Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 91 of 226
Found at i:28690622 original size:14 final size:14
Alignment explanation
Indices: 28690601--28690636 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
28690591 AATTATAACA
28690601 AAAATATAAA-AAT
1 AAAATATAAACAAT
28690614 AATAATATAAACAAT
1 AA-AATATAAACAAT
28690629 AAAATATA
1 AAAATATA
28690637 TTTTTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 14 0.67
15 5 0.24
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAATATAAACAAT
Found at i:28692406 original size:23 final size:24
Alignment explanation
Indices: 28692366--28692414 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
28692356 ATTTTACAAA
*
28692366 AAAATTATAATAAAATTTTTATAT
1 AAAATTATAATAAAATTTATATAT
*
28692390 AAAATTA-ATTAAAATTTATATAT
1 AAAATTATAATAAAATTTATATAT
28692413 AA
1 AA
28692415 TAAAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATTATAATAAAATTTATATAT
Found at i:28692511 original size:13 final size:12
Alignment explanation
Indices: 28692466--28692503 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
28692456 CCATTTCATT
28692466 TAAAATTTTATA
1 TAAAATTTTATA
*
28692478 T-AATTTTTATA
1 TAAAATTTTATA
28692489 TAAAATTTTA-A
1 TAAAATTTTATA
28692500 TAAA
1 TAAA
28692504 TATATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 15 0.65
12 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAAATTTTATA
Found at i:28699935 original size:31 final size:31
Alignment explanation
Indices: 28699899--28699980 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
28699889 CTTAACCTAA
* ** *
28699899 TGACTTAAATAAAAACTTTTGAATAGTTTAG
1 TGACTTAAATGAAAACTTTCAAATAGTTCAG
*
28699930 TGACTTAAATGGAAACTTTCAAATAGTTCAG
1 TGACTTAAATGAAAACTTTCAAATAGTTCAG
**
28699961 TGACCAAAATGAAAACTTTC
1 TGACTTAAATGAAAACTTTC
28699981 CCATAATTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTCAAATAGTTCAG
Found at i:28699994 original size:31 final size:31
Alignment explanation
Indices: 28699905--28699995 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 31
28699895 CTAATGACTT
* ** * **
28699905 AAATAAAAACTTTTGAATAGTTTAGTGACTT
1 AAATGAAAACTTTCAAATAATTTAGTGACCA
* * *
28699936 AAATGGAAACTTTCAAATAGTTCAGTGACCA
1 AAATGAAAACTTTCAAATAATTTAGTGACCA
**
28699967 AAATGAAAACTTTCCCATAATTTAGTGAC
1 AAATGAAAACTTTCAAATAATTTAGTGAC
28699996 TAATAATGCA
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (31 bp):
AAATGAAAACTTTCAAATAATTTAGTGACCA
Found at i:28700567 original size:15 final size:15
Alignment explanation
Indices: 28700529--28700566 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
28700519 GATTTCGTAT
* *
28700529 TTAAATTTTCAATAC
1 TTAACTTTTCAACAC
28700544 TTAACTTTTCAACAC
1 TTAACTTTTCAACAC
28700559 TT-ACTTTT
1 TTAACTTTT
28700567 TTAGTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAACTTTTCAACAC
Found at i:28701043 original size:113 final size:112
Alignment explanation
Indices: 28700890--28701187 Score: 352
Period size: 113 Copynumber: 2.6 Consensus size: 112
28700880 AGAATTAGTG
* * *
28700890 GCGTTTTAT-AGAAAGCGCCGCAAAAAACCTAAGT-CGAACGACGTCGTTTACCGAGCTTTCGGG
1 GCGTTTT-TGAGAAAGCGCCGCAAAAAACCTAA-TCCCAACGACGCCGTTT-CTGAGCTTTCGGG
28700953 GGTTTAGCGGCATTTTTAATAA-AGCGCCGCTAATG-TTCAGGGCTTTAGCC
63 GGTTTAGCGGCATTTTTAATAACA-CGCCGCTAATGCTT-AGGGCTTTAGCC
* * *
28701003 GCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCCAACGATGCCGTTTTCTGAGCTTTCGAGTG
1 GCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCCAACGACGCCG-TTTCTGAGCTTTCGGGGG
* * * * *
28701068 ATTAGTGGCGTTTTTAATAACATGCCGCTAATGCTTAGGGCTTTAGCG
65 TTTAGCGGCATTTTTAATAACACGCCGCTAATGCTTAGGGCTTTAGCC
* * * *
28701116 GCGTTTTTGAAAAAGCGCCGCAAGAAAACCTAAGCACAACGACACCGTTTCTGAGCTTTTCGGGG
1 GCGTTTTTGAGAAAGCGCCGCAA-AAAACCTAATCCCAACGACGCCGTTTCTGAGC-TTTCGGGG
*
28701181 ATTTAGC
64 GTTTAGC
28701188 AAGAAGCGCC
Statistics
Matches: 157, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
112 2 0.01
113 120 0.76
114 35 0.22
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.27
Consensus pattern (112 bp):
GCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCCAACGACGCCGTTTCTGAGCTTTCGGGGGT
TTAGCGGCATTTTTAATAACACGCCGCTAATGCTTAGGGCTTTAGCC
Found at i:28701278 original size:104 final size:102
Alignment explanation
Indices: 28701091--28701287 Score: 234
Period size: 103 Copynumber: 1.9 Consensus size: 102
28701081 TTAATAACAT
* * * * *
28701091 GCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCAAGAAAACCTAAGCACAAC
1 GCCGCTAATGC-TAAGGATTTAGCAGCGTTTTTGAAAAAGCGCCGCAAAAAAAACTAAGCACAAC
28701156 GACACCGTTTCTGAGCTTTTCGGGGATTTAGCAAGAAGC
65 GACACCGTTTCTGAGC-TTTCGGGGATTTAGCAAGAAGC
* * *
28701195 GCCGCTAATGC-AAGGATTTAGCAGCGTTTTTGGAATAGCGCCGCAAAAAAAAACTAAGCCCAAC
1 GCCGCTAATGCTAAGGATTTAGCAGCGTTTTTGAAAAAGCGCCGC-AAAAAAAACTAAGCACAAC
*** * *
28701259 GGTGCTGTTTTCTGTGCTTTCGGGGATTT
65 GACACCG-TTTCTGAGCTTTCGGGGATTT
28701288 TGCGGCGTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
102 28 0.36
103 31 0.40
104 19 0.24
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (102 bp):
GCCGCTAATGCTAAGGATTTAGCAGCGTTTTTGAAAAAGCGCCGCAAAAAAAACTAAGCACAACG
ACACCGTTTCTGAGCTTTCGGGGATTTAGCAAGAAGC
Found at i:28701452 original size:73 final size:71
Alignment explanation
Indices: 28701208--28701453 Score: 223
Period size: 70 Copynumber: 3.4 Consensus size: 71
28701198 GCTAATGCAA
*
28701208 GGATTTAGCAGCGTTTTT-GGAATAGCGCCGCAAAAAAAAACTAAGCCCAACGGTGCTGTTTTCT
1 GGATTTAGCGGC-TTTTTAGGAA-AGCGCCGC-AAAAAAAACTAAGCCCAACGGTGC-GTTTTCT
*
28701272 GTGCTTTCGG
62 ATGCTTTCGG
* ** * * * ***
28701282 GGATTTTGCGGCGTTTTTAAAAAAGCGCCGCAAGAAAACCTAAGCCCAATGACACCG--TT-TA-
1 GGATTTAGCGGC-TTTTTAGGAAAGCGCCGCAAAAAAAACTAAGCCCAACG-GTGCGTTTTCTAT
28701343 GCCTTTCGG
64 G-CTTTCGG
* ** *
28701352 GGATTTAGCGGCGTTTTAGGTGTAGCGCCGCAAAAAAAACTAAACCCAACGGTGTCGTTTTCTAT
1 GGATTTAGCGGCTTTTTAGG-AAAGCGCCGCAAAAAAAACTAAGCCCAACGGTG-CGTTTTCTAT
28701417 GCTTTCGG
64 GCTTTCGG
*
28701425 GGATTTAGTGGCATTTTTAGGAAAGCGCC
1 GGATTTAGCGGC-TTTTTAGGAAAGCGCC
28701454 ACTAATGCTC
Statistics
Matches: 134, Mismatches: 28, Indels: 21
0.73 0.15 0.11
Matches are distributed among these distances:
69 6 0.04
70 45 0.34
71 2 0.01
72 2 0.01
73 44 0.33
74 33 0.25
75 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (71 bp):
GGATTTAGCGGCTTTTTAGGAAAGCGCCGCAAAAAAAACTAAGCCCAACGGTGCGTTTTCTATGC
TTTCGG
Found at i:28701781 original size:7 final size:7
Alignment explanation
Indices: 28701686--28701783 Score: 56
Period size: 7 Copynumber: 13.4 Consensus size: 7
28701676 CAGGTATGGA
28701686 TTTAGGG
1 TTTAGGG
28701693 TTT-GGG
1 TTTAGGG
*
28701699 ATTTAAGG
1 -TTTAGGG
28701707 TTTAGGG
1 TTTAGGG
* *
28701714 GTTA-AG
1 TTTAGGG
* *
28701720 TGTTATGC
1 T-TTAGGG
28701728 TTTAGGG
1 TTTAGGG
*
28701735 GTTAGGAGG
1 TTTA-G-GG
28701744 ATTTAGGG
1 -TTTAGGG
*
28701752 GTTAGGG
1 TTTAGGG
*
28701759 GTTAGGG
1 TTTAGGG
28701766 ATTTAGGG
1 -TTTAGGG
28701774 TTTAGGG
1 TTTAGGG
28701781 TTT
1 TTT
28701784 CAACGGTAAG
Statistics
Matches: 70, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
6 4 0.06
7 48 0.69
8 12 0.17
9 3 0.04
10 3 0.04
ACGTcount: A:0.18, C:0.01, G:0.41, T:0.40
Consensus pattern (7 bp):
TTTAGGG
Found at i:28701782 original size:21 final size:22
Alignment explanation
Indices: 28701686--28701780 Score: 88
Period size: 22 Copynumber: 4.3 Consensus size: 22
28701676 CAGGTATGGA
* *
28701686 TTTA-GGGTTTGGGATTTAAGG
1 TTTAGGGGTTAGGGATTTAGGG
* * *
28701707 TTTAGGGGTTA-AG-TGTTATGC
1 TTTAGGGGTTAGGGAT-TTAGGG
28701728 TTTAGGGGTTAGGAGGATTTAGGG
1 TTTAGGGGTTA-G-GGATTTAGGG
*
28701752 GTTAGGGGTTAGGGATTTAGGG
1 TTTAGGGGTTAGGGATTTAGGG
28701774 TTTAGGG
1 TTTAGGG
28701781 TTTCAACGGT
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
20 1 0.02
21 20 0.34
22 21 0.36
23 1 0.02
24 15 0.25
25 1 0.02
ACGTcount: A:0.19, C:0.01, G:0.42, T:0.38
Consensus pattern (22 bp):
TTTAGGGGTTAGGGATTTAGGG
Found at i:28702107 original size:38 final size:39
Alignment explanation
Indices: 28702056--28702141 Score: 120
Period size: 38 Copynumber: 2.2 Consensus size: 39
28702046 ATAAATTTTT
* * *
28702056 TTAGGGGTTATGCTTTAGGGGTTAGGGA-GATTTAAGGG
1 TTAGGGTTTATGCTTTAAGGGTTAAGGAGGATTTAAGGG
*
28702094 TTAGGGTTTATGCTTTAAGGGTTAAGGAGGATTTAGGGG
1 TTAGGGTTTATGCTTTAAGGGTTAAGGAGGATTTAAGGG
28702133 TTATGGGTT
1 TTA-GGGTT
28702142 AGGGATTTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 25 0.60
39 12 0.29
40 5 0.12
ACGTcount: A:0.21, C:0.02, G:0.40, T:0.37
Consensus pattern (39 bp):
TTAGGGTTTATGCTTTAAGGGTTAAGGAGGATTTAAGGG
Found at i:28704415 original size:31 final size:31
Alignment explanation
Indices: 28704377--28704456 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
28704367 TTGGATTTTA
*
28704377 ATTGGTTTTTGCAGCTAAGATGATACCTTCT
1 ATTGGTTTTTGCTGCTAAGATGATACCTTCT
* *
28704408 ATTGGTTTTTACTGCTAAGATGGTACCTTCT
1 ATTGGTTTTTGCTGCTAAGATGATACCTTCT
* *
28704439 ATTGATTTCTGCTGCTAA
1 ATTGGTTTTTGCTGCTAA
28704457 ATGGCTAAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (31 bp):
ATTGGTTTTTGCTGCTAAGATGATACCTTCT
Found at i:28707147 original size:21 final size:21
Alignment explanation
Indices: 28707121--28707191 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
28707111 CTACAACTTA
*
28707121 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
28707142 AAGCAGCGGCTGCAGTGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
28707163 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
28707184 AAGCAGAG
1 AAGCAGAG
28707192 CAGAACAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.31, C:0.18, G:0.46, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:28707573 original size:42 final size:42
Alignment explanation
Indices: 28707514--28707626 Score: 147
Period size: 42 Copynumber: 2.7 Consensus size: 42
28707504 GTATAAAAGT
* * *
28707514 GCCGCTAAATACCATGTTCTTTAGCGGTGCTTAGAA-AAAACC
1 GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTA-AACAAAAAC
*
28707556 GCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAAACAAAAAC
1 GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAACAAAAAC
** *
28707598 GCCGCTAAAGAATATGGTCTTTAGCGGCG
1 GCCGCTAAAGACCATGTTCTTTAGCGGCG
28707627 TTTTTGTTTG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 2 0.03
42 60 0.97
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (42 bp):
GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAACAAAAAC
Found at i:28712231 original size:12 final size:12
Alignment explanation
Indices: 28712214--28712239 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28712204 TCCAACTGAG
28712214 TTTTTGTTTGCT
1 TTTTTGTTTGCT
28712226 TTTTTGTTTGCT
1 TTTTTGTTTGCT
28712238 TT
1 TT
28712240 ATTAATTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.15, T:0.77
Consensus pattern (12 bp):
TTTTTGTTTGCT
Found at i:28713782 original size:18 final size:19
Alignment explanation
Indices: 28713740--28713790 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 19
28713730 ACAAATACAC
28713740 ATAAATT-AAATG-AAATG
1 ATAAATTGAAATGAAAATG
*
28713757 A-AATTTGAAATGAAAAT-
1 ATAAATTGAAATGAAAATG
28713774 ATAAATTGAAATGAAAA
1 ATAAATTGAAATGAAAA
28713791 AAAAAATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 4 0.14
17 7 0.24
18 18 0.62
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (19 bp):
ATAAATTGAAATGAAAATG
Found at i:28713801 original size:19 final size:19
Alignment explanation
Indices: 28713757--28713801 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
28713747 AAATGAAATG
* *
28713757 AAATTTGAAATGAAAATAT
1 AAATTTGAAATGAAAAAAA
28713776 AAA-TTGAAATGAAAAAAA
1 AAATTTGAAATGAAAAAAA
28713794 AAATTTGA
1 AAATTTGA
28713802 CAAGACATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (19 bp):
AAATTTGAAATGAAAAAAA
Found at i:28714006 original size:25 final size:24
Alignment explanation
Indices: 28713972--28714025 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
28713962 TTAAATGAGA
* * *
28713972 AAAAATTTGAATTTAAATGAAATTT
1 AAAATTTTGAAATAAAATGAAA-TT
28713997 AAAATTTTGAAATAAAATGAAATT
1 AAAATTTTGAAATAAAATGAAATT
28714021 AAAAT
1 AAAAT
28714026 ATAAATTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (24 bp):
AAAATTTTGAAATAAAATGAAATT
Found at i:28714029 original size:18 final size:18
Alignment explanation
Indices: 28714008--28714059 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
28713998 AAATTTTGAA
*
28714008 ATAAAATGAAATTAAAAT
1 ATAAAATGAAATGAAAAT
*
28714026 ATAAATTGAAATGAAAA-
1 ATAAAATGAAATGAAAAT
*
28714043 A-AAACTGAATATGAAAA
1 ATAAAATGAA-ATGAAAA
28714060 AAGAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 7 0.23
17 8 0.27
18 15 0.50
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.23
Consensus pattern (18 bp):
ATAAAATGAAATGAAAAT
Found at i:28714080 original size:5 final size:5
Alignment explanation
Indices: 28714070--28714165 Score: 50
Period size: 5 Copynumber: 17.6 Consensus size: 5
28714060 AAGAATAAAT
* *
28714070 TGAAA TGAAA TGAAA TGTGAAA TGAATA TGAAA TAAAA TGTAATT TGAAA
1 TGAAA TGAAA TGAAA --TGAAA TGAA-A TGAAA TGAAA TG-AA-A TGAAA
* * * *
28714120 TGAATC TAAAA CGAAA TGAAA GTTGAAA TGAAA -AAAA TTGAAA TGA
1 TGAA-A TGAAA TGAAA TGAAA --TGAAA TGAAA TGAAA -TGAAA TGA
28714166 GACAAAAAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
4 3 0.04
5 39 0.57
6 15 0.22
7 12 0.17
ACGTcount: A:0.55, C:0.02, G:0.18, T:0.25
Consensus pattern (5 bp):
TGAAA
Found at i:28714103 original size:28 final size:28
Alignment explanation
Indices: 28714070--28714270 Score: 104
Period size: 28 Copynumber: 7.5 Consensus size: 28
28714060 AAGAATAAAT
28714070 TGAAATGAAATGAAATGTGAAATGAATA
1 TGAAATGAAATGAAATGTGAAATGAATA
* * * *
28714098 TGAAATAAAATGTAATTTGAAATGAATC
1 TGAAATGAAATGAAATGTGAAATGAATA
* *
28714126 TAAAACGAAATGAAA-GTTGAAATGAA-A
1 TGAAATGAAATGAAATG-TGAAATGAATA
* * **** *
28714153 -AAAATTGAAATGAGACAAAAAATTAATA
1 TGAAA-TGAAATGAAATGTGAAATGAATA
*
28714181 AG-AA--AAAT-AAAT-TGAAAT-AATA
1 TGAAATGAAATGAAATGTGAAATGAATA
** * *
28714203 AAAAAT-AAATTTAAATG-GAAA--AAAA
1 TGAAATGAAA-TGAAATGTGAAATGAATA
* *
28714228 TTAAATGAAATGAAATGTGAAATGAAAA
1 TGAAATGAAATGAAATGTGAAATGAATA
28714256 TGAAATGAAATGAAA
1 TGAAATGAAATGAAA
28714271 AAAAAATGAT
Statistics
Matches: 132, Mismatches: 27, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
22 5 0.04
23 6 0.05
24 5 0.04
25 18 0.14
26 19 0.14
27 14 0.11
28 65 0.49
ACGTcount: A:0.60, C:0.01, G:0.15, T:0.23
Consensus pattern (28 bp):
TGAAATGAAATGAAATGTGAAATGAATA
Found at i:28714120 original size:17 final size:16
Alignment explanation
Indices: 28714004--28714120 Score: 68
Period size: 17 Copynumber: 7.4 Consensus size: 16
28713994 TTTAAAATTT
28714004 TGAAATAAAATGAA-A
1 TGAAATAAAATGAATA
*
28714019 TTAAAATATAAATTGAA-A
1 -TGAAATA-AAA-TGAATA
*
28714037 TGAAAAAAAACTGAATA
1 TGAAATAAAA-TGAATA
* *
28714054 TGAAAAAAGAATAAAT-
1 TGAAATAA-AATGAATA
*
28714070 TGAAATGAAATGAA-A
1 TGAAATAAAATGAATA
*
28714085 TG---TGAAATGAATA
1 TGAAATAAAATGAATA
*
28714098 TGAAATAAAATGTAATT
1 TGAAATAAAATG-AATA
28714115 TGAAAT
1 TGAAAT
28714121 GAATCTAAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
12 9 0.11
13 3 0.04
15 7 0.09
16 25 0.31
17 30 0.37
18 7 0.09
ACGTcount: A:0.60, C:0.01, G:0.14, T:0.26
Consensus pattern (16 bp):
TGAAATAAAATGAATA
Found at i:28714174 original size:18 final size:18
Alignment explanation
Indices: 28714150--28714207 Score: 66
Period size: 19 Copynumber: 3.3 Consensus size: 18
28714140 AGTTGAAATG
*
28714150 AAAAAAATTGAAATGAGA
1 AAAAAAATTGAAATAAGA
*
28714168 CAAAAAATT--AATAAGA
1 AAAAAAATTGAAATAAGA
*
28714184 AAAATAAATTGAAATAATA
1 AAAA-AAATTGAAATAAGA
28714203 AAAAA
1 AAAAA
28714208 TAAATTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 9 0.27
17 5 0.15
18 9 0.27
19 10 0.30
ACGTcount: A:0.71, C:0.02, G:0.09, T:0.19
Consensus pattern (18 bp):
AAAAAAATTGAAATAAGA
Found at i:28714238 original size:5 final size:5
Alignment explanation
Indices: 28714225--28714270 Score: 56
Period size: 5 Copynumber: 8.6 Consensus size: 5
28714215 AAATGGAAAA
*
28714225 AAATT AAATG AAATG AAATGTG AAATG AAAATG AAATG AAATG AAA
1 AAATG AAATG AAATG AAA--TG AAATG -AAATG AAATG AAATG AAA
28714271 AAAAAATGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
5 27 0.73
6 5 0.14
7 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.22
Consensus pattern (5 bp):
AAATG
Found at i:28714238 original size:20 final size:20
Alignment explanation
Indices: 28714183--28714239 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
28714173 AATTAATAAG
*
28714183 AAAAATAAATTGAAAT-AATA
1 AAAAATAAATTGAAATGGA-A
*
28714203 AAAAATAAATTTAAATGGAA
1 AAAAATAAATTGAAATGGAA
28714223 AAAAATTAAA-TGAAATG
1 AAAAA-TAAATTGAAATG
28714240 AAATGTGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 27 0.84
21 5 0.16
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.25
Consensus pattern (20 bp):
AAAAATAAATTGAAATGGAA
Found at i:28714250 original size:12 final size:12
Alignment explanation
Indices: 28714233--28714267 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
28714223 AAAAATTAAA
28714233 TGAAATGAAATG
1 TGAAATGAAATG
*
28714245 TGAAATGAAA-A
1 TGAAATGAAATG
28714256 TGAAATGAAATG
1 TGAAATGAAATG
28714268 AAAAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (12 bp):
TGAAATGAAATG
Found at i:28714273 original size:18 final size:17
Alignment explanation
Indices: 28714230--28714271 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
28714220 GAAAAAAATT
28714230 AAATG-AAATGAAATGTG
1 AAATGAAAATGAAA-GTG
28714247 AAATGAAAATGAAA-TG
1 AAATGAAAATGAAAGTG
28714263 AAATGAAAA
1 AAATGAAAA
28714272 AAAAATGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.46
17 5 0.21
18 8 0.33
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (17 bp):
AAATGAAAATGAAAGTG
Found at i:28714277 original size:16 final size:16
Alignment explanation
Indices: 28714143--28714279 Score: 62
Period size: 17 Copynumber: 8.2 Consensus size: 16
28714133 AAATGAAAGT
*
28714143 TGAAATG-AAAAAAAT
1 TGAAATGAAAAAAAAA
*
28714158 TGAAATGAGACAAAAAA
1 TGAAATGA-AAAAAAAA
* * *
28714175 TTAATAAGAAAAATAAAT
1 TGAA-ATGAAAAA-AAAA
*
28714193 TGAAATAATAAAAAATAAA
1 TGAAAT--GAAAAAA-AAA
* *
28714212 TTTAAATG-GAAAAAAA
1 -TGAAATGAAAAAAAAA
* * **
28714228 TTAAATGAAATGAAATG
1 TGAAATGAAA-AAAAAA
**
28714245 TGAAATGAAAATGAAA
1 TGAAATGAAAAAAAAA
28714261 TGAAATGAAAAAAAAA
1 TGAAATGAAAAAAAAA
28714277 TGA
1 TGA
28714280 TAAGACATAT
Statistics
Matches: 87, Mismatches: 25, Indels: 19
0.66 0.19 0.15
Matches are distributed among these distances:
15 14 0.16
16 22 0.25
17 29 0.33
18 10 0.11
19 7 0.08
20 5 0.06
ACGTcount: A:0.65, C:0.01, G:0.13, T:0.21
Consensus pattern (16 bp):
TGAAATGAAAAAAAAA
Found at i:28714855 original size:18 final size:17
Alignment explanation
Indices: 28714834--28714868 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28714824 TTATTATTAA
*
28714834 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28714852 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28714869 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28714934 original size:157 final size:157
Alignment explanation
Indices: 28714721--28715037 Score: 571
Period size: 157 Copynumber: 2.0 Consensus size: 157
28714711 TAGAATACCC
*
28714721 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
* * *
28714786 TTATCAATAATAAATATTTTAATCATATTTAAAAATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAAAATAATTATTATTAAATATATTATAATTAAAA
28714851 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
* *
28714878 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
*
28714943 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAAAATAATTATTATTAAATATATTATAATTAAAA
28715008 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
28715035 TTA
1 TTA
28715038 ATATTCTTAT
Statistics
Matches: 153, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 153 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAAAATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:28715008 original size:16 final size:16
Alignment explanation
Indices: 28714971--28715012 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28714961 TTAATCATAT
*
28714971 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
28714987 TT-AAATATATTATAA
1 TTAAAATATATTATAA
28715002 TTAAAATATAT
1 TTAAAATATAT
28715013 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:28715019 original size:14 final size:15
Alignment explanation
Indices: 28714980--28715021 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28714970 TTTAAACATA
*
28714980 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28714995 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
28715009 A-TATAATTTAATA
1 ATTATAATTAAATA
28715022 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:28715109 original size:120 final size:121
Alignment explanation
Indices: 28714969--28715266 Score: 496
Period size: 120 Copynumber: 2.5 Consensus size: 121
28714959 ATTTAATCAT
*
28714969 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
28715034 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AA
*
28715091 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTCATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
28715154 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
* * *
28715210 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
28715267 TAAAATAATT
Statistics
Matches: 168, Mismatches: 5, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
119 7 0.04
120 156 0.93
121 4 0.02
122 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
Found at i:28715139 original size:14 final size:15
Alignment explanation
Indices: 28715090--28715141 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
28715080 GTAAAATATA
28715090 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
28715105 TATTAAATATATTAT
1 AATTAAATATATTAT
28715120 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
28715133 AATTTAATA
1 AATTAAATA
28715142 AAATTCTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:28715353 original size:24 final size:25
Alignment explanation
Indices: 28715307--28715354 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
28715297 TATGAATTTG
28715307 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
28715333 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
28715355 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:28715358 original size:92 final size:92
Alignment explanation
Indices: 28715262--28715471 Score: 232
Period size: 92 Copynumber: 2.3 Consensus size: 92
28715252 TGATTTAATA
* * *
28715262 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
28715324 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
28715354 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* *
28715419 ATTAAATATAATTTAAT-AGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* *
28715444 ATAATTTCATAAAATTCTTAATAATAAA
1 A-AATTTCAAAAAATTCATAATAATAAA
28715472 ATGTTCTTAT
Statistics
Matches: 102, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
90 2 0.02
91 30 0.29
92 62 0.61
93 8 0.08
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:28715479 original size:92 final size:92
Alignment explanation
Indices: 28715297--28715490 Score: 268
Period size: 92 Copynumber: 2.1 Consensus size: 92
28715287 AATTATATTT
* * * *
28715297 TATGAATTTGTATAATTTAAAATAATAATTATTACATATAATTTAATAATTAATATTAAATTTCA
1 TATGAATTTATACAATTTAAAATAATAATTATTAAATATAATTTAATAATGAATATTAAATTTCA
* *
28715362 TAAAATTCTTGATAATAAATTTTCTTA
66 TAAAATTCTTAATAATAAATGTTCTTA
*
28715389 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAGTG-ATA-TATAATTT
1 TATGAATTTATACAATTTAAAATAA-TAATTATTAAATATAATTTAATAATGAATATTA-AATTT
28715451 CATAAAATTCTTAATAATAAAATGTTCTTA
64 CATAAAATTCTTAATAAT-AAATGTTCTTA
*
28715481 TATGTATTTA
1 TATGAATTTA
28715491 CTAAAATCAA
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
90 2 0.02
91 25 0.27
92 61 0.67
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATAATTATTAAATATAATTTAATAATGAATATTAAATTTCA
TAAAATTCTTAATAATAAATGTTCTTA
Found at i:28718595 original size:33 final size:33
Alignment explanation
Indices: 28718556--28718631 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
28718546 ATTATAAAGC
*
28718556 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
28718589 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
28718622 ATGTATAATT
1 ATGTATAATT
28718632 CAAGTTTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTAT
Found at i:28718729 original size:37 final size:37
Alignment explanation
Indices: 28718674--28718755 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
28718664 GTATAAATAT
* *
28718674 ATTGATTAGTTCATTAAAGCATGTTCAAAGTTTTAAC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
*
28718711 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
28718748 ATTGATTA
1 ATTGATTA
28718756 ATAAATATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.40
Consensus pattern (37 bp):
ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
Found at i:28721944 original size:5 final size:5
Alignment explanation
Indices: 28721904--28721929 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28721894 GCAAATCGGC
28721904 AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA A
28721930 TCGGATGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:28722550 original size:33 final size:33
Alignment explanation
Indices: 28722490--28722558 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
28722480 TTGTTAATTT
* *
28722490 TTTTCATTTCAAATTTAATTTAATTTCATTTCA
1 TTTTCATTTCAAATTCAATTTAATTTCACTTCA
* *
28722523 TTTTCATTTC-ACTTCATTTTAATTTTCACTTCA
1 TTTTCATTTCAAATTCAATTTAA-TTTCACTTCA
28722556 TTT
1 TTT
28722559 AAAATTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 9 0.29
33 22 0.71
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (33 bp):
TTTTCATTTCAAATTCAATTTAATTTCACTTCA
Found at i:28722560 original size:16 final size:16
Alignment explanation
Indices: 28722508--28722558 Score: 75
Period size: 16 Copynumber: 3.1 Consensus size: 16
28722498 TCAAATTTAA
*
28722508 TTTAATTTCATTTCAT
1 TTTAATTTCACTTCAT
*
28722524 TTTCATTTCACTTCAT
1 TTTAATTTCACTTCAT
28722540 TTTAATTTTCACTTCAT
1 TTTAA-TTTCACTTCAT
28722557 TT
1 TT
28722559 AAAATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
16 18 0.58
17 13 0.42
ACGTcount: A:0.22, C:0.18, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAATTTCACTTCAT
Found at i:28722586 original size:20 final size:19
Alignment explanation
Indices: 28722563--28722605 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
28722553 TCATTTAAAA
28722563 TTTTTTC-CATTTAAATTTAT
1 TTTTTTCTCATTT-AATTT-T
28722583 TTTTTTCTCATTTAATTTT
1 TTTTTTCTCATTTAATTTT
28722602 TTTT
1 TTTT
28722606 CATATTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.23
20 12 0.55
21 5 0.23
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTTCTCATTTAATTTT
Found at i:28722595 original size:54 final size:56
Alignment explanation
Indices: 28722536--28722656 Score: 135
Period size: 54 Copynumber: 2.2 Consensus size: 56
28722526 TCATTTCACT
28722536 TCATTTTAATTTTCACTTCAT-TTAAAATTTTT-TC-CATTTAAATTTATTT-TTTTC
1 TCATTTTAATTTT-ACTTCATATT-AAATTTTTGTCTCATTTAAATTTATTTATTTTC
** * * *
28722590 TCA-TTTAATTTTTTTTCATATTAATTTTTTGTCTCATTTCAATTTATTTATTTTT
1 TCATTTTAATTTTACTTCATATTAAATTTTTGTCTCATTTAAATTTATTTATTTTC
*
28722645 TCATTTCAATTT
1 TCATTTTAATTT
28722657 ATATTTTATT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
52 12 0.21
53 13 0.23
54 17 0.30
55 7 0.12
56 7 0.12
ACGTcount: A:0.24, C:0.12, G:0.01, T:0.64
Consensus pattern (56 bp):
TCATTTTAATTTTACTTCATATTAAATTTTTGTCTCATTTAAATTTATTTATTTTC
Found at i:28722602 original size:16 final size:16
Alignment explanation
Indices: 28722577--28722634 Score: 75
Period size: 16 Copynumber: 3.6 Consensus size: 16
28722567 TTCCATTTAA
28722577 ATTT-ATTTTTTTCTC
1 ATTTAATTTTTTTCTC
28722592 ATTTAATTTTTTT-TC
1 ATTTAATTTTTTTCTC
28722607 ATATTAATTTTTTGTCTC
1 AT-TTAATTTTTT-TCTC
28722625 ATTTCAATTT
1 ATTT-AATTT
28722635 ATTTATTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.21
16 18 0.47
17 3 0.08
18 9 0.24
ACGTcount: A:0.21, C:0.10, G:0.02, T:0.67
Consensus pattern (16 bp):
ATTTAATTTTTTTCTC
Found at i:28722629 original size:23 final size:22
Alignment explanation
Indices: 28722603--28722669 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 22
28722593 TTTAATTTTT
28722603 TTTCATATTAATTT-TTTGTCTCA
1 TTTCA-ATTAATTTATTT-TCTCA
* *
28722626 TTTCAATTTATTTATTTTTTCA
1 TTTCAATTAATTTATTTTCTCA
28722648 TTTCAATTTATATTTTATTTTC
1 TTTCAA-TTA-A-TTTATTTTC
28722670 ATTCCAACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 17 0.47
23 10 0.28
24 1 0.03
25 8 0.22
ACGTcount: A:0.22, C:0.10, G:0.01, T:0.66
Consensus pattern (22 bp):
TTTCAATTAATTTATTTTCTCA
Found at i:28722672 original size:23 final size:22
Alignment explanation
Indices: 28722613--28722685 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 22
28722603 TTTCATATTA
28722613 ATTTTTTGTCTCATTTCAATTTAT
1 ATTTTTT-T-TCATTTCAATTTAT
28722637 -TTATTTTTTCATTTCAATTTAT
1 ATT-TTTTTTCATTTCAATTTAT
*
28722659 ATTTTATTTTCATTCCAACTTT-T
1 ATTTT-TTTTCATTTCAA-TTTAT
28722682 ATTT
1 ATTT
28722686 CATAGATCCT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
22 16 0.36
23 21 0.48
24 7 0.16
ACGTcount: A:0.22, C:0.12, G:0.01, T:0.64
Consensus pattern (22 bp):
ATTTTTTTTCATTTCAATTTAT
Found at i:28724969 original size:89 final size:87
Alignment explanation
Indices: 28724867--28725220 Score: 321
Period size: 89 Copynumber: 4.0 Consensus size: 87
28724857 ATTTGATAAA
* ** *
28724867 AAAATATATAATTCGAAA-AATTAATAATACGCAAC-AAATTAAATTTATAGATACAAGAAAATA
1 AAAATATAAAATTC-AAACAACAAATAATACG-AACTAAATTAAATTTACAGATACAA-AAAATA
28724930 CAAACATTCTAGAATAATAATACACG
63 CAAACATTCTA-AATAATAATACACG
* **
28724956 AAAATATAAAATTCAAACAACAAACAATAC-AGACTAAATTAAATTTACAGACCCAACAAAATAC
1 AAAATATAAAATTCAAACAACAAATAATACGA-ACTAAATTAAATTTACAGATACAA-AAAATAC
*
28725020 AAACAGATGGGTC-AAAT--TAATACACA
64 AAAC--AT---TCTAAATAATAATACACG
* * * *
28725046 AAAATTTAAAATTCAAATTAA-AAATAATACGGACTAAATTAAATTTACATATACAAAAAATACA
1 AAAATATAAAATTCAAA-CAACAAATAATACGAACTAAATTAAATTTACAGATACAAAAAATACA
* *
28725110 AACATTTTAAGA-AATTATTACACG
65 AACATTCTAA-ATAA-TAATACACG
* * * *
28725134 AAAATATAAAATTGAAACCACAAATAATACTGAA-TAAATTAAATTTACAAATATAAAAAAATAC
1 AAAATATAAAATTCAAACAACAAATAATAC-GAACTAAATTAAATTTACAGATA-CAAAAAATAC
*
28725198 AAACATTCTAAAGAAATAATACA
64 AAACATTCTAAA-TAATAATACA
28725221 AAAATTTTGA
Statistics
Matches: 217, Mismatches: 28, Indels: 40
0.76 0.10 0.14
Matches are distributed among these distances:
84 1 0.00
85 2 0.01
86 1 0.00
87 4 0.02
88 55 0.25
89 89 0.41
90 55 0.25
91 4 0.02
92 3 0.01
93 1 0.00
94 2 0.01
ACGTcount: A:0.58, C:0.12, G:0.05, T:0.25
Consensus pattern (87 bp):
AAAATATAAAATTCAAACAACAAATAATACGAACTAAATTAAATTTACAGATACAAAAAATACAA
ACATTCTAAATAATAATACACG
Found at i:28725075 original size:90 final size:89
Alignment explanation
Indices: 28724947--28725202 Score: 257
Period size: 90 Copynumber: 2.9 Consensus size: 89
28724937 TCTAGAATAA
* *
28724947 TAATACACGAAAATATAAAATTCAAACAACAAACAATACAGACTAAATTAAATTTACAGACCCAA
1 TAATACACAAAAATATAAAATTCAAACAACAAACAATACAGACTAAATTAAATTTACAGACACAA
28725012 CAAAATACAAACAGATGGGTCAAAT
66 -AAAATACAAACAGATGGGTCAAAT
* * * * * *
28725037 TAATACACAAAAATTTAAAATTCAAATTAA-AAATAATACGGACTAAATTAAATTTACATATACA
1 TAATACACAAAAATATAAAATTCAAA-CAACAAACAATACAGACTAAATTAAATTTACAGACACA
** **
28725101 AAAAATACAAACATTTTAAG--AAAT
65 AAAAATACAAACA-GATGGGTCAAAT
* * * * * * * * * *
28725125 TATTACACGAAAATATAAAATTGAAACCACAAATAATACTGAATAAATTAAATTTACAAATATAA
1 TAATACACAAAAATATAAAATTCAAACAACAAACAATACAGACTAAATTAAATTTACAGACA-CA
28725190 AAAAATACAAACA
65 AAAAATACAAACA
28725203 TTCTAAAGAA
Statistics
Matches: 140, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
87 1 0.01
88 55 0.39
89 26 0.19
90 56 0.40
91 2 0.01
ACGTcount: A:0.58, C:0.13, G:0.05, T:0.24
Consensus pattern (89 bp):
TAATACACAAAAATATAAAATTCAAACAACAAACAATACAGACTAAATTAAATTTACAGACACAA
AAAATACAAACAGATGGGTCAAAT
Found at i:28741847 original size:44 final size:44
Alignment explanation
Indices: 28741678--28742115 Score: 169
Period size: 44 Copynumber: 10.0 Consensus size: 44
28741668 CAAATCAGTA
* * **
28741678 AAGATAGCAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCA
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTG
* * * *
28741722 AAGAT-GACAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTT
1 AAGATAG-CAGATCTTATC-TCCCTAAGCAGTAGT-GG-AGTAGATTG
* * * * * *
28741766 AAGCCACTA--AG-CCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTG
1 AAG--A-TAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTG
**
28741810 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCA
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTG
* * * * * *
28741854 AAGACAGCAAATCTTATCTTTCC-AA-TA-TAGTGGGAAGCAGATTT
1 AAGATAGCAGATCTTATC-TCCCTAAGCAGTAGT-GG-AGTAGATTG
* * * *
28741898 AAGCCACTA--AG-CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTG
1 AAG--A-TAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTG
* **
28741942 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTG
** * * ** * *
28741986 AAGACGGCAAATCTTAACT-TTTCAAG-A-TAGTGGGAAATAGATTT
1 AAGATAGCAGATCTTATCTCCCT-AAGCAGTAGT-GG-AGTAGATTG
* * * *
28742030 AAGCCACTA--AG-TCTTGTCT-CCAAGAGCAGCAGTGGAGTAGGTTG
1 AAG--A-TAGCAGATCTTATCTCCCTA-AGCAGTAGTGGAGTAGATTG
* *
28742074 AAGATAGCAGATCTCATCTCCCTAAGCAGTAGTGGAGCAGAT
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGAT
28742116 CAAAGACGAC
Statistics
Matches: 280, Mismatches: 75, Indels: 78
0.65 0.17 0.18
Matches are distributed among these distances:
41 6 0.02
42 15 0.05
43 24 0.09
44 201 0.72
45 21 0.08
46 11 0.04
47 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (44 bp):
AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTG
Found at i:28741918 original size:132 final size:132
Alignment explanation
Indices: 28741678--28742210 Score: 852
Period size: 132 Copynumber: 4.0 Consensus size: 132
28741668 CAAATCAGTA
* *
28741678 AAGATAGCAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACAAATCTTATCTTT
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTT
*
28741743 CCAAGATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
66 CCAAGATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTATCTCCCTGAGCAGCAGCGGAGTAGGT
28741808 TG
131 TG
*
28741810 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGAC-AGCAAATCTTATCTT
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGA-CAAATCTTATCTT
* *
28741874 TCCAATATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGG
65 TCCAAGATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTATCTCCCTGAGCAGCAGCGGAGTAGG
28741939 TTG
130 TTG
* *
28741942 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTAACTTT
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTT
* ** * * ** *
28742007 TCAAGATAGTGGGAAATAGATTTAAGCCACTAAGTCTTGTCTCCAAGAGCAGCAGTGGAGTAGGT
66 CCAAGATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTATCTCCCTGAGCAGCAGCGGAGTAGGT
28742072 TG
131 TG
*
28742074 AAGATAGCAGATCTCATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTT
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTT
* ** * *
28742139 CCAAGATAGTGGGAAGCAGGTTTAAGCCACCGAGCCTTATCTCCCTAAGCAGTAGCGGAGTAGGT
66 CCAAGATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTATCTCCCTGAGCAGCAGCGGAGTAGGT
28742204 TG
131 TG
28742206 AAGAT
1 AAGAT
28742211 TACAAATCCT
Statistics
Matches: 366, Mismatches: 33, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
131 1 0.00
132 365 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (132 bp):
AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTT
CCAAGATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTATCTCCCTGAGCAGCAGCGGAGTAGGT
TG
Found at i:28744019 original size:22 final size:22
Alignment explanation
Indices: 28743994--28744040 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
28743984 TACACCAAAA
*
28743994 TAGGCTTTTAGCCGCGCTTTTT
1 TAGGCCTTTAGCCGCGCTTTTT
*
28744016 TAGGCCTTTAGCGGCGCTTTTT
1 TAGGCCTTTAGCCGCGCTTTTT
28744038 TAG
1 TAG
28744041 CGCCGCAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.11, C:0.21, G:0.26, T:0.43
Consensus pattern (22 bp):
TAGGCCTTTAGCCGCGCTTTTT
Found at i:28744562 original size:86 final size:86
Alignment explanation
Indices: 28744303--28744568 Score: 381
Period size: 86 Copynumber: 3.1 Consensus size: 86
28744293 TTTTTTTCTC
*
28744303 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCACAAACGCCACTAAAGAACCTAAT
1 AAACGCCGCAATAGACCATGATCTATAGCGGCGCTTTGACCACAAACGCCACTAAAGAACCTAAT
* *
28744368 CTTTAGCGGCGCTTTCCCCTA
66 CTTTAGCGGTGCTTTCCCCAA
* *
28744389 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTCGACCACAAAACGCCACTAAAGAACCTAA
1 AAACGCCGCAATAGACCATGATCTATAGCGGCGCTTTGACCAC-AAACGCCACTAAAGAACCTAA
28744454 TCTTTAGCGGTGCTTTCCCCAA
65 TCTTTAGCGGTGCTTTCCCCAA
* * ** * * *
28744476 AAACGCCGCTAA-AGACCATGATCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAAAGACCCTTA
1 AAACGCCGC-AATAGACCATGATCTATAGCGGCGCTTTGACCACAAACGCCACTAAAGAACCTAA
**
28744540 TCTTTAGCGGTGCTTTGACCAA
65 TCTTTAGCGGTGCTTTCCCCAA
28744562 AAACGCC
1 AAACGCC
28744569 ACTAAAGGCC
Statistics
Matches: 164, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
86 87 0.53
87 75 0.46
88 2 0.01
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (86 bp):
AAACGCCGCAATAGACCATGATCTATAGCGGCGCTTTGACCACAAACGCCACTAAAGAACCTAAT
CTTTAGCGGTGCTTTCCCCAA
Found at i:28744566 original size:43 final size:43
Alignment explanation
Indices: 28744303--28744575 Score: 289
Period size: 43 Copynumber: 6.3 Consensus size: 43
28744293 TTTTTTTCTC
* *
28744303 AAACGCCGC-AATAGACCCTGATCTATAGCGGCGCTTTGACCAC
1 AAACGCCGCTAA-AGACCCTGATCTTTAGCGGCGCTTTGACCAA
* * * ** *
28744346 AAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCCCCTA
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTGACCAA
* *
28744389 AAACGCCGC-AATAGACCCTGATCTATAGCGGCGCTTCGACCACA
1 AAACGCCGCTAA-AGACCCTGATCTTTAGCGGCGCTTTGACCA-A
* * * * **
28744433 AAACGCCACTAAAGAACCTAATCTTTAGCGGTGCTTTCCCCAA
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTGACCAA
* * ** *
28744476 AAACGCCGCTAAAGACCATGATCTTTAGTGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTGACCAA
* *
28744519 AAACGCCGCTAAAGACCCTTATCTTTAGCGGTGCTTTGACCAA
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTGACCAA
*
28744562 AAACGCCACTAAAG
1 AAACGCCGCTAAAG
28744576 GCCAACACCT
Statistics
Matches: 185, Mismatches: 41, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
42 2 0.01
43 147 0.79
44 34 0.18
45 2 0.01
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTGACCAA
Found at i:28744947 original size:21 final size:21
Alignment explanation
Indices: 28744918--28745010 Score: 105
Period size: 21 Copynumber: 4.4 Consensus size: 21
28744908 TTTGACGCTG
* *
28744918 CTCTACTTCCCTCGCTGCAAC
1 CTCTGCTTCCCTCGCTGCAGC
**
28744939 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
28744960 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * * *
28744981 CTATACTTCTCTAGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
28745002 CTCTGCTTC
1 CTCTGCTTC
28745011 TCTTGCTGTC
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.09, C:0.44, G:0.14, T:0.33
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:28745112 original size:66 final size:66
Alignment explanation
Indices: 28745040--28745170 Score: 174
Period size: 66 Copynumber: 2.0 Consensus size: 66
28745030 TTAAACTACT
* * * * *
28745040 GCTGGAGTTCTTCGTA-CTTTCGTTGATCCTCAGCTTCTCTCGTTGCTGCATCTGCTTTCAGTTG
1 GCTGGAGTTCTTCATATCTTT-GTTGAACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTG
28745104 TA
65 TA
* * *
28745106 GCTGGAGTTCTTCATATCTTTTTTGAACCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTTGT
1 GCTGGAGTTCTTCATATCTTTGTTGAACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
28745171 GTAATTTGCT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 52 0.93
67 4 0.07
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.43
Consensus pattern (66 bp):
GCTGGAGTTCTTCATATCTTTGTTGAACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
A
Found at i:28750609 original size:16 final size:16
Alignment explanation
Indices: 28750588--28750623 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28750578 ATAATTAAGC
*
28750588 TATGTAGGTTATGTAT
1 TATGTAAGTTATGTAT
*
28750604 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
28750620 TATG
1 TATG
28750624 AAAACTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:28750632 original size:25 final size:25
Alignment explanation
Indices: 28750604--28750657 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
28750594 GGTTATGTAT
*
28750604 TATGTAAGTTATTTATTATGAAAAC
1 TATGTAAGTTATGTATTATGAAAAC
* *
28750629 TATGTAAGTTGTGTATTATGAAAAT
1 TATGTAAGTTATGTATTATGAAAAC
28750654 TATG
1 TATG
28750658 CTATGTAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (25 bp):
TATGTAAGTTATGTATTATGAAAAC
Found at i:28750688 original size:25 final size:25
Alignment explanation
Indices: 28750659--28750712 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
28750649 AAAATTATGC
28750659 TATGTAAGTCATATAAGTTATGTAT
1 TATGTAAGTCATATAAGTTATGTAT
* * *
28750684 TATGTAAGTTATGTAAGTTATTTAT
1 TATGTAAGTCATATAAGTTATGTAT
28750709 TATG
1 TATG
28750713 CAAATTGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (25 bp):
TATGTAAGTCATATAAGTTATGTAT
Found at i:28750695 original size:9 final size:9
Alignment explanation
Indices: 28750659--28750704 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
28750649 AAAATTATGC
28750659 TATGTAAGT
1 TATGTAAGT
* *
28750668 CATATAAGT
1 TATGTAAGT
28750677 TATGT-A-T
1 TATGTAAGT
28750684 TATGTAAGT
1 TATGTAAGT
28750693 TATGTAAGT
1 TATGTAAGT
28750702 TAT
1 TAT
28750705 TTATTATGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
7 6 0.19
8 2 0.06
9 23 0.74
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (9 bp):
TATGTAAGT
Found at i:28750775 original size:34 final size:34
Alignment explanation
Indices: 28750727--28750856 Score: 174
Period size: 34 Copynumber: 3.8 Consensus size: 34
28750717 TTGTTAAAAT
* *
28750727 GTTATGTAAGTTATGTATAATATTAATTAACTAA
1 GTTATGTAATTTATGTATAATATTAATTAATTAA
*
28750761 GTTATGTAATTTATGTATAATATTTATGT-A-TAA
1 GTTATGTAATTTATGTATAATATTAAT-TAATTAA
* *
28750794 TATTAATGTAAGTTATGTATAATATTAATTAATTAA
1 -GTT-ATGTAATTTATGTATAATATTAATTAATTAA
28750830 GTTATGTAATTTATGTATAATATTAAT
1 GTTATGTAATTTATGTATAATATTAAT
28750857 GTAAGTTATG
Statistics
Matches: 84, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
33 3 0.04
34 52 0.62
35 26 0.31
36 3 0.04
ACGTcount: A:0.40, C:0.01, G:0.11, T:0.48
Consensus pattern (34 bp):
GTTATGTAATTTATGTATAATATTAATTAATTAA
Found at i:28750787 original size:13 final size:13
Alignment explanation
Indices: 28750769--28750803 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
28750759 AAGTTATGTA
28750769 ATTTATGTATAAT
1 ATTTATGTATAAT
28750782 ATTTATGTATAAT
1 ATTTATGTATAAT
*
28750795 ATTAATGTA
1 ATTTATGTA
28750804 AGTTATGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (13 bp):
ATTTATGTATAAT
Found at i:28750810 original size:69 final size:69
Alignment explanation
Indices: 28750730--28750859 Score: 242
Period size: 69 Copynumber: 1.9 Consensus size: 69
28750720 TTAAAATGTT
*
28750730 ATGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATATTTATGTATAAT
1 ATGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATATTAATGTATAAT
28750795 ATTA
66 ATTA
*
28750799 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTA
1 ATGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATATTAATGTA
28750860 AGTTATGTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.48
Consensus pattern (69 bp):
ATGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATATTAATGTATAAT
ATTA
Found at i:28750827 original size:56 final size:56
Alignment explanation
Indices: 28750782--28750908 Score: 254
Period size: 56 Copynumber: 2.3 Consensus size: 56
28750772 TATGTATAAT
28750782 ATTTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTA
1 ATTTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTA
28750838 ATTTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTA
1 ATTTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTA
28750894 ATTTATGTATAATAT
1 ATTTATGTATAATAT
28750909 CACATCACCC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 71 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (56 bp):
ATTTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTA
Found at i:28750858 original size:22 final size:22
Alignment explanation
Indices: 28750833--28750883 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
28750823 TAATTAAGTT
28750833 ATGTAATTTATGTATAATATTA
1 ATGTAATTTATGTATAATATTA
*
28750855 ATGTAAGTTATGTATAATATTA
1 ATGTAATTTATGTATAATATTA
28750877 AT-TAATT
1 ATGTAATT
28750884 AAGTTATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (22 bp):
ATGTAATTTATGTATAATATTA
Found at i:28750991 original size:13 final size:15
Alignment explanation
Indices: 28750972--28751012 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
28750962 CATATAAGTT
28750972 TATGTAAGTTATG-A
1 TATGTAAGTTATGTA
28750986 -ATGTAAGTTATGTA
1 TATGTAAGTTATGTA
28751000 TTATGTAAGTTAT
1 -TATGTAAGTTAT
28751013 TTAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (15 bp):
TATGTAAGTTATGTA
Found at i:28751007 original size:16 final size:16
Alignment explanation
Indices: 28750971--28751049 Score: 74
Period size: 16 Copynumber: 5.0 Consensus size: 16
28750961 ACATATAAGT
28750971 TTATGTAAGTTATG-A
1 TTATGTAAGTTATGTA
28750986 --ATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
28751000 TTATGTAAGTTATTTAAA
1 TTATGTAAGTTATGT--A
* *
28751018 TTATTTAAGTTGTGTA
1 TTATGTAAGTTATGTA
* *
28751034 TTATATAAGTCATGTA
1 TTATGTAAGTTATGTA
28751050 GGCTATGTGT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
13 12 0.23
14 1 0.02
16 26 0.50
18 13 0.25
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.48
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:28752081 original size:12 final size:12
Alignment explanation
Indices: 28752061--28752093 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
28752051 AAACTAAAAT
*
28752061 TGAACATATATA
1 TGAATATATATA
28752073 TGAATATATATA
1 TGAATATATATA
28752085 TGAATATAT
1 TGAATATAT
28752094 GTTGAAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (12 bp):
TGAATATATATA
Found at i:28753642 original size:10 final size:10
Alignment explanation
Indices: 28753627--28753662 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
28753617 ATTAATAACT
28753627 ATATATATCC
1 ATATATATCC
28753637 ATATATAT-C
1 ATATATATCC
28753646 ATATATATCC
1 ATATATATCC
28753656 ATATATA
1 ATATATA
28753663 AGTAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATATATCC
Found at i:28755387 original size:15 final size:15
Alignment explanation
Indices: 28755362--28755404 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
28755352 ACATGACCAT
28755362 TCAAA-CCCTAAATC
1 TCAAACCCCTAAATC
*
28755376 TCAAACCCCTAAACC
1 TCAAACCCCTAAATC
*
28755391 TCTAACCCCTAAAT
1 TCAAACCCCTAAAT
28755405 TAACCTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.21
Consensus pattern (15 bp):
TCAAACCCCTAAATC
Found at i:28758433 original size:38 final size:37
Alignment explanation
Indices: 28758383--28758566 Score: 140
Period size: 38 Copynumber: 4.7 Consensus size: 37
28758373 ATAGTATTAT
*
28758383 ATATTATG-ATTTTATTAAATTCATATAAGAATATTTA
1 ATATTAAGAATTTTATTAAATT-ATATAAGAATATTTA
**** *
28758420 ATATTAAGAATTTTATTAAATTATATATTTTTATTAAATT
1 ATATTAAGAATTTTATTAAATTATATAAGAATATT---TA
* * * *
28758460 ATATTTAATAATAATTATTTTAAATTATATTA-TATAGTATTA
1 ATA-TTAAGAAT--TT-TATTAAATTATATAAGAATA-T-TTA
*
28758502 TATATTATG-ATTTTATTAAATTCATATAAGAATATTTA
1 -ATATTAAGAATTTTATTAAATT-ATATAAGAATATTTA
28758540 ATATTAAGAATTTTATTAAATTATATA
1 ATATTAAGAATTTTATTAAATTATATA
28758567 TTTTTATTAA
Statistics
Matches: 115, Mismatches: 18, Indels: 28
0.71 0.11 0.17
Matches are distributed among these distances:
37 28 0.24
38 37 0.32
39 8 0.07
40 7 0.06
41 9 0.08
42 4 0.03
43 8 0.07
44 13 0.11
45 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (37 bp):
ATATTAAGAATTTTATTAAATTATATAAGAATATTTA
Found at i:28758451 original size:18 final size:18
Alignment explanation
Indices: 28758430--28758583 Score: 76
Period size: 18 Copynumber: 8.9 Consensus size: 18
28758420 ATATTAAGAA
28758430 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
28758448 TTTTATTAAA-T-TATA-
1 TTTTATTAAATTATATAT
* *
28758463 -TTTAAT-AATAAT-TAT
1 TTTTATTAAATTATATAT
* * *
28758478 TTTAAATTATATTATATAG
1 TTT-TATTAAATTATATAT
* * *
28758497 TATTA-TATATTAT-GA-
1 TTTTATTAAATTATATAT
*
28758512 TTTTATTAAATTCATATAA
1 TTTTATTAAATT-ATATAT
*** * *
28758531 GAATATTTAATATTA-AGAA
1 TTTTA-TTAA-ATTATATAT
28758550 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
28758568 TTTTATTAAATTATAT
1 TTTTATTAAATTATAT
28758584 TTAATAATAA
Statistics
Matches: 100, Mismatches: 22, Indels: 28
0.67 0.15 0.19
Matches are distributed among these distances:
13 2 0.02
14 7 0.07
15 5 0.05
16 12 0.12
17 17 0.17
18 38 0.38
19 11 0.11
20 5 0.05
21 3 0.03
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.55
Consensus pattern (18 bp):
TTTTATTAAATTATATAT
Found at i:28758504 original size:120 final size:120
Alignment explanation
Indices: 28758365--28758845 Score: 768
Period size: 120 Copynumber: 4.0 Consensus size: 120
28758355 ATTATTAATC
* * *
28758365 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
1 TATATTATATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTTAATATTAAGAA
* *
28758430 TTTTATTAAATTATATATTTTTATTA-AATTATATTTAATAATAATTATTTTAAAT
66 TTTTATTAAATTATATATTTTAATTATAA-TATATTTAATAATAATTATGTTAAAT
* * *
28758485 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
1 TATATTATATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTTAATATTAAGAA
*
28758550 TTTTATTAAATTATATATTTTTATTA-AATTATATTTAATAATAATTATGTTAAAT
66 TTTTATTAAATTATATATTTTAATTATAA-TATATTTAATAATAATTATGTTAAAT
* * *
28758605 TATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTTATTATTAATAA
1 TATATTATATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTTAATATTAAGAA
* *
28758670 TATTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATT
66 TTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAAT
* * *
28758725 TATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAA
1 TATATTATATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTTAATATTAAGAA
28758790 TTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
66 TTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
28758846 ATGATTAAAT
Statistics
Matches: 345, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
120 338 0.98
121 7 0.02
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (120 bp):
TATATTATATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTTAATATTAAGAA
TTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAAT
Found at i:28758706 original size:15 final size:15
Alignment explanation
Indices: 28758666--28758724 Score: 61
Period size: 15 Copynumber: 4.0 Consensus size: 15
28758656 TTTATTATTA
*
28758666 ATAATATTATTAAATT
1 ATAATA-TATTTAATT
28758682 AT-ATAT-TTTAATT
1 ATAATATATTTAATT
*
28758695 ATAATATATTTAATA
1 ATAATATATTTAATT
28758710 ATAAT-TATGTTAATT
1 ATAATATAT-TTAATT
28758725 TATATTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 8 0.22
14 8 0.22
15 19 0.51
16 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
ATAATATATTTAATT
Found at i:28758823 original size:16 final size:16
Alignment explanation
Indices: 28758802--28758843 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28758792 TTATTAAATT
*
28758802 ATATATTTTAATTATA
1 ATATATTTTAATAATA
28758818 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
28758833 AT-TATGTTTAA
1 ATATAT-TTTAA
28758844 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:28758828 original size:15 final size:15
Alignment explanation
Indices: 28758793--28758834 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28758783 TTAAGAATTT
*
28758793 TATTAAATTAT-ATA
1 TATTTAATTATAATA
28758807 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
28758821 TATTTAATAATAAT
1 TATTTAATTATAAT
28758835 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:28759082 original size:16 final size:16
Alignment explanation
Indices: 28759061--28759128 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
28759051 GATTTGCTAT
28759061 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
28759077 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
28759093 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28759109 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28759125 TACA
1 TACA
28759129 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:28759902 original size:41 final size:41
Alignment explanation
Indices: 28759627--28759945 Score: 228
Period size: 41 Copynumber: 7.8 Consensus size: 41
28759617 TTTTGTTACT
* * * *
28759627 ATTAGCGGCGCTTCGGA-AAAAACACCGCTAAAGG-TAG--C
1 ATTAGTGGCGC-TCAGATAAAAACGCCGCTAAAGGACAGAAC
* * * **
28759665 ATTAGTGGCGCTTACATATAAAACGCCGCTAAAGGCCAGAGT
1 ATTAGTGGCGCTCAGATA-AAAACGCCGCTAAAGGACAGAAC
* *
28759707 ACTAGTGGCGCTCAGATAAAAACGCCACTGAAA--ACACGAAC
1 ATTAGTGGCGCTCAGATAAAAACGCCGCT-AAAGGACA-GAAC
* * * * *
28759748 TTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACAGAGA-
1 ATTAGTGGCGCTCAGATAAAAACGCCGCTAAAGGACAGA-AC
* * * * * *
28759789 ATTAGTGGCGCTCAGACAATAACGCCACT-AATGATACGAGC
1 ATTAGTGGCGCTCAGATAAAAACGCCGCTAAAGGACA-GAAC
* * *
28759830 ATTAGTGGCGCTTAGACAAAAACGCCGCTAAAGGCCAGAAC
1 ATTAGTGGCGCTCAGATAAAAACGCCGCTAAAGGACAGAAC
*
28759871 ATTAGTGGCGCTCAGATAAAAACGCCGCTAAA-GATCGGAGA-
1 ATTAGTGGCGCTCAGATAAAAACGCCGCTAAAGGA-CAGA-AC
* *
28759912 ATTAGCGGCGCT-AAAGTAAAAACGCCGCTAAAGG
1 ATTAGTGGCGCTCAGA-TAAAAACGCCGCTAAAGG
28759946 TTTAAAAATC
Statistics
Matches: 221, Mismatches: 43, Indels: 30
0.75 0.15 0.10
Matches are distributed among these distances:
37 2 0.01
38 11 0.05
39 15 0.07
40 14 0.06
41 151 0.68
42 28 0.13
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (41 bp):
ATTAGTGGCGCTCAGATAAAAACGCCGCTAAAGGACAGAAC
Found at i:28759916 original size:82 final size:80
Alignment explanation
Indices: 28759665--28759945 Score: 300
Period size: 82 Copynumber: 3.4 Consensus size: 80
28759655 TAAAGGTAGC
* * * *
28759665 ATTAGTGGCGCTTACATATAAAACGCCGCTAAAGGCCAGAGTACTAGTGGCGCTCAGATAAAAAC
1 ATTAGCGGCGCTTAGATA-AAAACGCCGCTAAAGGCCAGA-AATTAGTGGCGCTCAGATAAAAAC
28759730 GCCACTGAAA-A-C-ACGA
64 GCCACT-AAAGATCGA-GA
* ** * *
28759746 ACTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACAGAGAATTAGTGGCGCTCAGACAATAA
1 A--TTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGA-AATTAGTGGCGCTCAGATAAAAA
* *
28759811 CGCCACTAATGATACGAGC
63 CGCCACTAAAGAT-CGAGA
* *
28759830 ATTAGTGGCGCTTAGACAAAAACGCCGCTAAAGGCCAGAACATTAGTGGCGCTCAGATAAAAACG
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAA-ATTAGTGGCGCTCAGATAAAAACG
*
28759895 CCGCTAAAGATCGGAGA
65 CCACTAAAGATC-GAGA
*
28759912 ATTAGCGGCGC-TAAAGTAAAAACGCCGCTAAAGG
1 ATTAGCGGCGCTTAGA-TAAAAACGCCGCTAAAGG
28759946 TTTAAAAATC
Statistics
Matches: 168, Mismatches: 23, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
81 8 0.05
82 142 0.85
83 14 0.08
84 3 0.02
85 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.16
Consensus pattern (80 bp):
ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAAATTAGTGGCGCTCAGATAAAAACGC
CACTAAAGATCGAGA
Found at i:28771006 original size:38 final size:39
Alignment explanation
Indices: 28770943--28771020 Score: 140
Period size: 38 Copynumber: 2.0 Consensus size: 39
28770933 CAAGGAGGGG
28770943 AAAGAAAGAAAGAAAAACTCAAAATGTGAGAAGAGAGAA
1 AAAGAAAGAAAGAAAAACTCAAAATGTGAGAAGAGAGAA
*
28770982 AAAGAAAGAAA-AAAAAGTCAAAATGTGAGAAGAGAGAA
1 AAAGAAAGAAAGAAAAACTCAAAATGTGAGAAGAGAGAA
28771020 A
1 A
28771021 CGTGAAAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 27 0.71
39 11 0.29
ACGTcount: A:0.65, C:0.04, G:0.23, T:0.08
Consensus pattern (39 bp):
AAAGAAAGAAAGAAAAACTCAAAATGTGAGAAGAGAGAA
Found at i:28772949 original size:23 final size:23
Alignment explanation
Indices: 28772903--28772951 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
28772893 TTAAATGAAC
* * **
28772903 AAATTTAACTTACAAGGAGGAAA
1 AAATTCAAATTACAAGGACAAAA
28772926 AAATTCAAATTACAAGGACAAAA
1 AAATTCAAATTACAAGGACAAAA
28772949 AAA
1 AAA
28772952 AAGACGAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.59, C:0.10, G:0.12, T:0.18
Consensus pattern (23 bp):
AAATTCAAATTACAAGGACAAAA
Found at i:28776656 original size:21 final size:21
Alignment explanation
Indices: 28776632--28776689 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
28776622 GTGCTAAACA
28776632 GAAACCCATAAGGGTTGAACG
1 GAAACCCATAAGGGTTGAACG
* * *
28776653 GAAACTCATAAGAGCTGAACG
1 GAAACCCATAAGGGTTGAACG
28776674 GAAACCCATAAGGGTT
1 GAAACCCATAAGGGTT
28776690 AAATTCAAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.16
Consensus pattern (21 bp):
GAAACCCATAAGGGTTGAACG
Found at i:28778392 original size:94 final size:94
Alignment explanation
Indices: 28778282--28778704 Score: 456
Period size: 94 Copynumber: 4.5 Consensus size: 94
28778272 AGATTCGAGG
* * * * * *
28778282 TTGTAGCTTTATCTTGCTCCACTGCATCTTCAGGGAGATTAGATTTGCTATTGTAGTTTCAATCT
1 TTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATTGTAGCTTCATTCC
** ** *
28778347 ATTCCATTACAACTTCAGGGATATAGGAT
66 AAACCATTGTAACTTCAGGGGTATAGGAT
* * * *** *
28778376 TTGTAGCTCCATCTTGC-CCTACTGCAACTTTAGAGAGATAAGACACGCCATTGTAGCTTCATTC
1 TTGTAGCTTCATCTTGCTCC-ACTGCAACTTCAGGGAGATAAGATTTGCTATTGTAGCTTCATTC
* * * *
28778440 CAAACTACTGTAACTTTAGGGGTATAAGAT
65 CAAACCATTGTAACTTCAGGGGTATAGGAT
* * *
28778470 TTGTAGCTTCATCTTGCTCCACTGCAAGTTCAGGGAGATAAAATTTGTTATTGTAGCTTCATTCC
1 TTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATTGTAGCTTCATTCC
*
28778535 AAACCATTGTAACTGT-AGGGGTATAGGAC
66 AAACCATTGTAACT-TCAGGGGTATAGGAT
* * * *
28778564 TTGTAGCTTTATCTTGCTCCACTGTAACTTCAGGGAGATAAGATTTGCTATTATAGTTTCATTCC
1 TTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATTGTAGCTTCATTCC
* * *
28778629 -GACTCATTTTAACTTCAGGGGTACAGGAT
66 AAAC-CATTGTAACTTCAGGGGTATAGGAT
* * * **
28778658 TTATAGCTTCATCTTACTTCACTAAAACTTCAGGGAGATAAGATTTG
1 TTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTG
28778705 TAGCTTCATT
Statistics
Matches: 271, Mismatches: 53, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
93 5 0.02
94 263 0.97
95 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (94 bp):
TTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATTGTAGCTTCATTCC
AAACCATTGTAACTTCAGGGGTATAGGAT
Found at i:28778731 original size:44 final size:44
Alignment explanation
Indices: 28778446--28778746 Score: 152
Period size: 44 Copynumber: 6.6 Consensus size: 44
28778436 ATTCCAAACT
*
28778446 ACTGTAACTTTAGGG-GTATAAGATTTGTAGCTTCATCTTGCTCC
1 ACTGTAACTTCAGGGAG-ATAAGATTTGTAGCTTCATCTTGCTCC
* * * * *
28778490 ACTGCAAGTTCAGGGAGATAAAATTTGTTATTGTAGCTTCA--TTCCAAACC
1 ACTGTAACTTCAGGGAGAT--AA---GAT-TTGTAGCTTCATCTTGC--TCC
* * * *
28778540 ATTGTAACTGT-AGGG-GTATAGGACTTGTAGCTTTATCTTGCTCC
1 ACTGTAACT-TCAGGGAG-ATAAGATTTGTAGCTTCATCTTGCTCC
* *
28778584 ACTGTAACTTCAGGGAGATAAGATTTGCTATTATAGTTTCAT-TCCGACT-C
1 ACTGTAACTTCAGGGAGATAAGATTTG------TAGCTTCATCT-TG-CTCC
* * * * *
28778634 ATTTTAACTTCAGGG-G-TACAGGATTTATAGCTTCATCTTACTTC
1 ACTGTAACTTCAGGGAGATA-A-GATTTGTAGCTTCATCTTGCTCC
** *
28778678 ACTAAAACTTCAGGGAGATAAGATTTGTAGCTTCATTTTGCTCC
1 ACTGTAACTTCAGGGAGATAAGATTTGTAGCTTCATCTTGCTCC
* *
28778722 ACTGTAACTTCAGGTAGATGAGATT
1 ACTGTAACTTCAGGGAGATAAGATT
28778747 CGCCATTGTA
Statistics
Matches: 190, Mismatches: 38, Indels: 58
0.66 0.13 0.20
Matches are distributed among these distances:
43 3 0.02
44 107 0.56
45 6 0.03
46 7 0.04
48 6 0.03
49 6 0.03
50 52 0.27
51 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (44 bp):
ACTGTAACTTCAGGGAGATAAGATTTGTAGCTTCATCTTGCTCC
Found at i:28783851 original size:34 final size:34
Alignment explanation
Indices: 28783811--28783880 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
28783801 TAACATAACA
28783811 TCAATTATATCATACCTTTCATAAACATAAATAT
1 TCAATTATATCATACCTTTCATAAACATAAATAT
28783845 TCAATTATATCATACCTTTCATAAACATAAATAT
1 TCAATTATATCATACCTTTCATAAACATAAATAT
28783879 TC
1 TC
28783881 TCATAAACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.39
Consensus pattern (34 bp):
TCAATTATATCATACCTTTCATAAACATAAATAT
Found at i:28783884 original size:18 final size:18
Alignment explanation
Indices: 28783863--28783898 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28783853 ATCATACCTT
28783863 TCATAAACATAAATATTC
1 TCATAAACATAAATATTC
28783881 TCATAAACATAAATATTC
1 TCATAAACATAAATATTC
28783899 ATACTTTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (18 bp):
TCATAAACATAAATATTC
Found at i:28783900 original size:34 final size:34
Alignment explanation
Indices: 28783811--28783901 Score: 87
Period size: 34 Copynumber: 2.7 Consensus size: 34
28783801 TAACATAACA
* **
28783811 TCAATTATATCATACCTTTCATAAACATAAATAT
1 TCAATTATAACATAAATTTCATAAACATAAATAT
* **
28783845 TCAATTATATCATACCTTTCATAAACATAAATAT
1 TCAATTATAACATAAATTTCATAAACATAAATAT
*
28783879 TC--TCATAAACATAAATATTCATA
1 TCAATTAT-AACATAAAT-TTCATA
28783902 CTTTCACCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
32 3 0.06
33 6 0.12
34 42 0.82
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (34 bp):
TCAATTATAACATAAATTTCATAAACATAAATAT
Found at i:28784073 original size:30 final size:29
Alignment explanation
Indices: 28784006--28784133 Score: 114
Period size: 29 Copynumber: 4.4 Consensus size: 29
28783996 GTCGTAACCG
* * ** * *
28784006 TCCCTTTTCATATTCGATGGTTAAAACCA
1 TCCCTTTTCATAATCGATAGTCGAAGCTA
* * *
28784035 TCCATTTTCATTAATCGATGGTCGTCA-CTA
1 TCCCTTTTCA-TAATCGATAGTCG-AAGCTA
*
28784065 TCCCTTTTCATATTCGATAGTCGAAGCTA
1 TCCCTTTTCATAATCGATAGTCGAAGCTA
* * *
28784094 TCCCTTTTCATAATCGATAGCCAAATCTA
1 TCCCTTTTCATAATCGATAGTCGAAGCTA
28784123 TCCCTTTTCAT
1 TCCCTTTTCAT
28784134 TGGTCGATGA
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
28 1 0.01
29 59 0.72
30 21 0.26
31 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.10, T:0.39
Consensus pattern (29 bp):
TCCCTTTTCATAATCGATAGTCGAAGCTA
Found at i:28784102 original size:59 final size:58
Alignment explanation
Indices: 28783992--28784111 Score: 150
Period size: 59 Copynumber: 2.1 Consensus size: 58
28783982 TGTGCTAAAT
* * *
28783992 GATGGTCGTAACCGTCCCTTTTCATATTCGATGGTTAAAACCATCCATTTTCATTAATC
1 GATGGTCGTAACCATCCCTTTTCATATTCGATAGTCAAAACCATCCATTTTCA-TAATC
* * * * * *
28784051 GATGGTCGTCACTATCCCTTTTCATATTCGATAGTCGAAGCTATCCCTTTTCATAATC
1 GATGGTCGTAACCATCCCTTTTCATATTCGATAGTCAAAACCATCCATTTTCATAATC
28784109 GAT
1 GAT
28784112 AGCCAAATCT
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
58 8 0.15
59 44 0.85
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (58 bp):
GATGGTCGTAACCATCCCTTTTCATATTCGATAGTCAAAACCATCCATTTTCATAATC
Found at i:28786992 original size:14 final size:14
Alignment explanation
Indices: 28786973--28786999 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28786963 GGGACCTTTT
28786973 ATGTAATGAAATGC
1 ATGTAATGAAATGC
28786987 ATGTAATGAAATG
1 ATGTAATGAAATG
28787000 TAATACTAAT
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:0.44, C:0.04, G:0.22, T:0.30
Consensus pattern (14 bp):
ATGTAATGAAATGC
Found at i:28789127 original size:18 final size:19
Alignment explanation
Indices: 28789092--28789130 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
28789082 ATCGAGTTTC
**
28789092 ATTCATTTTATCGGGAATT
1 ATTCATTTTATCAAGAATT
28789111 ATTCA-TTTATCAAGAATT
1 ATTCATTTTATCAAGAATT
28789129 AT
1 AT
28789131 CGGATATGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (19 bp):
ATTCATTTTATCAAGAATT
Found at i:28791776 original size:21 final size:21
Alignment explanation
Indices: 28791750--28791794 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
28791740 GATATTTATA
* *
28791750 TTTCTTTAC-ATTTTGTATAAT
1 TTTC-TTACGATTTTATAAAAT
28791771 TTTCTTACGATTTTATAAAAT
1 TTTCTTACGATTTTATAAAAT
28791792 TTT
1 TTT
28791795 ATAAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.27, C:0.09, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTCTTACGATTTTATAAAAT
Found at i:28791795 original size:10 final size:9
Alignment explanation
Indices: 28791780--28791859 Score: 56
Period size: 10 Copynumber: 8.6 Consensus size: 9
28791770 TTTTCTTACG
28791780 ATTTTATAAA
1 ATTTTAT-AA
28791790 ATTTTATAA
1 ATTTTATAA
* *
28791799 ATTTTTTAT
1 ATTTTATAA
*
28791808 ATTTCTATAT
1 ATTT-TATAA
28791818 ATTTTATAA
1 ATTTTATAA
*
28791827 CTTGTTACT-A
1 ATT-TTA-TAA
*
28791837 TTTTTATAAA
1 ATTTTAT-AA
28791847 ATTTTAT-A
1 ATTTTATAA
28791855 ATTTT
1 ATTTT
28791860 TTTTATTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
8 7 0.12
9 22 0.38
10 28 0.48
11 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (9 bp):
ATTTTATAA
Found at i:28791802 original size:19 final size:18
Alignment explanation
Indices: 28791780--28791859 Score: 65
Period size: 19 Copynumber: 4.3 Consensus size: 18
28791770 TTTTCTTACG
28791780 ATTTTATAAAATTTTATAA
1 ATTTTATAAAATTTTAT-A
* *
28791799 ATTTT-TTATATTTCTATA
1 ATTTTATAAAATTT-TATA
*
28791817 TATTTTAT-AACTTGTTACTA
1 -ATTTTATAAAATT-TTA-TA
*
28791837 TTTTTATAAAATTTTATA
1 ATTTTATAAAATTTTATA
28791855 ATTTT
1 ATTTT
28791860 TTTTATTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
18 13 0.27
19 27 0.56
20 8 0.17
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (18 bp):
ATTTTATAAAATTTTATA
Found at i:28791860 original size:19 final size:17
Alignment explanation
Indices: 28791781--28791905 Score: 56
Period size: 19 Copynumber: 6.8 Consensus size: 17
28791771 TTTCTTACGA
28791781 TTTTATAAAATTTTATAAAT
1 TTTTAT-AAATTTTAT--AT
*
28791801 TTTT-TATATTTCTATAT
1 TTTTATAAATTT-TATAT
*
28791818 ATTTTATAACTTGTTACTAT
1 -TTTTATAAATT-TTA-TAT
28791838 TTTTATAAAATTTTATAATT
1 TTTTAT-AAATTTTAT-A-T
* **
28791858 TTTTTTATTTTTTATGAT
1 TTTTATAAATTTTAT-AT
* * *
28791876 TTATATATATTCTA-AT
1 TTTTATAAATTTTATAT
28791892 TTTTAATAAATTTT
1 TTTT-ATAAATTTT
28791906 TAATATTGAA
Statistics
Matches: 81, Mismatches: 15, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
16 5 0.06
17 9 0.11
18 21 0.26
19 28 0.35
20 18 0.22
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (17 bp):
TTTTATAAATTTTATAT
Found at i:28791986 original size:35 final size:35
Alignment explanation
Indices: 28791866--28791986 Score: 82
Period size: 35 Copynumber: 3.4 Consensus size: 35
28791856 TTTTTTTTAT
* * * *
28791866 TTTTTATGATTTATATATATTCTAATTTTTAATAA
1 TTTTTATAATTTTTATTTATTTTAATTTTTAATAA
* ** * **
28791901 ATTTT-TAATATTGAATTTTTTATTAAAATTTAATAA
1 TTTTTATAAT-TTTTATTTATT-TTAATTTTTAATAA
* ** * *
28791937 TATTTATAGCTTTTATTTATTTTAATTTTTTATAT
1 TTTTTATAATTTTTATTTATTTTAATTTTTAATAA
28791972 TTTTTATAATTTTTA
1 TTTTTATAATTTTTA
28791987 ATAAAAGCAA
Statistics
Matches: 60, Mismatches: 23, Indels: 6
0.67 0.26 0.07
Matches are distributed among these distances:
34 3 0.05
35 33 0.55
36 22 0.37
37 2 0.03
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (35 bp):
TTTTTATAATTTTTATTTATTTTAATTTTTAATAA
Found at i:28792214 original size:89 final size:87
Alignment explanation
Indices: 28791999--28792213 Score: 249
Period size: 89 Copynumber: 2.4 Consensus size: 87
28791989 AAAAGCAAGG
* * *
28791999 GCTTAATTGCTTTTTTGAAAA-ATTTTG-AGGATCTTTTTGATGTATTTTGAAAGTTCAAGTACC
1 GCTTAATTGCTTTTTTGAAAATA-TTTGAAGG-TCTTTTTGATGCACTTTAAAAGTTCAAGTACC
* * * *
28792062 CAATTGAGTGCAAAAAAATGTAGG
64 CAAATGAGTGAAAAAAAAAGTAGA
* *
28792086 GACTTAATTGCTTTTTTAAAAAATGTTTGAAGGTCTTTTTGATGCACTTTAAAAGTTCAAGTACC
1 G-CTTAATTGCTTTTTT-GAAAATATTTGAAGGTCTTTTTGATGCACTTTAAAAGTTCAAGTACC
*
28792151 GAAATGAGTGAAAAAAAAAAGTAGAA
64 CAAATGAGTG-AAAAAAAAAGTAG-A
28792177 GCTTAATTG-TATTTTTGAAAATATTTGAAGG-CTTTTT
1 GCTTAATTGCT-TTTTTGAAAATATTTGAAGGTCTTTTT
28792214 TCACCCCTAA
Statistics
Matches: 109, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
87 1 0.01
88 21 0.19
89 59 0.54
90 27 0.25
91 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (87 bp):
GCTTAATTGCTTTTTTGAAAATATTTGAAGGTCTTTTTGATGCACTTTAAAAGTTCAAGTACCCA
AATGAGTGAAAAAAAAAGTAGA
Found at i:28796645 original size:16 final size:15
Alignment explanation
Indices: 28796624--28796653 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28796614 TTAAGCTTTT
28796624 AAGAATAAATGAAGAA
1 AAGAATAAAT-AAGAA
28796640 AAGAATAAATAAGA
1 AAGAATAAATAAGA
28796654 GACAAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (15 bp):
AAGAATAAATAAGAA
Found at i:28797294 original size:16 final size:16
Alignment explanation
Indices: 28797257--28797298 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28797247 TTAATCATAT
*
28797257 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
28797273 TT-AAATATATTATAA
1 TTAAAATATATTATAA
28797288 TTAAAATATAT
1 TTAAAATATAT
28797299 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:28797305 original size:14 final size:15
Alignment explanation
Indices: 28797266--28797307 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28797256 TTTAAACATA
*
28797266 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28797281 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
28797295 A-TATAATTTAATA
1 ATTATAATTAAATA
28797308 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:28797358 original size:61 final size:60
Alignment explanation
Indices: 28797286--28797475 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 60
28797276 AATATATTAT
* *
28797286 AATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCA
1 AATTATAATATATAATTTAATAAAATTCTTAA-AATTAATATTCTTATATAAATTTACTCA
* * * * * * * **
28797347 AATCATAATATATGATACT-ATAAAA-T-AT-AAATTAACATAATTATTAT-TAAATATATTGT
1 AATTATAATATATAAT-TTAATAAAATTCTTAAAATT-A-AT-ATTCTTATATAAATTTACTCA
*
28797406 AATTAAAATATATAATTTAATAAAATTCTTAAAAATTAATATTCTTATATAAATTTACTCA
1 AATTATAATATATAATTTAATAAAATTCTT-AAAATTAATATTCTTATATAAATTTACTCA
28797467 AATTATAAT
1 AATTATAAT
28797476 GTATGATACT
Statistics
Matches: 97, Mismatches: 22, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
57 4 0.04
58 3 0.03
59 29 0.30
60 16 0.16
61 38 0.39
62 2 0.02
63 5 0.05
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (60 bp):
AATTATAATATATAATTTAATAAAATTCTTAAAATTAATATTCTTATATAAATTTACTCA
Found at i:28797475 original size:120 final size:120
Alignment explanation
Indices: 28797260--28797544 Score: 516
Period size: 120 Copynumber: 2.4 Consensus size: 120
28797250 ATCATATTTA
*
28797260 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAAAATTAA
*
28797325 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATAAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
*
28797380 AACATAATTATTATTAAATATATTGTAATTAAAATATATAATTTAATAAAATTCTTAAAAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAAAATTAA
* *
28797445 TATTCTTATATAAATTTACTCAAATTATAATGTATGATACTATAAAATATAAATT
66 TATTCTTATATAAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
*
28797500 AACATATTTATTATTAAATATATTATAATTAAAATATATAATTTA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTA
28797545 TTATTAAATA
Statistics
Matches: 158, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 158 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAAAATTAA
TATTCTTATATAAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:28797530 original size:30 final size:33
Alignment explanation
Indices: 28797501--28797564 Score: 85
Period size: 35 Copynumber: 1.9 Consensus size: 33
28797491 ATATAAATTA
*
28797501 ACAT-ATTTATTATTAAATATATTATAATTAAAAT
1 ACATAATTTATTATTAAATATATTACAATT--AAT
*
28797535 ATATAATTTATTATTAAATATATTACAATT
1 ACATAATTTATTATTAAATATATTACAATT
28797565 TAAAATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
34 3 0.11
35 24 0.89
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (33 bp):
ACATAATTTATTATTAAATATATTACAATTAAT
Found at i:28797534 original size:16 final size:16
Alignment explanation
Indices: 28797496--28797587 Score: 59
Period size: 15 Copynumber: 5.8 Consensus size: 16
28797486 ATAAAATATA
*
28797496 AATTAACATAT-TTAT
1 AATTAAAATATATTAT
*
28797511 TATT-AAATATATTAT
1 AATTAAAATATATTAT
*
28797526 AATTAAAATATATAATT
1 AATTAAAATATATTA-T
* *
28797543 TATTATTAAATATATTAC
1 AATTA--AAATATATTAT
28797561 AATTTAAAAT-TATTA-
1 AA-TTAAAATATATTAT
28797576 ACATT-AAATATA
1 A-ATTAAAATATA
28797588 ATTTAATAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
14 9 0.15
15 15 0.25
16 15 0.25
17 9 0.15
18 1 0.02
19 12 0.20
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTAAAATATATTAT
Found at i:28800811 original size:13 final size:13
Alignment explanation
Indices: 28800793--28800818 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28800783 TTCTTTTGAG
28800793 TTCAAAAATAATT
1 TTCAAAAATAATT
28800806 TTCAAAAATAATT
1 TTCAAAAATAATT
28800819 CTGATTTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
TTCAAAAATAATT
Found at i:28802692 original size:43 final size:43
Alignment explanation
Indices: 28802626--28802710 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
28802616 GAAATCGATT
*
28802626 AACTCAAACAAATAATGCAATACAGGCAAGAATCGAAACAAAG
1 AACTCAAACAAATAATGCAATACAGGCAAGAACCGAAACAAAG
*
28802669 AACTGAAACAAATAATGCAATACAGGCAAGAACCGAAACAAA
1 AACTCAAACAAATAATGCAATACAGGCAAGAACCGAAACAAA
28802711 CTATTTAGCC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.56, C:0.19, G:0.14, T:0.11
Consensus pattern (43 bp):
AACTCAAACAAATAATGCAATACAGGCAAGAACCGAAACAAAG
Found at i:28818641 original size:19 final size:19
Alignment explanation
Indices: 28818600--28818641 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
28818590 ACAATATTAT
* *
28818600 TATGTGGTGAACTATTAAT
1 TATGTGGTGAACTACTAAA
28818619 TATGTGGTGTAA-TACTAAA
1 TATGTGGTG-AACTACTAAA
28818638 TATG
1 TATG
28818642 CACTTGGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.40
Consensus pattern (19 bp):
TATGTGGTGAACTACTAAA
Found at i:28819636 original size:24 final size:24
Alignment explanation
Indices: 28819609--28819657 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
28819599 TGTGTTAGGA
28819609 AAATTTACTAATTTAATAAGTATG
1 AAATTTACTAATTTAATAAGTATG
28819633 AAATTTACTAATTTAATAAGTATG
1 AAATTTACTAATTTAATAAGTATG
28819657 A
1 A
28819658 TTTCATGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (24 bp):
AAATTTACTAATTTAATAAGTATG
Found at i:28820418 original size:14 final size:14
Alignment explanation
Indices: 28820397--28820437 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
28820387 TTTTTCCAAA
*
28820397 AAAAATCATTTTCT
1 AAAAATCATTTTCC
*
28820411 AGAAATCATTTTCC
1 AAAAATCATTTTCC
*
28820425 AAAAATTATTTTC
1 AAAAATCATTTTC
28820438 AATGAAACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.41, C:0.15, G:0.02, T:0.41
Consensus pattern (14 bp):
AAAAATCATTTTCC
Found at i:28821087 original size:29 final size:29
Alignment explanation
Indices: 28821054--28821122 Score: 104
Period size: 28 Copynumber: 2.4 Consensus size: 29
28821044 CGAGTTGTTT
* * *
28821054 TCTCATTTTCTCCCAACCTTTTTTTCTTC
1 TCTCATTTTCTCCCAAACATATTTTCTTC
28821083 TCTCATTTTCT-CCAAACATATTTTCTTC
1 TCTCATTTTCTCCCAAACATATTTTCTTC
28821111 TCTCATTTTCTC
1 TCTCATTTTCTC
28821123 TCAAGCACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 25 0.69
29 11 0.31
ACGTcount: A:0.14, C:0.32, G:0.00, T:0.54
Consensus pattern (29 bp):
TCTCATTTTCTCCCAAACATATTTTCTTC
Found at i:28822570 original size:79 final size:79
Alignment explanation
Indices: 28822461--28822690 Score: 302
Period size: 79 Copynumber: 2.9 Consensus size: 79
28822451 TACGCCTCCG
* * * * *
28822461 TGTTACTCTGTTGATGAAGAATATGT--GATATCTGATTATGTTAGATTGATTGTTACTGGTTTT
1 TGTTACTTTGTTGAT-AAGGA-ATGTACGATATCTGAATATGTTAGATTGATTGTTACTGATTCT
*
28822524 GGTTTATAATCCTCTA
64 GATTTATAATCCTCTA
*
28822540 TGTTACTTTGTTGATAAGGAATGTACGATATCTGAATATGTTAGATTAATTGTTACTGATTCTGA
1 TGTTACTTTGTTGATAAGGAATGTACGATATCTGAATATGTTAGATTGATTGTTACTGATTCTGA
* *
28822605 TTTATGATCTTCTA
66 TTTATAATCCTCTA
* * * * *
28822619 CGTTACTTTGTTGATGAGGAATATACGATATCTGAACATGTTAGATTGATTGTTACTGATTCTAA
1 TGTTACTTTGTTGATAAGGAATGTACGATATCTGAATATGTTAGATTGATTGTTACTGATTCTGA
28822684 TTTATAA
66 TTTATAA
28822691 CCGTGCATGT
Statistics
Matches: 133, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
77 4 0.03
78 4 0.03
79 125 0.94
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.45
Consensus pattern (79 bp):
TGTTACTTTGTTGATAAGGAATGTACGATATCTGAATATGTTAGATTGATTGTTACTGATTCTGA
TTTATAATCCTCTA
Found at i:28823510 original size:13 final size:13
Alignment explanation
Indices: 28823492--28823516 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28823482 TATGATTTGA
28823492 TCTTTTGGGTTTT
1 TCTTTTGGGTTTT
28823505 TCTTTTGGGTTT
1 TCTTTTGGGTTT
28823517 GTAATCTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.24, T:0.68
Consensus pattern (13 bp):
TCTTTTGGGTTTT
Found at i:28825925 original size:21 final size:21
Alignment explanation
Indices: 28825899--28825939 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
28825889 AAATGATCAA
28825899 GAATCGATACTTTATGCCAGG
1 GAATCGATACTTTATGCCAGG
28825920 GAATCGATACTTTATGCCAG
1 GAATCGATACTTTATGCCAG
28825940 AATTGATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (21 bp):
GAATCGATACTTTATGCCAGG
Found at i:28828300 original size:13 final size:13
Alignment explanation
Indices: 28828282--28828307 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28828272 CGAAATTATA
28828282 ATTATAATAATTT
1 ATTATAATAATTT
28828295 ATTATAATAATTT
1 ATTATAATAATTT
28828308 CGATAAACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATAATAATTT
Found at i:28830935 original size:11 final size:11
Alignment explanation
Indices: 28830919--28830945 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
28830909 TAACCATACA
28830919 TACTGAATATT
1 TACTGAATATT
28830930 TACTGAATATT
1 TACTGAATATT
28830941 TACTG
1 TACTG
28830946 TGGGACTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (11 bp):
TACTGAATATT
Found at i:28837937 original size:14 final size:14
Alignment explanation
Indices: 28837918--28837944 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28837908 ATATTTTAGG
28837918 GTTATGATATTCAA
1 GTTATGATATTCAA
28837932 GTTATGATATTCA
1 GTTATGATATTCA
28837945 CATTCTCCAA
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:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (14 bp):
GTTATGATATTCAA
Found at i:28844491 original size:25 final size:24
Alignment explanation
Indices: 28844390--28844515 Score: 127
Period size: 22 Copynumber: 5.3 Consensus size: 24
28844380 CACTAATGAA
* *
28844390 CAGAGAGCACTAAAGTGCTAT-A-
1 CAGAGAGCACCAACGTGCTATAAT
*
28844412 CAGAGAGCA-CAGATGTGCTA-AA-
1 CAGAGAGCACCA-ACGTGCTATAAT
** *
28844434 CAGAGAGCACTGACGTGCTAAAAT
1 CAGAGAGCACCAACGTGCTATAAT
*
28844458 CAGAGAGCACCAACGTGCTAGTAGT
1 CAGAGAGCACCAACGTGCTA-TAAT
28844483 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCT-ATAAT
28844508 CAGAGAGC
1 CAGAGAGC
28844516 GCGCTAAAGT
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
21 1 0.01
22 33 0.38
23 2 0.02
24 18 0.21
25 32 0.37
26 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.15
Consensus pattern (24 bp):
CAGAGAGCACCAACGTGCTATAAT
Found at i:28848373 original size:21 final size:20
Alignment explanation
Indices: 28848322--28848391 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 20
28848312 ATTCATAAAA
*
28848322 AAAATATAACCAAAAATCATT
1 AAAATATAA-AAAAAATCATT
28848343 ACAAATTATAAAAAAAATCATAT
1 A-AAA-TATAAAAAAAATCAT-T
**
28848366 AAAATATATTTAAAAATCATT
1 AAAATATA-AAAAAAATCATT
28848387 AAAAT
1 AAAAT
28848392 CATTAATGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
21 11 0.26
22 24 0.57
23 7 0.17
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATATAAAAAAAATCATT
Found at i:28852786 original size:20 final size:21
Alignment explanation
Indices: 28852757--28852795 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
28852747 GGACTAAATA
*
28852757 AAAAACATTTGGAAATTTTAG
1 AAAAACATTTGAAAATTTTAG
28852778 AAAAA-ATTTGAAAATTTT
1 AAAAACATTTGAAAATTTT
28852796 GGACTACAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (21 bp):
AAAAACATTTGAAAATTTTAG
Done.