Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 169 of 170
Found at i:50418126 original size:28 final size:28
Alignment explanation
Indices: 50418087--50418216 Score: 80
Period size: 26 Copynumber: 4.9 Consensus size: 28
50418077 TTGTTGAAAA
*
50418087 TATAACAA-ATATATATGTATATATAAAT
1 TATAA-AATATATATAAGTATATATAAAT
* *
50418115 TATAAAATATATGTACA-TATATGT--AT
1 TATAAAATATATATA-AGTATATATAAAT
* ** *
50418141 TATAAAATGTATATAAGTATACGTATAT
1 TATAAAATATATATAAGTATATATAAAT
* *
50418169 TTTAAAAT-TATA-AAGTATATACAAA-
1 TATAAAATATATATAAGTATATATAAAT
* *
50418194 -A-AAAATATATGTATGTATATATA
1 TATAAAATATATATAAGTATATATA
50418217 TAGGAGTTAT
Statistics
Matches: 80, Mismatches: 15, Indels: 17
0.71 0.13 0.15
Matches are distributed among these distances:
23 5 0.06
24 3 0.04
25 10 0.12
26 30 0.38
27 6 0.08
28 26 0.32
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (28 bp):
TATAAAATATATATAAGTATATATAAAT
Found at i:50418161 original size:26 final size:25
Alignment explanation
Indices: 50418087--50418189 Score: 75
Period size: 28 Copynumber: 3.9 Consensus size: 25
50418077 TTGTTGAAAA
* *
50418087 TATAACAAATATATATGTATATATAAAT
1 TATAA-AATTATATAAGTATATAT--AT
* *
50418115 TATAAAATATATGTACA-TATATGTAT
1 TATAAAAT-TATATA-AGTATATATAT
50418141 TATAAAATGTATATAAGTATACGTATAT
1 TATAAAAT-TATATAAGTATA--TATAT
*
50418169 TTTAAAATTATA-AAGTATATA
1 TATAAAATTATATAAGTATATA
50418190 CAAAAAAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
24 2 0.03
25 1 0.02
26 26 0.42
27 6 0.10
28 27 0.44
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.41
Consensus pattern (25 bp):
TATAAAATTATATAAGTATATATAT
Found at i:50418264 original size:58 final size:59
Alignment explanation
Indices: 50418202--50418312 Score: 172
Period size: 58 Copynumber: 1.9 Consensus size: 59
50418192 AAAAAAATAT
* *
50418202 ATGTATGTATATATA-TAGGAGTTATAGAATATAAAACACATATATAT-TATAAGAATGC
1 ATGTATATATATATATTA-AAGTTATAGAATATAAAACACATATATATGTATAAGAATGC
*
50418260 ATGTATATATATATATTAAAGTTATAGAATATAAAACACATATGTATGTATAA
1 ATGTATATATATATATTAAAGTTATAGAATATAAAACACATATATATGTATAA
50418313 ATATATAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
58 41 0.85
59 7 0.15
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.36
Consensus pattern (59 bp):
ATGTATATATATATATTAAAGTTATAGAATATAAAACACATATATATGTATAAGAATGC
Found at i:50418448 original size:20 final size:22
Alignment explanation
Indices: 50418397--50418448 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
50418387 AATTTTGAAT
*
50418397 AATAATACATGGTAAATTTATAC
1 AATAATA-ATGATAAATTTATAC
* *
50418420 AATATTAATGATAGATTTA-A-
1 AATAATAATGATAAATTTATAC
50418440 AATAATAAT
1 AATAATAAT
50418449 ATATTATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 8 0.32
21 1 0.04
22 10 0.40
23 6 0.24
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.37
Consensus pattern (22 bp):
AATAATAATGATAAATTTATAC
Found at i:50420031 original size:23 final size:24
Alignment explanation
Indices: 50419987--50420031 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
50419977 GAAAAAGGTT
*
50419987 TTCTTTTTTCCTTTTTCAATTGGG
1 TTCTTTTTTCCTTTTCCAATTGGG
*
50420011 TTCTTTTTT-CTTTTCCGATTG
1 TTCTTTTTTCCTTTTCCAATTG
50420032 CTCTTCTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.07, C:0.18, G:0.11, T:0.64
Consensus pattern (24 bp):
TTCTTTTTTCCTTTTCCAATTGGG
Found at i:50434670 original size:12 final size:12
Alignment explanation
Indices: 50434653--50434695 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
50434643 TTAATCGAGC
50434653 TTGAGCTAAGTA
1 TTGAGCTAAGTA
50434665 TTGAGCTCAA--A
1 TTGAGCT-AAGTA
50434676 CTTGAGCTAAGTA
1 -TTGAGCTAAGTA
50434689 TTGAGCT
1 TTGAGCT
50434696 CAAACTTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
11 3 0.11
12 21 0.78
13 3 0.11
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (12 bp):
TTGAGCTAAGTA
Found at i:50434684 original size:24 final size:24
Alignment explanation
Indices: 50434652--50434707 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
50434642 TTTAATCGAG
50434652 CTTGAGCTAAGTATTGAGCTCAAA
1 CTTGAGCTAAGTATTGAGCTCAAA
50434676 CTTGAGCTAAGTATTGAGCTCAAA
1 CTTGAGCTAAGTATTGAGCTCAAA
50434700 CTTGAGCT
1 CTTGAGCT
50434708 TGAGCTTGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (24 bp):
CTTGAGCTAAGTATTGAGCTCAAA
Found at i:50434704 original size:12 final size:12
Alignment explanation
Indices: 50434665--50434707 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
50434655 GAGCTAAGTA
50434665 TTGAGCTCAAAC
1 TTGAGCTCAAAC
50434677 TTGAGCT-AAGTA-
1 TTGAGCTCAA--AC
50434689 TTGAGCTCAAAC
1 TTGAGCTCAAAC
50434701 TTGAGCT
1 TTGAGCT
50434708 TGAGCTTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
11 3 0.11
12 21 0.78
13 3 0.11
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (12 bp):
TTGAGCTCAAAC
Found at i:50441677 original size:20 final size:20
Alignment explanation
Indices: 50441652--50441691 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
50441642 TACGAAAAAT
* *
50441652 TAAAATTTTTGACTCTTAAC
1 TAAAATTTTTAACTATTAAC
50441672 TAAAATTTTTAACTATTAAC
1 TAAAATTTTTAACTATTAAC
50441692 ATCACATAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (20 bp):
TAAAATTTTTAACTATTAAC
Found at i:50444604 original size:12 final size:12
Alignment explanation
Indices: 50444583--50444619 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
50444573 GTTATTTCCA
50444583 TTTCCACCGCCG
1 TTTCCACCGCCG
*
50444595 TTTGCACCGCCG
1 TTTCCACCGCCG
*
50444607 TTTCCACCACCG
1 TTTCCACCGCCG
50444619 T
1 T
50444620 CATCTTCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.11, C:0.46, G:0.16, T:0.27
Consensus pattern (12 bp):
TTTCCACCGCCG
Found at i:50452145 original size:42 final size:42
Alignment explanation
Indices: 50452086--50452172 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
50452076 TGCTTACATG
50452086 TGGCATCCCATGTCTCATACGTAAGCTCTCTCACCTAAATAA
1 TGGCATCCCATGTCTCATACGTAAGCTCTCTCACCTAAATAA
50452128 TGGCATCCCATGTCTCATACGTAAGCTCTCTCACCTAAATAA
1 TGGCATCCCATGTCTCATACGTAAGCTCTCTCACCTAAATAA
50452170 TGG
1 TGG
50452173 AAGCATATGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.29
Consensus pattern (42 bp):
TGGCATCCCATGTCTCATACGTAAGCTCTCTCACCTAAATAA
Found at i:50452963 original size:28 final size:28
Alignment explanation
Indices: 50452909--50452964 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
50452899 CTTCTCATAA
*
50452909 TCTCATCCTCTCTTCACAACGATTCTCT
1 TCTCATCCTCTCTTCACAACGACTCTCT
*
50452937 TCTCATCCTCTAC-TCACAACGGCTCTCT
1 TCTCATCCTCT-CTTCACAACGACTCTCT
50452965 ACCCTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.18, C:0.41, G:0.05, T:0.36
Consensus pattern (28 bp):
TCTCATCCTCTCTTCACAACGACTCTCT
Found at i:50460687 original size:19 final size:19
Alignment explanation
Indices: 50460661--50460703 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
50460651 AACATCATGA
*
50460661 TATATATATTATATATTTTAT
1 TATATA-ATTACATA-TTTAT
50460682 TATATAATTACATATTTAT
1 TATATAATTACATATTTAT
50460701 TAT
1 TAT
50460704 TTTATTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 7 0.33
21 6 0.29
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATAATTACATATTTAT
Found at i:50463839 original size:18 final size:18
Alignment explanation
Indices: 50463816--50463860 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
50463806 TTTTATATAT
*
50463816 TTCATGTTTGTTTTGTGA
1 TTCATGTTTGTTTTATGA
50463834 TTCATGTTTGTTTTATGA
1 TTCATGTTTGTTTTATGA
50463852 TTCATGTTT
1 TTCATGTTT
50463861 AGGGTTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.13, C:0.07, G:0.18, T:0.62
Consensus pattern (18 bp):
TTCATGTTTGTTTTATGA
Found at i:50466806 original size:23 final size:23
Alignment explanation
Indices: 50466776--50466825 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
50466766 TTTTTCCTAC
50466776 TTATAATTGTAATTGATTTTGAT
1 TTATAATTGTAATTGATTTTGAT
50466799 TTATAATTGTAATTGATTTTGAT
1 TTATAATTGTAATTGATTTTGAT
50466822 TTAT
1 TTAT
50466826 GAATGATTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (23 bp):
TTATAATTGTAATTGATTTTGAT
Found at i:50468709 original size:39 final size:39
Alignment explanation
Indices: 50468664--50468744 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
50468654 TGCCAGCTTG
50468664 TTATTTTCACATATACTAACTAAAAATCTAGTTAATGAA
1 TTATTTTCACATATACTAACTAAAAATCTAGTTAATGAA
*
50468703 TTATTTTCACATATACTAACTAAAAATCTAGTTACTGAA
1 TTATTTTCACATATACTAACTAAAAATCTAGTTAATGAA
50468742 TTA
1 TTA
50468745 ACGACTATCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.40
Consensus pattern (39 bp):
TTATTTTCACATATACTAACTAAAAATCTAGTTAATGAA
Found at i:50469196 original size:15 final size:16
Alignment explanation
Indices: 50469176--50469207 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
50469166 GTTATTATCG
50469176 TATTTAA-TATATATT
1 TATTTAATTATATATT
50469191 TATTTAATTATATATT
1 TATTTAATTATATATT
50469207 T
1 T
50469208 GTATGGCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTAATTATATATT
Found at i:50471046 original size:6 final size:6
Alignment explanation
Indices: 50471035--50471060 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
50471025 ATTAATGATA
50471035 AATTTT AATTTT AATTTT AATTTT AA
1 AATTTT AATTTT AATTTT AATTTT AA
50471061 AATATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
AATTTT
Found at i:50471178 original size:22 final size:22
Alignment explanation
Indices: 50471128--50471178 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
50471118 AAACATACAT
*
50471128 ATTTAATTATTTATATTTATTA
1 ATTTAATTATATATATTTATTA
*
50471150 ATATAATTA-ATATGATTTATTA
1 ATTTAATTATATAT-ATTTATTA
*
50471172 TTTTAAT
1 ATTTAAT
50471179 AAGTTATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
ATTTAATTATATATATTTATTA
Found at i:50476609 original size:3 final size:3
Alignment explanation
Indices: 50476603--50476628 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
50476593 ACACCAGACC
50476603 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
50476629 AGTTAACCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:50477750 original size:16 final size:16
Alignment explanation
Indices: 50477729--50477766 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
50477719 CATTTGTTAC
*
50477729 TTGAATTTAAAATAAT
1 TTGAATCTAAAATAAT
50477745 TTGAATCTAAAATAAT
1 TTGAATCTAAAATAAT
*
50477761 TCGAAT
1 TTGAAT
50477767 GAGTAACCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (16 bp):
TTGAATCTAAAATAAT
Found at i:50480221 original size:29 final size:29
Alignment explanation
Indices: 50480147--50480221 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
50480137 TTTTTCTTTT
* * *
50480147 TTGGTCACCCAACTATGAAAAGTTAGAAA
1 TTGGTCACTCAACTATTAAAAGTTACAAA
*
50480176 ATGGTCA-TCCAACTATTAAAAGTTACAAA
1 TTGGTCACT-CAACTATTAAAAGTTACAAA
50480205 TTGGTCACTCAACTATT
1 TTGGTCACTCAACTATT
50480222 CAATTTTGTC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 38 0.97
30 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (29 bp):
TTGGTCACTCAACTATTAAAAGTTACAAA
Found at i:50481031 original size:5 final size:5
Alignment explanation
Indices: 50481003--50481041 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
50480993 GTTCACTTAA
*
50481003 AATTT AGATTT AA-TT AATTC AATTT AATTT AATTT AATT
1 AATTT A-ATTT AATTT AATTT AATTT AATTT AATTT AATT
50481042 ATTAAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 4 0.13
5 21 0.70
6 5 0.17
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (5 bp):
AATTT
Found at i:50481050 original size:24 final size:25
Alignment explanation
Indices: 50481003--50481052 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
50480993 GTTCACTTAA
*
50481003 AATTTAGATTTAATTAATTCAATTT
1 AATTTAGATTTAATTAATTAAATTT
*
50481028 AATTTA-ATTTAATT-ATTAAAATT
1 AATTTAGATTTAATTAATTAAATTT
50481051 AA
1 AA
50481053 ATAATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 9 0.39
24 8 0.35
25 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (25 bp):
AATTTAGATTTAATTAATTAAATTT
Found at i:50491480 original size:154 final size:147
Alignment explanation
Indices: 50491174--50491729 Score: 516
Period size: 148 Copynumber: 3.7 Consensus size: 147
50491164 TATTTAATTG
* ** ** *
50491174 TTAACTTTATGTAATCAAATCAATTCGA-CTTGATTTTAAATTCCAATTAGAATTAACATATATA
1 TTAACTTTATATAATCAAATCAATTTAATC-CAATTTTAAATTCCAATTAGAATTAA-AAATATA
* * * * *
50491238 GTTATCAGAAATTGAGAAAGTAGGTAGTAGGAAGTAATG-TTTCGGAACCCGAATTGGGATTAGT
64 GTTATC----A---A-AAAGTAGGCAGCAAGAAGCAATGTTTTCGGAACCCGAGTTGGGA-TAGT
**
50491302 TTGGATTCAAATTGAACAAGTTTTTAAT
120 TTAAATTCAAATTGAACAAGTTTTTAAT
* * * *
50491330 CATTAACTTTATAGAATCCAATCAGTTTAATCCAATTTTAACATTCCAATTAGAATCAATAAATA
1 --TTAACTTTATATAATCAAATCAATTTAATCCAATTTTAA-ATTCCAATTAGAATTAA-AAATA
* * *
50491395 TAGTTATCAAAAAGTAGGCAGTAAGAAACAATGTTTTCGGAAACCCCGAGTTGGGATCGGTTTAA
62 TAGTTATCAAAAAGTAGGCAGCAAGAAGCAATGTTTTCGG-AA-CCCGAGTTGGGAT-AGTTTAA
*
50491460 ATTCAAATTGAACAAATTTTTAATT
124 ATTCAAATTGAACAAGTTTTTAA-T
* * *
50491485 GTTAACTTTATATAATCAAATCAATTT-ATCCAACTTTAAATTCCAATTATAATTAACAA-AT--
1 -TTAACTTTATATAATCAAATCAATTTAATCCAATTTTAAATTCCAATTAGAATTAAAAATATAG
* * * * * * * *
50491546 TTATCAAAAAGTAGGCAACATGAAGCAATGTTTTTGGAACTCAAGTTAGGATAATTTAAATTTAA
65 TTATCAAAAAGTAGGCAGCAAGAAGCAATGTTTTCGGAACCCGAGTTGGGATAGTTTAAATTCAA
50491611 ATTGAACAAGTTTTTAAT
130 ATTGAACAAGTTTTTAAT
* * **
50491629 TTAACTTTATATAATCAAATTAATTCAAT-CAATTTTTAAATTTTAATTAGAATTAACAAATATA
1 TTAACTTTATATAATCAAATCAATTTAATCCAA-TTTTAAATTCCAATTAGAATTAA-AAATATA
*
50491693 GTTATTAAAAA-TGAGGCAGCAAGAAGCAATGTTTTCG
64 GTTATCAAAAAGT-AGGCAGCAAGAAGCAATGTTTTCG
50491730 AAACTCGGGG
Statistics
Matches: 333, Mismatches: 51, Indels: 38
0.79 0.12 0.09
Matches are distributed among these distances:
143 27 0.08
144 22 0.07
145 28 0.08
146 12 0.04
147 3 0.01
148 62 0.19
150 2 0.01
151 21 0.06
152 22 0.07
153 14 0.04
154 60 0.18
155 2 0.01
158 29 0.09
159 29 0.09
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (147 bp):
TTAACTTTATATAATCAAATCAATTTAATCCAATTTTAAATTCCAATTAGAATTAAAAATATAGT
TATCAAAAAGTAGGCAGCAAGAAGCAATGTTTTCGGAACCCGAGTTGGGATAGTTTAAATTCAAA
TTGAACAAGTTTTTAAT
Found at i:50496598 original size:5 final size:6
Alignment explanation
Indices: 50496581--50496606 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
50496571 AATATATTCA
50496581 TATTTT TATTTT TATTTT TATTTT TA
1 TATTTT TATTTT TATTTT TATTTT TA
50496607 AAAATATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:50504026 original size:23 final size:23
Alignment explanation
Indices: 50503996--50504041 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
50503986 AGTGCCCCAA
*
50503996 TTTTTTGATGTCTTATTGGTGGG
1 TTTTTTGATGCCTTATTGGTGGG
50504019 TTTTTTGATGCCTTATTGGTGGG
1 TTTTTTGATGCCTTATTGGTGGG
50504042 GTTATCATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.09, C:0.07, G:0.30, T:0.54
Consensus pattern (23 bp):
TTTTTTGATGCCTTATTGGTGGG
Found at i:50507855 original size:20 final size:20
Alignment explanation
Indices: 50507832--50507874 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
50507822 TATTTTACAA
50507832 TTAACTCT-AAATTCTAAATT
1 TTAACTCTAAAATT-TAAATT
* *
50507852 TTAATTTTAAAATTTAAATT
1 TTAACTCTAAAATTTAAATT
50507872 TTA
1 TTA
50507875 CATTTACCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAACTCTAAAATTTAAATT
Found at i:50512380 original size:14 final size:14
Alignment explanation
Indices: 50512361--50512387 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
50512351 AAATAAAATA
50512361 TACATATATATATG
1 TACATATATATATG
50512375 TACATATATATAT
1 TACATATATATAT
50512388 AACTTAGAAT
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:0.07, G:0.04, T:0.44
Consensus pattern (14 bp):
TACATATATATATG
Found at i:50525919 original size:24 final size:23
Alignment explanation
Indices: 50525875--50525920 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
50525865 TTTATTTACG
* * *
50525875 TTTTATTATTTTTATTTTTATTC
1 TTTTATAATTTTTAATATTATTC
50525898 TTTTATAATGTTTTAATATTATT
1 TTTTATAAT-TTTTAATATTATT
50525921 TGTTTGTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTTATAATTTTTAATATTATTC
Found at i:50525934 original size:12 final size:13
Alignment explanation
Indices: 50525917--50525945 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
50525907 GTTTTAATAT
50525917 TATTTG-TTTGTA
1 TATTTGTTTTGTA
50525929 TATTTGTTTTGTA
1 TATTTGTTTTGTA
50525942 TATT
1 TATT
50525946 ATGGGTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (13 bp):
TATTTGTTTTGTA
Found at i:50532380 original size:27 final size:27
Alignment explanation
Indices: 50532342--50532396 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
50532332 TTGATTTGAT
*
50532342 AGTTCTTTTTGGTTTATATTCCGATTA
1 AGTTCTTTTTGGTTTATACTCCGATTA
50532369 AGTTCTTTTTGGTTTATACTCCGATTA
1 AGTTCTTTTTGGTTTATACTCCGATTA
50532396 A
1 A
50532397 TTTGGTGGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.20, C:0.13, G:0.15, T:0.53
Consensus pattern (27 bp):
AGTTCTTTTTGGTTTATACTCCGATTA
Found at i:50536574 original size:36 final size:36
Alignment explanation
Indices: 50536534--50536613 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 36
50536524 ATACATATAA
*
50536534 ATATATATACT-TATAAAAATAAAAAT-ATGTATATGT
1 ATATATATA-TATATAAAAAGAAAAATGA-GTATATGT
* *
50536570 ATATAGATATATATAAAAAGAAATATGAGTATATGT
1 ATATATATATATATAAAAAGAAAAATGAGTATATGT
50536606 ATATATAT
1 ATATATAT
50536614 TAAACAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 1 0.03
36 36 0.95
37 1 0.03
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.38
Consensus pattern (36 bp):
ATATATATATATATAAAAAGAAAAATGAGTATATGT
Found at i:50536755 original size:3 final size:3
Alignment explanation
Indices: 50536744--50536813 Score: 97
Period size: 3 Copynumber: 23.3 Consensus size: 3
50536734 CAATAATACC
* * *
50536744 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
50536789 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
50536814 GCAAAAGTAC
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
2 1 0.02
3 58 0.98
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:50537889 original size:31 final size:29
Alignment explanation
Indices: 50537854--50537922 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
50537844 TTGTTTGTAA
**
50537854 TTGGGCTGAGGGTCTATTTTGGGTCTTGGGT
1 TTGGGCTGAGGGT-TATTTT-GGTAATGGGT
* *
50537885 TTGGGCTGGTGGGTTGTTTTGGTAATGGGT
1 TTGGGCT-GAGGGTTATTTTGGTAATGGGT
50537915 TTGGGCTG
1 TTGGGCTG
50537923 GGTTAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 1 0.03
30 15 0.45
31 12 0.36
32 5 0.15
ACGTcount: A:0.06, C:0.07, G:0.45, T:0.42
Consensus pattern (29 bp):
TTGGGCTGAGGGTTATTTTGGTAATGGGT
Found at i:50538997 original size:12 final size:12
Alignment explanation
Indices: 50538980--50539004 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50538970 TATTTTATAA
50538980 TTTTTAACCTAT
1 TTTTTAACCTAT
50538992 TTTTTAACCTAT
1 TTTTTAACCTAT
50539004 T
1 T
50539005 CTCTAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTTAACCTAT
Found at i:50549586 original size:15 final size:15
Alignment explanation
Indices: 50549566--50549594 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
50549556 GTTCTAAGTC
50549566 TGTGTCTGGTTAATT
1 TGTGTCTGGTTAATT
50549581 TGTGTCTGGTTAAT
1 TGTGTCTGGTTAAT
50549595 AAGGTTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.28, T:0.52
Consensus pattern (15 bp):
TGTGTCTGGTTAATT
Found at i:50555157 original size:12 final size:13
Alignment explanation
Indices: 50555140--50555171 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
50555130 TTTGGAGTTG
50555140 GTGGTTCAAT-AT
1 GTGGTTCAATCAT
50555152 GTGGTTC-ATCAT
1 GTGGTTCAATCAT
50555164 GTGGTTCA
1 GTGGTTCA
50555172 GTATTTGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 16 0.89
ACGTcount: A:0.19, C:0.12, G:0.28, T:0.41
Consensus pattern (13 bp):
GTGGTTCAATCAT
Found at i:50555191 original size:33 final size:33
Alignment explanation
Indices: 50555152--50555220 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
50555142 GGTTCAATAT
50555152 GTGGTTC-ATCATGTGGTTCAGTATTTGTGGGTG
1 GTGGTTCAAT-ATGTGGTTCAGTATTTGTGGGTG
50555185 GTGGTTCAATATGTGGTTCAGTATTTGTGGGTG
1 GTGGTTCAATATGTGGTTCAGTATTTGTGGGTG
50555218 GTG
1 GTG
50555221 ATGGTGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 33 0.94
34 2 0.06
ACGTcount: A:0.13, C:0.07, G:0.38, T:0.42
Consensus pattern (33 bp):
GTGGTTCAATATGTGGTTCAGTATTTGTGGGTG
Found at i:50561309 original size:27 final size:27
Alignment explanation
Indices: 50561277--50561328 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
50561267 AACTTTTAAA
*
50561277 GGATTAAA-TCACAATTTTATTATTTTG
1 GGATTAAAGT-ACAATTTTATCATTTTG
*
50561304 GGATTAAAGTATAATTTTATCATTT
1 GGATTAAAGTACAATTTTATCATTT
50561329 ACTAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.48
Consensus pattern (27 bp):
GGATTAAAGTACAATTTTATCATTTTG
Found at i:50564990 original size:146 final size:143
Alignment explanation
Indices: 50564725--50564994 Score: 398
Period size: 146 Copynumber: 1.9 Consensus size: 143
50564715 GCTTTTGCTC
* * *
50564725 AAATAATAAAATTGATAGAGTAAACTTTAAGGTTTATTAGGTATAAATCCATATGTTTTTTTAGA
1 AAATAATAAAATTGAAAGAGTAAACTTTAAGGTTTACTAGATATAAATCCATATGTTTTTTTAGA
* *
50564790 TTTATTAAAATATAAAAAGACATAAATATCCTCAAAATAATATTTATTGATTTATAAAATGAAAC
66 TTTATCAAAATATAAAAAGACATAAATACCCTCAAAATAATATTTATTGATTTATAAAATGAAAC
50564855 GAGACTTTTATTA
131 GAGACTTTTATTA
*
50564868 AAATAATAAAATTGAAAGAGTAAACTTTAAGGTTTCCTAGAT-TCAAATCCATATGCTTTTTTTC
1 AAATAATAAAATTGAAAGAGTAAACTTTAAGGTTTACTAGATAT-AAATCCATATG--TTTTTT-
* * * * *
50564932 TCGATTTATCGAAATATAGAAAGGCATAAATACCCTCAAAATAATATTTATTGGTTTATAAAA
62 TAGATTTATCAAAATATAAAAAGACATAAATACCCTCAAAATAATATTTATTGATTTATAAAA
50564995 CGAATGTGTT
Statistics
Matches: 112, Mismatches: 11, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
142 1 0.01
143 49 0.44
145 6 0.05
146 56 0.50
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (143 bp):
AAATAATAAAATTGAAAGAGTAAACTTTAAGGTTTACTAGATATAAATCCATATGTTTTTTTAGA
TTTATCAAAATATAAAAAGACATAAATACCCTCAAAATAATATTTATTGATTTATAAAATGAAAC
GAGACTTTTATTA
Found at i:50567010 original size:28 final size:29
Alignment explanation
Indices: 50566985--50567060 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
50566975 CTCTTTCAAA
*
50566985 TATTTTAACATTTTTAATTTATTTCAACT
1 TATTTTAACATTTTTAATTTATTTCAATT
* * *
50567014 TATTTCAATATTGTTAATTTA-TTCAATTT
1 TATTTTAACATTTTTAATTTATTTCAA-TT
50567043 TATTTTAACA-TTTTAATT
1 TATTTTAACATTTTTAATT
50567061 CATATATTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 12 0.31
29 27 0.69
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.59
Consensus pattern (29 bp):
TATTTTAACATTTTTAATTTATTTCAATT
Found at i:50568155 original size:31 final size:31
Alignment explanation
Indices: 50568102--50568160 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
50568092 ACAATATGGT
* *
50568102 CATTGAATTATTTAAAAATTTTCATTTAAGC
1 CATTGAACTATTCAAAAATTTTCATTTAAGC
*
50568133 CATTGAACTATTCAAAATTTTTCATTTA
1 CATTGAACTATTCAAAAATTTTCATTTA
50568161 GGTCACCGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (31 bp):
CATTGAACTATTCAAAAATTTTCATTTAAGC
Found at i:50576393 original size:6 final size:6
Alignment explanation
Indices: 50576382--50576559 Score: 356
Period size: 6 Copynumber: 29.7 Consensus size: 6
50576372 GGCCAGTAGT
50576382 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
50576430 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
50576478 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
50576526 TACACA TACACA TACACA TACACA TACACA TACA
1 TACACA TACACA TACACA TACACA TACACA TACA
50576560 TTATATAACT
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 172 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (6 bp):
TACACA
Found at i:50576619 original size:55 final size:56
Alignment explanation
Indices: 50576542--50576668 Score: 229
Period size: 56 Copynumber: 2.3 Consensus size: 56
50576532 TACACATACA
*
50576542 CATACACATACACATACATTATATAACTTAAGG-CCAGTAGTTACACAAATAAGAG
1 CATACACATACACATACATTATATAACTTAAGGAACAGTAGTTACACAAATAAGAG
50576597 CATACACATACACATACATTATATAACTTAAGGAACAGTAGTTACACAAATAAGAG
1 CATACACATACACATACATTATATAACTTAAGGAACAGTAGTTACACAAATAAGAG
*
50576653 AATACACATACACATA
1 CATACACATACACATA
50576669 GACATACATC
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
55 33 0.48
56 36 0.52
ACGTcount: A:0.48, C:0.20, G:0.09, T:0.23
Consensus pattern (56 bp):
CATACACATACACATACATTATATAACTTAAGGAACAGTAGTTACACAAATAAGAG
Found at i:50581002 original size:21 final size:21
Alignment explanation
Indices: 50580976--50581016 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
50580966 ATCTGCTCAA
* *
50580976 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
50580997 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
50581017 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:50584646 original size:6 final size:6
Alignment explanation
Indices: 50584638--50584695 Score: 107
Period size: 6 Copynumber: 9.7 Consensus size: 6
50584628 TGTATATACA
*
50584638 TGTATA TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
50584686 TGTATG TGTA
1 TGTATG TGTA
50584696 CAAGTACGTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (6 bp):
TGTATG
Found at i:50584914 original size:145 final size:145
Alignment explanation
Indices: 50584680--50584974 Score: 473
Period size: 145 Copynumber: 2.0 Consensus size: 145
50584670 TATGTGTATG
* **
50584680 TGTATGTGTATGTGTACAAGTACGTACATCGCAATGCAACATAATTCTAATTATGTCATGGACAT
1 TGTATGTGTATGTATACAAGTACGTACATCGCAATGCAACATAATTCTAACCATGTCATGGACAT
* * * *
50584745 GAAGGATATGAGGGATAGATGATTCTTTTCGTAAATGTGTTGTTGTTGGTGGTATGATTTGCAGC
66 GAAGGATATGAGGGATAGATGATTCTTTTCCTAAATGTGCTATTGTTGATGGTATGATTTGCAGC
50584810 CAAGTGAATCCTATA
131 CAAGTGAATCCTATA
* * * * *
50584825 TGTATTTGTATGTATATATGTACGTATATTGCAATGCAACATAATTCTAACCATGTCATGGACAT
1 TGTATGTGTATGTATACAAGTACGTACATCGCAATGCAACATAATTCTAACCATGTCATGGACAT
50584890 GAAGGATATGAGGGATAGATGATTCTTTTCCTAAATGTGCTATTGTTGATGGTATGATTTGCAGC
66 GAAGGATATGAGGGATAGATGATTCTTTTCCTAAATGTGCTATTGTTGATGGTATGATTTGCAGC
*
50584955 CATGTGAATCCTATA
131 CAAGTGAATCCTATA
50584970 TGTAT
1 TGTAT
50584975 ATGTGTACGT
Statistics
Matches: 137, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
145 137 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (145 bp):
TGTATGTGTATGTATACAAGTACGTACATCGCAATGCAACATAATTCTAACCATGTCATGGACAT
GAAGGATATGAGGGATAGATGATTCTTTTCCTAAATGTGCTATTGTTGATGGTATGATTTGCAGC
CAAGTGAATCCTATA
Found at i:50587549 original size:16 final size:17
Alignment explanation
Indices: 50587528--50587560 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
50587518 AATGTTTTGG
*
50587528 TTATTT-ATTTTCTTTT
1 TTATTTGATTTTATTTT
50587544 TTATTTGATTTTATTTT
1 TTATTTGATTTTATTTT
50587561 ATGTGAATTT
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:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (17 bp):
TTATTTGATTTTATTTT
Found at i:50589884 original size:29 final size:28
Alignment explanation
Indices: 50589826--50589884 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
50589816 TCGTTCTTAT
* * *
50589826 TTTGGTCATCCTAAATTTTTTTTGTTAA
1 TTTGGTCACCCTAAATTTTTTTTATAAA
50589854 TTTGGTCACCCTAAATTTTTTTTATCAAA
1 TTTGGTCACCCTAAATTTTTTTTAT-AAA
50589883 TT
1 TT
50589885 AATCACTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.24, C:0.14, G:0.08, T:0.54
Consensus pattern (28 bp):
TTTGGTCACCCTAAATTTTTTTTATAAA
Found at i:50589890 original size:28 final size:28
Alignment explanation
Indices: 50589835--50589890 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
50589825 TTTTGGTCAT
* * * **
50589835 CCTAAATTTTTTTTGTTAATTTGGTCAC
1 CCTAAATTTTTTTTATCAAATTAATCAC
50589863 CCTAAATTTTTTTTATCAAATTAATCAC
1 CCTAAATTTTTTTTATCAAATTAATCAC
50589891 TCCACCATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.50
Consensus pattern (28 bp):
CCTAAATTTTTTTTATCAAATTAATCAC
Found at i:50594674 original size:24 final size:24
Alignment explanation
Indices: 50594617--50594678 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
50594607 GCACCATATA
* *
50594617 CACCAGCACCTCCACCACCAGAAC
1 CACCTGCACCACCACCACCAGAAC
*
50594641 CACCTCCACCACCACCACCATG-AC
1 CACCTGCACCACCACCACCA-GAAC
*
50594665 CGCCTGCACCACCA
1 CACCTGCACCACCA
50594679 AAACCTCCTC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 31 0.97
25 1 0.03
ACGTcount: A:0.29, C:0.56, G:0.08, T:0.06
Consensus pattern (24 bp):
CACCTGCACCACCACCACCAGAAC
Found at i:50594732 original size:30 final size:30
Alignment explanation
Indices: 50594698--50594776 Score: 108
Period size: 30 Copynumber: 2.6 Consensus size: 30
50594688 CCAGCTCCTT
50594698 CTCCACCACCATATCCACCTGCA-TGTGCCC
1 CTCCACCACCATATCCACCTGCACT-TGCCC
* *
50594728 CTCCACCACCATATCCTCCTGCACTTGCTC
1 CTCCACCACCATATCCACCTGCACTTGCCC
50594758 CTCCACCACCACT-TCCACC
1 CTCCACCACCA-TATCCACC
50594777 ACCACCTCCA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 42 0.95
31 2 0.05
ACGTcount: A:0.19, C:0.53, G:0.06, T:0.22
Consensus pattern (30 bp):
CTCCACCACCATATCCACCTGCACTTGCCC
Found at i:50594774 original size:12 final size:12
Alignment explanation
Indices: 50594757--50594786 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
50594747 TGCACTTGCT
50594757 CCTCCACCACCA
1 CCTCCACCACCA
*
50594769 CTTCCACCACCA
1 CCTCCACCACCA
50594781 CCTCCA
1 CCTCCA
50594787 TGTCCACCGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.23, C:0.63, G:0.00, T:0.13
Consensus pattern (12 bp):
CCTCCACCACCA
Found at i:50595100 original size:135 final size:135
Alignment explanation
Indices: 50594823--50595728 Score: 1447
Period size: 135 Copynumber: 6.7 Consensus size: 135
50594813 AGCACCACCA
* * *
50594823 GCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACCATATCCAGAAGCTCCACCACCATATCC
1 GCACCACCAGCTCCACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCACCATATCC
50594888 ACCTGCACTAGCTCCGCCGCCACCACTACCACCACCACCACCACCTCCATGTCCACCTGCTCCTC
66 ACCTGCACTAGCTCCGCCGCCACCACT------ACCACCACCACCTCCATGTCCACCTGCTCCTC
*
50594953 CATACCCCCCG
125 CATACCCGCCG
*
50594964 GCACCACCAGTTCCACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCACCATATCC
1 GCACCACCAGCTCCACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCACCATATCC
*
50595029 ACCTGCACTAGCTCCACCGCCACCACTACCACCACCACCTCCATGTCCACCTGCTCCTCCATACC
66 ACCTGCACTAGCTCCGCCGCCACCACTACCACCACCACCTCCATGTCCACCTGCTCCTCCATACC
50595094 CGCCG
131 CGCCG
* * * *
50595099 GCACCACCAGCTCCGCCTCCTTCGCCACCTCCACCACCATATCCAGAAGGTCCACCACCGTATCC
1 GCACCACCAGCTCCACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCACCATATCC
* * * *
50595164 ACCTGTACTAGCTCCGCCGCCACCACTACCACCACCACCTCCATGTCCACCTGCACCACCA-GCT
66 ACCTGCACTAGCTCCGCCGCCACCACTACCACCACCACCTCCATGTCCACCTGCTCCTCCATAC-
*
50595228 CCACCG
130 CCGCCG
* *
50595234 GCACCACCAGCTCCACCTCCTTCACCACCCCCACCGCCATATCCAGAAGCTCCACCACCATATCC
1 GCACCACCAGCTCCACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCACCATATCC
* * *
50595299 ACCTGCACTAGCTCCGCCACTACCACCACCACCACCACCTCCATGTCCACCTGCTCCTCCATACC
66 ACCTGCACTAGCTCCGCCGCCACCACTACCACCACCACCTCCATGTCCACCTGCTCCTCCATACC
*
50595364 CCCCG
131 CGCCG
*
50595369 GCACCACCAGTTCCACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCACCATATCC
1 GCACCACCAGCTCCACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCACCATATCC
*
50595434 ACCTGCACTAGCTCCACCGCCACCACTACCACCACCACCTCCATGTCCACCTGCTCCTCCATACC
66 ACCTGCACTAGCTCCGCCGCCACCACTACCACCACCACCTCCATGTCCACCTGCTCCTCCATACC
50595499 CGCCG
131 CGCCG
50595504 GCACCACCAGCTCCACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCACCATATCC
1 GCACCACCAGCTCCACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCACCATATCC
* *
50595569 ACCTGCACTAGCTCCGCCACCACCACTACCACCACCACCTCCAAT-TCCACCCGCTCCTCCATAC
66 ACCTGCACTAGCTCCGCCGCCACCACTACCACCACCACCTCC-ATGTCCACCTGCTCCTCCATAC
50595633 CCGCCG
130 CCGCCG
* * * *
50595639 GCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACCATATCCAGAAGCTCCACCGCCATATCC
1 GCACCACCAGCTCCACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCACCATATCC
* *
50595704 ACCTGCACTAGCTCCACCACCACCA
66 ACCTGCACTAGCTCCGCCGCCACCA
50595729 TTGCCACCTC
Statistics
Matches: 714, Mismatches: 48, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
134 1 0.00
135 623 0.87
136 3 0.00
141 87 0.12
ACGTcount: A:0.22, C:0.53, G:0.09, T:0.15
Consensus pattern (135 bp):
GCACCACCAGCTCCACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCACCATATCC
ACCTGCACTAGCTCCGCCGCCACCACTACCACCACCACCTCCATGTCCACCTGCTCCTCCATACC
CGCCG
Found at i:50595220 original size:18 final size:18
Alignment explanation
Indices: 50595209--50595251 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
50595199 CACCTCCATG
50595209 TCCACCTGCACCACCAGC
1 TCCACCTGCACCACCAGC
*
50595227 TCCACCGGCACCACCAGC
1 TCCACCTGCACCACCAGC
50595245 TCCACCT
1 TCCACCT
50595252 CCTTCACCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.56, G:0.12, T:0.12
Consensus pattern (18 bp):
TCCACCTGCACCACCAGC
Found at i:50595417 original size:405 final size:404
Alignment explanation
Indices: 50594728--50595728 Score: 1608
Period size: 405 Copynumber: 2.4 Consensus size: 404
50594718 GCATGTGCCC
* * * *
50594728 CTCCACCACCATATCCTCCTGCACTTGCTCCTCCACCACCACTTCCACCACCACCTCCATGTCCA
1 CTCCACCACCATATCCACCTGCACTAGCTCCGCCACCACCACTACCACCACCACCTCCATGTCCA
* * *
50594793 CCGGCTCCTCCATACCCGCCAGCACCACCAGCACCACCAGCTCCGCCTCCTTCACCACCTCCACC
66 ------CCTGC--A-CCACCAGC-CCACCGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACC
50594858 ACCATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCGCCGCCACCACTACCACCAC
121 ACCATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCT---CCG---CCACTACCACCAC
50594923 CACCACCACCTCCATGTCCACCTGCTCCTCCATACCCCCCGGCACCACCAGTTCCACCTCCTTCG
180 CACCACCACCTCCATGTCCACCTGCTCCTCCATACCCCCCGGCACCACCAGTTCCACCTCCTTCG
50594988 CCACCTCCACCGCCATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCACCGCCACC
245 CCACCTCCACCGCCATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCACCGCCACC
*
50595053 ACTACCACCACCACCTCCATGTCCACCTGCTCCTCCATACCCGCCGGCACCACCAGCTCCGCCTC
310 ACTACCACCACCACCTCCATGTCCACCTGCTCCTCCATACCCGCCGGCACCACCAGCTCCACCTC
50595118 CTTCGCCACCTCCACCACCATATCCAGAAG
375 CTTCGCCACCTCCACCACCATATCCAGAAG
* * * *
50595148 GTCCACCACCGTATCCACCTGTACTAGCTCCGCCGCCACCACTACCACCACCACCTCCATGTCCA
1 CTCCACCACCATATCCACCTGCACTAGCTCCGCCACCACCACTACCACCACCACCTCCATGTCCA
* * *
50595213 CCTGCACCACCAGCTCCACCGGCACCACCAGCTCCACCTCCTTCACCACCCCCACCGCCATATCC
66 CCTGCACCACCAGC-CCACCGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACCATATCC
50595278 AGAAGCTCCACCACCATATCCACCTGCACTAGCTCCGCCACTACCACCACCACCACCACCTCCAT
130 AGAAGCTCCACCACCATATCCACCTGCACTAGCTCCGCCACTACCACCACCACCACCACCTCCAT
50595343 GTCCACCTGCTCCTCCATACCCCCCGGCACCACCAGTTCCACCTCCTTCGCCACCTCCACCGCCA
195 GTCCACCTGCTCCTCCATACCCCCCGGCACCACCAGTTCCACCTCCTTCGCCACCTCCACCGCCA
50595408 TATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCACCGCCACCACTACCACCACCACC
260 TATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCACCGCCACCACTACCACCACCACC
50595473 TCCATGTCCACCTGCTCCTCCATACCCGCCGGCACCACCAGCTCCACCTCCTTCGCCACCTCCAC
325 TCCATGTCCACCTGCTCCTCCATACCCGCCGGCACCACCAGCTCCACCTCCTTCGCCACCTCCAC
*
50595538 CGCCATATCCAGAAG
390 CACCATATCCAGAAG
50595553 CTCCACCACCATATCCACCTGCACTAGCTCCGCCACCACCACTACCACCACCACCTCCAAT-TCC
1 CTCCACCACCATATCCACCTGCACTAGCTCCGCCACCACCACTACCACCACCACCTCC-ATGTCC
* * * * *
50595617 ACCCGCTCCTCCATACCCGCCGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACCATATC
65 ACCTGCACCACCA-GCCCACCGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACCATATC
* * *
50595682 CAGAAGCTCCACCGCCATATCCACCTGCACTAGCTCCACCACCACCA
129 CAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCGCCACTACCA
50595729 TTGCCACCTC
Statistics
Matches: 547, Mismatches: 32, Indels: 19
0.91 0.05 0.03
Matches are distributed among these distances:
405 392 0.72
406 3 0.01
408 3 0.01
411 87 0.16
412 1 0.00
414 4 0.01
420 57 0.10
ACGTcount: A:0.22, C:0.53, G:0.09, T:0.15
Consensus pattern (404 bp):
CTCCACCACCATATCCACCTGCACTAGCTCCGCCACCACCACTACCACCACCACCTCCATGTCCA
CCTGCACCACCAGCCCACCGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACCATATCCA
GAAGCTCCACCACCATATCCACCTGCACTAGCTCCGCCACTACCACCACCACCACCACCTCCATG
TCCACCTGCTCCTCCATACCCCCCGGCACCACCAGTTCCACCTCCTTCGCCACCTCCACCGCCAT
ATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCACCGCCACCACTACCACCACCACCT
CCATGTCCACCTGCTCCTCCATACCCGCCGGCACCACCAGCTCCACCTCCTTCGCCACCTCCACC
ACCATATCCAGAAG
Found at i:50597672 original size:19 final size:20
Alignment explanation
Indices: 50597637--50597674 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
50597627 AAAATGAATT
50597637 AAATAAAAATTTCATATATA
1 AAATAAAAATTTCATATATA
*
50597657 AAATTAAAATTT-ATATAT
1 AAATAAAAATTTCATATAT
50597675 GACATTGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATAAAAATTTCATATATA
Found at i:50603342 original size:26 final size:26
Alignment explanation
Indices: 50603310--50603364 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
50603300 TGACAATTGT
*
50603310 TTACTTAATCAAAT-AATATAATATTA
1 TTACTTAA-AAAATCAATATAATATTA
*
50603336 TTACTTAAAAAATCAATTTAATATTA
1 TTACTTAAAAAATCAATATAATATTA
50603362 TTA
1 TTA
50603365 TACATTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (26 bp):
TTACTTAAAAAATCAATATAATATTA
Found at i:50603954 original size:3 final size:3
Alignment explanation
Indices: 50603948--50603975 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
50603938 ACCAGAGCCG
50603948 CCA CCA CCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA C
50603976 TAACACCTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:50604092 original size:18 final size:18
Alignment explanation
Indices: 50604071--50604145 Score: 53
Period size: 18 Copynumber: 4.2 Consensus size: 18
50604061 ACTCCCGCCA
*
50604071 CCACCACCACCTCCATGT
1 CCACCACCACCTCCATAT
* * *
50604089 CCACTAGCTCCTCCATAT
1 CCACCACCACCTCCATAT
* * *
50604107 CCAGCTCCACCTCCTTCA-
1 CCACCACCACCTCCAT-AT
* *
50604125 CCACCTCCACTTCCATAT
1 CCACCACCACCTCCATAT
50604143 CCA
1 CCA
50604146 GAAGCTCCTC
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
17 1 0.02
18 40 0.95
19 1 0.02
ACGTcount: A:0.21, C:0.52, G:0.04, T:0.23
Consensus pattern (18 bp):
CCACCACCACCTCCATAT
Found at i:50604291 original size:123 final size:117
Alignment explanation
Indices: 50604164--50604537 Score: 408
Period size: 123 Copynumber: 3.0 Consensus size: 117
50604154 TCCACCATAT
* * * ** *
50604164 CCACCAGCACTAGCTCCTCCACCACCATTGCCACCACCACCTCCGTGTCCATTAGCTCCTTCATA
1 CCACCTGCACTAGCTCCTCCTCCACCATTGCCACCACCACCTCCATGTCCACCAGCTCCTCCATA
*
50604229 GCCGCCACCACTACCAGCTCCACCTCCGTT-GCCACCTCCACTGCCATACCCAGAAGCA
66 ------ACCACCACCAGCTCCACCTCC-TTCGCCACCTCCACTGCCATACCCAGAAGCA
*
50604287 CCACCTGCACTAGCTCCGCCTCCACCATTACCGCCACCAGCACCACCTCCATGTCCACCAGCTCC
1 CCACCTGCACTAGCTCCTCCTCCACCATT---GCCA-C--CACCACCTCCATGTCCACCAGCTCC
*
50604352 TCCATAACCACCACCAGCTCCACCTCCTTCGCCACCTCCATTGCCATACCCAGAAGCA
60 TCCATAACCACCACCAGCTCCACCTCCTTCGCCACCTCCACTGCCATACCCAGAAGCA
* * *
50604410 CCACCTGCACTAGCTCCTCCTCCACCACTGCCACCACCAGCACCACCTCCTTGTCCACCGGCTCC
1 CCACCTGCACTAGCTCCTCCTCCACCATTG---CCA-C--CACCACCTCCATGTCCACCAGCTCC
* * ** * *
50604475 TCCATAACCACCACCAGCTCCACCTCCTTCACCAGCTCCACCACCATATCCAGAAGCT
60 TCCATAACCACCACCAGCTCCACCTCCTTCGCCACCTCCACTGCCATACCCAGAAGCA
50604533 CCACC
1 CCACC
50604538 ACCATGTCCA
Statistics
Matches: 221, Mismatches: 20, Indels: 20
0.85 0.08 0.08
Matches are distributed among these distances:
120 1 0.00
122 2 0.01
123 186 0.84
126 4 0.02
127 1 0.00
129 27 0.12
ACGTcount: A:0.22, C:0.51, G:0.10, T:0.17
Consensus pattern (117 bp):
CCACCTGCACTAGCTCCTCCTCCACCATTGCCACCACCACCTCCATGTCCACCAGCTCCTCCATA
ACCACCACCAGCTCCACCTCCTTCGCCACCTCCACTGCCATACCCAGAAGCA
Found at i:50604366 original size:42 final size:40
Alignment explanation
Indices: 50604306--50604513 Score: 128
Period size: 42 Copynumber: 5.1 Consensus size: 40
50604296 CTAGCTCCGC
* *
50604306 CTCCACCATTACCGCCACCAGCACCACCTCCATGTCCACCAG
1 CTCCTCCA-TACCACCACCAGCACCACCTCC-TGTCCACCAG
* * *
50604348 CTCCTCCATAACCACCACCAGCTCCACCTCCT-T-CGCCAC
1 CTCCTCCAT-ACCACCACCAGCACCACCTCCTGTCCACCAG
** *
50604387 CTCCATTGCCATA-C-CCAGAAGCACCACCTGCACTAGCTCC-TC--
1 CTCC--T-CCATACCACCACCAGCACCACCT-C-CT-G-TCCACCAG
* * *
50604429 CTCCACCACTGCCACCACCAGCACCACCTCCTTGTCCACCGG
1 CTCCTCCA-TACCACCACCAGCACCACCTCC-TGTCCACCAG
*
50604471 CTCCTCCATAACCACCACCAGCTCCACCTCCT-T-CACCAG
1 CTCCTCCAT-ACCACCACCAGCACCACCTCCTGTCCACCAG
50604510 CTCC
1 CTCC
50604514 ACCACCATAT
Statistics
Matches: 130, Mismatches: 18, Indels: 39
0.70 0.10 0.21
Matches are distributed among these distances:
39 35 0.27
40 8 0.06
41 11 0.08
42 73 0.56
44 2 0.02
45 1 0.01
ACGTcount: A:0.22, C:0.53, G:0.09, T:0.17
Consensus pattern (40 bp):
CTCCTCCATACCACCACCAGCACCACCTCCTGTCCACCAG
Found at i:50604527 original size:18 final size:18
Alignment explanation
Indices: 50604488--50604547 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
50604478 ATAACCACCA
* *
50604488 CCAGCTCCACCTCCTTCA-
1 CCAGCTCCACCACCAT-AT
50604506 CCAGCTCCACCACCATAT
1 CCAGCTCCACCACCATAT
*
50604524 CCAGAAGCTCCACCACCATGT
1 CC---AGCTCCACCACCATAT
50604545 CCA
1 CCA
50604548 CCTACACTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
17 1 0.03
18 17 0.49
21 17 0.49
ACGTcount: A:0.25, C:0.50, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAGCTCCACCACCATAT
Found at i:50604532 original size:21 final size:21
Alignment explanation
Indices: 50604508--50604547 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
50604498 CTCCTTCACC
50604508 AGCTCCACCACCATATCCAGA
1 AGCTCCACCACCATATCCAGA
*
50604529 AGCTCCACCACCATGTCCA
1 AGCTCCACCACCATATCCA
50604548 CCTACACTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.45, G:0.10, T:0.15
Consensus pattern (21 bp):
AGCTCCACCACCATATCCAGA
Found at i:50604567 original size:123 final size:123
Alignment explanation
Indices: 50604053--50604688 Score: 397
Period size: 123 Copynumber: 5.1 Consensus size: 123
50604043 TCCTGCACCG
* * * * *
50604053 CCTCCACCACTCCCGCCACCACCACCACCTCCATGTCCACTAGCTCCTCCAT----A--TCCAGC
1 CCTCCACCACCCCCACCACCAGCACCACCTCCATGTCCACCAGCTCCTCCATAACCACCACCAGC
** * * *
50604112 TCCACCTCCTTCACCACCTCCACTTCCATATCCAGAAGCTCCTCCACCA-TA--TCCA
66 TCCACCTCCTTCACCACCTCCACCACCATACCCAGAAGCACCACCACCACTAGCTCCA
** * * ** *
50604167 CCAGCACTAGCTCCTCCACCACCATTGCCACCACCACCTCCGTGTCCATTAGCTCCTTCATAGCC
1 CCTCCACCA-C-CC-CCACCACCA--G----CACCACCTCCATGTCCACCAGCTCCTCCATA---
* * ** **
50604232 GCCACCACTACCAGCTCCACCTCCGTT-GCCACCTCCACTGCCATACCCAGAAGCACCACCTGCA
54 ---ACCACCACCAGCTCCACCTCC-TTCACCACCTCCACCACCATACCCAGAAGCACCACCACCA
*
50604296 CTAGCTCCG
115 CTAGCTCCA
*** *
50604305 CCTCCACCATTACCGCCACCAGCACCACCTCCATGTCCACCAGCTCCTCCATAACCACCACCAGC
1 CCTCCACCACCCCCACCACCAGCACCACCTCCATGTCCACCAGCTCCTCCATAACCACCACCAGC
* *** ** *
50604370 TCCACCTCCTTCGCCACCTCCATTGCCATACCCAGAAGCACCACCTGCACTAGCTCCT
66 TCCACCTCCTTCACCACCTCCACCACCATACCCAGAAGCACCACCACCACTAGCTCCA
** * *
50604428 CCTCCACCACTGCCACCACCAGCACCACCTCCTTGTCCACCGGCTCCTCCATAACCACCACCAGC
1 CCTCCACCACCCCCACCACCAGCACCACCTCCATGTCCACCAGCTCCTCCATAACCACCACCAGC
* * *
50604493 TCCACCTCCTTCACCAGCTCCACCACCATATCCAGAAGCTCCACCACCATGTCCACCTACACTAC
66 TCCACCTCCTTCACCACCTCCACCACCATACCCAGAAG---CACCACCA---CCA-CTA-GCT-C
*
50604558 CT
122 CA
* * * * * * *
50604560 CCCCCACCACCACTACCACTACCACCACCACCTCCATGTCCACCGGCTTCTCCATACCCACTACC
1 CCTCCACCACC-C--CCACCACCAGCACCACCTCCATGTCCACCAGCTCCTCCATAACCACCACC
** * *
50604625 A-CT--A---CCAGCACCACCTCCACTACCATATCCAGAAGCACCACCTA-CACTAGCTCCA
63 AGCTCCACCTCCTTCACCACCTCCACCACCATACCCAGAAGCACCACC-ACCACTAGCTCCA
*
50604680 CCACCACCA
1 CCTCCACCA
50604689 TTGCCACCTC
Statistics
Matches: 421, Mismatches: 62, Indels: 72
0.76 0.11 0.13
Matches are distributed among these distances:
114 6 0.01
115 1 0.00
116 1 0.00
117 8 0.02
120 10 0.02
121 2 0.00
122 5 0.01
123 185 0.44
126 14 0.03
127 1 0.00
129 56 0.13
130 3 0.01
131 2 0.00
132 13 0.03
133 2 0.00
134 2 0.00
135 97 0.23
136 4 0.01
138 9 0.02
ACGTcount: A:0.23, C:0.51, G:0.08, T:0.17
Consensus pattern (123 bp):
CCTCCACCACCCCCACCACCAGCACCACCTCCATGTCCACCAGCTCCTCCATAACCACCACCAGC
TCCACCTCCTTCACCACCTCCACCACCATACCCAGAAGCACCACCACCACTAGCTCCA
Found at i:50604573 original size:18 final size:18
Alignment explanation
Indices: 50604552--50604590 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
50604542 TGTCCACCTA
* *
50604552 CACTACCTCCCCCACCAC
1 CACTACCACCACCACCAC
*
50604570 CACTACCACTACCACCAC
1 CACTACCACCACCACCAC
50604588 CAC
1 CAC
50604591 CTCCATGTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.62, G:0.00, T:0.10
Consensus pattern (18 bp):
CACTACCACCACCACCAC
Found at i:50604663 original size:24 final size:24
Alignment explanation
Indices: 50604617--50604663 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
50604607 TTCTCCATAC
*
50604617 CCACTACCACTACCAGCACCACCT
1 CCACTACCACTACCAGAACCACCT
*
50604641 CCACTACCA-TATCCAGAAGCACC
1 CCACTACCACTA-CCAGAACCACC
50604664 ACCTACACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.32, C:0.49, G:0.06, T:0.13
Consensus pattern (24 bp):
CCACTACCACTACCAGAACCACCT
Found at i:50614509 original size:38 final size:37
Alignment explanation
Indices: 50614452--50614527 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 37
50614442 TATATTTTTA
*
50614452 TTTTTATTTTTTAATTTTAAAATACTTTTAAAATATT
1 TTTTTATTTTTTAATTTTAAAATAATTTTAAAATATT
* **
50614489 TTTTTATTTTTTTATTTTTAAAATAATTTTTTAATATT
1 TTTTTA-TTTTTTAATTTTAAAATAATTTTAAAATATT
50614527 T
1 T
50614528 ATTAAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
37 6 0.18
38 28 0.82
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (37 bp):
TTTTTATTTTTTAATTTTAAAATAATTTTAAAATATT
Found at i:50614517 original size:20 final size:22
Alignment explanation
Indices: 50614494--50614534 Score: 59
Period size: 20 Copynumber: 1.9 Consensus size: 22
50614484 ATATTTTTTT
50614494 ATTTTTT-TATTT-TTAAAATA
1 ATTTTTTATATTTATTAAAATA
50614514 ATTTTTTAATATTTATTAAAA
1 ATTTTTT-ATATTTATTAAAA
50614535 AATGGGTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
22 5 0.28
23 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTTTTATATTTATTAAAATA
Found at i:50619762 original size:5 final size:5
Alignment explanation
Indices: 50619752--50619779 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
50619742 ATTAGCTATT
50619752 GTGGA GTGGA GTGGA GTGGA GTGGA GTG
1 GTGGA GTGGA GTGGA GTGGA GTGGA GTG
50619780 ATAAGAGTTT
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:0.18, C:0.00, G:0.61, T:0.21
Consensus pattern (5 bp):
GTGGA
Found at i:50629232 original size:15 final size:15
Alignment explanation
Indices: 50629212--50629258 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
50629202 TGGTTACTAG
*
50629212 TAATAATAAGGTTAA
1 TAATAATAAGGATAA
*
50629227 TAATAATAATGATAA
1 TAATAATAAGGATAA
* *
50629242 TAATAATGATGATAA
1 TAATAATAAGGATAA
50629257 TA
1 TA
50629259 TATTAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (15 bp):
TAATAATAAGGATAA
Found at i:50629241 original size:12 final size:12
Alignment explanation
Indices: 50629226--50629258 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
50629216 AATAAGGTTA
50629226 ATAATAATAATG
1 ATAATAATAATG
50629238 ATAATAATAATG
1 ATAATAATAATG
*
50629250 ATGATAATA
1 ATAATAATA
50629259 TATTAAAATA
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:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (12 bp):
ATAATAATAATG
Found at i:50630943 original size:45 final size:42
Alignment explanation
Indices: 50630846--50630961 Score: 135
Period size: 45 Copynumber: 2.6 Consensus size: 42
50630836 TTTTAATCCA
* * *
50630846 CTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTG
1 CTCCACTGTAAC-TCAGGGAGATAAGATAGTGGCTTCAATCTG
*
50630889 CTCCGCTGTAATCTCAGGGAGATAAGAT-GCTCTGGCTTCAATCTG
1 CTCCACTGTAA-CTCAGGGAGATAAGATAG---TGGCTTCAATCTG
50630934 CTCCACTGTAACCTCAGGGAGATAAGAT
1 CTCCACTGTAA-CTCAGGGAGATAAGAT
50630962 CTGAAATTCT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
42 1 0.02
43 24 0.38
44 1 0.02
45 37 0.59
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (42 bp):
CTCCACTGTAACTCAGGGAGATAAGATAGTGGCTTCAATCTG
Found at i:50630997 original size:46 final size:45
Alignment explanation
Indices: 50630846--50631176 Score: 232
Period size: 46 Copynumber: 7.6 Consensus size: 45
50630836 TTTTAATCCA
* * *
50630846 CTCCACTGTAA-CTTCAGGGAGATAGGA--T-AGTGTCTTCGATCTG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTGAAT-TCTTTGATCTG
* * * **
50630889 CTCCGCTGTAATCTCAGGGAGATAAGATGCT--CTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGAT-CTGAAT-TCTTTGATCTG
* *
50630934 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTTGATCTG
* * * *
50630980 TTCCACTGTAATCTCAGGGAGATAAGACCTG-A---TGTGATCTT
1 CTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTTGATCTG
* * * *
50631021 CTCTACTGTAA-CTTCAGAGAGATAAGATC------CTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTGAATTCTTTGATCTG
* * * *
50631060 CTCCATTGTAATCTCAAGGAGATAGGAT-T-ACTATCTTTGATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTGAAT-TCTTTGATCTG
* *
50631104 CTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTTGATCTG
*
50631150 TTCCACTGTAATCTCAGGGAGATAAGA
1 CTCCACTGTAATCTCAGGGAGATAAGA
50631177 CCTGTATAAT
Statistics
Matches: 228, Mismatches: 41, Indels: 35
0.75 0.13 0.12
Matches are distributed among these distances:
39 26 0.11
40 2 0.01
41 29 0.13
43 23 0.10
44 36 0.16
45 38 0.17
46 71 0.31
47 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (45 bp):
CTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTTGATCTG
Found at i:50643346 original size:11 final size:11
Alignment explanation
Indices: 50643330--50643358 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
50643320 AAAGAAAATT
50643330 AAATAAATACA
1 AAATAAATACA
50643341 AAATAAATACA
1 AAATAAATACA
50643352 AAATAAA
1 AAATAAA
50643359 ATAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (11 bp):
AAATAAATACA
Found at i:50643927 original size:15 final size:15
Alignment explanation
Indices: 50643907--50643953 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
50643897 TGGTTACTAG
*
50643907 TAATAATAAGGTTAA
1 TAATAATAAGGATAA
*
50643922 TAATAATAATGATAA
1 TAATAATAAGGATAA
* *
50643937 TAATAATGATGATAA
1 TAATAATAAGGATAA
50643952 TA
1 TA
50643954 TATTAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (15 bp):
TAATAATAAGGATAA
Found at i:50643936 original size:12 final size:12
Alignment explanation
Indices: 50643921--50643953 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
50643911 AATAAGGTTA
50643921 ATAATAATAATG
1 ATAATAATAATG
50643933 ATAATAATAATG
1 ATAATAATAATG
*
50643945 ATGATAATA
1 ATAATAATA
50643954 TATTAAAATA
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:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (12 bp):
ATAATAATAATG
Found at i:50645724 original size:18 final size:19
Alignment explanation
Indices: 50645692--50645737 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
50645682 TTTAATTTTG
* * *
50645692 TATTATAAATTACATAGTA
1 TATTAGAAATAACATAATA
50645711 TA-TAGAAATAACATAATA
1 TATTAGAAATAACATAATA
50645729 TATTAGAAA
1 TATTAGAAA
50645738 AAAAAACAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (19 bp):
TATTAGAAATAACATAATA
Found at i:50651928 original size:19 final size:20
Alignment explanation
Indices: 50651904--50651945 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
50651894 TACTTTGATT
* *
50651904 ATATTATTTATT-TTTATTA
1 ATATTATTGATTCTTTAATA
50651923 ATATTATTGATTCTTTAATA
1 ATATTATTGATTCTTTAATA
50651943 ATA
1 ATA
50651946 AAAATTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
ATATTATTGATTCTTTAATA
Found at i:50665718 original size:27 final size:27
Alignment explanation
Indices: 50665651--50665721 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
50665641 CGGGTGGCGG
*
50665651 CTCATAGGGAGGCACCATTAAAAGTGC
1 CTCATAGGGAGGCGCCATTAAAAGTGC
*
50665678 CTCATAAGGAGGCGCCATTAAAAGTGC
1 CTCATAGGGAGGCGCCATTAAAAGTGC
50665705 CTCATAGGGAGGCGCCA
1 CTCATAGGGAGGCGCCA
50665722 ATGGGTAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.31, C:0.24, G:0.28, T:0.17
Consensus pattern (27 bp):
CTCATAGGGAGGCGCCATTAAAAGTGC
Found at i:50665775 original size:19 final size:19
Alignment explanation
Indices: 50665726--50666250 Score: 207
Period size: 19 Copynumber: 26.3 Consensus size: 19
50665716 GCGCCAATGG
*
50665726 GTAATTTTGTATGTATATT
1 GTAATTTTGTATGAATATT
50665745 GTAACTTTTTGTATGAATATT
1 GTAA--TTTTGTATGAATATT
*
50665766 ATAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
50665785 GTAATTATTTTAT-AATTAATTTT
1 GTAATT-TTGTATGAA-T-A--TT
* * *
50665808 GT-ATTTATAGTTTTGGAT-TA
1 GTAATTT-T-G-TATGAATATT
*
50665828 GT-ATTTTGTATGAATAGT
1 GTAATTTTGTATGAATATT
50665846 GTAATTTTTTGTATGAATATT
1 GTAA--TTTTGTATGAATATT
*
50665867 GTAATTTTTTATGAATATT
1 GTAATTTTGTATGAATATT
*
50665886 GTAATTTTTTATGAATATT
1 GTAATTTTGTATGAATATT
*
50665905 GTAATTATT-T-T--ATAAT
1 GTAATT-TTGTATGAATATT
* *
50665921 -TAATTTTGTATTTATAGTTTTT
1 GTAATTTTGTA-TGA-A--TATT
50665943 GATTAGTATTTTGTATGAATATT
1 G--TA--ATTTTGTATGAATATT
*
50665966 GTAATTTTG--T-AATTTT
1 GTAATTTTGTATGAATATT
* *
50665982 GTATGAATATTG--T-AATTTT
1 G--T-AATTTTGTATGAATATT
50666001 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
50666020 GTAATTATT-T-T--ATAAT
1 GTAATT-TTGTATGAATATT
* *
50666036 -TAATTTTGTATTTATAGTTTTT
1 GTAATTTTGTA-TGA-A--TATT
50666058 GATTAGTATTTTGTATGAATATT
1 G--TA--ATTTTGTATGAATATT
* *
50666081 ATAATGTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
50666100 GTAATTATTTTAT-AATTAATTTT
1 GTAATT-TTGTATGAA-T-A--TT
* * *
50666123 GT-ATTTATAGTTTTGGAT-TA
1 GTAATTT-T-G-TATGAATATT
*
50666143 GT-ATTTTGTATGGATATT
1 GTAATTTTGTATGAATATT
*
50666161 GTAATTTTGTATGGATATT
1 GTAATTTTGTATGAATATT
50666180 GTAATATTGTTTGTATGAATATT
1 GT-A-A-T-TTTGTATGAATATT
50666203 GTAATATTGTTTGTATGAATATT
1 GT-A-A-T-TTTGTATGAATATT
50666226 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
50666245 GTAATT
1 GTAATT
50666251 ATTTTATAAT
Statistics
Matches: 402, Mismatches: 40, Indels: 128
0.71 0.07 0.22
Matches are distributed among these distances:
14 4 0.01
15 12 0.03
16 20 0.05
17 15 0.04
18 11 0.03
19 160 0.40
20 34 0.08
21 45 0.11
22 14 0.03
23 53 0.13
24 6 0.01
25 8 0.02
26 4 0.01
27 16 0.04
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (19 bp):
GTAATTTTGTATGAATATT
Found at i:50665784 original size:40 final size:38
Alignment explanation
Indices: 50665726--50666250 Score: 205
Period size: 40 Copynumber: 13.2 Consensus size: 38
50665716 GCGCCAATGG
*
50665726 GTAATTTTGTATGTATATTGTAACTTTTTGTATGAATATT
1 GTAATTTTGTATGAATATTGTAA-TTTTT-TATGAATATT
*
50665766 ATAATTTTGTATGAATATTGTAATTATTTTAT-AATTAATTTT
1 GTAATTTTGTATGAATATTGTAATT-TTTTATGAA-T-A--TT
* * * * *
50665808 GT-ATTTATAGTTTTGGAT-TAGT-ATTTTGTATGAATAGT
1 GTAATTT-T-G-TATGAATATTGTAATTTTTTATGAATATT
50665846 GTAATTTTTTGTATGAATATTGTAATTTTTTATGAATATT
1 GTAA--TTTTGTATGAATATTGTAATTTTTTATGAATATT
*
50665886 GTAATTTTTTATGAATATTGTAATTATTTTAT--A-A-T
1 GTAATTTTGTATGAATATTGTAATT-TTTTATGAATATT
* * *
50665921 -TAATTTTGTATTTATAGTTTTTGATTAGTATTTTGTATGAATATT
1 GTAATTTTGTA-TGA-A--TATTG--TA--ATTTTTTATGAATATT
* *** *
50665966 GTAATTTTG--T-AATTTTGT-A-TGAATATTGTAATTTT
1 GTAATTTTGTATGAATATTGTAATTTTTTA-TG-AATATT
50666001 GTAATTTTGTATGAATATTGTAATTATTTTAT--A-A-T
1 GTAATTTTGTATGAATATTGTAATT-TTTTATGAATATT
* * *
50666036 -TAATTTTGTATTTATAGTTTTTGATTAGTATTTTGTATGAATATT
1 GTAATTTTGTA-TGA-A--TATTG--TA--ATTTTTTATGAATATT
* *
50666081 ATAATGTTGTATGAATATTGTAATTATTTTAT-AATTAATTTT
1 GTAATTTTGTATGAATATTGTAATT-TTTTATGAA-T-A--TT
* * * * *
50666123 GT-ATTTATAGTTTTGGAT-TAGT-ATTTTGTATGGATATT
1 GTAATTT-T-G-TATGAATATTGTAATTTTTTATGAATATT
*
50666161 GTAATTTTGTATGGATATTGTAATATTGTTTGTATGAATATT
1 GTAATTTTGTATGAATATTGT-A-ATT-TTT-TATGAATATT
*
50666203 GTAATATTGTTTGTATGAATATTGTAATTTTGTATGAATATT
1 GT-A-A-T-TTTGTATGAATATTGTAATTTTTTATGAATATT
50666245 GTAATT
1 GTAATT
50666251 ATTTTATAAT
Statistics
Matches: 369, Mismatches: 47, Indels: 140
0.66 0.08 0.25
Matches are distributed among these distances:
33 3 0.01
34 22 0.06
35 20 0.05
36 9 0.02
37 8 0.02
38 56 0.15
39 34 0.09
40 59 0.16
41 38 0.10
42 51 0.14
43 14 0.04
44 17 0.05
45 6 0.02
46 32 0.09
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (38 bp):
GTAATTTTGTATGAATATTGTAATTTTTTATGAATATT
Found at i:50665835 original size:61 final size:62
Alignment explanation
Indices: 50665769--50666166 Score: 286
Period size: 61 Copynumber: 6.4 Consensus size: 62
50665759 GAATATTATA
50665769 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGT-ATTTATAGTTTTGGATTAGT
1 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTAATTTATAGTTTTGGATTAGT
* * * * * * *
50665830 ATTTTGTATGAATAGTGTAATT-TTTTGT-ATGAATATTGTAATTT-T--TTATGAATATTGT
1 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTAATTTATAGTTTTGGAT-TAGT
* *
50665888 AATTTTTTATGAATATTGTAATTATTTTATAATTAATTTTGT-ATTTATAGTTTTTGATTAGT
1 -ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTAATTTATAGTTTTGGATTAGT
* * * * * *
50665950 ATTTTGTATGAATATTGTAATTTTGTAATTTTGT-ATGAATATTGTAATTTTGTAATTTTGTA-T
1 ATTTTGTATGAATATTGTAA---T-T-ATTTTATAATTAATTTTGTAA-TTTATAGTTTTGGATT
*
50666013 -GA
60 AGT
* * * * * * *
50666015 ATATTGTAAT-TATTTTATAATTAATTTTGTATTTATAGTTTT-TGA-TTAGTA-TTTTGTATGA
1 ATTTTGT-ATGAATATTGTAATT-ATTTTATAATTA-A-TTTTGTAATTTA-TAGTTTTG---GA
* *
50666076 ATATT
58 TTAGT
50666081 ATAATGTTGTATGAATATTGTAATTATTTTATAATTAATTTTGT-ATTTATAGTTTTGGATTAGT
1 AT--T-TTGTATGAATATTGTAATTATTTTATAATTAATTTTGTAATTTATAGTTTTGGATTAGT
*
50666145 ATTTTGTATGGATATTGTAATT
1 ATTTTGTATGAATATTGTAATT
50666167 TTGTATGGAT
Statistics
Matches: 259, Mismatches: 46, Indels: 64
0.70 0.12 0.17
Matches are distributed among these distances:
57 6 0.02
58 3 0.01
59 30 0.12
60 18 0.07
61 84 0.32
62 9 0.03
63 8 0.03
64 12 0.05
65 25 0.10
66 19 0.07
67 20 0.08
68 12 0.05
69 13 0.05
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (62 bp):
ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTAATTTATAGTTTTGGATTAGT
Found at i:50665939 original size:120 final size:118
Alignment explanation
Indices: 50665726--50666112 Score: 568
Period size: 115 Copynumber: 3.3 Consensus size: 118
50665716 GCGCCAATGG
* *
50665726 GTAATTTTGTATGTATATTGTAACTTTTTGTATGAATATTATAATTTTGTATGAATATTGTAATT
1 GTAATTTTGTATGAATATTGTAA-TTTTT-TATGAATATTGTAATTTTGTATGAATATTGTAATT
* *
50665791 ATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTATTTTGTATGAATAGT
64 ATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGTATTTTGTATGAATATT
*
50665846 GTAATTTTTTGTATGAATATTGTAATTTTTTATGAATATTGTAATTTTTTATGAATATTGTAATT
1 GTAA--TTTTGTATGAATATTGTAATTTTTTATGAATATTGTAATTTTGTATGAATATTGTAATT
50665911 ATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGTATTTTGTATGAATATT
64 ATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGTATTTTGTATGAATATT
* *** *
50665966 GTAATTTTG--T-AATTTTGT-A-TGAATATTGTAATTTTGTAATTTTGTATGAATATTGTAATT
1 GTAATTTTGTATGAATATTGTAATTTTTTA-TG-AATATTGTAATTTTGTATGAATATTGTAATT
50666026 ATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGTATTTTGTATGAATATT
64 ATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGTATTTTGTATGAATATT
* *
50666081 ATAATGTTGTATGAATATTGTAATTATTTTAT
1 GTAATTTTGTATGAATATTGTAATT-TTTTAT
50666113 AATTAATTTT
Statistics
Matches: 240, Mismatches: 17, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
113 3 0.01
114 3 0.01
115 98 0.41
116 1 0.00
117 1 0.00
118 12 0.05
119 1 0.00
120 96 0.40
121 7 0.03
122 18 0.08
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (118 bp):
GTAATTTTGTATGAATATTGTAATTTTTTATGAATATTGTAATTTTGTATGAATATTGTAATTAT
TTTATAATTAATTTTGTATTTATAGTTTTTGATTAGTATTTTGTATGAATATT
Found at i:50665977 original size:8 final size:8
Alignment explanation
Indices: 50665964--50666011 Score: 60
Period size: 8 Copynumber: 5.6 Consensus size: 8
50665954 TGTATGAATA
50665964 TTGTAATT
1 TTGTAATT
50665972 TTGTAATT
1 TTGTAATT
*
50665980 TTGTATGAATA
1 TTG--T-AATT
50665991 TTGTAATT
1 TTGTAATT
50665999 TTGTAATT
1 TTGTAATT
50666007 TTGTA
1 TTGTA
50666012 TGAATATTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 27 0.77
9 1 0.03
10 1 0.03
11 6 0.17
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (8 bp):
TTGTAATT
Found at i:50665980 original size:27 final size:27
Alignment explanation
Indices: 50665950--50666025 Score: 152
Period size: 27 Copynumber: 2.8 Consensus size: 27
50665940 TTTGATTAGT
50665950 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
50665977 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
50666004 ATTTTGTATGAATATTGTAATT
1 ATTTTGTATGAATATTGTAATT
50666026 ATTTTATAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.55
Consensus pattern (27 bp):
ATTTTGTATGAATATTGTAATTTTGTA
Found at i:50666205 original size:80 final size:80
Alignment explanation
Indices: 50665751--50666250 Score: 376
Period size: 80 Copynumber: 6.3 Consensus size: 80
50665741 TATTGTAACT
* * *
50665751 TTTTGTATGAATATTATAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTAT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATGAATATTGTATTTAT
50665816 AGTTTTGGATTAGTA
66 AGTTTTGGATTAGTA
*
50665831 TTTTGTATGAATAGTGTAATTTTTTGTATGAATATTGTAA-T-TTTT-T-ATGAATATTGTAATT
1 TTTTGTATGAATATTGTAA--TTTTGTATGAATATTGTAATTATTTTATAATGAATATTGT-ATT
* * *
50665892 T-T--TTATGAATATTGTAA
63 TATAGTTTTGGAT-TAGT-A
* ** * * *
50665909 TTATT-T-T--ATAAT-TAATTTTGTATTTATAGTTTTTGATTAGTATTT-TGTATGAATATTGT
1 TT-TTGTATGAATATTGTAATTTTGTATGAATA--TTGTAATTA-T-TTTAT-AATGAATATTGT
* * * *
50665968 AATTTTGTAATTTTGTA-T-GAA
60 -A-TTTATAGTTTTGGATTAGTA
* * * *
50665989 TATTG--T-AATTTTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTAT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATGAATATTGTATTTAT
*
50666051 AGTTTTTGATTAGTA
66 AGTTTTGGATTAGTA
* * * *
50666066 TTTTGTATGAATATTATAATGTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTAT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATGAATATTGTATTTAT
50666131 AGTTTTGGATTAGTA
66 AGTTTTGGATTAGTA
* * * *
50666146 TTTTGTATGGATATTGTAATTTTGTATGGATATTGTAA-TATTGTT-TGTATGAATATTGTA-AT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATT-TTAT-AATGAATATTGTATTT
* * *
50666208 ATTGTTTGTATGAATATTGTAA
64 ATAG-TT-T-TGGAT-TAGT-A
50666230 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
50666251 ATTTTATAAT
Statistics
Matches: 339, Mismatches: 47, Indels: 64
0.75 0.10 0.14
Matches are distributed among these distances:
72 11 0.03
74 7 0.02
75 15 0.04
76 8 0.02
77 23 0.07
78 20 0.06
79 27 0.08
80 154 0.45
81 20 0.06
82 25 0.07
83 3 0.01
84 26 0.08
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (80 bp):
TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATGAATATTGTATTTAT
AGTTTTGGATTAGTA
Found at i:50666324 original size:60 final size:60
Alignment explanation
Indices: 50666244--50666362 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 60
50666234 GTATGAATAT
* * * * *
50666244 TGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGTC
1 TGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGTC
50666304 TGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
1 TGTAATTATTTTAAAA-TTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
50666363 TTAGTTTAGT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
59 6 0.11
60 47 0.89
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (60 bp):
TGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGTC
Found at i:50666519 original size:15 final size:16
Alignment explanation
Indices: 50666483--50666519 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
50666473 CTCATTTAAT
50666483 TTTTATATAATGTAAC
1 TTTTATATAATGTAAC
*
50666499 TTTTATATTATGTAA-
1 TTTTATATAATGTAAC
50666514 TTTTAT
1 TTTTAT
50666520 TTGATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTTATATAATGTAAC
Found at i:50667903 original size:25 final size:24
Alignment explanation
Indices: 50667875--50667925 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
50667865 AAAATGTTCT
* *
50667875 AAAATTCTGAAAAGAAAATGAAAAA
1 AAAAATCTGAAAA-AAAAAGAAAAA
*
50667900 AAAAATCTGAAAAAAAAAGAAGAA
1 AAAAATCTGAAAAAAAAAGAAAAA
50667924 AA
1 AA
50667926 TGACATCGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.73, C:0.04, G:0.12, T:0.12
Consensus pattern (24 bp):
AAAAATCTGAAAAAAAAAGAAAAA
Found at i:50675844 original size:81 final size:81
Alignment explanation
Indices: 50675709--50675870 Score: 202
Period size: 81 Copynumber: 2.0 Consensus size: 81
50675699 ATTCTGAAGT
* * * * * * *
50675709 CAACAGCCAAGATACACAAGCATGTGATAAACATCTGCAAAATTTTCCCACTGAAAATTTATTAC
1 CAACAGCCAAGATACACAAGCAAGTGACAAAAATATGCAAAATATTCCCACTGAAAATCTATCAC
*
50675774 AAATTAAAAAATGTAC
66 AAATTAAAAAAGGTAC
*
50675790 CAACAGCCAAGATACACAAGTAAGTGACAAAGAATAT-CAATAA-ATTCCCACTGAAAATCTATC
1 CAACAGCCAAGATACACAAGCAAGTGACAAA-AATATGCAA-AATATTCCCACTGAAAATCTATC
*
50675853 ACAAATTCAAAAAGGTAC
64 ACAAATTAAAAAAGGTAC
50675871 ATTAAGCAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
81 64 0.93
82 5 0.07
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.22
Consensus pattern (81 bp):
CAACAGCCAAGATACACAAGCAAGTGACAAAAATATGCAAAATATTCCCACTGAAAATCTATCAC
AAATTAAAAAAGGTAC
Found at i:50678909 original size:18 final size:20
Alignment explanation
Indices: 50678866--50678918 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
50678856 ATTTTTAAAA
*
50678866 TAAACATTAAAAAATTATTT
1 TAAAAATTAAAAAATTATTT
50678886 TAAAAA-TAAAAAATTATTT
1 TAAAAATTAAAAAATTATTT
50678905 T-AAAATTAAAAAAT
1 TAAAAATTAAAAAAT
50678919 AAAAATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 4 0.13
19 22 0.71
20 5 0.16
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAAATTAAAAAATTATTT
Found at i:50691567 original size:21 final size:21
Alignment explanation
Indices: 50691541--50691582 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
50691531 GAGTTTATAT
*
50691541 ATAAAATCAATTATAAATTAA
1 ATAAAATAAATTATAAATTAA
* *
50691562 ATAAAATAAATTTTAATTTAA
1 ATAAAATAAATTATAAATTAA
50691583 TTCATAATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAAAATAAATTATAAATTAA
Found at i:50702475 original size:6 final size:6
Alignment explanation
Indices: 50702464--50702508 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
50702454 ACAACATCAC
50702464 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TAT
50702509 GGTGGGAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:50713982 original size:31 final size:32
Alignment explanation
Indices: 50713948--50714009 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
50713938 TTAAAAAGAA
50713948 AAAAAATCTT-AATAGCCAAA-TAACTTAAAT
1 AAAAAATCTTGAATAGCCAAAGTAACTTAAAT
* **
50713978 AAAAAATTTTGAATAGTTAAAGTAACTTAAAT
1 AAAAAATCTTGAATAGCCAAAGTAACTTAAAT
50714010 GAATACTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 9 0.33
31 8 0.30
32 10 0.37
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (32 bp):
AAAAAATCTTGAATAGCCAAAGTAACTTAAAT
Found at i:50714509 original size:16 final size:16
Alignment explanation
Indices: 50714472--50714509 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
50714462 AGTTTATAAT
50714472 ATTT-TATATTATGTA
1 ATTTATATATTATGTA
50714487 ATTTTTATATATTATGTA
1 A--TTTATATATTATGTA
50714505 ATTTA
1 ATTTA
50714510 GAACACATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.05
16 4 0.20
17 3 0.15
18 12 0.60
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (16 bp):
ATTTATATATTATGTA
Found at i:50720841 original size:13 final size:14
Alignment explanation
Indices: 50720823--50720851 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
50720813 TCATTTCCTC
50720823 TTCTTTTTT-TTTT
1 TTCTTTTTTCTTTT
50720836 TTCTTTTTTCTTTT
1 TTCTTTTTTCTTTT
50720850 TT
1 TT
50720852 TAAAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTCTTTTTTCTTTT
Found at i:50720842 original size:7 final size:7
Alignment explanation
Indices: 50720823--50720851 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
50720813 TCATTTCCTC
50720823 TTCTTTT
1 TTCTTTT
50720830 TT-TTTT
1 TTCTTTT
50720836 TTCTTTT
1 TTCTTTT
50720843 TTCTTTT
1 TTCTTTT
50720850 TT
1 TT
50720852 TAAAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTCTTTT
Found at i:50728737 original size:24 final size:24
Alignment explanation
Indices: 50728710--50728756 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
50728700 CCTTACCATG
*
50728710 TATTTTTTAAATAATAA-ATTTTTT
1 TATTTTGTAAA-AATAATATTTTTT
*
50728734 TATTTTGTGAAAATAATATTTTT
1 TATTTTGTAAAAATAATATTTTT
50728757 ATTAGAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
TATTTTGTAAAAATAATATTTTTT
Found at i:50734060 original size:29 final size:29
Alignment explanation
Indices: 50734027--50734082 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
50734017 ATATAGATAG
50734027 GATCAAATTAGTCCCTT-TACTATTAAATA
1 GATCAAATTAGT-CCTTGTACTATTAAATA
* *
50734056 GATCAATTTAGTCCTTGTATTATTAAA
1 GATCAAATTAGTCCTTGTACTATTAAA
50734083 AGGAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (29 bp):
GATCAAATTAGTCCTTGTACTATTAAATA
Found at i:50737278 original size:95 final size:93
Alignment explanation
Indices: 50737165--50737431 Score: 412
Period size: 95 Copynumber: 2.9 Consensus size: 93
50737155 GGGTTCTTTT
* *
50737165 TATTTTCTTCTTTAATCGGCTGTGTTTTCCATTGAATTTGAATATGTATATATAACTTCGAATCG
1 TATTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAATCG
*
50737230 ATTTTTTAGCTTCATTGGGATTTTTGGG
66 ATTTTTCAGCTTCATTGGGATTTTTGGG
* *
50737258 TTCTTTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAGTATGTATATATAACTTTGAAT
1 -T-ATTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAAT
**
50737323 CGCCTTTTCAGCTTCATTGGGATTTTTGGG
64 CGATTTTTCAGCTTCATTGGGATTTTTGGG
**
50737353 TATTTTCCCCTTTAATCGGCTGTATTTTCCATTGAATTTG-A-ATGTATATATAACTTTGAATCG
1 TATTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAATCG
*
50737416 ATGTTTCAGCTTCATT
66 ATTTTTCAGCTTCATT
50737432 TGCATGCGGG
Statistics
Matches: 158, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
91 35 0.22
93 36 0.23
94 2 0.01
95 85 0.54
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (93 bp):
TATTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAATCG
ATTTTTCAGCTTCATTGGGATTTTTGGG
Found at i:50740181 original size:15 final size:14
Alignment explanation
Indices: 50740163--50740210 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
50740153 TTTTAAATAC
50740163 AAAACTTTTAATATT
1 AAAA-TTTTAATATT
*
50740178 AAAATATTACATATT
1 AAAATTTTA-ATATT
50740193 AAAATTTTAA-A-T
1 AAAATTTTAATATT
50740205 AAAATT
1 AAAATT
50740211 CTATTAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 7 0.23
13 1 0.03
14 5 0.17
15 17 0.57
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (14 bp):
AAAATTTTAATATT
Found at i:50746812 original size:11 final size:11
Alignment explanation
Indices: 50746798--50746838 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
50746788 TGTTTTCTCT
50746798 CTATTTTGCTA
1 CTATTTTGCTA
*
50746809 CTATTTTACTA
1 CTATTTTGCTA
* *
50746820 TTATGTTGCTA
1 CTATTTTGCTA
50746831 CTATTTTG
1 CTATTTTG
50746839 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:50746911 original size:30 final size:30
Alignment explanation
Indices: 50746875--50746937 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
50746865 ACTTATTTTA
*
50746875 TTGTTAATTTTATTATTATTTTAAAGACAT
1 TTGTTAAATTTATTATTATTTTAAAGACAT
* * *
50746905 TTGTTAAATTTGTTATTATTTTAGAGGCAT
1 TTGTTAAATTTATTATTATTTTAAAGACAT
50746935 TTG
1 TTG
50746938 CTAGTTAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.56
Consensus pattern (30 bp):
TTGTTAAATTTATTATTATTTTAAAGACAT
Found at i:50747218 original size:6 final size:6
Alignment explanation
Indices: 50747207--50747238 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
50747197 AGTGATCTCT
50747207 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT
50747239 CACTGCTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:50748115 original size:10 final size:10
Alignment explanation
Indices: 50748102--50748130 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
50748092 ATATTTTTTT
50748102 TAATTTTTAA
1 TAATTTTTAA
50748112 TAA-TTTTAA
1 TAATTTTTAA
50748121 TAATTTTTAA
1 TAATTTTTAA
50748131 ATTTCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:50757391 original size:16 final size:17
Alignment explanation
Indices: 50757370--50757408 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
50757360 TTTTTTTAAA
50757370 TTAATTGATTAA-AATT
1 TTAATTGATTAATAATT
* *
50757386 TTAATTTATTAATATTT
1 TTAATTGATTAATAATT
50757403 TTAATT
1 TTAATT
50757409 ATCTTTTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTAATTGATTAATAATT
Found at i:50767495 original size:2 final size:2
Alignment explanation
Indices: 50767488--50767524 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
50767478 GCTCTGTCCC
50767488 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
50767525 TTTGCTTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:50769621 original size:31 final size:31
Alignment explanation
Indices: 50769586--50769644 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
50769576 GAAACTTTTT
* * *
50769586 ACTAGGTCTATTTTGGTACATGAACTTGACA
1 ACTAGATCCATTTTGGTACATAAACTTGACA
* *
50769617 ACTAGATCCATTTTTGTCCATAAACTTG
1 ACTAGATCCATTTTGGTACATAAACTTG
50769645 GATTTCATCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (31 bp):
ACTAGATCCATTTTGGTACATAAACTTGACA
Found at i:50785857 original size:21 final size:21
Alignment explanation
Indices: 50785751--50785883 Score: 88
Period size: 21 Copynumber: 6.3 Consensus size: 21
50785741 CATAAGTGCT
*
50785751 AACAGAAACCCATAAGGGTTG
1 AACAGAAACCCATAAGGGTTA
** * * * *
50785772 AATGGAAGCTCAT-AGGAGCTG
1 AACAGAAACCCATAAGG-GTTA
*
50785793 AACGGAAACCCATAAGGGTTA
1 AACAGAAACCCATAAGGGTTA
* * * * *
50785814 AACAGAAGCTCAAAAGAGCTA
1 AACAGAAACCCATAAGGGTTA
* *
50785835 AACGGAAACCCATTAGGGTTA
1 AACAGAAACCCATAAGGGTTA
* * *
50785856 AACAGAAACTCATATGAGTTA
1 AACAGAAACCCATAAGGGTTA
50785877 AACAGAA
1 AACAGAA
50785884 GCTCACGAGA
Statistics
Matches: 82, Mismatches: 28, Indels: 4
0.72 0.25 0.04
Matches are distributed among these distances:
20 3 0.04
21 76 0.93
22 3 0.04
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (21 bp):
AACAGAAACCCATAAGGGTTA
Found at i:50785879 original size:42 final size:42
Alignment explanation
Indices: 50785732--50785879 Score: 172
Period size: 42 Copynumber: 3.5 Consensus size: 42
50785722 CAATGGCTGC
* * * *
50785732 ACAGAAGCACATAAGTGCT-AACAGAAACCCATAAGGGTTGA
1 ACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTAA
** * *
50785773 ATGGAAGCTCATAGGAGCTGAACGGAAACCCATAAGGGTTAA
1 ACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTAA
* *
50785815 ACAGAAGCTCAAAAGAGCTAAACGGAAACCCATTAGGGTTAA
1 ACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTAA
* * *
50785857 ACAGAAACTCATATGAGTTAAAC
1 ACAGAAGCTCATAAGAGCTAAAC
50785880 AGAAGCTCAC
Statistics
Matches: 89, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 14 0.16
42 75 0.84
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.16
Consensus pattern (42 bp):
ACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTAA
Found at i:50785899 original size:21 final size:20
Alignment explanation
Indices: 50785780--50785905 Score: 63
Period size: 21 Copynumber: 6.0 Consensus size: 20
50785770 TGAATGGAAG
* *
50785780 CTCATAGGAGCTGAACGGAAA
1 CTCATA-GAGCTAAACAGAAA
* * * *
50785801 CCCATAAGGGTTAAACAGAAG
1 CTCAT-AGAGCTAAACAGAAA
* *
50785822 CTCAAAAGAGCTAAACGGAAA
1 CTC-ATAGAGCTAAACAGAAA
* * *
50785843 CCCATTAGGGTTAAACAGAAA
1 CTCA-TAGAGCTAAACAGAAA
* *
50785864 CTCATATGAGTTAAACAGAAG
1 CTCATA-GAGCTAAACAGAAA
* *
50785885 CTCACGAGAGCTAAACGGAAA
1 CTCA-TAGAGCTAAACAGAAA
50785906 GTAAACACAA
Statistics
Matches: 76, Mismatches: 24, Indels: 10
0.69 0.22 0.09
Matches are distributed among these distances:
20 3 0.04
21 70 0.92
22 3 0.04
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (20 bp):
CTCATAGAGCTAAACAGAAA
Found at i:50788122 original size:20 final size:20
Alignment explanation
Indices: 50788085--50788123 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
50788075 TCTAATTGTC
*
50788085 TATAATATTTTTATTTTTCT
1 TATAATATTTGTATTTTTCT
50788105 TATAATATTTAGTATTTTT
1 TATAATATTT-GTATTTTT
50788124 TTAATGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (20 bp):
TATAATATTTGTATTTTTCT
Found at i:50796042 original size:29 final size:28
Alignment explanation
Indices: 50795984--50796042 Score: 66
Period size: 28 Copynumber: 2.0 Consensus size: 28
50795974 AATTTAATAG
**
50795984 TTTATATTTTTAAAAGATTAAATCAAAAT
1 TTTATATTTTT-AAAGATTAAAAAAAAAT
50796013 TTTATTATTTTT-AAGATTAAAAAAATAAT
1 TTTA-TATTTTTAAAGATTAAAAAAA-AAT
50796042 T
1 T
50796043 CTTTCATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 11 0.42
29 8 0.31
30 7 0.27
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (28 bp):
TTTATATTTTTAAAGATTAAAAAAAAAT
Found at i:50803580 original size:19 final size:19
Alignment explanation
Indices: 50803556--50803593 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
50803546 ATTTAAAGGA
50803556 TAGTTATTTGATACATAGG
1 TAGTTATTTGATACATAGG
50803575 TAGTTATTTGATACATAGG
1 TAGTTATTTGATACATAGG
50803594 CGGTGAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (19 bp):
TAGTTATTTGATACATAGG
Found at i:50828331 original size:24 final size:24
Alignment explanation
Indices: 50828304--50828352 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
50828294 TATGATAGAT
50828304 TCTGCTCTGCATATAATGTGTTAG
1 TCTGCTCTGCATATAATGTGTTAG
50828328 TCTGCTCTGCATATAATGTGTTAG
1 TCTGCTCTGCATATAATGTGTTAG
50828352 T
1 T
50828353 TCAGATCGCA
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:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (24 bp):
TCTGCTCTGCATATAATGTGTTAG
Found at i:50839163 original size:19 final size:22
Alignment explanation
Indices: 50839133--50839181 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
50839123 GGGGAACAAT
50839133 AGAAAAACATT-GAG-AAGAAG
1 AGAAAAACATTAGAGAAAGAAG
50839153 AGAAAAA-ATTGAGAGAAAGAAG
1 AGAAAAACATT-AGAGAAAGAAG
50839175 AGAAAAA
1 AGAAAAA
50839182 GAGAATACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 3 0.12
20 7 0.27
21 3 0.12
22 13 0.50
ACGTcount: A:0.65, C:0.02, G:0.24, T:0.08
Consensus pattern (22 bp):
AGAAAAACATTAGAGAAAGAAG
Found at i:50845118 original size:32 final size:31
Alignment explanation
Indices: 50845073--50845168 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
50845063 CTTAGATAAT
50845073 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
50845104 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
50845136 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
50845167 TT
1 TT
50845169 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:50846623 original size:10 final size:9
Alignment explanation
Indices: 50846606--50846631 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
50846596 CTACTCTCTC
50846606 TCTTTTTTT
1 TCTTTTTTT
50846615 TCTTTTTTT
1 TCTTTTTTT
50846624 TCTTTTTT
1 TCTTTTTT
50846632 GCTTTTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TCTTTTTTT
Done.