Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 37 of 198
Found at i:11153640 original size:19 final size:19
Alignment explanation
Indices: 11153603--11153683 Score: 53
Period size: 19 Copynumber: 4.4 Consensus size: 19
11153593 ATAACAAATG
* *
11153603 AAATTTAAAAATATAAAAA
1 AAATTAAAAAAAATAAAAA
*
11153622 AAATTAAAAAAAAT--TAA
1 AAATTAAAAAAAATAAAAA
* *
11153639 AAATTACAGAAAATAAAAA
1 AAATTAAAAAAAATAAAAA
* *
11153658 TAAA--AACAAAAATAATGAA
1 -AAATTAAAAAAAATAA-AAA
11153677 AAATTAA
1 AAATTAA
11153684 TTCGGTGTTG
Statistics
Matches: 46, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
17 14 0.30
18 11 0.24
19 16 0.35
20 5 0.11
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
AAATTAAAAAAAATAAAAA
Found at i:11153653 original size:38 final size:38
Alignment explanation
Indices: 11153610--11153682 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
11153600 ATGAAATTTA
** *
11153610 AAAATATAAAA-AAAATTAAAAAAAATTAAAAATTACAG
1 AAAATA-AAAATAAAAACAAAAAAAATGAAAAATTACAG
*
11153648 AAAATAAAAATAAAAACAAAAATAATGAAAAATTA
1 AAAATAAAAATAAAAACAAAAAAAATGAAAAATTA
11153683 ATTCGGTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 4 0.13
38 26 0.87
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (38 bp):
AAAATAAAAATAAAAACAAAAAAAATGAAAAATTACAG
Found at i:11153662 original size:28 final size:29
Alignment explanation
Indices: 11153584--11153671 Score: 72
Period size: 28 Copynumber: 3.0 Consensus size: 29
11153574 TTTTAAGATC
* *
11153584 TAAAAATATATAACAAATGAAATTTAAAAATA
1 TAAAAA-AAATAA-AAAT-AAAATTAAAAATA
*
11153616 TAAAAAAAATTAAAA-AAAATTAAAAAT-
1 TAAAAAAAATAAAAATAAAATTAAAAATA
* * **
11153643 TACAGAAAATAAAAATAAAAACAAAAATA
1 TAAAAAAAATAAAAATAAAATTAAAAATA
11153672 ATGAAAAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
27 12 0.26
28 21 0.46
30 3 0.07
31 4 0.09
32 6 0.13
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (29 bp):
TAAAAAAAATAAAAATAAAATTAAAAATA
Found at i:11153984 original size:18 final size:20
Alignment explanation
Indices: 11153940--11153986 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
11153930 TAATTTATAT
11153940 ATTTCTTATATTTTTTTAACA
1 ATTT-TTATATTTTTTTAACA
* *
11153961 AGTTTTAT-TTTTTTTCA-A
1 ATTTTTATATTTTTTTAACA
11153979 ATTTTTAT
1 ATTTTTAT
11153987 GGATTTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 8 0.35
19 8 0.35
20 4 0.17
21 3 0.13
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (20 bp):
ATTTTTATATTTTTTTAACA
Found at i:11154571 original size:18 final size:18
Alignment explanation
Indices: 11154550--11154584 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11154540 CCAACATACG
* *
11154550 TAAAAGATTCTAAAAAAT
1 TAAAAAATTATAAAAAAT
11154568 TAAAAAATTATAAAAAA
1 TAAAAAATTATAAAAAA
11154585 ATTTCAATTT
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:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (18 bp):
TAAAAAATTATAAAAAAT
Found at i:11154916 original size:22 final size:22
Alignment explanation
Indices: 11154886--11154928 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
11154876 ACACCAAAAC
*
11154886 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
11154908 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
11154929 AGCGCCACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:11160660 original size:82 final size:82
Alignment explanation
Indices: 11160514--11160915 Score: 439
Period size: 82 Copynumber: 4.9 Consensus size: 82
11160504 TTTTGTTACT
* * *** * * * * *
11160514 ATTAGCGGCGCTTCGGCAAAAACGCCGCTAAAGA-TTAATACATTCGTGGCGCTTAGATACAAAC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCCGA-GCATTAGCGGCGCTTAGACAAAAAC
* *
11160578 GCCGCTGA-ATACAGGAGA
65 GCCGCT-ATAGACAGGAGC
* * * * * *
11160596 ATTAGCGGCGCATATATAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGCATAGGCGAAAACG
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGCTTAGACAAAAACG
*
11160661 CCGCTATAGACACAGAGC
66 CCGCTATAGACA-GGAGC
* * * * * *
11160679 ATTATCGGCGCTTAGACGAAAACGCCGCTAAAGACTCGGAGCATTAGCGGTGCTTAGACGAAAGC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGAC-CCGAGCATTAGCGGCGCTTAGACAAAAAC
* *
11160744 GCCGCTAAAGACTCGGAGC
65 GCCGCTATAGAC-AGGAGC
* * * *
11160763 ATTAGCGGCGCTTATACGAAAACGCCACTATAGACCCGAGCATTAGCGGCGCTTAGACAAAAACG
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGCTTAGACAAAAACG
**
11160828 CCGCTATAGACCCGAGC
66 CCGCTATAGACAGGAGC
*
11160845 ATTAGCGGCGCTTAGACAAAAACGCCGCTATAGACCCGAGCATTAGCGGCGCTTAGACAAAAACG
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGCTTAGACAAAAACG
11160910 CCGCTA
66 CCGCTA
11160916 AATGTTTAAA
Statistics
Matches: 270, Mismatches: 45, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
81 1 0.00
82 129 0.48
83 70 0.26
84 70 0.26
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.16
Consensus pattern (82 bp):
ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGCTTAGACAAAAACG
CCGCTATAGACAGGAGC
Found at i:11160699 original size:42 final size:41
Alignment explanation
Indices: 11160596--11160915 Score: 433
Period size: 41 Copynumber: 7.7 Consensus size: 41
11160586 ATACAGGAGA
* * ** *
11160596 ATTAGCGGCGCATATATAAAAACGCCGCTAAAGACCCGAGC
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTATAGACCCGAGC
* * *
11160637 ATTAGCGGCGCATAGGCGAAAACGCCGCTATAGACACAGAGC
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTATAGAC-CCGAGC
* * *
11160679 ATTATCGGCGCTTAGACGAAAACGCCGCTAAAGACTCGGAGC
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTATAGAC-CCGAGC
* * * *
11160721 ATTAGCGGTGCTTAGACGAAAGCGCCGCTAAAGACTCGGAGC
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTATAGAC-CCGAGC
* *
11160763 ATTAGCGGCGCTTATACGAAAACGCCACTATAGACCCGAGC
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTATAGACCCGAGC
*
11160804 ATTAGCGGCGCTTAGACAAAAACGCCGCTATAGACCCGAGC
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTATAGACCCGAGC
*
11160845 ATTAGCGGCGCTTAGACAAAAACGCCGCTATAGACCCGAGC
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTATAGACCCGAGC
*
11160886 ATTAGCGGCGCTTAGACAAAAACGCCGCTA
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTA
11160916 AATGTTTAAA
Statistics
Matches: 254, Mismatches: 24, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
41 144 0.57
42 110 0.43
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.15
Consensus pattern (41 bp):
ATTAGCGGCGCTTAGACGAAAACGCCGCTATAGACCCGAGC
Found at i:11160860 original size:23 final size:23
Alignment explanation
Indices: 11160793--11160902 Score: 64
Period size: 23 Copynumber: 5.2 Consensus size: 23
11160783 AACGCCACTA
11160793 TAGACCCGAGCATTAGCGGCGCT
1 TAGACCCGAGCATTAGCGGCGCT
* * *
11160816 TAGA--C-A--A-AAACGCCGCT
1 TAGACCCGAGCATTAGCGGCGCT
11160833 ATAGACCCGAGCATTAGCGGCGCT
1 -TAGACCCGAGCATTAGCGGCGCT
* * *
11160857 TAGA--C-A--A-AAACGCCGCT
1 TAGACCCGAGCATTAGCGGCGCT
11160874 ATAGACCCGAGCATTAGCGGCGCT
1 -TAGACCCGAGCATTAGCGGCGCT
11160898 TAGAC
1 TAGAC
11160903 AAAAACGCCG
Statistics
Matches: 61, Mismatches: 12, Indels: 28
0.60 0.12 0.28
Matches are distributed among these distances:
17 14 0.23
18 10 0.16
20 4 0.07
21 4 0.07
23 15 0.25
24 14 0.23
ACGTcount: A:0.30, C:0.29, G:0.25, T:0.15
Consensus pattern (23 bp):
TAGACCCGAGCATTAGCGGCGCT
Found at i:11161353 original size:88 final size:88
Alignment explanation
Indices: 11161204--11161371 Score: 259
Period size: 88 Copynumber: 1.9 Consensus size: 88
11161194 TCATGTTTAA
* *
11161204 TAGTACAAATTGTAATTACACAGTTATATAATTTATATTTTAATAAAATATATTAATTACTATAA
1 TAGTACAAATTGTAATTACACAATTACATAATTTATATTTTAATAAAATATATTAATTACTAT-A
11161269 AAAATT-TTAGTATGAATATTTGG
65 AAAATTATTAGTATGAATATTTGG
* **
11161292 TAGTACAAATTGTAATTGCACAATTACATAATTTATATATTTTTTAAAA-ATATTAATTACTATA
1 TAGTACAAATTGTAATTACACAATTACATAATTTATAT-TTTAATAAAATATATTAATTACTATA
11161356 AAAATTATTAGTATGA
65 AAAATTATTAGTATGA
11161372 TAAGTATAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
87 7 0.10
88 58 0.79
89 8 0.11
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (88 bp):
TAGTACAAATTGTAATTACACAATTACATAATTTATATTTTAATAAAATATATTAATTACTATAA
AAATTATTAGTATGAATATTTGG
Found at i:11162251 original size:41 final size:41
Alignment explanation
Indices: 11162144--11162418 Score: 428
Period size: 41 Copynumber: 6.7 Consensus size: 41
11162134 GACCTTTCGG
* *
11162144 GGCTTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCA
1 GGCTTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
*
11162185 GAGC-TTT-GCGGCGTTTTTGAGAAAGCGCCGCTAATACTCA
1 G-GCTTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
*
11162225 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
1 GGCTTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
11162266 GGCTTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
1 GGCTTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
*
11162307 GGCTTTTAGCGGCGTTTTTGAGAAAGCACCGCTAATGCTCA
1 GGCTTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * * *
11162348 GGCTTTTAGCGGTGTTTGTCAGAAAGCGTCGCTAATGCTCA
1 GGCTTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* *
11162389 GGCTTTTAGCGGTGTTTTTGAAAAAGCGCC
1 GGCTTTTAGCGGCGTTTTTGAGAAAGCGCC
11162419 ACAAAAACAT
Statistics
Matches: 215, Mismatches: 16, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
39 2 0.01
40 34 0.16
41 177 0.82
42 2 0.01
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (41 bp):
GGCTTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
Found at i:11162914 original size:7 final size:7
Alignment explanation
Indices: 11162857--11162915 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
11162847 AGGGTTGTGA
11162857 TTTAGGG
1 TTTAGGG
* *
11162864 GTTAAGG
1 TTTAGGG
*
11162871 CTTAGGG
1 TTTAGGG
*
11162878 GTTAGGG
1 TTTAGGG
11162885 ATTT-GGG
1 -TTTAGGG
11162892 -TTAGGG
1 TTTAGGG
11162898 TTTAGGG
1 TTTAGGG
*
11162905 TTTAGAG
1 TTTAGGG
11162912 TTTA
1 TTTA
11162916 AATTAAATAG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
5 2 0.05
6 3 0.07
7 35 0.83
8 2 0.05
ACGTcount: A:0.19, C:0.02, G:0.41, T:0.39
Consensus pattern (7 bp):
TTTAGGG
Found at i:11162978 original size:7 final size:7
Alignment explanation
Indices: 11162955--11162999 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
11162945 TAAATAAGGT
11162955 TTAGGGG
1 TTAGGGG
**
11162962 TTAGTAG
1 TTAGGGG
11162969 TTAGGGG
1 TTAGGGG
11162976 TTAGGGG
1 TTAGGGG
*
11162983 TTTGGGG
1 TTAGGGG
11162990 TTAGGGG
1 TTAGGGG
11162997 TTA
1 TTA
11163000 AGAGTTAGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.16, C:0.00, G:0.49, T:0.36
Consensus pattern (7 bp):
TTAGGGG
Found at i:11162979 original size:21 final size:21
Alignment explanation
Indices: 11162955--11163008 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
11162945 TAAATAAGGT
11162955 TTAGGGGTTAGTAGTTAGGGG
1 TTAGGGGTTAGTAGTTAGGGG
* **
11162976 TTAGGGGTTTGGGGTTAGGGG
1 TTAGGGGTTAGTAGTTAGGGG
* *
11162997 TTAAGAGTTAGT
1 TTAGGGGTTAGT
11163009 GATTTAAGGT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.46, T:0.35
Consensus pattern (21 bp):
TTAGGGGTTAGTAGTTAGGGG
Found at i:11167628 original size:24 final size:23
Alignment explanation
Indices: 11167600--11167647 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
11167590 AATTTAAAAA
11167600 ATAAAACATAATATAATATTT-ATT
1 ATAAAA-ATAA-ATAATATTTGATT
*
11167624 ATAAAAATAAATATTATTTGATT
1 ATAAAAATAAATAATATTTGATT
11167647 A
1 A
11167648 AAATATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 8 0.36
24 6 0.27
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
ATAAAAATAAATAATATTTGATT
Found at i:11167769 original size:43 final size:43
Alignment explanation
Indices: 11167692--11167919 Score: 289
Period size: 43 Copynumber: 5.3 Consensus size: 43
11167682 TTTTTGCTAG
* *
11167692 AAGCGCCGCTAAAGGT-TTGTTCTTTAGCGGCGTTTGTGGAAA
1 AAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGGAAA
* *
11167734 AAGCGTCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTTTGGGAAA
1 AAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGT-GGAAA
* * *
11167778 AAGCGCCGCTAAAGGTTGTGGTCTTTAGTGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGGAAA
*
11167821 AAGCGCCGCTAAAGGTCGTGGTCTTTAGC-GCGTTTGTGTAAA
1 AAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGGAAA
* * * * * **
11167863 AAGCGCCGCTAAAGATTGTAGTATTTAGCGGCGTTTATTTAAA
1 AAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGGAAA
*
11167906 AAACGCCGCTAAAG
1 AAGCGCCGCTAAAG
11167920 TTAGCGACGC
Statistics
Matches: 163, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
42 51 0.31
43 73 0.45
44 39 0.24
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.29
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGGAAA
Found at i:11167908 original size:129 final size:128
Alignment explanation
Indices: 11167672--11167919 Score: 329
Period size: 129 Copynumber: 1.9 Consensus size: 128
11167662 AGATTATATT
* * * * *
11167672 TTTAGTGGCGTTTTTGCTAGAAGCGCCGCTAAAGGTTTGTTCTTTAGCGGCGTTTGTGGAAAAAG
1 TTTAGTGGCGTTTGTGCGAAAAGCGCCGCTAAAGGTGTGGTCTTTAGCGGCGTTTGTGGAAAAAG
* * * * *
11167737 CGTCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTTTGGGAAAAAGCGCCGCTAAAGGTTGTGGTC
66 CGCCGCTAAAGATCGTAGTATTTAGCGGCGTTTTT-GGAAAAAACGCCGCTAAAGGTTGTGGTC
* *
11167801 TTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTTTAGC-GCGTTTGTGTAAAAA
1 TTTAGTGGCGTTTGTGCGAAAAGCGCCGCTAAAGGT-GTGGTCTTTAGCGGCGTTTGTGGAAAAA
* *
11167865 GCGCCGCTAAAGATTGTAGTATTTAGCGGCGTTTATT-TAAAAAACGCCGCTAAAG
65 GCGCCGCTAAAGATCGTAGTATTTAGCGGCGTTT-TTGGAAAAAACGCCGCTAAAG
11167920 TTAGCGACGC
Statistics
Matches: 103, Mismatches: 14, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
128 16 0.16
129 75 0.73
130 12 0.12
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.31
Consensus pattern (128 bp):
TTTAGTGGCGTTTGTGCGAAAAGCGCCGCTAAAGGTGTGGTCTTTAGCGGCGTTTGTGGAAAAAG
CGCCGCTAAAGATCGTAGTATTTAGCGGCGTTTTTGGAAAAAACGCCGCTAAAGGTTGTGGTC
Found at i:11167989 original size:22 final size:22
Alignment explanation
Indices: 11167961--11168003 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
11167951 AAGCGGCGCT
*
11167961 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
11167983 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
11168004 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:11168696 original size:6 final size:6
Alignment explanation
Indices: 11168685--11168719 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
11168675 CTTCATACAT
11168685 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
11168720 TACTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:11168699 original size:18 final size:18
Alignment explanation
Indices: 11168678--11168717 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
11168668 GGTACATCTT
*
11168678 CATACATATATACATATA
1 CATACACATATACATATA
*
11168696 CATATACATATACATATA
1 CATACACATATACATATA
11168714 CATA
1 CATA
11168718 TATACTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (18 bp):
CATACACATATACATATA
Found at i:11169447 original size:41 final size:41
Alignment explanation
Indices: 11169401--11169506 Score: 122
Period size: 41 Copynumber: 2.6 Consensus size: 41
11169391 ACCGGCATGT
* * **
11169401 AGCCTGCTAGGCTTAAAGCCTGATTTAGAACACCGACATTA
1 AGCCTGCTAGACGTAAAGCCTGAAATAGAACACCGACATTA
* ***
11169442 AGCCTGCTAGACGTAAAGTCTGAAATATTTCACCGACATTA
1 AGCCTGCTAGACGTAAAGCCTGAAATAGAACACCGACATTA
* *
11169483 AGCCTGCTAAACGTAAAGTCTGAA
1 AGCCTGCTAGACGTAAAGCCTGAA
11169507 TTATTTCACT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGCCTGAAATAGAACACCGACATTA
Found at i:11169512 original size:41 final size:41
Alignment explanation
Indices: 11169431--11169533 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
11169421 TGATTTAGAA
*
11169431 CACCGACATTAAGCCTGCTAGACGTAAAGTCTGAAATATTT
1 CACCGACATTAAGCCTGCTAAACGTAAAGTCTGAAATATTT
*
11169472 CACCGACATTAAGCCTGCTAAACGTAAAGTCTGAATTATTT
1 CACCGACATTAAGCCTGCTAAACGTAAAGTCTGAAATATTT
* * *
11169513 CACTGGCATTAAGCCAGCTAA
1 CACCGACATTAAGCCTGCTAA
11169534 GCACAGAGCC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (41 bp):
CACCGACATTAAGCCTGCTAAACGTAAAGTCTGAAATATTT
Found at i:11169547 original size:41 final size:41
Alignment explanation
Indices: 11169431--11169548 Score: 110
Period size: 41 Copynumber: 2.9 Consensus size: 41
11169421 TGATTTAGAA
* * ** * *
11169431 CACCGACATTAAGCCTGCTAGACGTAAAGTCTGAAATATTT
1 CACCGACATTAAGCCAGCTAAACACAAAGCCTGAATTATTT
* ** *
11169472 CACCGACATTAAGCCTGCTAAACGTAAAGTCTGAATTATTT
1 CACCGACATTAAGCCAGCTAAACACAAAGCCTGAATTATTT
* * * *
11169513 CACTGGCATTAAGCCAGCTAAGCACAGAGCCTGAAT
1 CACCGACATTAAGCCAGCTAAACACAAAGCCTGAAT
11169549 AACTCAGATA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (41 bp):
CACCGACATTAAGCCAGCTAAACACAAAGCCTGAATTATTT
Found at i:11171465 original size:18 final size:20
Alignment explanation
Indices: 11171421--11171469 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
11171411 CCTAAACAAA
*
11171421 AAGTATCGATACTTATTAGT
1 AAGTATCGATACCTATTAGT
11171441 AAGTATCGATACCT-TTAGT
1 AAGTATCGATACCTATTAGT
11171460 -AGTATCGATA
1 AAGTATCGATA
11171470 TGTATTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 10 0.36
19 5 0.18
20 13 0.46
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (20 bp):
AAGTATCGATACCTATTAGT
Found at i:11176720 original size:21 final size:21
Alignment explanation
Indices: 11176661--11176720 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 21
11176651 AGAATAATGA
*
11176661 TGAATTGCACATACGTGCCCC
1 TGAATTGCACATACGTACCCC
* *
11176682 T--ATCTGTAC-TTCGGTACCCC
1 TGAAT-TGCACATAC-GTACCCC
11176702 TGAATTGCACATACGTACC
1 TGAATTGCACATACGTACC
11176721 ACTGTTTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 10
0.66 0.11 0.23
Matches are distributed among these distances:
19 4 0.14
20 11 0.38
21 10 0.34
22 4 0.14
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (21 bp):
TGAATTGCACATACGTACCCC
Found at i:11176736 original size:41 final size:41
Alignment explanation
Indices: 11176661--11176743 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
11176651 AGAATAATGA
* *
11176661 TGAATTGCACATACGTGCCCCTATCTGTACTTCGGTACCCC
1 TGAATTGCACATACGTACCACTATCTGTACTTCGGTACCCC
* *
11176702 TGAATTGCACATACGTACCACTGTTTGTTA-TTCGGTACCCC
1 TGAATTGCACATACGTACCACTATCTG-TACTTCGGTACCCC
11176743 T
1 T
11176744 AGATGTTCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 35 0.95
42 2 0.05
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.33
Consensus pattern (41 bp):
TGAATTGCACATACGTACCACTATCTGTACTTCGGTACCCC
Found at i:11183573 original size:103 final size:103
Alignment explanation
Indices: 11183388--11183587 Score: 303
Period size: 103 Copynumber: 1.9 Consensus size: 103
11183378 GTTACATTTA
* *
11183388 TATGGTAATGCTCTGTAACCCTACTCCCGCGACGGATACGAGATAAGGGTGTTACATTTGCTCCC
1 TATGGTAATGCTCCGTAACCCTACTCCAGCGACGGATACGAGATAAGGGTGTTACATTTGCTCCC
*
11183453 TTCAGTGTGCAGACTTTCCTTTTCTTTTTCCCCAAACG
66 TTCAGTGTACAGACTTTCCTTTTCTTTTTCCCCAAACG
* * * *
11183491 TATGGTAATGCTCCGTAACCCTATTCCAGTGACGTATACGAGATAAGGGTGTTACATTTTCT-CC
1 TATGGTAATGCTCCGTAACCCTACTCCAGCGACGGATACGAGATAAGGGTGTTACATTTGCTCCC
* *
11183555 TCTCCGTGTACAGCCTTTCCTTTTCTTTTTCCC
66 T-TCAGTGTACAGACTTTCCTTTTCTTTTTCCC
11183588 TATTCTTTTC
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
102 3 0.03
103 84 0.97
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (103 bp):
TATGGTAATGCTCCGTAACCCTACTCCAGCGACGGATACGAGATAAGGGTGTTACATTTGCTCCC
TTCAGTGTACAGACTTTCCTTTTCTTTTTCCCCAAACG
Found at i:11187692 original size:12 final size:11
Alignment explanation
Indices: 11187665--11187698 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
11187655 TATATATATT
*
11187665 TAAAAATTATA
1 TAAAAATAATA
11187676 TAAAAATAATA
1 TAAAAATAATA
11187687 TAAAAAATAATA
1 T-AAAAATAATA
11187699 CGGTTGGGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:11194142 original size:41 final size:41
Alignment explanation
Indices: 11194087--11194226 Score: 185
Period size: 41 Copynumber: 3.4 Consensus size: 41
11194077 TATATGATTG
**
11194087 GCACTAAGTGTGCGAAGTTAAATAATGATGTTGAATAACGA
1 GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
*
11194128 GCACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACGA
1 GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
* * *
11194169 GCACTAAGTGTGCGAAACAAAATAATAATGTT-AATAGC-A
1 GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
* *
11194208 GGCATTAAGTGTGTGAAAC
1 -GCACTAAGTGTGCGAAAC
11194227 CGAGATCAAG
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 1 0.01
40 21 0.24
41 67 0.75
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (41 bp):
GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
Found at i:11196545 original size:18 final size:18
Alignment explanation
Indices: 11196522--11196556 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11196512 TCTAAGAAGC
11196522 ACTTTTGAGACAAAAACT
1 ACTTTTGAGACAAAAACT
*
11196540 ACTTTTGAGATAAAAAC
1 ACTTTTGAGACAAAAAC
11196557 ATTGCTAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (18 bp):
ACTTTTGAGACAAAAACT
Found at i:11203063 original size:6 final size:6
Alignment explanation
Indices: 11203052--11203100 Score: 62
Period size: 6 Copynumber: 7.7 Consensus size: 6
11203042 ATAATAAAAT
*
11203052 AAAACA AAAACA AAAACAAA AAAATA AAAAGCA AAAACA AAAACA AAAA
1 AAAACA AAAACA AAAAC--A AAAACA AAAA-CA AAAACA AAAACA AAAA
11203101 ATATAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
6 28 0.74
7 5 0.13
8 5 0.13
ACGTcount: A:0.84, C:0.12, G:0.02, T:0.02
Consensus pattern (6 bp):
AAAACA
Found at i:11203091 original size:27 final size:26
Alignment explanation
Indices: 11203047--11203108 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 26
11203037 AGTGCATAAT
11203047 AAAAT-AAAACAAAAACAAAAACAAA
1 AAAATAAAAACAAAAACAAAAACAAA
11203072 AAAATAAAAAGCAAAAACAAAAACAAA
1 AAAATAAAAA-CAAAAACAAAAACAAA
11203099 AAATATAAAA
1 AAA-ATAAAA
11203109 TATAAAACTA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
25 5 0.15
26 4 0.12
27 19 0.56
28 6 0.18
ACGTcount: A:0.82, C:0.10, G:0.02, T:0.06
Consensus pattern (26 bp):
AAAATAAAAACAAAAACAAAAACAAA
Found at i:11203101 original size:21 final size:20
Alignment explanation
Indices: 11203052--11203094 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
11203042 ATAATAAAAT
*
11203052 AAAACAAAAACAAAAACAAA
1 AAAATAAAAACAAAAACAAA
11203072 AAAATAAAAAGCAAAAACAAA
1 AAAATAAAAA-CAAAAACAAA
11203093 AA
1 AA
11203095 CAAAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.84, C:0.12, G:0.02, T:0.02
Consensus pattern (20 bp):
AAAATAAAAACAAAAACAAA
Found at i:11206008 original size:14 final size:14
Alignment explanation
Indices: 11205986--11206015 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11205976 CGTAAAAATT
11205986 AAATAAAAATAAAA
1 AAATAAAAATAAAA
*
11206000 AAATTAAAATAAAA
1 AAATAAAAATAAAA
11206014 AA
1 AA
11206016 TGGCTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAATAAAAATAAAA
Found at i:11207966 original size:93 final size:93
Alignment explanation
Indices: 11207804--11207989 Score: 291
Period size: 93 Copynumber: 2.0 Consensus size: 93
11207794 CAATCATAGT
*
11207804 CATACATATCATAGAGCAAATCAGTCATACATAACATAAAGCCATAACATTCATTTCATCTCCTA
1 CATACATATCATAGAGCAAATCAGTCATACATAACATAAAGCCATAACAGTCATTTCATCTCCTA
*
11207869 GGGGTATAACATCCATTTTACCCTATGG
66 GGGGTATAACAGCCATTTTACCCTATGG
* * * *
11207897 CATACATATCATAGAGCAAATCAGTCATACATAATATAAGGCCATAACAGTCATTTCATCTCTTG
1 CATACATATCATAGAGCAAATCAGTCATACATAACATAAAGCCATAACAGTCATTTCATCTCCTA
** *
11207962 GGGGTATTCCGGCCATTTTACCCTATGG
66 GGGGTATAACAGCCATTTTACCCTATGG
11207990 GGGTAATTCA
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 84 1.00
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (93 bp):
CATACATATCATAGAGCAAATCAGTCATACATAACATAAAGCCATAACAGTCATTTCATCTCCTA
GGGGTATAACAGCCATTTTACCCTATGG
Found at i:11207990 original size:27 final size:27
Alignment explanation
Indices: 11207960--11208581 Score: 679
Period size: 27 Copynumber: 23.0 Consensus size: 27
11207950 TTTCATCTCT
* *
11207960 TGGGGGTATTCCGGCCATTTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* * * *
11207987 TGGGGGTAATTCAGTCAATTTACCTTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* *
11208014 TGGGGGTATTTCGATCATTTTCCCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* *
11208041 TCGGGCTATTTCGGTCATTTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
** *
11208068 TAAGGGTATTTCGATCATTTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
*
11208095 TGGGGGTATTTCGGTCATTTTACTCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* * * *
11208122 TGAGGATGTTTCGATCATTTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* *
11208149 TAGGGGTATTTCGGTCAATTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* * *
11208176 TGGGAGTATTTCGATCAATTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* *
11208203 TGGGGGTATTTCGAAT-AATTTACCCTA
1 TGGGGGTATTTCG-GTCATTTTACCCTA
** *
11208230 TAAGGGTATTTCGGTCAATTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* * ** *
11208257 TAGGGCTATTTCAATCATTTTACTCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
*
11208284 TGGGGGTATTTCGATCATTTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* * *
11208311 TGGGGGTATTCCAGTCATTTTACCCTG
1 TGGGGGTATTTCGGTCATTTTACCCTA
** *
11208338 TAAGGGTATTTCGATCATTTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* * * *
11208365 TAGGGGTATTTTGGTCATTTTACCTTG
1 TGGGGGTATTTCGGTCATTTTACCCTA
* ** *
11208392 TGGGCGTATTTTAGTCATTTTATCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* *
11208419 TGGGGCTATTTCGATCATTTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* *
11208446 TGGGGGTATTTTGGTCATTTTATCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* * * *
11208473 TAGGGGTATTTCGATTATTTTATCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
11208500 TGGGGGTATTTCGGTCATTTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* *
11208527 TAGGGGTATTTCGGTCATTTTATCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* * *
11208554 TAGGGTTATTTCGGTCATTTTATCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
11208581 T
1 T
11208582 AGGGTTTTAA
Statistics
Matches: 499, Mismatches: 94, Indels: 4
0.84 0.16 0.01
Matches are distributed among these distances:
26 1 0.00
27 496 0.99
28 2 0.00
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.42
Consensus pattern (27 bp):
TGGGGGTATTTCGGTCATTTTACCCTA
Found at i:11213644 original size:59 final size:60
Alignment explanation
Indices: 11213573--11213689 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 60
11213563 ATCACTTTCA
* * * *
11213573 TATTAAATTAATATAATATTTATC-AAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTATCTAAGATAAACATTAAATTAAATTTAATATTAAATCT
* *
11213632 TATTAAAATAATAGAATGTTTATCTTGTAGATAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATAGAATATTTATC-T-AAGATAAACATTAAATTAAATTTAATATTAA
11213690 GATAATCACT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 21 0.43
62 28 0.57
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (60 bp):
TATTAAAATAATAGAATATTTATCTAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:11215392 original size:15 final size:15
Alignment explanation
Indices: 11215368--11215399 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11215358 TATGCATGCA
*
11215368 AAATATAAAAGACAT
1 AAATACAAAAGACAT
11215383 AAATACAAAAGACAT
1 AAATACAAAAGACAT
11215398 AA
1 AA
11215400 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:11222002 original size:15 final size:15
Alignment explanation
Indices: 11221982--11222012 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11221972 AAAATTCATA
11221982 TTAATTTTAATTAAT
1 TTAATTTTAATTAAT
*
11221997 TTAATTTTACTTAAT
1 TTAATTTTAATTAAT
11222012 T
1 T
11222013 AAAATTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TTAATTTTAATTAAT
Found at i:11224414 original size:25 final size:25
Alignment explanation
Indices: 11224331--11224405 Score: 114
Period size: 25 Copynumber: 3.0 Consensus size: 25
11224321 CCATAGATTT
*
11224331 TATGAGTTTCCCGTTATTCAGCTCA
1 TATGAGCTTCCCGTTATTCAGCTCA
* *
11224356 TATGAGCTTCCCCTTATTCAGCTCG
1 TATGAGCTTCCCGTTATTCAGCTCA
*
11224381 TATGAGCTTCCCGTTATTCAACTCA
1 TATGAGCTTCCCGTTATTCAGCTCA
11224406 AAAAAGCTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.37
Consensus pattern (25 bp):
TATGAGCTTCCCGTTATTCAGCTCA
Found at i:11224414 original size:50 final size:49
Alignment explanation
Indices: 11224331--11224436 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 49
11224321 CCATAGATTT
* * * ** * * *
11224331 TATGAGTTTCCCGTTATTCAGCTCATATGAGCTTCCCCTTATTCAGCTCG
1 TATGAGCTTCCCGTTATTCAACTCAAAAAAGCTTACCATT-TACAGCTCG
*
11224381 TATGAGCTTCCCGTTATTCAACTCAAAAAAGCTTACTATTTACAGCTCG
1 TATGAGCTTCCCGTTATTCAACTCAAAAAAGCTTACCATTTACAGCTCG
11224430 TATGAGC
1 TATGAGC
11224437 ATACATAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
49 15 0.32
50 32 0.68
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (49 bp):
TATGAGCTTCCCGTTATTCAACTCAAAAAAGCTTACCATTTACAGCTCG
Found at i:11231615 original size:25 final size:25
Alignment explanation
Indices: 11231580--11231673 Score: 91
Period size: 25 Copynumber: 3.7 Consensus size: 25
11231570 CTCTTATGAG
*
11231580 TTTCCTGTTATTCAACTCGTATAAGC
1 TTTCC-GTTATTCAACTCATATAAGC
* *
11231606 TTTCCGTTATTCAGCTCATATGAGC
1 TTTCCGTTATTCAACTCATATAAGC
* ** *
11231631 TTCCCGTTATTCAACTCCCATGAGC
1 TTTCCGTTATTCAACTCATATAAGC
*
11231656 -TTCCTGTTATTCAGCTCA
1 TTTCC-GTTATTCAACTCA
11231674 GAAAAGATTA
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
24 3 0.05
25 49 0.86
26 5 0.09
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.39
Consensus pattern (25 bp):
TTTCCGTTATTCAACTCATATAAGC
Found at i:11231642 original size:50 final size:50
Alignment explanation
Indices: 11231567--11231673 Score: 144
Period size: 50 Copynumber: 2.1 Consensus size: 50
11231557 GGATACATCA
* * * **
11231567 CAGCTCTTATGAGTTTCCTGTTATTCAACTCGTATAAGCTTTCC-GTTATT
1 CAGCTCATATGAGCTTCCCGTTATTCAACTCCCATAAGC-TTCCTGTTATT
*
11231617 CAGCTCATATGAGCTTCCCGTTATTCAACTCCCATGAGCTTCCTGTTATT
1 CAGCTCATATGAGCTTCCCGTTATTCAACTCCCATAAGCTTCCTGTTATT
11231667 CAGCTCA
1 CAGCTCA
11231674 GAAAAGATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
49 4 0.08
50 46 0.92
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.38
Consensus pattern (50 bp):
CAGCTCATATGAGCTTCCCGTTATTCAACTCCCATAAGCTTCCTGTTATT
Found at i:11240205 original size:40 final size:40
Alignment explanation
Indices: 11240092--11240196 Score: 183
Period size: 40 Copynumber: 2.6 Consensus size: 40
11240082 TATCTGCATT
11240092 CTGTATCTGATATGGGCCAAGGCCCTTATTTATTTTTGAGA
1 CTGTATCTGA-ATGGGCCAAGGCCCTTATTTATTTTTGAGA
*
11240133 CTGTATCTGAATGGGCCGAGGCCCTTATTTATTTTTGAGA
1 CTGTATCTGAATGGGCCAAGGCCCTTATTTATTTTTGAGA
*
11240173 CTGTATCTGAATGGGCTAAGGCCC
1 CTGTATCTGAATGGGCCAAGGCCC
11240197 AAACTTATTC
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
40 51 0.84
41 10 0.16
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (40 bp):
CTGTATCTGAATGGGCCAAGGCCCTTATTTATTTTTGAGA
Found at i:11243219 original size:18 final size:18
Alignment explanation
Indices: 11243196--11243234 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
11243186 GTGACCCATG
11243196 TTTCCC-AAATTTTTATGT
1 TTTCCCAAAATTTTT-TGT
11243214 TTTCCCAAAATTTTTTGT
1 TTTCCCAAAATTTTTTGT
11243232 TTT
1 TTT
11243235 GTTCAAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.21, C:0.15, G:0.05, T:0.59
Consensus pattern (18 bp):
TTTCCCAAAATTTTTTGT
Found at i:11244130 original size:130 final size:130
Alignment explanation
Indices: 11243908--11244530 Score: 747
Period size: 130 Copynumber: 4.8 Consensus size: 130
11243898 AATAACTCAT
* **
11243908 TGATTTAATATCACAACTGATATTATTAAGGCTCGTTGATTTACAATCACAATTTAAGTTCATTG
1 TGATTTAATATCACAACTGATATTATTAAGGCTCGTTGATTTACGATCACAACCTAAGTTCATTG
* * *
11243973 ATTTACTATCATAAACAATTTTCTATGACTTAGTTGATTTACTATCT-CTACTCCAAATAGCTCG
66 ATTTACTATCATGAACAATCTTCTATGAGTTAGTTGATTTACTAT-TGCTACTCCAAATAGCTCG
*
11244037 T
130 C
* * ** * *
11244038 TGAATTAAGATCACAGTTGATATTATTAAGGCTCGCTGATTTACGATCACAACCTAAGTTCATTT
1 TGATTTAATATCACAACTGATATTATTAAGGCTCGTTGATTTACGATCACAACCTAAGTTCATTG
* * *
11244103 ATTTACTATTATGAACAATCTTCTATGAGTTAGTTGATTTACTATCAG-TACTCCAAACAGCTCG
66 ATTTACTATCATGAACAATCTTCTATGAGTTAGTTGATTTACTAT-TGCTACTCCAAATAGCTCG
11244167 C
130 C
** ** * * *
11244168 TGATTTAATATCACAGTTGATATTATTGGGGCTCATTGATTTACGATCGCAACCTAAGTTCGTTG
1 TGATTTAATATCACAACTGATATTATTAAGGCTCGTTGATTTACGATCACAACCTAAGTTCATTG
* * ** * * *
11244233 ATTTACTATCATGAAAAATCTTCTATGATTTAGTTGATTTACTATTGCTACTTTAAACATCTCAC
66 ATTTACTATCATGAACAATCTTCTATGAGTTAGTTGATTTACTATTGCTACTCCAAATAGCTCGC
* * * *
11244298 TGATTTAATATCACAAATGATATTATTAAGGCTCGTTGATTTACGATCGCAGCCTAAGTTTATTG
1 TGATTTAATATCACAACTGATATTATTAAGGCTCGTTGATTTACGATCACAACCTAAGTTCATTG
* *
11244363 A-TTACTATCATGAACAATCTTCTATAAGTTAGTTGATTTACAATTGCTACTCCAAATAGCTCGC
66 ATTTACTATCATGAACAATCTTCTATGAGTTAGTTGATTTACTATTGCTACTCCAAATAGCTCGC
* * * * *
11244427 T-AGTTTAAGATCACAACTGATATTATTAAGGCT-GACTGGTTTAGGATCACAGCCTAAGTTCAT
1 TGA-TTTAATATCACAACTGATATTATTAAGGCTCG-TTGATTTACGATCACAACCTAAGTTCAT
* * *
11244490 TAATTTACAATCATGAATAATCCTTCCTA--AGTTAGTTGATT
64 TGATTTACTATCATGAACAAT-CTT-CTATGAGTTAGTTGATT
11244531 CATAGTCATA
Statistics
Matches: 426, Mismatches: 60, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
128 2 0.00
129 109 0.26
130 309 0.73
131 3 0.01
132 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (130 bp):
TGATTTAATATCACAACTGATATTATTAAGGCTCGTTGATTTACGATCACAACCTAAGTTCATTG
ATTTACTATCATGAACAATCTTCTATGAGTTAGTTGATTTACTATTGCTACTCCAAATAGCTCGC
Found at i:11250814 original size:19 final size:19
Alignment explanation
Indices: 11250790--11250826 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
11250780 GAAAAAAACA
11250790 ATCATTTTTTAAATTTTTT
1 ATCATTTTTTAAATTTTTT
*
11250809 ATCATTTTTTTAATTTTT
1 ATCATTTTTTAAATTTTT
11250827 GGAACTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
ATCATTTTTTAAATTTTTT
Found at i:11257390 original size:38 final size:38
Alignment explanation
Indices: 11257348--11257421 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
11257338 AATGCTAGAC
* *
11257348 AAGATATTTCCAATAAACAAATTTTTCTGATCAAAATT
1 AAGATATTGCCAATAAACAAATTTCTCTGATCAAAATT
*
11257386 AAGATATTGCCAATAAACAAATTTCTCTTATCAAAA
1 AAGATATTGCCAATAAACAAATTTCTCTGATCAAAA
11257422 CGATTGACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (38 bp):
AAGATATTGCCAATAAACAAATTTCTCTGATCAAAATT
Found at i:11259463 original size:17 final size:17
Alignment explanation
Indices: 11259441--11259475 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
11259431 TGAATGGTAC
11259441 ATATGAACATTGTAGAT
1 ATATGAACATTGTAGAT
11259458 ATATGAACATTGTAGAT
1 ATATGAACATTGTAGAT
11259475 A
1 A
11259476 AATCAATGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (17 bp):
ATATGAACATTGTAGAT
Found at i:11260535 original size:13 final size:12
Alignment explanation
Indices: 11260515--11260541 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
11260505 CCAAACAACA
11260515 TCAAAAAAAATT
1 TCAAAAAAAATT
11260527 TCAAAAAAAATT
1 TCAAAAAAAATT
11260539 TCA
1 TCA
11260542 CTTTAATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (12 bp):
TCAAAAAAAATT
Found at i:11262829 original size:21 final size:21
Alignment explanation
Indices: 11262800--11262959 Score: 128
Period size: 21 Copynumber: 7.6 Consensus size: 21
11262790 GAAGCTTGTA
*
11262800 AGCTGAACAGAAGCTCATAAG
1 AGCTGAACAGAAACTCATAAG
* *
11262821 AGCTAAACAGAAACCCATAA-
1 AGCTGAACAGAAACTCATAAG
* * *
11262841 AGGTTGAACAGAATCTCGTAAG
1 A-GCTGAACAGAAACTCATAAG
** *
11262863 ATTTGAACAGAAACTCTTAAG
1 AGCTGAACAGAAACTCATAAG
* *
11262884 AGTTGAACAGAAGCTCGA-AAG
1 AGCTGAACAGAAACTC-ATAAG
*
11262905 AGCTGAAC-GAAAACTTATAAG
1 AGCTGAACAG-AAACTCATAAG
* * * *
11262926 AGTTAAACAGAAGCTCGTAAG
1 AGCTGAACAGAAACTCATAAG
11262947 AGCTGAACAGAAA
1 AGCTGAACAGAAA
11262960 GTAAAACACG
Statistics
Matches: 108, Mismatches: 25, Indels: 12
0.74 0.17 0.08
Matches are distributed among these distances:
20 3 0.03
21 103 0.95
22 2 0.02
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.17
Consensus pattern (21 bp):
AGCTGAACAGAAACTCATAAG
Found at i:11262851 original size:42 final size:42
Alignment explanation
Indices: 11262803--11262959 Score: 160
Period size: 42 Copynumber: 3.7 Consensus size: 42
11262793 GCTTGTAAGC
* *
11262803 TGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAAG-GT
1 TGAACAGAAGCTCATAAGAGCTGAACAGAAACAC-TAAAGAGT
* * ** * *
11262845 TGAACAGAATCTCGTAAGATTTGAACAGAAACTCTTAAGAGT
1 TGAACAGAAGCTCATAAGAGCTGAACAGAAACACTAAAGAGT
11262887 TGAACAGAAGCTCGA-AAGAGCTGAAC-GAAA-ACTTATAAGAGT
1 TGAACAGAAGCTC-ATAAGAGCTGAACAGAAACAC-TA-AAGAGT
* *
11262929 TAAACAGAAGCTCGTAAGAGCTGAACAGAAA
1 TGAACAGAAGCTCATAAGAGCTGAACAGAAA
11262960 GTAAAACACG
Statistics
Matches: 94, Mismatches: 15, Indels: 11
0.78 0.12 0.09
Matches are distributed among these distances:
40 1 0.01
41 9 0.10
42 80 0.85
43 4 0.04
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (42 bp):
TGAACAGAAGCTCATAAGAGCTGAACAGAAACACTAAAGAGT
Found at i:11267763 original size:18 final size:17
Alignment explanation
Indices: 11267731--11267765 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11267721 GTGTTTTGAA
11267731 TTGTTTTAATTTAATTT
1 TTGTTTTAATTTAATTT
*
11267748 TTGTTATTATTTTAATTT
1 TTGTT-TTAATTTAATTT
11267766 ATACGCTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTGTTTTAATTTAATTT
Found at i:11268152 original size:2 final size:2
Alignment explanation
Indices: 11268145--11268191 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
11268135 TTAGTACATT
*
11268145 TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11268187 TA TA T
1 TA TA T
11268192 TCGTTTGAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:11270520 original size:22 final size:24
Alignment explanation
Indices: 11270492--11270535 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
11270482 TATGGCAAGA
11270492 AATTAAG-TAGAAAAG-AAGTATG
1 AATTAAGTTAGAAAAGTAAGTATG
11270514 AATTAAGTTAGAAAAGTAAGTA
1 AATTAAGTTAGAAAAGTAAGTA
11270536 AACTTAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (24 bp):
AATTAAGTTAGAAAAGTAAGTATG
Found at i:11270925 original size:36 final size:36
Alignment explanation
Indices: 11270845--11270936 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 36
11270835 ATATGTGTGG
* *
11270845 AATTGAAATGAATAT-TGACTTGAAAATGGAAAAGTA
1 AATTGAATTGAAT-TGTGACTTGAAAATGAAAAAGTA
*
11270881 AATTTTGAATTGAATTGTGA-TTGAAAGTGAAAAAGTGA
1 AA--TTGAATTGAATTGTGACTTGAAAATGAAAAAGT-A
*
11270919 AATTGAATTGAAATGTGA
1 AATTGAATTGAATTGTGA
11270937 ATTTGGAGAC
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
36 17 0.35
37 15 0.31
38 16 0.33
ACGTcount: A:0.46, C:0.01, G:0.22, T:0.32
Consensus pattern (36 bp):
AATTGAATTGAATTGTGACTTGAAAATGAAAAAGTA
Found at i:11272006 original size:18 final size:17
Alignment explanation
Indices: 11271966--11272014 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
11271956 GTGTGACCCC
* *
11271966 TATTTTTTAAATTTTTT
1 TATTTTTAAAATTATTT
11271983 TAATTTTTAAAATTAATTT
1 T-ATTTTTAAAATT-ATTT
*
11272002 TATTTTAAAAATT
1 TATTTTTAAAATT
11272015 TAAAAACAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 1 0.04
18 22 0.81
19 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTTTTAAAATTATTT
Found at i:11275114 original size:2 final size:2
Alignment explanation
Indices: 11275107--11275150 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
11275097 GATATTTAAA
11275107 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
11275149 AT
1 AT
11275151 TAAAGTCCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11275842 original size:18 final size:18
Alignment explanation
Indices: 11275805--11275842 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
11275795 AAAAAATCAC
*
11275805 ATTTTTTATATTTAATAT
1 ATTTTTTATATTTAAAAT
11275823 ATTTTTTA-ATTTCAAAAT
1 ATTTTTTATATTT-AAAAT
11275841 AT
1 AT
11275843 ATAGTGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTTTATATTTAAAAT
Found at i:11281705 original size:26 final size:26
Alignment explanation
Indices: 11281676--11281736 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
11281666 ATAAGGTTAA
* *
11281676 TTATTTTAAGTT-CTTTATATATTATT
1 TTATTTTAAGTTACTTTACATATTA-C
* *
11281702 TTATTTAAAGTTATTTTACATATTAC
1 TTATTTTAAGTTACTTTACATATTAC
11281728 TTATTTTAA
1 TTATTTTAA
11281737 AATTAACCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (26 bp):
TTATTTTAAGTTACTTTACATATTAC
Found at i:11281735 original size:27 final size:25
Alignment explanation
Indices: 11281675--11281737 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 25
11281665 TATAAGGTTA
*
11281675 ATTATTTT-AAGTTCTTTATATATT
1 ATTATTTTAAAGTTCTTTACATATT
* *
11281699 ATTTTATTTAAAGTTATTTTACATATT
1 ATTAT-TTTAAAGTT-CTTTACATATT
11281726 ACTTATTTTAAA
1 A-TTATTTTAAA
11281738 ATTAACCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 4 0.13
25 3 0.10
26 5 0.16
27 16 0.52
28 3 0.10
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (25 bp):
ATTATTTTAAAGTTCTTTACATATT
Found at i:11284786 original size:18 final size:18
Alignment explanation
Indices: 11284725--11284786 Score: 52
Period size: 21 Copynumber: 3.1 Consensus size: 18
11284715 AAGCTATAAA
11284725 ATTAATATAGATTGATATTTT
1 ATTAATATA-ATT-ATA-TTT
* *
11284746 AATAATCTAATTATTGAATTT
1 ATTAATATAATTA-T--ATTT
11284767 ATTAATATAATTATATTT
1 ATTAATATAATTATATTT
11284785 AT
1 AT
11284787 CATACATCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
18 6 0.18
19 1 0.03
20 5 0.15
21 21 0.62
22 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (18 bp):
ATTAATATAATTATATTT
Found at i:11284796 original size:42 final size:41
Alignment explanation
Indices: 11284725--11284826 Score: 106
Period size: 41 Copynumber: 2.5 Consensus size: 41
11284715 AAGCTATAAA
11284725 ATTAATATAGATTGATATTT-TAATAATCT-AATTATTGAATTT
1 ATTAATATA-ATT-ATATTTATAATAATCTAAATT-TTGAATTT
*
11284767 ATTAATATAATTATATTTATCATACATCTAAAATTTTGAATTT
1 ATTAATATAATTATATTTATAATA-ATCT-AAATTTTGAATTT
11284810 A-T-AT-TAATATATATTTA
1 ATTAATATAAT-TATATTTA
11284827 ACTGTTGAAG
Statistics
Matches: 54, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
40 10 0.19
41 17 0.31
42 14 0.26
43 9 0.17
44 4 0.07
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (41 bp):
ATTAATATAATTATATTTATAATAATCTAAATTTTGAATTT
Found at i:11285902 original size:20 final size:20
Alignment explanation
Indices: 11285870--11285914 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
11285860 AAAAAAAATC
*
11285870 ATTTTGTTTATAATTTTTAT
1 ATTTTGTTTATAATTTTTAA
11285890 ATTTT-TTTAATAATTTTTAA
1 ATTTTGTTT-ATAATTTTTAA
11285910 ATTTT
1 ATTTT
11285915 AAAAGGGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
ATTTTGTTTATAATTTTTAA
Found at i:11286364 original size:5 final size:5
Alignment explanation
Indices: 11286356--11286383 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
11286346 AAATAAAAAT
11286356 AACGA AACGA AACGA AACGA AACGA AAC
1 AACGA AACGA AACGA AACGA AACGA AAC
11286384 AGTACAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.21, G:0.18, T:0.00
Consensus pattern (5 bp):
AACGA
Found at i:11286845 original size:17 final size:17
Alignment explanation
Indices: 11286823--11286855 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
11286813 GTTTGGTTGT
11286823 TAACTTTCAAGACTTAG
1 TAACTTTCAAGACTTAG
11286840 TAACTTTCAAGACTTA
1 TAACTTTCAAGACTTA
11286856 TGTAGAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (17 bp):
TAACTTTCAAGACTTAG
Found at i:11287840 original size:18 final size:17
Alignment explanation
Indices: 11287817--11287851 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
11287807 ATCTTTTTAG
11287817 ATTAAAACAAAAATAATT
1 ATTAAAA-AAAAATAATT
*
11287835 ATTAAAATAAAATAATT
1 ATTAAAAAAAAATAATT
11287852 CTAAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
ATTAAAAAAAAATAATT
Found at i:11287858 original size:16 final size:17
Alignment explanation
Indices: 11287826--11287858 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11287816 GATTAAAACA
*
11287826 AAAATAATTATTAAAAT
1 AAAATAATTACTAAAAT
11287843 AAAATAATT-CTAAAAT
1 AAAATAATTACTAAAAT
11287859 TTAAAATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATAATTACTAAAAT
Found at i:11288623 original size:125 final size:125
Alignment explanation
Indices: 11288371--11288746 Score: 533
Period size: 124 Copynumber: 3.0 Consensus size: 125
11288361 TTAGGGTTTT
* *** * **
11288371 TAGGTCCTGGAAGAAATAATTTCGAGTTGAAGTTTCTGATAAAATAGTATAAAATCGCTTCTAGC
1 TAGGTCATGGAAGAAATAATTT-TTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* * *
11288436 AGGATGCTATTTGAGAATAATTTGTG-AAATCGCGCCCTAGTGGACGCGCTTTTGCTATAG
65 AGGATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* *
11288496 TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAACCGCTTCTAGTA
1 TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
* *
11288561 GGATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACACACTTTTGCTACAG
66 GGATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* * * * *
11288621 TAGGTCATGGAAGAAATAA-ATTTTTTGACGTTTCTGAGCAAACAGTATAAAATCGCTCCAAGGA
1 TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
* *
11288685 GGAT-CTATTTGAGAAGAATTTGTAAAAATCGCGCCCTCGTGGATGCGCTTTTGCTACAG
66 GGATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
11288744 TAG
1 TAG
11288747 CATGTTTGGA
Statistics
Matches: 226, Mismatches: 24, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
123 54 0.24
124 102 0.45
125 70 0.31
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (125 bp):
TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
GGATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:11290504 original size:23 final size:23
Alignment explanation
Indices: 11290456--11290921 Score: 525
Period size: 23 Copynumber: 20.8 Consensus size: 23
11290446 GCAAGCCCGT
* *
11290456 TTAGTGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAAGTTAATTAGG
***
11290477 TTAGGGTTTTTAAGTTAAGGGGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
11290500 TTAGGGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAAGTTAATTAGG
* **
11290521 TTAGAGTTTTTAAG-TAA-CGGG
1 TTAGGGTTTTTAAGTTAATTAGG
11290542 TTAGGGTTTTTAAG-T--TTAGGG
1 TTAGGGTTTTTAAGTTAATTA-GG
11290563 TTTAGGGTTTTTAA-TTAAATTAGG
1 -TTAGGGTTTTTAAGTT-AATTAGG
* *
11290587 TTAGAGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
11290608 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
11290631 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
11290654 TTAGGATTTTTAAGTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
* *
11290677 TTAGGTTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
11290700 TTAGGGTTTTTAAGTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
* *
11290723 TTAGGGCTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
11290746 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
11290769 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
11290792 TTAGGGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAAGTTAATTAGG
* *
11290813 TTAGGATTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
11290836 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
11290859 TTAGGGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
11290880 TTTAAGGTTTTTAA-TTAAATTAGG
1 -TTAGGGTTTTTAAGTT-AATTAGG
*
11290904 TTAGGATTTTTAAGTTAA
1 TTAGGGTTTTTAAGTTAA
11290922 GGGTATTAAT
Statistics
Matches: 394, Mismatches: 31, Indels: 38
0.85 0.07 0.08
Matches are distributed among these distances:
20 3 0.01
21 92 0.23
22 28 0.07
23 260 0.66
24 8 0.02
25 3 0.01
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (23 bp):
TTAGGGTTTTTAAGTTAATTAGG
Found at i:11290694 original size:69 final size:67
Alignment explanation
Indices: 11290456--11290921 Score: 611
Period size: 69 Copynumber: 6.9 Consensus size: 67
11290446 GCAAGCCCGT
* * *** * *
11290456 TTAGTGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGGGTTAGGGTTTTTAAGTTAA--G
1 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTA
11290519 GG
66 GG
* * *
11290521 TTAGAGTTTTTAAG-TAACGGGTTAGGGTTTTTAAGTTT-A--GGGTTTAGGGTTTTTAATTAAA
1 TTAGGGTTTTTAAGTTAA-GGGTTAGGGTTTTTAA-TTTAATTAGG-TTAGGGTTTTTAATTTAA
11290582 TTAGG
63 TTAGG
*
11290587 TTAGAGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTA
1 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTA
11290652 GG
66 GG
* * * *
11290654 TTAGGATTTTTAAGTTAATTAGGTTAGGTTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAT
1 TTAGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAAT
11290719 TAGG
64 TAGG
* * *
11290723 TTAGGGCTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAAT
1 TTAGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAAT
11290788 TAGG
64 TAGG
*
11290792 TTAGGGTTTTTAAGTTAAGGGTTAGGATTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTA
1 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTA
11290857 GG
66 GG
* * * *
11290859 TTAGGGTTTTTAAGTTAAGGGTTTAAGGTTTTTAATTAAATTAGGTTAGGATTTTTAAGTTAA
1 TTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAA
11290922 GGGTATTAAT
Statistics
Matches: 363, Mismatches: 26, Indels: 21
0.89 0.06 0.05
Matches are distributed among these distances:
63 3 0.01
64 19 0.05
65 33 0.09
66 35 0.10
67 109 0.30
68 38 0.10
69 126 0.35
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (67 bp):
TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTA
GG
Found at i:11290807 original size:205 final size:197
Alignment explanation
Indices: 11290462--11290921 Score: 627
Period size: 205 Copynumber: 2.3 Consensus size: 197
11290452 CCGTTTAGTG
* *** *
11290462 TTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGGGTTAGGGTTTTTAAGTTAAGGGTTAGAG
1 TTTTTAAGTTAAGGGTTA-GGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAAGGTTAGAG
* * *
11290527 TTTTTAAGTAACGGGTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGA
65 CTTTTAAGTAACAGGTTAGGGTTTTTAAGTTTAAGGTTTAGGGTTTTTAATTAAATTAGGTTAGA
*
11290592 GTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTA
130 GTTTTTAAGTTAAGGGTTAGGATTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTA
11290657 GGA
195 GGA
*
11290660 TTTTTAAGTTAATTAGGTTAGGTTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTT
1 TTTTTAAGTTAA--GGGTTAGG-TTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--AGGTT
* * * *
11290725 AGGGCTTTTAATTTAATTAGGTTAGGGTTTTTAA-TTTAATTAGG-TTAGGGTTTTTAATTTAAT
61 AGAGCTTTTAA-GTAA-CAGGTTAGGGTTTTTAAGTTT-A--AGGTTTAGGGTTTTTAATTAAAT
*
11290788 TAGGTTAGGGTTTTTAAGTTAAGGGTTAGGATTTTTAATTTAATTAGGTTAGGGTTTTTAATTTA
121 TAGGTTAGAGTTTTTAAGTTAAGGGTTAGGATTTTTAATTTAATTAGGTTAGGGTTTTTAATTTA
*
11290853 ATTAGGTTAGGG
186 ATTAGGTTAGGA
* *
11290865 TTTTTAAGTTAAGGGTTTAAGGTTTTTAATTAAATTAGGTTAGGATTTTTAAGTTAA
1 TTTTTAAGTTAAGGG-TT-AGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA
11290922 GGGTATTAAT
Statistics
Matches: 231, Mismatches: 19, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
198 12 0.05
199 2 0.01
200 36 0.16
202 13 0.06
203 8 0.03
204 51 0.22
205 107 0.46
206 2 0.01
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (197 bp):
TTTTTAAGTTAAGGGTTAGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAAGGTTAGAGC
TTTTAAGTAACAGGTTAGGGTTTTTAAGTTTAAGGTTTAGGGTTTTTAATTAAATTAGGTTAGAG
TTTTTAAGTTAAGGGTTAGGATTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAG
GA
Found at i:11290970 original size:9 final size:9
Alignment explanation
Indices: 11290952--11290988 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
11290942 ATTCTCAAAT
11290952 AATA-TCAA
1 AATATTCAA
11290960 AATATTCAA
1 AATATTCAA
11290969 AATATTCAA
1 AATATTCAA
11290978 AATATTCAA
1 AATATTCAA
11290987 AA
1 AA
11290989 ATTTCTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 4 0.14
9 24 0.86
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (9 bp):
AATATTCAA
Found at i:11291020 original size:25 final size:25
Alignment explanation
Indices: 11290991--11291108 Score: 131
Period size: 25 Copynumber: 4.9 Consensus size: 25
11290981 ATTCAAAAAT
11290991 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
11291016 TTCTATTTTATTACATCAAAT-AA-
1 TTCTATTTTATTACATCAAATAAAC
** * * * *
11291039 TATC-A--AAATAAC-TAAAAAAAAT
1 T-TCTATTTTATTACATCAAATAAAC
11291061 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
11291086 TTCTATTTTATTACATCAAATAA
1 TTCTATTTTATTACATCAAATAA
11291109 TATCAAAATA
Statistics
Matches: 75, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
20 4 0.05
21 8 0.11
22 2 0.03
23 2 0.03
24 8 0.11
25 51 0.68
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.42
Consensus pattern (25 bp):
TTCTATTTTATTACATCAAATAAAC
Found at i:11291067 original size:70 final size:70
Alignment explanation
Indices: 11290985--11291118 Score: 268
Period size: 70 Copynumber: 1.9 Consensus size: 70
11290975 CAAAATATTC
11290985 AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
1 AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
11291050 CTAAA
66 CTAAA
11291055 AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATA
1 AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATA
11291119 TTCAAAATAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.40
Consensus pattern (70 bp):
AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
CTAAA
Found at i:11291561 original size:18 final size:18
Alignment explanation
Indices: 11291538--11291577 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
11291528 GACTCGAAAA
*
11291538 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGCT
11291556 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
11291574 AGGA
1 AGGA
11291578 AACGCACTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:11292234 original size:7 final size:7
Alignment explanation
Indices: 11292224--11292248 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
11292214 TTATATACAT
11292224 AATACTA
1 AATACTA
11292231 AATACTA
1 AATACTA
11292238 AATACTA
1 AATACTA
11292245 AATA
1 AATA
11292249 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:11292444 original size:20 final size:20
Alignment explanation
Indices: 11292419--11292456 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11292409 TTTATTTTTA
11292419 AAAATCT-ATATAATAATTGT
1 AAAATCTAATATAA-AATTGT
11292439 AAAATCTAATATAAAATT
1 AAAATCTAATATAAAATT
11292457 TACCTCGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (20 bp):
AAAATCTAATATAAAATTGT
Found at i:11293368 original size:12 final size:12
Alignment explanation
Indices: 11293351--11293392 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
11293341 TTTACGGTTT
11293351 AAAAAGATTTTA
1 AAAAAGATTTTA
11293363 AAAAAGATTTTA
1 AAAAAGATTTTA
** *
11293375 AAAATTATTTAA
1 AAAAAGATTTTA
11293387 AAAAAG
1 AAAAAG
11293393 GGAGTTAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (12 bp):
AAAAAGATTTTA
Found at i:11293503 original size:14 final size:11
Alignment explanation
Indices: 11293460--11293499 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
11293450 AAGAGAATTT
11293460 TTGA-AGGAAA
1 TTGAGAGGAAA
11293470 TTGAGAGGAAA
1 TTGAGAGGAAA
11293481 TTGAGAGGAAA
1 TTGAGAGGAAA
11293492 TTTGAGAG
1 -TTGAGAG
11293500 AGGATTAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 4 0.14
11 17 0.61
12 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:11301822 original size:17 final size:18
Alignment explanation
Indices: 11301800--11301833 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
11301790 CTAAACACTT
11301800 CTAAAATAACC-TAAACC
1 CTAAAATAACCATAAACC
11301817 CTAAAATAACCATAAAC
1 CTAAAATAACCATAAAC
11301834 TATATCCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.18
Consensus pattern (18 bp):
CTAAAATAACCATAAACC
Found at i:11304480 original size:19 final size:19
Alignment explanation
Indices: 11304456--11304493 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
11304446 AATTTATAAC
*
11304456 TAATTAACCTTAATTACTT
1 TAATTAAACTTAATTACTT
11304475 TAATTAAACTTAATTACTT
1 TAATTAAACTTAATTACTT
11304494 AACCTTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATTAAACTTAATTACTT
Found at i:11308682 original size:30 final size:29
Alignment explanation
Indices: 11308642--11308701 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 29
11308632 GATACATGGG
11308642 AATAAGTTGCTCACACAAGCTGACATTAT
1 AATAAGTTGCTCACACAAGCTGACATTAT
*
11308671 AATAGAGTTGCTCACACAAGTTGACATTAT
1 AATA-AGTTGCTCACACAAGCTGACATTAT
11308701 A
1 A
11308702 TCGAGGTTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (29 bp):
AATAAGTTGCTCACACAAGCTGACATTAT
Found at i:11322785 original size:27 final size:26
Alignment explanation
Indices: 11322741--11322791 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
11322731 ATATTACAAA
* *
11322741 TTTTCTTTTTATTTTCTTTAATTTCT
1 TTTTCATTTGATTTTCTTTAATTTCT
11322767 TTTTCATTTGATTGTTCTTTAATTT
1 TTTTCATTTGATT-TTCTTTAATTT
11322792 TTATCAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.14, C:0.10, G:0.04, T:0.73
Consensus pattern (26 bp):
TTTTCATTTGATTTTCTTTAATTTCT
Found at i:11326766 original size:2 final size:2
Alignment explanation
Indices: 11326759--11326785 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11326749 CTTATGTTTT
11326759 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
11326786 CTTGAATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11332141 original size:17 final size:17
Alignment explanation
Indices: 11332121--11332188 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 17
11332111 ATAAATTGAT
11332121 ATAAATATATAAAAATC
1 ATAAATATATAAAAATC
* *
11332138 ATAAATATTTATAAATATT
1 ATAAATA--TATAAAAATC
*
11332157 ATAAA-AAATAAAAATC
1 ATAAATATATAAAAATC
11332173 GAATAAAT-TATAAAAA
1 --ATAAATATATAAAAA
11332189 ATTATAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
16 7 0.17
17 7 0.17
18 13 0.32
19 13 0.32
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (17 bp):
ATAAATATATAAAAATC
Found at i:11332158 original size:9 final size:9
Alignment explanation
Indices: 11332120--11332161 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
11332110 TATAAATTGA
11332120 TATAAATA-
1 TATAAATAT
*
11332128 TATAAAAAT
1 TATAAATAT
*
11332137 CATAAATATT
1 TATAAATA-T
11332147 TATAAATAT
1 TATAAATAT
11332156 TATAAA
1 TATAAA
11332162 AAATAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
8 7 0.25
9 13 0.46
10 8 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (9 bp):
TATAAATAT
Found at i:11332160 original size:19 final size:17
Alignment explanation
Indices: 11332120--11332196 Score: 59
Period size: 19 Copynumber: 4.4 Consensus size: 17
11332110 TATAAATTGA
11332120 TATAAATATATAAAAAT
1 TATAAATATATAAAAAT
* *
11332137 CATAAATATTTATAAATAT
1 TATAAATA--TATAAAAAT
*
11332156 TATAAA-AAATAAAAAT
1 TATAAATATATAAAAAT
*
11332172 CGAATAAAT-TATAAAAAAT
1 --TATAAATATAT-AAAAAT
11332191 TATAAA
1 TATAAA
11332197 ATTAATAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
16 7 0.15
17 12 0.26
18 8 0.17
19 19 0.41
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (17 bp):
TATAAATATATAAAAAT
Found at i:11332197 original size:27 final size:26
Alignment explanation
Indices: 11332103--11332205 Score: 86
Period size: 27 Copynumber: 3.8 Consensus size: 26
11332093 TTAAAAATAA
*
11332103 AAAAAATTATAAATTGATATAAA-TAT
1 AAAAAATTATAAAATGA-ATAAATTAT
* **
11332129 ATAAAAATCATAAATATTTATAAATATTAT
1 A-AAAAATTATAAA-ATGAAT-AA-ATTAT
11332159 AAAAAA-TA-AAAATCGAATAAATTAT
1 AAAAAATTATAAAAT-GAATAAATTAT
*
11332184 AAAAAATTATAAAATTAATAAA
1 AAAAAATTATAAAATGAATAAA
11332206 ACATATTTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
25 11 0.18
26 13 0.21
27 23 0.38
28 4 0.07
29 6 0.10
30 4 0.07
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (26 bp):
AAAAAATTATAAAATGAATAAATTAT
Found at i:11333894 original size:49 final size:50
Alignment explanation
Indices: 11333824--11333918 Score: 138
Period size: 49 Copynumber: 1.9 Consensus size: 50
11333814 CATTGAGATT
* * *
11333824 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACAAGGCATTGGCACTAAG
1 ATGAGAGGGCCCACGTAAGACCATGTCTGGGACAAGGCATGGGCACTAAG
* *
11333874 ATGAGAGGGCCC-CGTAAGACCATGTTTGGGACATGGCATGGGCAC
1 ATGAGAGGGCCCACGTAAGACCATGTCTGGGACAAGGCATGGGCAC
11333919 CGATATGAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
49 29 0.73
50 11 0.28
ACGTcount: A:0.27, C:0.21, G:0.33, T:0.19
Consensus pattern (50 bp):
ATGAGAGGGCCCACGTAAGACCATGTCTGGGACAAGGCATGGGCACTAAG
Found at i:11333927 original size:49 final size:50
Alignment explanation
Indices: 11333823--11333928 Score: 133
Period size: 49 Copynumber: 2.1 Consensus size: 50
11333813 TCATTGAGAT
* * * *
11333823 TATGAGAGGTCCCATGTAAGACCATGTCTGGGACAAGGCATTGGCACTAA
1 TATGAGAGGGCCCACGTAAGACCATGTCTGGGACAAGGCATGGGCACCAA
* * * *
11333873 GATGAGAGGGCCC-CGTAAGACCATGTTTGGGACATGGCATGGGCACCGA
1 TATGAGAGGGCCCACGTAAGACCATGTCTGGGACAAGGCATGGGCACCAA
11333922 TATGAGA
1 TATGAGA
11333929 ACTCCCATGT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
49 36 0.77
50 11 0.23
ACGTcount: A:0.28, C:0.20, G:0.32, T:0.20
Consensus pattern (50 bp):
TATGAGAGGGCCCACGTAAGACCATGTCTGGGACAAGGCATGGGCACCAA
Found at i:11347650 original size:9 final size:9
Alignment explanation
Indices: 11347636--11347690 Score: 74
Period size: 9 Copynumber: 6.1 Consensus size: 9
11347626 TATAGTTTGA
11347636 TATTCGAAT
1 TATTCGAAT
11347645 TATTCGAAT
1 TATTCGAAT
*
11347654 TATTCGAGT
1 TATTCGAAT
11347663 TATTCGAAT
1 TATTCGAAT
* *
11347672 TATTTGAGT
1 TATTCGAAT
*
11347681 TATTCAAAT
1 TATTCGAAT
11347690 T
1 T
11347691 CGAAAACTCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (9 bp):
TATTCGAAT
Found at i:11347659 original size:18 final size:18
Alignment explanation
Indices: 11347636--11347690 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
11347626 TATAGTTTGA
*
11347636 TATTCGAATTATTCGAAT
1 TATTCGAGTTATTCGAAT
11347654 TATTCGAGTTATTCGAAT
1 TATTCGAGTTATTCGAAT
* *
11347672 TATTTGAGTTATTCAAAT
1 TATTCGAGTTATTCGAAT
11347690 T
1 T
11347691 CGAAAACTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (18 bp):
TATTCGAGTTATTCGAAT
Found at i:11347871 original size:24 final size:24
Alignment explanation
Indices: 11347842--11347904 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
11347832 AGTGTTGCGG
* *
11347842 ACAAATCGCCAGAACAGTATTCAA
1 ACAAATCGCCAGAACAATATGCAA
* * *
11347866 ACAAATTGCCAAAATAATATGCAA
1 ACAAATCGCCAGAACAATATGCAA
*
11347890 ACAAATCGCTAGAAC
1 ACAAATCGCCAGAAC
11347905 TCCAAACAGA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.17
Consensus pattern (24 bp):
ACAAATCGCCAGAACAATATGCAA
Found at i:11347957 original size:30 final size:29
Alignment explanation
Indices: 11347911--11347983 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
11347901 GAACTCCAAA
* * *
11347911 CAGAACTCC-AAAATTGCGGATTTACTGC
1 CAGAACTCCAAAAATTGCAGATATACCGC
*
11347939 TAGAACTCCAATAAATTGCAGATATACCGC
1 CAGAACTCCAA-AAATTGCAGATATACCGC
*
11347969 CAGAACTCCACAAAT
1 CAGAACTCCAAAAAT
11347984 CTCCTGTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 8 0.22
29 5 0.14
30 24 0.65
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (29 bp):
CAGAACTCCAAAAATTGCAGATATACCGC
Found at i:11350662 original size:9 final size:9
Alignment explanation
Indices: 11350645--11350711 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
11350635 GTAGTGATTC
*
11350645 AATTCGGTT
1 AATTCGGGT
* *
11350654 AATTTGGTT
1 AATTCGGGT
11350663 AATTCGGGT
1 AATTCGGGT
*
11350672 AATTTGGGT
1 AATTCGGGT
*
11350681 AATTCAGGT
1 AATTCGGGT
11350690 AATTCGGGT
1 AATTCGGGT
*
11350699 AATTCGGTT
1 AATTCGGGT
11350708 AATT
1 AATT
11350712 TTTAACCAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.42
Consensus pattern (9 bp):
AATTCGGGT
Found at i:11350668 original size:18 final size:18
Alignment explanation
Indices: 11350645--11350712 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
11350635 GTAGTGATTC
*
11350645 AATTCGGTTAATTTGGTT
1 AATTCGGTTAATTTGGGT
*
11350663 AATTCGGGTAATTTGGGT
1 AATTCGGTTAATTTGGGT
*
11350681 AATTCAGG-TAATTCGGGT
1 AATTC-GGTTAATTTGGGT
11350699 AATTCGGTTAATTT
1 AATTCGGTTAATTT
11350713 TTAACCAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.05
18 40 0.91
19 2 0.05
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (18 bp):
AATTCGGTTAATTTGGGT
Found at i:11356306 original size:25 final size:25
Alignment explanation
Indices: 11356277--11356324 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
11356267 TGACGTAAAT
*
11356277 TGAATGTGAATAATGTTTAATCGCA
1 TGAATGTGAATAATGGTTAATCGCA
*
11356302 TGAATGTGAATGATGGTTAATCG
1 TGAATGTGAATAATGGTTAATCG
11356325 ATTCTAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.35
Consensus pattern (25 bp):
TGAATGTGAATAATGGTTAATCGCA
Found at i:11361557 original size:2 final size:2
Alignment explanation
Indices: 11361550--11361574 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11361540 AATGATACAA
11361550 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
11361575 TATTCATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:11362847 original size:20 final size:19
Alignment explanation
Indices: 11362822--11362915 Score: 61
Period size: 20 Copynumber: 4.9 Consensus size: 19
11362812 GATCGTTACA
11362822 TTATAAAAATTAATAAAAAC
1 TTATAAAAATT-ATAAAAAC
*
11362842 TTATAAATAA-TATTAAAAAA
1 TTATAAA-AATTA-TAAAAAC
* *
11362862 TCATAAAAAATTAT-TAAAC
1 TTAT-AAAAATTATAAAAAC
* *
11362881 --ATTAAAATTGATATAAAC
1 TTATAAAAATT-ATAAAAAC
*
11362899 TTATAAATATTATAAAA
1 TTATAAAAATTATAAAA
11362916 CTCTAACAAG
Statistics
Matches: 58, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
16 6 0.10
17 4 0.07
18 5 0.09
19 9 0.16
20 27 0.47
21 7 0.12
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (19 bp):
TTATAAAAATTATAAAAAC
Found at i:11363706 original size:9 final size:9
Alignment explanation
Indices: 11363694--11363770 Score: 52
Period size: 9 Copynumber: 8.4 Consensus size: 9
11363684 TTTTGTGAAT
11363694 TTTTATAAA
1 TTTTATAAA
11363703 TTTTA-AATA
1 TTTTATAA-A
* *
11363712 TTGTATATA
1 TTTTATAAA
* *
11363721 TATTATTAA
1 TTTTATAAA
*
11363730 TTTTATAAT
1 TTTTATAAA
11363739 TTATTA-AAA
1 TT-TTATAAA
11363748 TTTT-TATAA
1 TTTTATA-AA
11363757 TATTTATAAA
1 T-TTTATAAA
11363767 TTTT
1 TTTT
11363771 TATGATTTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 14
0.68 0.13 0.19
Matches are distributed among these distances:
8 5 0.10
9 34 0.67
10 10 0.20
11 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (9 bp):
TTTTATAAA
Found at i:11363752 original size:19 final size:19
Alignment explanation
Indices: 11363675--11363785 Score: 70
Period size: 19 Copynumber: 5.8 Consensus size: 19
11363665 TATGATATTA
* *
11363675 TTTATAAGTTTTTGTGAATT
1 TTTATAA-TTTTTATAAATT
*
11363695 TTTATAA-ATTT-TAAATAT
1 TTTATAATTTTTATAAAT-T
* * *
11363713 TGTAT-ATATATTATTAA-T
1 TTTATAAT-TTTTATAAATT
11363731 TTTATAATTTATTA-AAATT
1 TTTATAATTT-TTATAAATT
*
11363750 TTTATAATATTTATAAATT
1 TTTATAATTTTTATAAATT
*
11363769 TTTATGATTTTTTATAA
1 TTTAT-AATTTTTATAA
11363786 TTCTTGTAAG
Statistics
Matches: 70, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
17 5 0.07
18 19 0.27
19 27 0.39
20 19 0.27
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTATAATTTTTATAAATT
Found at i:11363760 original size:36 final size:37
Alignment explanation
Indices: 11363694--11363770 Score: 88
Period size: 36 Copynumber: 2.1 Consensus size: 37
11363684 TTTTGTGAAT
*
11363694 TTTTATAAATTTTAAATATTGTATATATA-TTATTAA
1 TTTTATAAATTTTAAATATTGTATATATATTTATAAA
* *
11363730 TTTTATAATTTATTAAA-ATT-TTTATAATATTTATAAA
1 TTTTATAAATT-TTAAATATTGTATAT-ATATTTATAAA
11363767 TTTT
1 TTTT
11363771 TATGATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
35 4 0.11
36 16 0.46
37 15 0.43
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (37 bp):
TTTTATAAATTTTAAATATTGTATATATATTTATAAA
Found at i:11363778 original size:9 final size:9
Alignment explanation
Indices: 11363632--11363787 Score: 86
Period size: 10 Copynumber: 16.6 Consensus size: 9
11363622 TTATAATTCC
*
11363632 TAATTTTTC
1 TAATTTTTA
11363641 TAATTTATTA
1 TAATTT-TTA
11363651 TAATTTATTA
1 TAATTT-TTA
* * *
11363661 AAATTATGA
1 TAATTTTTA
11363670 T-ATTATTTA
1 TAATT-TTTA
*
11363679 TAAGTTTTTG
1 TAA-TTTTTA
11363689 TGAATTTTTA
1 T-AATTTTTA
*
11363699 TAAATTTTA
1 TAATTTTTA
*
11363708 -AATATTGTA
1 TAAT-TTTTA
*
11363717 T-ATATATTA
1 TAAT-TTTTA
11363726 TTAA-TTTTA
1 -TAATTTTTA
11363735 TAATTTATTA
1 TAATTT-TTA
*
11363745 AAATTTTTA
1 TAATTTTTA
*
11363754 TAATATTTA
1 TAATTTTTA
11363763 TAAATTTTTA
1 T-AATTTTTA
*
11363773 TGATTTTTTA
1 T-AATTTTTA
11363783 TAATT
1 TAATT
11363788 CTTGTAAGTA
Statistics
Matches: 113, Mismatches: 22, Indels: 24
0.71 0.14 0.15
Matches are distributed among these distances:
8 8 0.07
9 48 0.42
10 52 0.46
11 5 0.04
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (9 bp):
TAATTTTTA
Found at i:11363825 original size:14 final size:14
Alignment explanation
Indices: 11363806--11363832 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11363796 TATATCTCAA
11363806 TTTTACTATTTTTT
1 TTTTACTATTTTTT
11363820 TTTTACTATTTTT
1 TTTTACTATTTTT
11363833 AATTTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTACTATTTTTT
Found at i:11363840 original size:17 final size:16
Alignment explanation
Indices: 11363806--11363851 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
11363796 TATATCTCAA
11363806 TTTTACTA-TTTT-TT
1 TTTTACTATTTTTATT
11363820 TTTTACTATTTTTAATT
1 TTTTACTATTTTT-ATT
11363837 TTTTA-TAATTTTTAT
1 TTTTACT-ATTTTTAT
11363852 GAGAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.29
15 4 0.14
16 3 0.11
17 13 0.46
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTACTATTTTTATT
Found at i:11364467 original size:19 final size:19
Alignment explanation
Indices: 11364425--11364482 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
11364415 AAAACACCCA
*
11364425 AAATAATTCAAAATAATTTTT
1 AAAT-ATTCAAAAT-ATTTAT
11364446 AAATATTCAAAATATTTAT
1 AAATATTCAAAATATTTAT
*
11364465 AAAAATTCCAAAAT-TTTA
1 AAATATT-CAAAATATTTA
11364483 AAAAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.44
20 15 0.44
21 4 0.12
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATATTCAAAATATTTAT
Found at i:11372365 original size:7 final size:7
Alignment explanation
Indices: 11372353--11372399 Score: 94
Period size: 7 Copynumber: 6.7 Consensus size: 7
11372343 TTTTTACCAT
11372353 GAACCTC
1 GAACCTC
11372360 GAACCTC
1 GAACCTC
11372367 GAACCTC
1 GAACCTC
11372374 GAACCTC
1 GAACCTC
11372381 GAACCTC
1 GAACCTC
11372388 GAACCTC
1 GAACCTC
11372395 GAACC
1 GAACC
11372400 CAAACCTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.30, C:0.43, G:0.15, T:0.13
Consensus pattern (7 bp):
GAACCTC
Found at i:11372434 original size:18 final size:19
Alignment explanation
Indices: 11372396--11372451 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 19
11372386 TCGAACCTCG
* *
11372396 AACCCAAACCTTAACCTTA
1 AACCCAAACCCTAAACTTA
* *
11372415 AACTCAAACTC-AAACTTA
1 AACCCAAACCCTAAACTTA
11372433 AACCCAAACCCTAAACTTA
1 AACCCAAACCCTAAACTTA
11372452 GACCTAAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (19 bp):
AACCCAAACCCTAAACTTA
Found at i:11372552 original size:78 final size:78
Alignment explanation
Indices: 11372423--11372578 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
11372413 TAAACTCAAA
11372423 CTCAAACTTAAACCCAAACCCTAAACTTAGACCTAAATCTTAAATCTTAAATCTTGAATCTCGAA
1 CTCAAACTTAAACCCAAACCCTAAACTTAGACCTAAATCTTAAATCTTAAATCTTGAATCTCGAA
11372488 CCCATTCAAGATT
66 CCCATTCAAGATT
11372501 CTCAAACTTAAACCCAAACCCTAAACTTAGACCTAAATCTTAAATCTTAAATCTTGAATCTCGAA
1 CTCAAACTTAAACCCAAACCCTAAACTTAGACCTAAATCTTAAATCTTAAATCTTGAATCTCGAA
11372566 CCCATTCAAGATT
66 CCCATTCAAGATT
11372579 TAAAATTTAG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.40, C:0.27, G:0.05, T:0.28
Consensus pattern (78 bp):
CTCAAACTTAAACCCAAACCCTAAACTTAGACCTAAATCTTAAATCTTAAATCTTGAATCTCGAA
CCCATTCAAGATT
Found at i:11377151 original size:16 final size:16
Alignment explanation
Indices: 11377118--11377151 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11377108 ACTCATTTAA
*
11377118 TTTTCTTTTTGAATTT
1 TTTTCTTTTTGAACTT
*
11377134 TTTTCTTTTTGCACTT
1 TTTTCTTTTTGAACTT
11377150 TT
1 TT
11377152 AAGCTAACCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTCTTTTTGAACTT
Found at i:11377497 original size:22 final size:22
Alignment explanation
Indices: 11377471--11377521 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
11377461 CAACCAAATA
*
11377471 ATCACAGCTTCAACAATTTACC
1 ATCACAACTTCAACAATTTACC
*
11377493 ATCACAACTTCAACAATTTATC
1 ATCACAACTTCAACAATTTACC
11377515 ATTCACA
1 A-TCACA
11377522 CTAGCGTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.39, C:0.29, G:0.02, T:0.29
Consensus pattern (22 bp):
ATCACAACTTCAACAATTTACC
Found at i:11383549 original size:12 final size:12
Alignment explanation
Indices: 11383528--11383637 Score: 55
Period size: 12 Copynumber: 8.9 Consensus size: 12
11383518 AAAAACTTAA
*
11383528 TGATTAAAAACT
1 TGATGAAAAACT
*
11383540 TGATGGAAAACT
1 TGATGAAAAACT
*
11383552 TTATGAAAAGACT
1 TGATGAAAA-ACT
* *
11383565 TGATGAGAAGCT
1 TGATGAAAAACT
*
11383577 T-A-AAAAGAACT
1 TGATGAAA-AACT
*
11383588 TGATG-CAAACT
1 TGATGAAAAACT
* *
11383599 TAATAAAAAAAAACT
1 TGAT---GAAAAACT
*
11383614 TGATAAAAGAACT
1 TGATGAAA-AACT
11383627 TGATGAAAAAC
1 TGATGAAAAAC
11383638 ACTTGAAGAA
Statistics
Matches: 72, Mismatches: 17, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
10 2 0.03
11 12 0.17
12 29 0.40
13 21 0.29
15 8 0.11
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.25
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:11383626 original size:13 final size:14
Alignment explanation
Indices: 11383605--11383654 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
11383595 AACTTAATAA
11383605 AAAAAAACTTGAT-
1 AAAAAAACTTGATG
*
11383618 AAAAGAACTTGATG
1 AAAAAAACTTGATG
* *
11383632 AAAAACACTTGAAG
1 AAAAAAACTTGATG
11383646 AAAGAAAAC
1 AAA-AAAAC
11383655 ACTTAATGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 12 0.40
14 14 0.47
15 4 0.13
ACGTcount: A:0.60, C:0.10, G:0.14, T:0.16
Consensus pattern (14 bp):
AAAAAAACTTGATG
Found at i:11383635 original size:14 final size:13
Alignment explanation
Indices: 11383518--11383648 Score: 53
Period size: 12 Copynumber: 10.2 Consensus size: 13
11383508 AGCTTAATTG
*
11383518 AAAAACTTAATGA
1 AAAAACTTGATGA
11383531 TTAAAAACTTGATG-
1 --AAAAACTTGATGA
* *
11383545 GAAAACTTTATGA
1 AAAAACTTGATGA
*
11383558 AAAGACTTGATG-
1 AAAAACTTGATGA
* *
11383570 AGAAGCTT-A--A
1 AAAAACTTGATGA
11383580 AAAGAACTTGATG-
1 AAA-AACTTGATGA
* * *
11383593 -CAAACTTAATAAAA
1 AAAAACTTGAT--GA
11383607 AAAAACTTGAT-A
1 AAAAACTTGATGA
11383619 AAAGAACTTGATGA
1 AAA-AACTTGATGA
*
11383633 AAAACACTTGAAGA
1 AAAA-ACTTGATGA
11383647 AA
1 AA
11383649 GAAAACACTT
Statistics
Matches: 86, Mismatches: 17, Indels: 27
0.66 0.13 0.21
Matches are distributed among these distances:
10 2 0.02
11 12 0.14
12 21 0.24
13 18 0.21
14 14 0.16
15 19 0.22
ACGTcount: A:0.53, C:0.09, G:0.15, T:0.24
Consensus pattern (13 bp):
AAAAACTTGATGA
Found at i:11391881 original size:14 final size:14
Alignment explanation
Indices: 11391846--11391895 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
11391836 AGAAAGAAAA
11391846 GATTAAAAACTTAATT
1 GATT-AAAACTTAA-T
11391862 GA--AAAACTTAAT
1 GATTAAAACTTAAT
11391874 GATTAAAACTTAAT
1 GATTAAAACTTAAT
11391888 GATTAAAA
1 GATTAAAA
11391896 ACTTGATGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.09
13 9 0.28
14 18 0.56
16 2 0.06
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (14 bp):
GATTAAAACTTAAT
Found at i:11391931 original size:13 final size:12
Alignment explanation
Indices: 11391850--11391995 Score: 66
Period size: 13 Copynumber: 11.5 Consensus size: 12
11391840 AGAAAAGATT
*
11391850 AAAAACTTAATTG
1 AAAAACTTGA-TG
*
11391863 AAAAACTTAATG
1 AAAAACTTGATG
*
11391875 ATTAAAACTTAATGATT
1 A--AAAAC-T--TGATG
11391892 AAAAACTTGATGG
1 AAAAACTTGAT-G
*
11391905 AAAAA-TTTATG
1 AAAAACTTGATG
11391916 AAAAGACTTGATG
1 AAAA-ACTTGATG
* *
11391929 AAAAGCTT-A-A
1 AAAAACTTGATG
11391939 AAATAACTTGATG
1 AAA-AACTTGATG
* * *
11391952 -CAAACTTAATAAA
1 AAAAACTTGAT--G
*
11391965 AAAAACTTGATA
1 AAAAACTTGATG
11391977 AAAGAACTTGATG
1 AAA-AACTTGATG
11391990 AAAAAC
1 AAAAAC
11391996 ACTTGAATAA
Statistics
Matches: 103, Mismatches: 15, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
10 3 0.03
11 17 0.17
12 24 0.23
13 35 0.34
14 14 0.14
15 6 0.06
17 4 0.04
ACGTcount: A:0.53, C:0.08, G:0.12, T:0.27
Consensus pattern (12 bp):
AAAAACTTGATG
Found at i:11391972 original size:14 final size:14
Alignment explanation
Indices: 11391953--11392019 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
11391943 AACTTGATGC
11391953 AAACTTAATAAAAA
1 AAACTTAATAAAAA
*
11391967 AAACTTGAT-AAAA
1 AAACTTAATAAAAA
* * *
11391980 GAACTTGATGAAAA
1 AAACTTAATAAAAA
*
11391994 ACACTTGAATAAAGAA
1 AAACTT-AATAAA-AA
11392010 AACACTTAAT
1 AA-ACTTAAT
11392020 GAATGACTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
13 12 0.29
14 16 0.38
15 4 0.10
16 6 0.14
17 4 0.10
ACGTcount: A:0.58, C:0.10, G:0.09, T:0.22
Consensus pattern (14 bp):
AAACTTAATAAAAA
Found at i:11391984 original size:27 final size:28
Alignment explanation
Indices: 11391954--11392006 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
11391944 ACTTGATGCA
11391954 AACTTAATAAAAAAAACTTG-ATAAAAG
1 AACTTAATAAAAAAAACTTGAATAAAAG
* * *
11391981 AACTTGATGAAAAACACTTGAATAAA
1 AACTTAATAAAAAAAACTTGAATAAA
11392007 GAAAACACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.23
Consensus pattern (28 bp):
AACTTAATAAAAAAAACTTGAATAAAAG
Found at i:11394432 original size:18 final size:18
Alignment explanation
Indices: 11394409--11394443 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11394399 CTCATGGATC
11394409 TGATAAACAAAATAAACT
1 TGATAAACAAAATAAACT
* *
11394427 TGATAAAGATAATAAAC
1 TGATAAACAAAATAAAC
11394444 ATAAAGAGCA
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:0.09, T:0.23
Consensus pattern (18 bp):
TGATAAACAAAATAAACT
Done.