204132 TTTTCATGTTTTAATGACCAGTCAAGTTAGGCCCTTACCTATTCACTACAGGAAAACAAGTTTTT
1 TTTTCATGTTTTAATGACCAGTCAAGTTAGGCCCTTACCTATTCACTACAGGAAAACAAGTTTTT
*
36204197 AGCAGTGTTTTTTGAGCCTATAGACGTCGCTAAAATATTGTAAAAGCGTCGTAAAAAACGCCGCT
66 AGCAGTGTTTTTTGAGCCTATAGACGTCGCTAAAATATTGTAAAAGCGCCGTAAAAAACGCCGCT
*
36204262 AAAAATCATGAGGTTTATGAAGAAAAATGTCGCTATAGAACATGGTCTTTAGCGACGTTTTTCTC
131 AAAAATCATGAGGTTTATGAAGAAAAATGTCGCTATAGAACATGGTCTTTAGCGGCGTTTTTCTC
36204327 ACAAACACCGCTAAAGAACATGATCTTTAGCAACGTTTTTCTCACAAATGCTGCTAAAATTAACA
196 ACAAACACCGCTAAAGAACATGATCTTTAGCAACGTTTTTCTCACAAATGCTGCTAAAATTAACA
*
36204392 GATTTTAACAGCTCATTTTAATTCATATAGAATCTTAATTTTCAATACTTTTTCCTATAAATTCA
261 GATTTTAACAGCTCATTTTAATTCATATAGAATCTTAATTTTCAACACTTTTTCCTATAAATTCA
36204457 AATCCAACCAATAACTTCAAATCTAAATGTAATGATACTATCACGAAAAAAATATATATATGATT
326 AATCCAACCAATAACTTCAAATCTAAATGTAATGATACTATCACGAAAAAAATATATATATGATT
*
36204522 TAAATTAATAAATAAATGAAAAATATTATACAAAAATAGTATTGCATATATTATTCTCACAATAA
391 TAAATTAATAAATAAATGAAAAATATTATACAAAAATAGTATTGTATATATTATTCTCACAATAA
*
36204587 TAAAAAACAAAAGTTTAAGATGACGGATTCTGGGG
456 TAAAAAACAAAAGTCTAAGATGACGGATTCTGGGG
*
36204622 TTTTCATGTTTTAATGACCAATCAAGTTAGGCCCTTACCTATTCACTACAGGAAAACAAGTTTTT
1 TTTTCATGTTTTAATGACCAGTCAAGTTAGGCCCTTACCTATTCACTACAGGAAAACAAGTTTTT
36204687 AGCAGTGTTTTTTGAGCCTATAGACGTCGCTAAAATATTGTAAAAGCGCCGTAAAAAACGCCGCT
66 AGCAGTGTTTTTTGAGCCTATAGACGTCGCTAAAATATTGTAAAAGCGCCGTAAAAAACGCCGCT
*
36204752 AAAAATCATGAGGTTTATGAAGAAAAATGTCACTATAGAACATGGTCTTTAGCGGCGTTTTTCTC
131 AAAAATCATGAGGTTTATGAAGAAAAATGTCGCTATAGAACATGGTCTTTAGCGGCGTTTTTCTC
36204817 ACAAACACCGCTAAAGAACATGATCTTTAGCAACGTTTTTCTCACAAATGCTGCTAAAATTAACA
196 ACAAACACCGCTAAAGAACATGATCTTTAGCAACGTTTTTCTCACAAATGCTGCTAAAATTAACA
* *
36204882 AATTTTAACAGCTCATTTTAATTCATATAGAATCTTAATTTTCAACATTTTTTCCTATAAATTCA
261 GATTTTAACAGCTCATTTTAATTCATATAGAATCTTAATTTTCAACACTTTTTCCTATAAATTCA
*
36204947 AATCCAACCAATAACTTCAAATCTAAATGTAATGATACTATCACGAAAAATATATATATATGATT
326 AATCCAACCAATAACTTCAAATCTAAATGTAATGATACTATCACGAAAAAAATATATATATGATT
36205012 TAAATTAATAAATAAATGAAAAATATTATACAAAAATAGTATTGTATATATTATTCTCACAATAA
391 TAAATTAATAAATAAATGAAAAATATTATACAAAAATAGTATTGTATATATTATTCTCACAATAA
*
36205077 TAAAAAACAAAAGTCTAAGATAACGGATTCTGGGG
456 TAAAAAACAAAAGTCTAAGATGACGGATTCTGGGG
36205112 TTTTCATGTTTTAATGACCAGTCAAGTTAGGCCCTTACCTATTCACTACAGGAAAACAAGTTTTT
1 TTTTCATGTTTTAATGACCAGTCAAGTTAGGCCCTTACCTATTCACTACAGGAAAACAAGTTTTT
*
36205177 AGCAATGTTTTTTGAGCCTATAGACGTCGCTAAAATATTGTAAAAGCGCCGTAAAAAACGCCGCT
66 AGCAGTGTTTTTTGAGCCTATAGACGTCGCTAAAATATTGTAAAAGCGCCGTAAAAAACGCCGCT
*
36205242 AAAAATCATGAGGTTTATGAAGAAAAATGTCGCTATAGAACATGATCTTTAGCGGCGTTTTTCTC
131 AAAAATCATGAGGTTTATGAAGAAAAATGTCGCTATAGAACATGGTCTTTAGCGGCGTTTTTCTC
*
36205307 ACAAACACCGCTAAAGAACATGATCTTTAGCAACGTTTTCCTCACAAATGCTGCTAAAATTAACA
196 ACAAACACCGCTAAAGAACATGATCTTTAGCAACGTTTTTCTCACAAATGCTGCTAAAATTAACA
36205372 GATTTTAACAGCTCATTTTAATTCATATAGAATCTTAATTTTCAACACTTTTTCCTATAAATTCA
261 GATTTTAACAGCTCATTTTAATTCATATAGAATCTTAATTTTCAACACTTTTTCCTATAAATTCA
36205437 AATCCAACCAATAACTTCAAATCTAAATGTAATGATACTATCACGAAAAAAATATATATATGATT
326 AATCCAACCAATAACTTCAAATCTAAATGTAATGATACTATCACGAAAAAAATATATATATGATT
36205502 TAAATTAATAAATAAATGAAAAATATTATACAAAAATAGTATTGTATATATTATTCTCACAATAA
391 TAAATTAATAAATAAATGAAAAATATTATACAAAAATAGTATTGTATATATTATTCTCACAATAA
36205567 TAAAAAACAAAAGTCTAAGATGACGGATTCTGGGG
456 TAAAAAACAAAAGTCTAAGATGACGGATTCTGGGG
36205602 TT
1 TT
36205604 GGTCACTATT
Statistics
Matches: 962, Mismatches: 20, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
490 962 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.32
Consensus pattern (490 bp):
TTTTCATGTTTTAATGACCAGTCAAGTTAGGCCCTTACCTATTCACTACAGGAAAACAAGTTTTT
AGCAGTGTTTTTTGAGCCTATAGACGTCGCTAAAATATTGTAAAAGCGCCGTAAAAAACGCCGCT
AAAAATCATGAGGTTTATGAAGAAAAATGTCGCTATAGAACATGGTCTTTAGCGGCGTTTTTCTC
ACAAACACCGCTAAAGAACATGATCTTTAGCAACGTTTTTCTCACAAATGCTGCTAAAATTAACA
GATTTTAACAGCTCATTTTAATTCATATAGAATCTTAATTTTCAACACTTTTTCCTATAAATTCA
AATCCAACCAATAACTTCAAATCTAAATGTAATGATACTATCACGAAAAAAATATATATATGATT
TAAATTAATAAATAAATGAAAAATATTATACAAAAATAGTATTGTATATATTATTCTCACAATAA
TAAAAAACAAAAGTCTAAGATGACGGATTCTGGGG
Found at i:36205364 original size:43 final size:43
Alignment explanation
Indices: 36205272--36205354 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
36205262 AGAAAAATGT
* ** *
36205272 CGCTATAGAACATGATCTTTAGCGGCGTTTTTCTCACAAACAC
1 CGCTAAAGAACATGATCTTTAGCAACGTTTTCCTCACAAACAC
36205315 CGCTAAAGAACATGATCTTTAGCAACGTTTTCCTCACAAA
1 CGCTAAAGAACATGATCTTTAGCAACGTTTTCCTCACAAA
36205355 TGCTGCTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (43 bp):
CGCTAAAGAACATGATCTTTAGCAACGTTTTCCTCACAAACAC
Found at i:36209928 original size:11 final size:11
Alignment explanation
Indices: 36209912--36209988 Score: 58
Period size: 11 Copynumber: 7.4 Consensus size: 11
36209902 AAACCCAATT
36209912 TTTATTTTAAA
1 TTTATTTTAAA
*
36209923 TTTATTTTAAG
1 TTTATTTTAAA
36209934 TTTA----AAA
1 TTTATTTTAAA
36209941 -TTATTTTAAA
1 TTTATTTTAAA
* *
36209951 TTTAAATTT-AT
1 TTT-ATTTTAAA
*
36209962 TTTAAATTTAAA
1 TTT-ATTTTAAA
36209974 TTTATTTTAAA
1 TTTATTTTAAA
36209985 TTTA
1 TTTA
36209989 AAATTTGAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
6 3 0.06
7 2 0.04
10 3 0.06
11 37 0.70
12 8 0.15
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (11 bp):
TTTATTTTAAA
Found at i:36209937 original size:17 final size:17
Alignment explanation
Indices: 36209917--36209990 Score: 130
Period size: 17 Copynumber: 4.4 Consensus size: 17
36209907 CAATTTTTAT
*
36209917 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAA
*
36209934 TTTAAAATTATTTTAAA
1 TTTAAATTTATTTTAAA
36209951 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
36209968 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
36209985 TTTAAA
1 TTTAAA
36209991 ATTTGAAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:36211693 original size:29 final size:30
Alignment explanation
Indices: 36211650--36211710 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
36211640 CCTTAATGCC
36211650 AATTTTAATTTA-TTTCAAATTTA-TCCATT
1 AATTTTAATTTATTTTC-AATTTAGTCCATT
*
36211679 AATTTT-ATTTAATTTTCAATTTAGTCCGTT
1 AATTTTAATTT-ATTTTCAATTTAGTCCATT
36211709 AA
1 AA
36211711 CCATTTTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 4 0.14
29 13 0.46
30 11 0.39
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.54
Consensus pattern (30 bp):
AATTTTAATTTATTTTCAATTTAGTCCATT
Found at i:36212029 original size:29 final size:29
Alignment explanation
Indices: 36211933--36212228 Score: 196
Period size: 29 Copynumber: 10.1 Consensus size: 29
36211923 CCCAGAAGAT
* * *
36211933 CCCTAAACTGTCCAAAAA-TCATATTTTGAC
1 CCCTGAACTTTCCAAAAATTC-CATTTTG-C
* * *
36211963 CCCCGAACTTTCTAAAAATTACATTTTGAC
1 CCCTGAACTTTCCAAAAATTCCATTTTG-C
* * *
36211993 CCTTGAACTGTCTAAAAATTCCATTTTGC
1 CCCTGAACTTTCCAAAAATTCCATTTTGC
* *
36212022 CCCTGAAC-TTCTAAAAAATTTCATTTTG-
1 CCCTGAACTTTC-CAAAAATTCCATTTTGC
* *
36212050 ACCTCGAACTTTCCAAAAATTACCATTTTAC
1 CCCT-GAACTTTCCAAAAATT-CCATTTTGC
* * *
36212081 TCCC-GAA-TTTTCAAAAATTTCATTTTTGA
1 -CCCTGAACTTTCCAAAAATTCCA-TTTTGC
* * *
36212110 CCTTGAACTTTCCAAAAATTGCCATCTT-A
1 CCCTGAACTTTCCAAAAATT-CCATTTTGC
* *
36212139 CCCTCGAA-TTTCCAAAAATTCTATTTTGA
1 CCCT-GAACTTTCCAAAAATTCCATTTTGC
* *
36212168 CCCTAAACTTTCCAAAAATTACCATTTT-A
1 CCCTGAACTTTCCAAAAATT-CCATTTTGC
*
36212197 CCCTCGAA-TTTTCAAAAATTCCATTTTTGC
1 CCCT-GAACTTTCCAAAAATTCCA-TTTTGC
36212227 CC
1 CC
36212229 TTGAGTTTCT
Statistics
Matches: 213, Mismatches: 35, Indels: 36
0.75 0.12 0.13
Matches are distributed among these distances:
28 19 0.09
29 104 0.49
30 85 0.40
31 3 0.01
32 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCTGAACTTTCCAAAAATTCCATTTTGC
Found at i:36212198 original size:58 final size:57
Alignment explanation
Indices: 36211963--36212258 Score: 264
Period size: 58 Copynumber: 5.1 Consensus size: 57
36211953 ATATTTTGAC
* * * *
36211963 CCCCGAACTTTCTAAAAATTAC-ATTTTGACCCTTGAACTGTCTAAAAATT-CCATTTTG
1 CCCCGAA-TTTCCAAAAATT-CTATTTTGACCC-TGAACTTTCCAAAAATTACCATTTTA
* *
36212021 CCCCTGAACTTCTAAAAAATT-TCATTTTGA-CCTCGAACTTTCCAAAAATTACCATTTTA
1 CCCC-GAATTTC-CAAAAATTCT-ATTTTGACCCT-GAACTTTCCAAAAATTACCATTTTA
* * * *
36212080 CTCCCGAATTTTCAAAAATT-TCATTTTTGACCTTGAACTTTCCAAAAATTGCCATCTTA
1 C-CCCGAATTTCCAAAAATTCT-A-TTTTGACCCTGAACTTTCCAAAAATTACCATTTTA
*
36212139 CCCTCGAATTTCCAAAAATTCTATTTTGACCCTAAACTTTCCAAAAATTACCATTTTA
1 CCC-CGAATTTCCAAAAATTCTATTTTGACCCTGAACTTTCCAAAAATTACCATTTTA
* * * ** *
36212197 CCCTCGAATTTTCAAAAATTCCATTTTTG-CCCTTG-AGTTTCTTAAAATTACCGTTTTA
1 CCC-CGAATTTCCAAAAATTCTA-TTTTGACCC-TGAACTTTCCAAAAATTACCATTTTA
36212255 CCCC
1 CCCC
36212259 CGAACCTCTA
Statistics
Matches: 202, Mismatches: 23, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
57 2 0.01
58 112 0.55
59 82 0.41
60 6 0.03
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (57 bp):
CCCCGAATTTCCAAAAATTCTATTTTGACCCTGAACTTTCCAAAAATTACCATTTTA
Found at i:36212301 original size:117 final size:117
Alignment explanation
Indices: 36211933--36212286 Score: 317
Period size: 117 Copynumber: 3.0 Consensus size: 117
36211923 CCCAGAAGAT
* * * * * *
36211933 CCCTAAACTGTCCAAAAATCA-TATTTTGACCCCCGAACTTTCTAAAAATTACA-TTTTGACCCT
1 CCCTAAACTATCCAAAAATTACCATTTT-ACTCCCGAATTTTC-AAAAATTCCATTTTTGA-CCT
* * * * * * * *
36211996 TGAACTGTCTAAAAATT-CCATTTTGCCCCTGAACTTCTAAAAAATTTCATTTTGA
63 TGAACTTTCCAAAAATTACCATCTTACCCCCGAACCTC-CAAAAATTCCATTTTGA
* * *
36212051 -CCTCGAACTTTCCAAAAATTACCATTTTACTCCCGAATTTTCAAAAATTTCATTTTTGACCTTG
1 CCCT-AAACTATCCAAAAATTACCATTTTACTCCCGAATTTTCAAAAATTCCATTTTTGACCTTG
* * ** *
36212115 AACTTTCCAAAAATTGCCATCTTACCCTCGAATTTCCAAAAATTCTATTTTGA
65 AACTTTCCAAAAATTACCATCTTACCCCCGAACCTCCAAAAATTCCATTTTGA
* *
36212168 CCCTAAACTTTCCAAAAATTACCATTTTAC-CCTCGAATTTTCAAAAATTCCATTTTTGCCCTTG
1 CCCTAAACTATCCAAAAATTACCATTTTACTCC-CGAATTTTCAAAAATTCCATTTTTGACCTTG
* ** * * * *
36212232 -AGTTTCTTAAAATTACCGTTTTACCCCCGAACCTCTATAAATTACCATTTT-A
65 AACTTTCCAAAAATTACCATCTTACCCCCGAACCTCCAAAAATT-CCATTTTGA
36212284 CCC
1 CCC
36212287 CTCGGACATC
Statistics
Matches: 197, Mismatches: 32, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
116 38 0.19
117 104 0.53
118 50 0.25
119 5 0.03
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.36
Consensus pattern (117 bp):
CCCTAAACTATCCAAAAATTACCATTTTACTCCCGAATTTTCAAAAATTCCATTTTTGACCTTGA
ACTTTCCAAAAATTACCATCTTACCCCCGAACCTCCAAAAATTCCATTTTGA
Found at i:36214674 original size:11 final size:11
Alignment explanation
Indices: 36214660--36214688 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
36214650 AATATATTAT
36214660 AAATTATAAAG
1 AAATTATAAAG
36214671 AAATTAT-AAG
1 AAATTATAAAG
36214681 AAATTATA
1 AAATTATA
36214689 TAAGTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (11 bp):
AAATTATAAAG
Found at i:36225590 original size:20 final size:17
Alignment explanation
Indices: 36225548--36225587 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
36225538 TATCTCCATA
36225548 TTTTGTACTCTTCGTTT
1 TTTTGTACTCTTCGTTT
*
36225565 TTTTGTACTCTTCGTTC
1 TTTTGTACTCTTCGTTT
36225582 TTTTGT
1 TTTTGT
36225588 TGTTATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.05, C:0.17, G:0.12, T:0.65
Consensus pattern (17 bp):
TTTTGTACTCTTCGTTT
Found at i:36227309 original size:319 final size:319
Alignment explanation
Indices: 36226720--36227342 Score: 1050
Period size: 319 Copynumber: 2.0 Consensus size: 319
36226710 TCGAAATAGA
*
36226720 CTTCGAGATCGAAATGGCCAGGACCTTAGAGAGGCATTGCTGCTTCATTATATAATTCATAGAAG
1 CTTCGAGATCGAAATGGCCAGGACCTTAGAGAGGCATTGCTGCTTCAGTATATAATTCATAGAAG
* *
36226785 CCTAATGTAGATTTTTTCAATAAGATAAAATTGATTGTGGGCAATGGGTGCTACTTGAACTTTTG
66 CCTAATGTAGATTTTTTCAATAAGATAAAATTGATTGTGGACAATGGGTGCTACTTGAACTTTTA
* * *
36226850 GTCAAATGTGTGAGTGGGTGACTGCCCTTTATATGAAGCCTTTCCGAGAATTTTTGCATTGGCTA
131 GTCAAATGTGTGAGTGGGTGACCGCCCCTTATATGAAGCCTTTCCCAGAATTTTTGCATTGGCTA
* *
36226915 CCATAAAGATAAGAAAAATAACTCAGTTTGGTGATTGGATTAATCAATTTTTGGTGTGAAGAGTC
196 CCATAAAGACAAGAAAAATAACTCAATTTGGTGATTGGATTAATCAATTTTTGGTGTGAAGAGTC
*
36226980 AAGTTAAGGAGGAATATTTAGGCATGGGAAGCTGACCAATGGAACAAAGTATATAATCT
261 AAGTTAAGGAGGAATATTTAAGCATGGGAAGCTGACCAATGGAACAAAGTATATAATCT
* * * *
36227039 CTTCTAGATTGAAATGGTCAGGACCTT-GAAGAGGCATTGTTGCTTCAGTATATAATTCATAGAA
1 CTTCGAGATCGAAATGGCCAGGACCTTAG-AGAGGCATTGCTGCTTCAGTATATAATTCATAGAA
36227103 GCCTAATGTAGATTTTTTCAATAAGATAAAATTGATTGTGGACAATGGGTGCTACTTGAACTTTT
65 GCCTAATGTAGATTTTTTCAATAAGATAAAATTGATTGTGGACAATGGGTGCTACTTGAACTTTT
* *
36227168 AGTCAAATGTGTGGGTGGGTGACCGCCCCTTATATGAAGCCTTTCCCAGAATTTTTGTATTGGCT
130 AGTCAAATGTGTGAGTGGGTGACCGCCCCTTATATGAAGCCTTTCCCAGAATTTTTGCATTGGCT
* * ** *
36227233 ACCATGAAGGCAAGAAAAATAGTTCAATTTGGTGATTGGATTAATCAATTTTTGGTGTGAGGAGT
195 ACCATAAAGACAAGAAAAATAACTCAATTTGGTGATTGGATTAATCAATTTTTGGTGTGAAGAGT
36227298 CAAGTTAAGGAGGAATATTTAAGCATGGGAAGCTGACCAATGGAA
260 CAAGTTAAGGAGGAATATTTAAGCATGGGAAGCTGACCAATGGAA
36227343 TAAGTTTTAA
Statistics
Matches: 283, Mismatches: 20, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
318 1 0.00
319 282 1.00
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (319 bp):
CTTCGAGATCGAAATGGCCAGGACCTTAGAGAGGCATTGCTGCTTCAGTATATAATTCATAGAAG
CCTAATGTAGATTTTTTCAATAAGATAAAATTGATTGTGGACAATGGGTGCTACTTGAACTTTTA
GTCAAATGTGTGAGTGGGTGACCGCCCCTTATATGAAGCCTTTCCCAGAATTTTTGCATTGGCTA
CCATAAAGACAAGAAAAATAACTCAATTTGGTGATTGGATTAATCAATTTTTGGTGTGAAGAGTC
AAGTTAAGGAGGAATATTTAAGCATGGGAAGCTGACCAATGGAACAAAGTATATAATCT
Found at i:36230658 original size:4 final size:4
Alignment explanation
Indices: 36230651--36230705 Score: 56
Period size: 4 Copynumber: 12.8 Consensus size: 4
36230641 GACTAGAATA
* *
36230651 AAAT AAAT AAAT ACAATT AAAA ACAAT TAAT AACAT AAAT AAAT AAAT
1 AAAT AAAT AAAT A-AA-T AAAT A-AAT AAAT AA-AT AAAT AAAT AAAT
36230699 AAAT AAA
1 AAAT AAA
36230706 ATATAGTAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
4 31 0.72
5 10 0.23
6 2 0.05
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:36230967 original size:11 final size:11
Alignment explanation
Indices: 36230889--36230967 Score: 50
Period size: 12 Copynumber: 6.6 Consensus size: 11
36230879 GTAAAATGGC
*
36230889 ATAAGAAATAA
1 ATAAAAAATAA
*
36230900 ATAACAAATAA
1 ATAAAAAATAA
*
36230911 ATAAGTAAAAACAAA
1 AT-A--AAAAA-TAA
36230926 ATAAAAAATAAA
1 ATAAAAAAT-AA
** *
36230938 ATGTAAATTAA
1 ATAAAAAATAA
36230949 ATACAAAAATAA
1 ATA-AAAAATAA
36230961 ATAAAAA
1 ATAAAAA
36230968 CAAAGAACTT
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
11 20 0.38
12 23 0.44
14 5 0.10
15 4 0.08
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (11 bp):
ATAAAAAATAA
Found at i:36231128 original size:23 final size:24
Alignment explanation
Indices: 36231085--36231131 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
36231075 ATTTAAAGTA
36231085 TAAATTAAAAAAATAATAAAAGAT
1 TAAATTAAAAAAATAATAAAAGAT
*
36231109 TAAATTAAAATAA-AATAAAAGAT
1 TAAATTAAAAAAATAATAAAAGAT
36231132 AAAAGGACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (24 bp):
TAAATTAAAAAAATAATAAAAGAT
Found at i:36239634 original size:43 final size:43
Alignment explanation
Indices: 36239471--36239781 Score: 320
Period size: 43 Copynumber: 7.3 Consensus size: 43
36239461 TTATGAGGAA
* *
36239471 AAACGCCGCTATAGAACATGGTCTTTAGCGGCGC-TTTCCCAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * *
36239513 AAATGCCACTAAAGAACATGGTCTTTAGCGGCGC-TTTCCCAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * * ***
36239555 AAACGCCGTTAAGGAACATGATCTTTAGCAATGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * * * * *
36239598 AAGCGTCGTTAAAGAACATGGTCTTTAGCGGCGCTTTTTCTAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * *** **
36239641 AAACACTGCTAAAGAACATGGTCTTTAGCATTGCTTTTTTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * * * * *
36239684 AAACACCACTAAAGAACGTGGCCTTTAGTGGCGCTTTTCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
36239727 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* *
36239770 AAATGCCACTAA
1 AAACGCCGCTAA
36239782 CATTAACAAA
Statistics
Matches: 218, Mismatches: 50, Indels: 1
0.81 0.19 0.00
Matches are distributed among these distances:
42 65 0.30
43 153 0.70
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
Found at i:36244719 original size:60 final size:59
Alignment explanation
Indices: 36244595--36244852 Score: 168
Period size: 59 Copynumber: 4.5 Consensus size: 59
36244585 AATCGGGTAT
* * * * * * *
36244595 AGGGGTGTTGGCCATTGCATGGTCAACACCAAAAAATTTAATTTTTTTATCAGATAAAT
1 AGGGGTGTCGGTCATGGCATGGTCAACACCAAAAAAATTAAATTTTTTATCAGACAAAA
* **
36244654 AGGGGTGTCGGTCATGGCATGGTTAACACCAAAAAAATTAAATTTTTTATTTGACAAAA
1 AGGGGTGTCGGTCATGGCATGGTCAACACCAAAAAAATTAAATTTTTTATCAGACAAAA
* ** * * * *
36244713 AGGGGGTGTCAGTCATGTAATGGCCAACGCC----AAATT---TTTTTTGTCAGATAAAAA
1 A-GGGGTGTCGGTCATGGCATGGTCAACACCAAAAAAATTAAATTTTTTATCAGA-CAAAA
* * *
36244767 AGGGGATGTCGGCCAT-GCAATGGCCAACACC--AAAAA-T--ATTTTTTGTCAGA-AAAA
1 AGGGG-TGTCGGTCATGGC-ATGGTCAACACCAAAAAAATTAAATTTTTTATCAGACAAAA
* *
36244821 AGGGGTGTCGGCCAT-GCAATGGCCAACACCAA
1 AGGGGTGTCGGTCATGGC-ATGGTCAACACCAA
36244853 TTTTTTTTAA
Statistics
Matches: 165, Mismatches: 25, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
53 38 0.23
54 33 0.20
55 1 0.01
56 20 0.12
59 50 0.30
60 23 0.14
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (59 bp):
AGGGGTGTCGGTCATGGCATGGTCAACACCAAAAAAATTAAATTTTTTATCAGACAAAA
Found at i:36244768 original size:54 final size:52
Alignment explanation
Indices: 36244709--36244860 Score: 200
Period size: 54 Copynumber: 2.9 Consensus size: 52
36244699 TTTATTTGAC
* * * *
36244709 AAAAAGGGGGTGTCAGTCATGTAATGGCCAACGCCAAATTTTTTTTGTCAGATA
1 AAAAAGGGGGTGTCGGCCATGCAATGGCCAACACCAAATTTTTTTTGTCAG--A
* *
36244763 AAAAAGGGGATGTCGGCCATGCAATGGCCAACACCAAAAATATTTTTTGTCAGA
1 AAAAAGGGGGTGTCGGCCATGCAATGGCCAACACC--AAATTTTTTTTGTCAGA
36244817 AAAAA-GGGGTGTCGGCCATGCAATGGCCAACACC-AATTTTTTTT
1 AAAAAGGGGGTGTCGGCCATGCAATGGCCAACACCAAATTTTTTTT
36244861 AAATTCTCGT
Statistics
Matches: 88, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
50 9 0.10
53 28 0.32
54 36 0.41
56 15 0.17
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (52 bp):
AAAAAGGGGGTGTCGGCCATGCAATGGCCAACACCAAATTTTTTTTGTCAGA
Found at i:36244843 original size:53 final size:54
Alignment explanation
Indices: 36244709--36244852 Score: 195
Period size: 53 Copynumber: 2.7 Consensus size: 54
36244699 TTTATTTGAC
* * * * * *
36244709 AAAAAGGGGGTGTCAGTCATGTAATGGCCAACGCC--AAATTTTTTTTGTCAGA
1 AAAAAAGGGGTGTCGGCCATGCAATGGCCAACACCAAAAATATTTTTTGTCAGA
36244761 TAAAAAAGGGGATGTCGGCCATGCAATGGCCAACACCAAAAATATTTTTTGTCAG-
1 -AAAAAAGGGG-TGTCGGCCATGCAATGGCCAACACCAAAAATATTTTTTGTCAGA
36244816 AAAAAAGGGGTGTCGGCCATGCAATGGCCAACACCAA
1 AAAAAAGGGGTGTCGGCCATGCAATGGCCAACACCAA
36244853 TTTTTTTTAA
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
53 36 0.44
54 31 0.38
56 15 0.18
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (54 bp):
AAAAAAGGGGTGTCGGCCATGCAATGGCCAACACCAAAAATATTTTTTGTCAGA
Found at i:36249977 original size:42 final size:42
Alignment explanation
Indices: 36249926--36250005 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
36249916 TGTATTTATG
*
36249926 AATCAACATGTATGAAATCAATACATATGAGCAAGTGGTATA
1 AATCAACATGTATGAAATCAATACATATAAGCAAGTGGTATA
*
36249968 AATCAACATGTATGAAATCAATATATATAAGCAAGTGG
1 AATCAACATGTATGAAATCAATACATATAAGCAAGTGG
36250006 AATCATCCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.26
Consensus pattern (42 bp):
AATCAACATGTATGAAATCAATACATATAAGCAAGTGGTATA
Found at i:36255287 original size:23 final size:23
Alignment explanation
Indices: 36255257--36255310 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
36255247 ACGCTAGCGA
*
36255257 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACCTCGTGT
*
36255280 GCTTACTGTTTTGCACCTCGTGT
1 GCTTACTGTTTCGCACCTCGTGT
*
36255303 GCCTACTG
1 GCTTACTG
36255311 ATATACGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.09, C:0.28, G:0.22, T:0.41
Consensus pattern (23 bp):
GCTTACTGTTTCGCACCTCGTGT
Found at i:36262671 original size:18 final size:18
Alignment explanation
Indices: 36262648--36262686 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
36262638 AAAAATCAAA
*
36262648 TTTCACTTCAATTCT-ATT
1 TTTCACATC-ATTCTCATT
36262666 TTTCACATCATTCTCATT
1 TTTCACATCATTCTCATT
36262684 TTT
1 TTT
36262687 GTCCCATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTCACATCATTCTCATT
Found at i:36266540 original size:19 final size:21
Alignment explanation
Indices: 36266501--36266540 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
36266491 AAATATACAT
*
36266501 TTAATTTTCTTTAAATATTTC
1 TTAATTTTCTTAAAATATTTC
36266522 TTAATTTT-TTAAAAT-TTTC
1 TTAATTTTCTTAAAATATTTC
36266541 ACAAACAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 6 0.33
21 8 0.44
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (21 bp):
TTAATTTTCTTAAAATATTTC
Found at i:36276484 original size:30 final size:29
Alignment explanation
Indices: 36276450--36276506 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
36276440 TATTCAAAAG
36276450 TATAAGAATTATTTAAACATTTAAAAATAT
1 TATAAGAATTATTTAAA-ATTTAAAAATAT
*
36276480 TATAAGAATTATTTAAAATTTTAAAAT
1 TATAAGAATTATTTAAAATTTAAAAAT
36276507 TTAAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (29 bp):
TATAAGAATTATTTAAAATTTAAAAATAT
Found at i:36276532 original size:22 final size:23
Alignment explanation
Indices: 36276498--36276540 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
36276488 TTATTTAAAA
36276498 TTTTAAAATTTAAAAAAAATATT
1 TTTTAAAATTTAAAAAAAATATT
*
36276521 TTTTGAAA-TTAAAAAAAATA
1 TTTTAAAATTTAAAAAAAATA
36276541 AAAAAATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TTTTAAAATTTAAAAAAAATATT
Found at i:36278246 original size:3 final size:3
Alignment explanation
Indices: 36278238--36278267 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
36278228 ATTTAAACAC
36278238 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
36278268 CAACTAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:36279488 original size:18 final size:18
Alignment explanation
Indices: 36279465--36279503 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
36279455 AAAAATCAAA
*
36279465 TTTCACTTCAATTCT-ATT
1 TTTCACATC-ATTCTCATT
36279483 TTTCACATCATTCTCATT
1 TTTCACATCATTCTCATT
36279501 TTT
1 TTT
36279504 GTCCCATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTCACATCATTCTCATT
Found at i:36279611 original size:23 final size:20
Alignment explanation
Indices: 36279584--36279626 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 20
36279574 AATATTTTCT
36279584 TACTCAAGCATTCAAAATCATAA
1 TACTCAAGC--TCAAAAT-ATAA
36279607 TACTCAAGCTCAAAATATAA
1 TACTCAAGCTCAAAATATAA
36279627 CCATGGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 7 0.35
23 9 0.45
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.26
Consensus pattern (20 bp):
TACTCAAGCTCAAAATATAA
Found at i:36280543 original size:8 final size:8
Alignment explanation
Indices: 36280530--36280567 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
36280520 TATTTATAAA
36280530 ATATTATT
1 ATATTATT
*
36280538 ATATTATA
1 ATATTATT
36280546 ATATTATT
1 ATATTATT
36280554 A-ATTATT
1 ATATTATT
*
36280561 AAATTAT
1 ATATTAT
36280568 CTTTTGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
ATATTATT
Found at i:36294298 original size:42 final size:43
Alignment explanation
Indices: 36294185--36294299 Score: 121
Period size: 40 Copynumber: 2.7 Consensus size: 43
36294175 TAATAATTTA
* *
36294185 CAAATAGTGTGGTTCATTCATGAACCAAGTGGCAGTTTTTATCTG
1 CAAATA-TGTGGTTCAATCATGAACCAAGTGACAG-TTTTATCTG
* * * *
36294230 CAATTATGTTGTGC-ATCCA-CAA-CAAGTGACAG-TTTATCTG
1 CAAATATGTGGTTCAAT-CATGAACCAAGTGACAGTTTTATCTG
36294270 CAAATATGTGGTTCAATCATGAACCAAGTG
1 CAAATATGTGGTTCAATCATGAACCAAGTG
36294300 CATACTGGAG
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
40 21 0.38
41 4 0.07
42 15 0.27
43 3 0.05
44 8 0.14
45 5 0.09
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (43 bp):
CAAATATGTGGTTCAATCATGAACCAAGTGACAGTTTTATCTG
Found at i:36295658 original size:2 final size:2
Alignment explanation
Indices: 36295651--36295680 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
36295641 TTTCGTATGA
36295651 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
36295681 GAAGTTCCTT
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):
AT
Found at i:36305894 original size:18 final size:18
Alignment explanation
Indices: 36305871--36305909 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
36305861 AAAAATCAAA
*
36305871 TTTCACTTCAATTCT-ATT
1 TTTCACATC-ATTCTCATT
36305889 TTTCACATCATTCTCATT
1 TTTCACATCATTCTCATT
36305907 TTT
1 TTT
36305910 GACCCATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTCACATCATTCTCATT
Found at i:36306948 original size:8 final size:8
Alignment explanation
Indices: 36306935--36306972 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
36306925 TATTTATAAA
36306935 ATATTATT
1 ATATTATT
*
36306943 ATATTATA
1 ATATTATT
36306951 ATATTATT
1 ATATTATT
36306959 A-ATTATT
1 ATATTATT
*
36306966 AAATTAT
1 ATATTAT
36306973 CTTTTGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
ATATTATT
Found at i:36318098 original size:18 final size:19
Alignment explanation
Indices: 36318075--36318116 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
36318065 TAGAATTTGC
36318075 CTTTCTCTCT-TATTC-TTT
1 CTTTCTCTCTCT-TTCTTTT
36318093 CTTTCTCTCTCTTTCTTTT
1 CTTTCTCTCTCTTTCTTTT
36318112 CTTTC
1 CTTTC
36318117 CTTTCTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (19 bp):
CTTTCTCTCTCTTTCTTTT
Found at i:36323350 original size:8 final size:8
Alignment explanation
Indices: 36323337--36323374 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
36323327 TATTTATAAA
36323337 ATATTATT
1 ATATTATT
*
36323345 ATATTATA
1 ATATTATT
36323353 ATATTATT
1 ATATTATT
36323361 A-ATTATT
1 ATATTATT
*
36323368 AAATTAT
1 ATATTAT
36323375 CTTTTGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
ATATTATT
Found at i:36334246 original size:18 final size:17
Alignment explanation
Indices: 36334222--36334267 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
36334212 GAATTTTGCC
36334222 TTCCTCTCTTTATTTCT
1 TTCCTCTCTTTATTTCT
36334239 TCTCCTCT-TTCT-TTTCT
1 T-TCCTCTCTT-TATTTCT
*
36334256 TTCCTTTCTTTA
1 TTCCTCTCTTTA
36334268 CATCATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
16 6 0.25
17 11 0.46
18 7 0.29
ACGTcount: A:0.04, C:0.30, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCCTCTCTTTATTTCT
Found at i:36337969 original size:22 final size:22
Alignment explanation
Indices: 36337920--36337971 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
36337910 ATATCCAAAC
*
36337920 AATAACAATAAAATAGTAGCAA
1 AATAATAATAAAATAGTAGCAA
* *
36337942 CATAATAATAAAATTGTAGCAA
1 AATAATAATAAAATAGTAGCAA
36337964 AATAATAA
1 AATAATAA
36337972 CATAACAGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (22 bp):
AATAATAATAAAATAGTAGCAA
Found at i:36339471 original size:15 final size:14
Alignment explanation
Indices: 36339451--36339502 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
36339441 ATATATGTTA
36339451 ATATTTTTATTTTT
1 ATATTTTTATTTTT
*
36339465 -TATATTTTATTTTA
1 ATAT-TTTTATTTTT
36339479 ATTATTTTTAGTTTTT
1 A-TATTTTTA-TTTTT
36339495 ATATTTTT
1 ATATTTTT
36339503 TTCAAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 3 0.09
14 9 0.28
15 12 0.38
16 8 0.25
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (14 bp):
ATATTTTTATTTTT
Found at i:36339474 original size:14 final size:14
Alignment explanation
Indices: 36339455--36339501 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
36339445 ATGTTAATAT
36339455 TTTTATTTTTTATA
1 TTTTATTTTTTATA
36339469 TTTTATTTTAATTAT-
1 TTTTATTTT--TTATA
*
36339484 TTTTAGTTTTTATA
1 TTTTATTTTTTATA
36339498 TTTT
1 TTTT
36339502 TTTCAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 4 0.14
14 13 0.45
15 8 0.28
16 4 0.14
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTTATTTTTTATA
Found at i:36339510 original size:29 final size:29
Alignment explanation
Indices: 36339452--36339510 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
36339442 TATATGTTAA
* *
36339452 TATTTTTATTTTTTATATTTTATTTTAAT
1 TATTTTTAGTTTTTATATTTTATTTAAAT
36339481 TATTTTTAGTTTTTATATTTT-TTTCAAAT
1 TATTTTTAGTTTTTATATTTTATTT-AAAT
36339510 T
1 T
36339511 TTCAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 3 0.11
29 24 0.89
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (29 bp):
TATTTTTAGTTTTTATATTTTATTTAAAT
Found at i:36342499 original size:20 final size:20
Alignment explanation
Indices: 36342474--36342538 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 20
36342464 TAGCACGATA
36342474 AATTTTATTATTTTTTTACG
1 AATTTTATTATTTTTTTACG
*
36342494 AATTTTA-TATTTCTTTAC-
1 AATTTTATTATTTTTTTACG
* * * *
36342512 ATTTTTATAATTTTCTTATG
1 AATTTTATTATTTTTTTACG
36342532 -ATTTTAT
1 AATTTTAT
36342539 AAAATTTTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
18 6 0.17
19 23 0.64
20 7 0.19
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (20 bp):
AATTTTATTATTTTTTTACG
Found at i:36342530 original size:29 final size:28
Alignment explanation
Indices: 36342498--36342578 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 28
36342488 TTTACGAATT
* *
36342498 TTATATTTCTTTACATTTTTATAATTTTC
1 TTATATTTCTATA-AATTTTATAATTTTC
*
36342527 TTATGATTT-TATAAAATTTTATAATTTTT
1 TTAT-ATTTCTAT-AAATTTTATAATTTTC
*
36342556 TTATATTTCTATATATTTTATAA
1 TTATATTTCTATAAATTTTATAA
36342579 AACAAATACG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
28 14 0.31
29 26 0.58
30 5 0.11
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (28 bp):
TTATATTTCTATAAATTTTATAATTTTC
Found at i:36360601 original size:18 final size:18
Alignment explanation
Indices: 36360575--36360609 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36360565 TCAATAAAAG
*
36360575 TATTGAAAAAAAAACATT
1 TATTCAAAAAAAAACATT
*
36360593 TATTCAAAAAATAACAT
1 TATTCAAAAAAAAACAT
36360610 CACAGACACT
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:0.60, C:0.09, G:0.03, T:0.29
Consensus pattern (18 bp):
TATTCAAAAAAAAACATT
Found at i:36361676 original size:18 final size:17
Alignment explanation
Indices: 36361625--36361676 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 17
36361615 GCCCAATCCA
* *
36361625 TTTTAAATT-TATAATA
1 TTTTATATTATATAATT
* *
36361641 TTTTATATTATGTTATT
1 TTTTATATTATATAATT
36361658 TTTATATATTATATAATT
1 TTT-TATATTATATAATT
36361676 T
1 T
36361677 AAAACAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 8 0.29
17 7 0.25
18 13 0.46
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTATATTATATAATT
Done.