Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 59 of 204
Found at i:17366554 original size:20 final size:19
Alignment explanation
Indices: 17366517--17366581 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
17366507 ATATGTTATC
*
17366517 ATTTAATTTTATAATATACT
1 ATTTAATTTAATAATATA-T
**
17366537 ATTTAATTTAATTTTATAT
1 ATTTAATTTAATAATATAT
*
17366556 ATATTAATTCAACGTAATATAT
1 AT-TTAATTTAA--TAATATAT
17366578 ATTT
1 ATTT
17366582 TTTAGATAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
19 3 0.08
20 23 0.64
21 2 0.06
22 8 0.22
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.54
Consensus pattern (19 bp):
ATTTAATTTAATAATATAT
Found at i:17370022 original size:21 final size:21
Alignment explanation
Indices: 17369998--17370046 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
17369988 CGATGACCAA
* *
17369998 CCGCCATCGGCAAACGGGACG
1 CCGCCATCGCCAAACAGGACG
* *
17370019 CCGCCATCGCCCACCAGGACG
1 CCGCCATCGCCAAACAGGACG
17370040 CCGCCAT
1 CCGCCAT
17370047 AGCTGCCACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.47, G:0.27, T:0.06
Consensus pattern (21 bp):
CCGCCATCGCCAAACAGGACG
Found at i:17380183 original size:44 final size:45
Alignment explanation
Indices: 17380132--17380228 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 45
17380122 TGTAAAACTT
* ** * *
17380132 TTGTTGTGCACCCACAGCCAGAGTTAGATTTCATCTGC-GGGTAC
1 TTGTTGTGCACCCACAACCAGAGGCAGATTCCATCTGCAGGGTAA
* * *
17380176 TTGTTGTGTATCCACAACCAGAGGCAGATTCCATCTGCAGGTTAA
1 TTGTTGTGCACCCACAACCAGAGGCAGATTCCATCTGCAGGGTAA
17380221 TTGTTGTG
1 TTGTTGTG
17380229 TAATTTACAA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 32 0.73
45 12 0.27
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (45 bp):
TTGTTGTGCACCCACAACCAGAGGCAGATTCCATCTGCAGGGTAA
Found at i:17382969 original size:24 final size:24
Alignment explanation
Indices: 17382918--17382969 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
17382908 TTTAAAATTT
* * *
17382918 ATTAATATAATATATTTAGCATTT
1 ATTAACATAACATATTTAGCATTG
17382942 ATTAACATAACATATTT-GACATTG
1 ATTAACATAACATATTTAG-CATTG
17382966 ATTA
1 ATTA
17382970 TAATTAGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (24 bp):
ATTAACATAACATATTTAGCATTG
Found at i:17384373 original size:24 final size:23
Alignment explanation
Indices: 17384336--17384380 Score: 81
Period size: 24 Copynumber: 1.9 Consensus size: 23
17384326 GAAGAATATG
17384336 AGAAGAGAGAAAAATAAAGAAGA
1 AGAAGAGAGAAAAATAAAGAAGA
17384359 AGAAGAAGAGAAAAATAAAGAA
1 AGAAG-AGAGAAAAATAAAGAA
17384381 ATAAAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.04
Consensus pattern (23 bp):
AGAAGAGAGAAAAATAAAGAAGA
Found at i:17386843 original size:45 final size:45
Alignment explanation
Indices: 17386766--17386861 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
17386756 GATAGATAAA
* *
17386766 ATATAA-ATTAATCTAAAATTTTAAATATATTTTAAATATTTAAT
1 ATATAATATTAATCTAAAATTTTAAATACATTTTAAATAATTAAT
* * * *
17386810 ATATAATATTCATCTAAATTTTTATATCCATTTTAAATAATTAAT
1 ATATAATATTAATCTAAAATTTTAAATACATTTTAAATAATTAAT
17386855 ATA-AATA
1 ATATAATA
17386862 AGATTATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 10 0.22
45 35 0.78
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (45 bp):
ATATAATATTAATCTAAAATTTTAAATACATTTTAAATAATTAAT
Found at i:17402463 original size:23 final size:23
Alignment explanation
Indices: 17402422--17402486 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
17402412 GAAAAGACAA
* * *
17402422 ATGAATAGTGAAAAATCTCAGGC-
1 ATGAACAGTGAAGATTCTC-GGCG
*
17402445 ATGAACAGTGAAGATTCTCTGCG
1 ATGAACAGTGAAGATTCTCGGCG
* *
17402468 ATGAAGAATGAAGATTCTC
1 ATGAACAGTGAAGATTCTC
17402487 CGAAAAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 2 0.06
23 33 0.94
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (23 bp):
ATGAACAGTGAAGATTCTCGGCG
Found at i:17413924 original size:28 final size:28
Alignment explanation
Indices: 17413863--17413986 Score: 178
Period size: 28 Copynumber: 4.4 Consensus size: 28
17413853 ATTAAGTCCA
*
17413863 CACACTCAGTGCTATATAATC-AACTCG
1 CACACTTAGTGCTATATAATCAAACTCG
17413890 CACACTTAGTGCTATATAATCAAACTCG
1 CACACTTAGTGCTATATAATCAAACTCG
*
17413918 CACACTTAGTGCTACATAATCAAACTCG
1 CACACTTAGTGCTATATAATCAAACTCG
* * * *
17413946 CACACTTAGTGCTGTACAATTTAAACCCG
1 CACACTTAGTGCTATATAA-TCAAACTCG
17413975 CACACTTAGTGC
1 CACACTTAGTGC
17413987 CAATCTCATG
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 20 0.23
28 49 0.56
29 19 0.22
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (28 bp):
CACACTTAGTGCTATATAATCAAACTCG
Found at i:17421860 original size:28 final size:28
Alignment explanation
Indices: 17421797--17421922 Score: 182
Period size: 28 Copynumber: 4.5 Consensus size: 28
17421787 ATATTAAGTC
*
17421797 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
17421824 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
17421852 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
17421880 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
17421909 CGCACACTTAGTGC
1 CGCACACTTAGTGC
17421923 CAATCTCATG
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.24
28 49 0.54
29 19 0.21
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:17425336 original size:56 final size:56
Alignment explanation
Indices: 17425250--17425369 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
17425240 ACAAGGGATG
17425250 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
17425306 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
17425362 ATGGGCAA
1 ATGGGCAA
17425370 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:17426906 original size:49 final size:47
Alignment explanation
Indices: 17426827--17427616 Score: 1133
Period size: 47 Copynumber: 16.6 Consensus size: 47
17426817 TATTTGAATA
*
17426827 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
17426874 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGTCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
17426923 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * * *
17426972 AATGTGAAAGTGTATATATATGTGATTAGGCCTAATGGCCGATGTGATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
17427021 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
17427068 AACGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
17427117 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
17427166 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
17427213 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
17427262 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
17427309 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
17427356 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
17427403 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
17427450 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
17427497 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
17427544 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
17427591 -GTGTGGAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
17427617 TCCCGAAGGG
Statistics
Matches: 701, Mismatches: 34, Indels: 17
0.93 0.05 0.02
Matches are distributed among these distances:
46 24 0.03
47 398 0.57
49 278 0.40
50 1 0.00
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:17427517 original size:25 final size:25
Alignment explanation
Indices: 17427489--17427567 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
17427479 CGAATGGCCA
17427489 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* * ***
17427514 ATGTGAT-AAGGCCG-AA-TGGCCA-
1 ATGTGATGAATG-TGAAAGTGTATAT
17427536 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
17427561 ATGTGAT
1 ATGTGAT
17427568 AAGGCCGAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 8 0.21
23 8 0.21
24 8 0.21
25 15 0.38
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:17427623 original size:94 final size:94
Alignment explanation
Indices: 17426827--17427616 Score: 1099
Period size: 96 Copynumber: 8.3 Consensus size: 94
17426817 TATTTGAATA
* *
17426827 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATAAATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG--TATA
* *
17426892 TATGTGATAAGGCCTAATGGTCAATGTGATG
64 TATGTGATAAGGCCGAATGGCCAATGTGATG
* *
17426923 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATA-A-ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG--TA
* * * *
17426988 TATATGTGATTAGGCCTAATGGCCGATGTGATA
62 TATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
17427021 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAACGTGAAAGTGTATATA
1 AATGTGAAAGTGTATAAATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG--TATA
*
17427086 TATGTGATAAGGCCTAATGGCCAATGTGATG
64 TATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
17427117 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATAAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATA-A-ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
17427182 TATGTGATAAGGCCGAATGGCCAATGTGATG
64 TATGTGATAAGGCCGAATGGCCAATGTGATG
*
17427213 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGTGT
1 AATGTGAAAGTGTATA-A-ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTGTAT
*
17427277 ATGTGTGATAAGGCCGAATGGCCAATGTGATG
63 ATATGTGATAAGGCCGAATGGCCAATGTGATG
* * * *
17427309 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGTGTA
1 AATGTGAA-AGTGTATAAATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTGTATA
*
17427372 TGTGTGATAAGGCCGAATGGCCAATGTGATG
64 TATGTGATAAGGCCGAATGGCCAATGTGATG
* *
17427403 AATGTGAACATGTGTAT--GTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGCAT
1 AATGTGAA-A-GTGTATAAATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTGTAT
*
17427465 ATATGAGATAAGGCCGAATGGCCAATGTGATG
63 ATATGTGATAAGGCCGAATGGCCAATGTGATG
*
17427497 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATAAATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
17427562 TGTGATAAGGCCGAATGGCCAATGTGATG
66 TGTGATAAGGCCGAATGGCCAATGTGATG
* *
17427591 -GTGTGGAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATAAATGTGATAAG
17427617 TCCCGAAGGG
Statistics
Matches: 645, Mismatches: 38, Indels: 25
0.91 0.05 0.04
Matches are distributed among these distances:
92 6 0.01
93 25 0.04
94 237 0.37
96 246 0.38
97 2 0.00
98 129 0.20
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.29
Consensus pattern (94 bp):
AATGTGAAAGTGTATAAATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
TGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:17429957 original size:40 final size:39
Alignment explanation
Indices: 17429873--17430096 Score: 202
Period size: 40 Copynumber: 5.6 Consensus size: 39
17429863 TCGAATGATG
* * * *
17429873 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* *
17429913 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
17429953 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
17429992 TCCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
** * * **
17430033 -CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA-TGTA
1 TCCGGGCTAAGT-CCGAAG-GCATTTGTGCGAGTTACTAAA
17430072 TCCGGGCTAAGTTCCGAAGAGCATT
1 TCCGGGCTAAG-TCCGAAG-GCATT
17430097 CATGCTAGTG
Statistics
Matches: 155, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
39 36 0.23
40 97 0.63
41 22 0.14
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:17430009 original size:79 final size:81
Alignment explanation
Indices: 17429873--17430056 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 81
17429863 TCGAATGATG
* *
17429873 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
*
17429937 TGTGCGAGTTACTA-A
66 TGTACGAGTTACTATA
* * * **
17429952 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
17430014 TTTGTACGAGTTACTATA
64 TTTGTACGAGTTACTATA
*
17430032 ACCGGGCTAAGTCCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAG-GCATT
17430057 CATGCTAGTG
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 25 0.28
81 5 0.06
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTACGAGTTACTATA
Found at i:17430305 original size:40 final size:40
Alignment explanation
Indices: 17430033--17430299 Score: 392
Period size: 40 Copynumber: 6.7 Consensus size: 40
17430023 GTTACTATAA
17430033 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
*
17430073 CCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
*
17430113 CCGAGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
*
17430153 CCGGGCTAAGTCCCGAAAAGCATTCATGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
** * *
17430193 CCGGGCTAAGTTTCGAAGAGCATTCGTGCTAGTGATATAT
1 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
* * * * * *
17430233 CCGTGCTAA-ACCCGAAGAGCATTCGTGCTGGTGTTATAT
1 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
* *
17430272 CCGGGCTAGGTCCCGAAGAGCAATCATG
1 CCGGGCTAAGTCCCGAAGAGCATTCATG
17430300 TTGGTGACGT
Statistics
Matches: 205, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
39 32 0.16
40 173 0.84
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
Found at i:17434006 original size:20 final size:21
Alignment explanation
Indices: 17433983--17434021 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
17433973 ATGACATTAG
*
17433983 ACAATTAAATAAAT-TAATGC
1 ACAAATAAATAAATCTAATGC
17434003 ACAAATAAATAAATCTAAT
1 ACAAATAAATAAATCTAAT
17434022 ATGCACACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (21 bp):
ACAAATAAATAAATCTAATGC
Found at i:17436025 original size:22 final size:21
Alignment explanation
Indices: 17435991--17436035 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
17435981 TTTTATTTGC
*
17435991 AAAATCAAAATTTTCTTTTAAA
1 AAAATCAAAATTTT-TCTTAAA
**
17436013 AAAATCATTATTTTTCTTAAA
1 AAAATCAAAATTTTTCTTAAA
17436034 AA
1 AA
17436036 TCAAAACATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATCAAAATTTTTCTTAAA
Found at i:17436418 original size:152 final size:149
Alignment explanation
Indices: 17436212--17436650 Score: 634
Period size: 152 Copynumber: 2.9 Consensus size: 149
17436202 AATCAAAACA
* * *
17436212 TTATTTCGAAATAGTTAAAAAAATCAAAACTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATGA
1 TTATTTTGAAATAGTTAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAA
17436277 CTTAAAAAAATATATTTTTATTTTTCAAAATCTAAACTTTCTCCTTTTTTTAAAAAAAAACACTA
66 CTTAAAAAAATATATTTTTATTTTTCAAAATCTAAACTTTCT-CTTTTTTT--AAAAAAACACTA
17436342 TTTTTCTTAAAGATTAAAGCTT
128 TTTTTCTTAAAGATTAAAGCTT
* * * *
17436364 TTATTTTGAAGTACTTAAAAAAATCAAAACTTTATTTTAAAAATTTAAATTTTCCTTTAAAATAA
1 TTATTTTGAAATAGTTAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAA
* *
17436429 C-TAAAAAATTA-ATTTTTATTTTTTAAAATCTAAACTTTCTCTTTTTCTT-AAAAAACACTATT
66 CTTAAAAAAATATATTTTTATTTTTCAAAATCTAAACTTTCTCTTTTT-TTAAAAAAACACTATT
17436491 TTTCTTAAAGATTAAAGCTT
130 TTTCTTAAAGATTAAAGCTT
*
17436511 TTACTTTGAAATAGTTGAAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAAT
1 TTATTTTGAAATAGTT--AAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAAT
* *
17436576 AACTAAAAAAACCATATATTTATT-TTTTTCAAAATCTAAACTTTCTACTTTTTTTTTAAAAAAC
64 AACTTAAAAAA--ATATATTT-TTATTTTTCAAAATCTAAACTTTCT-C--TTTTTTTAAAAAAA
17436640 CACTATTTTTC
123 CACTATTTTTC
17436651 CCAAAATCAA
Statistics
Matches: 257, Mismatches: 18, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
147 46 0.18
149 54 0.21
150 36 0.14
151 9 0.04
152 61 0.24
153 25 0.10
154 3 0.01
155 2 0.01
156 21 0.08
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.44
Consensus pattern (149 bp):
TTATTTTGAAATAGTTAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAA
CTTAAAAAAATATATTTTTATTTTTCAAAATCTAAACTTTCTCTTTTTTTAAAAAAACACTATTT
TTCTTAAAGATTAAAGCTT
Found at i:17438142 original size:23 final size:23
Alignment explanation
Indices: 17438116--17438248 Score: 126
Period size: 23 Copynumber: 5.8 Consensus size: 23
17438106 AATATTTGGC
*
17438116 ATGAATAGTGAAGATT-TGCTACA
1 ATGAACAGTGAAGATTCT-CTACA
* * *
17438139 ATGAATAGTAAAAATTCTCTGAC-
1 ATGAACAGTGAAGATTCTCT-ACA
* * *
17438162 ATGAACAGTGAAGATTCTTTGCG
1 ATGAACAGTGAAGATTCTCTACA
*
17438185 ATGAACAGTGAAGATTCTCTGCA
1 ATGAACAGTGAAGATTCTCTACA
* * *
17438208 ATAAACAATGAAGATTCTCTACG
1 ATGAACAGTGAAGATTCTCTACA
*
17438231 ATGAATAGTGAAGATTCT
1 ATGAACAGTGAAGATTCT
17438249 TTGAAAAAAA
Statistics
Matches: 91, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
22 1 0.01
23 87 0.96
24 3 0.03
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (23 bp):
ATGAACAGTGAAGATTCTCTACA
Found at i:17438189 original size:46 final size:46
Alignment explanation
Indices: 17438124--17438248 Score: 146
Period size: 46 Copynumber: 2.7 Consensus size: 46
17438114 GCATGAATAG
* * * * *
17438124 TGAAGATT-TGCTACAATGAATAGTAAAAATTCTCTG-ACATGAACAG
1 TGAAGATTCT-CTACGATGAATAGTGAAGATTCTCTGCA-ATAAACAA
* * *
17438170 TGAAGATTCTTTGCGATGAACAGTGAAGATTCTCTGCAATAAACAA
1 TGAAGATTCTCTACGATGAATAGTGAAGATTCTCTGCAATAAACAA
17438216 TGAAGATTCTCTACGATGAATAGTGAAGATTCT
1 TGAAGATTCTCTACGATGAATAGTGAAGATTCT
17438249 TTGAAAAAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
46 64 0.97
47 2 0.03
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (46 bp):
TGAAGATTCTCTACGATGAATAGTGAAGATTCTCTGCAATAAACAA
Found at i:17438195 original size:69 final size:69
Alignment explanation
Indices: 17438116--17438251 Score: 168
Period size: 69 Copynumber: 2.0 Consensus size: 69
17438106 AATATTTGGC
* * * *
17438116 ATGAATAGTGAAGATT-TGCTACAATGAATAGTAAAAATTCTCTGAC-ATGAACAGTGAAGATTC
1 ATGAACAGTGAAGATTCT-CTACAATAAACAATAAAAATTCTCT-ACGATGAACAGTGAAGATTC
17438179 TTTGCG
64 TTTGCG
* * * *
17438185 ATGAACAGTGAAGATTCTCTGCAATAAACAATGAAGATTCTCTACGATGAATAGTGAAGATTCTT
1 ATGAACAGTGAAGATTCTCTACAATAAACAATAAAAATTCTCTACGATGAACAGTGAAGATTCTT
17438250 TG
66 TG
17438252 AAAAAAATAC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
68 2 0.04
69 54 0.95
70 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (69 bp):
ATGAACAGTGAAGATTCTCTACAATAAACAATAAAAATTCTCTACGATGAACAGTGAAGATTCTT
TGCG
Found at i:17438523 original size:16 final size:16
Alignment explanation
Indices: 17438502--17438532 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17438492 TTTTAGCTTT
17438502 AAAAAATTTAATTTTA
1 AAAAAATTTAATTTTA
17438518 AAAAAATTTAATTTT
1 AAAAAATTTAATTTT
17438533 CAAATTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAAAATTTAATTTTA
Found at i:17457348 original size:26 final size:26
Alignment explanation
Indices: 17457306--17457359 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
17457296 CAAGTTTCAA
* *
17457306 AATATCATAACAGATATTATTTTTAG
1 AATATCATAACAGATATCAGTTTTAG
* *
17457332 AATATCATAGCATATATCAGTTTTAG
1 AATATCATAACAGATATCAGTTTTAG
17457358 AA
1 AA
17457360 CACTTACAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (26 bp):
AATATCATAACAGATATCAGTTTTAG
Found at i:17468618 original size:16 final size:16
Alignment explanation
Indices: 17468597--17468628 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17468587 TCAAATCTAT
*
17468597 TTGAAGTGATTTAAAA
1 TTGAAGTGATGTAAAA
17468613 TTGAAGTGATGTAAAA
1 TTGAAGTGATGTAAAA
17468629 GGCATGCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (16 bp):
TTGAAGTGATGTAAAA
Found at i:17477181 original size:16 final size:16
Alignment explanation
Indices: 17477160--17477191 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17477150 TCAAATCTAT
*
17477160 TTGAAGTGATTTAAAA
1 TTGAAGTGATGTAAAA
17477176 TTGAAGTGATGTAAAA
1 TTGAAGTGATGTAAAA
17477192 GGCATGCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (16 bp):
TTGAAGTGATGTAAAA
Found at i:17484814 original size:21 final size:20
Alignment explanation
Indices: 17484785--17484823 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
17484775 CTAGTCCCCT
*
17484785 TTTATTGTCAGGTAAACTACA
1 TTTAATGTCA-GTAAACTACA
*
17484806 TTTAATGTCATTAAACTA
1 TTTAATGTCAGTAAACTA
17484824 TTAGTAAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTAATGTCAGTAAACTACA
Found at i:17484909 original size:31 final size:31
Alignment explanation
Indices: 17484871--17484939 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
17484861 TCACAAAATG
*
17484871 GTCACTAAACTATTGAAAAGTT-TTCATTCAA
1 GTCACTAAACTATTCAAAAGTTATT-ATTCAA
*
17484902 GTCACTAAACTATTCAAAAGTTATTATTTAA
1 GTCACTAAACTATTCAAAAGTTATTATTCAA
17484933 GTCACTA
1 GTCACTA
17484940 GGGTTTTAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 33 0.94
32 2 0.06
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (31 bp):
GTCACTAAACTATTCAAAAGTTATTATTCAA
Found at i:17491218 original size:24 final size:24
Alignment explanation
Indices: 17491170--17491216 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
17491160 ACTGGTCATA
*
17491170 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
17491194 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
17491217 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:17491997 original size:54 final size:53
Alignment explanation
Indices: 17491907--17492039 Score: 160
Period size: 54 Copynumber: 2.5 Consensus size: 53
17491897 AGACCCCAAA
* * *
17491907 ATAGGTAAAATAACTAAAATACCCTCATAGGATAAAATGACCAAAATACCCCC
1 ATAGGTAAAATGACTGAAATACCCCCATAGGATAAAATGACCAAAATACCCCC
* * *
17491960 ATAGGATAAAATGACTGAAATGCCCCCATAAGG-TAAAATGATCGAAATACCCCC
1 ATAGG-TAAAATGACTGAAATACCCCCAT-AGGATAAAATGACCAAAATACCCCC
**
17492014 ATAGGGTAAAATGACTGTTATACCCC
1 ATA-GGTAAAATGACTGAAATACCCC
17492040 TAGGAGATGA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
53 5 0.07
54 58 0.85
55 5 0.07
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.20
Consensus pattern (53 bp):
ATAGGTAAAATGACTGAAATACCCCCATAGGATAAAATGACCAAAATACCCCC
Found at i:17492036 original size:27 final size:27
Alignment explanation
Indices: 17491910--17492039 Score: 145
Period size: 27 Copynumber: 4.8 Consensus size: 27
17491900 CCCCAAAATA
* * *
17491910 GGTAAAATAACTAAAATACCCTCATAG
1 GGTAAAATGACTGAAATACCCCCATAG
* **
17491937 GATAAAATGACCAAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCCCATAG
* * *
17491964 GATAAAATGACTGAAATGCCCCCATAA
1 GGTAAAATGACTGAAATACCCCCATAG
17491991 GGTAAAATGA-TCGAAATACCCCCATAG
1 GGTAAAATGACT-GAAATACCCCCATAG
**
17492018 GGTAAAATGACTGTTATACCCC
1 GGTAAAATGACTGAAATACCCC
17492040 TAGGAGATGA
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
26 1 0.01
27 86 0.98
28 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACTGAAATACCCCCATAG
Found at i:17492053 original size:54 final size:54
Alignment explanation
Indices: 17491907--17492055 Score: 147
Period size: 54 Copynumber: 2.8 Consensus size: 54
17491897 AGACCCCAAA
* * * * *
17491907 ATAGG-TAAAATAACTAAAATACCCTCATAGGATAAAATGACCAAAATACCCCC
1 ATAGGATAAAATGACTGAAATACCCCCAGAAGATAAAATGACCAAAATACCCCC
* * * * *
17491960 ATAGGATAAAATGACTGAAATGCCCCCATAAGGTAAAATGATCGAAATACCCCC
1 ATAGGATAAAATGACTGAAATACCCCCAGAAGATAAAATGACCAAAATACCCCC
* ** * * *
17492014 ATAGGGTAAAATGACTGTTATACCCCTAGGAGATGAAATGAC
1 ATAGGATAAAATGACTGAAATACCCCCAGAAGATAAAATGAC
17492056 TGTTATGGCA
Statistics
Matches: 77, Mismatches: 18, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
53 5 0.06
54 72 0.94
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (54 bp):
ATAGGATAAAATGACTGAAATACCCCCAGAAGATAAAATGACCAAAATACCCCC
Found at i:17497113 original size:18 final size:18
Alignment explanation
Indices: 17497090--17497124 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17497080 TTCGAAACTT
*
17497090 TAGTGGAGAAGACTAAGG
1 TAGTGGAAAAGACTAAGG
*
17497108 TAGTGGAAAAGATTAAG
1 TAGTGGAAAAGACTAAG
17497125 CTCGTGGAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.34, T:0.20
Consensus pattern (18 bp):
TAGTGGAAAAGACTAAGG
Found at i:17504683 original size:17 final size:17
Alignment explanation
Indices: 17504661--17504696 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17504651 ACGCACAACA
* *
17504661 AATGATTTTACGGAAAT
1 AATGATTTCACGCAAAT
17504678 AATGATTTCACGCAAAT
1 AATGATTTCACGCAAAT
17504695 AA
1 AA
17504697 ACATTTTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (17 bp):
AATGATTTCACGCAAAT
Found at i:17511126 original size:60 final size:62
Alignment explanation
Indices: 17511012--17511130 Score: 170
Period size: 63 Copynumber: 1.9 Consensus size: 62
17511002 TCAATTTGTA
* * *
17511012 TTAGATATTATAATTATTTAAGTTTACTTTTTTACCTAATTAATATTTAAATACTATTTATAC
1 TTAGATATTATAATTATTGAACTTTAC-TTTTTACCAAATTAATATTTAAATACTATTTATAC
* *
17511075 TTAGATATTGTAATTATTGAACTTTA-TTTTTA-CAAATTAATATTTAGATACTATTT
1 TTAGATATTATAATTATTGAACTTTACTTTTTACCAAATTAATATTTAAATACTATTT
17511131 GTATTAGTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
60 22 0.43
61 6 0.12
63 23 0.45
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (62 bp):
TTAGATATTATAATTATTGAACTTTACTTTTTACCAAATTAATATTTAAATACTATTTATAC
Found at i:17515571 original size:18 final size:18
Alignment explanation
Indices: 17515538--17515572 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17515528 ACCAGCAGAT
* *
17515538 GGCATACTGACTTGTTGG
1 GGCATACTAACCTGTTGG
17515556 GGCATACTAACCTGTTG
1 GGCATACTAACCTGTTG
17515573 TGGAGAGCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (18 bp):
GGCATACTAACCTGTTGG
Found at i:17517429 original size:37 final size:35
Alignment explanation
Indices: 17517373--17517534 Score: 104
Period size: 37 Copynumber: 4.5 Consensus size: 35
17517363 ATATTGTTAA
17517373 TGAATGCATGATTAAGCATGTCATTAAGATTTTCAAACC
1 TGAA-GCATGA-TAAGCATGTCATTAA-ATTTT-AAACC
* ** *
17517412 TGAAGCATGATAAGCATGCCACCGAAATTGTTAAATC
1 TGAAGCATGATAAGCATGTCA-TTAAATT-TTAAACC
* * *
17517449 -GAAAGCATGATGAGCAT-TCA-T-ACTGTT-AA--
1 TG-AAGCATGATAAGCATGTCATTAAATTTTAAACC
*
17517478 TGAATGCATGATTAAACATGTCATTAAGATTTTCAAACC
1 TGAA-GCATGA-TAAGCATGTCATTAA-ATTTT-AAACC
17517517 TGAAGCATGATAAGCATG
1 TGAAGCATGATAAGCATG
17517535 CCACCGAAAT
Statistics
Matches: 95, Mismatches: 14, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
29 2 0.02
30 7 0.07
31 7 0.07
32 5 0.05
33 3 0.03
34 1 0.01
35 3 0.03
36 3 0.03
37 40 0.42
38 16 0.17
39 8 0.08
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (35 bp):
TGAAGCATGATAAGCATGTCATTAAATTTTAAACC
Found at i:17517549 original size:105 final size:105
Alignment explanation
Indices: 17517367--17517570 Score: 399
Period size: 105 Copynumber: 1.9 Consensus size: 105
17517357 GACATGATAT
*
17517367 TGTTAATGAATGCATGATTAAGCATGTCATTAAGATTTTCAAACCTGAAGCATGATAAGCATGCC
1 TGTTAATGAATGCATGATTAAACATGTCATTAAGATTTTCAAACCTGAAGCATGATAAGCATGCC
17517432 ACCGAAATTGTTAAATCGAAAGCATGATGAGCATTCATAC
66 ACCGAAATTGTTAAATCGAAAGCATGATGAGCATTCATAC
17517472 TGTTAATGAATGCATGATTAAACATGTCATTAAGATTTTCAAACCTGAAGCATGATAAGCATGCC
1 TGTTAATGAATGCATGATTAAACATGTCATTAAGATTTTCAAACCTGAAGCATGATAAGCATGCC
17517537 ACCGAAATTGTTAAATCGAAAGCATGATGAGCAT
66 ACCGAAATTGTTAAATCGAAAGCATGATGAGCAT
17517571 GCCATTGATA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 98 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (105 bp):
TGTTAATGAATGCATGATTAAACATGTCATTAAGATTTTCAAACCTGAAGCATGATAAGCATGCC
ACCGAAATTGTTAAATCGAAAGCATGATGAGCATTCATAC
Found at i:17517562 original size:37 final size:37
Alignment explanation
Indices: 17517414--17517574 Score: 117
Period size: 37 Copynumber: 4.5 Consensus size: 37
17517404 TTCAAACCTG
17517414 AAGCATGATAAGCATGCCACCGAAATTGTTAAATCGA
1 AAGCATGATAAGCATGCCACCGAAATTGTTAAATCGA
* * * *
17517451 AAGCATGATGAGCAT----TC-ATACTGTT-AAT-GA
1 AAGCATGATAAGCATGCCACCGAAATTGTTAAATCGA
* * * ** *
17517481 ATGCATGATTAAACATGTCA-TTAAGATT-TTCAAACCTG-
1 AAGCATGA-TAAGCATGCCACCGAA-ATTGTT-AAATC-GA
17517519 AAGCATGATAAGCATGCCACCGAAATTGTTAAATCGA
1 AAGCATGATAAGCATGCCACCGAAATTGTTAAATCGA
*
17517556 AAGCATGATGAGCATGCCA
1 AAGCATGATAAGCATGCCA
17517575 TTGATATTTT
Statistics
Matches: 92, Mismatches: 18, Indels: 28
0.67 0.13 0.20
Matches are distributed among these distances:
30 9 0.10
31 8 0.09
32 6 0.07
33 1 0.01
35 3 0.03
36 3 0.03
37 50 0.54
38 11 0.12
39 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (37 bp):
AAGCATGATAAGCATGCCACCGAAATTGTTAAATCGA
Found at i:17526482 original size:14 final size:13
Alignment explanation
Indices: 17526465--17526510 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
17526455 ACTTAAATTC
17526465 TAATAATAATAAAA
1 TAATAA-AATAAAA
17526479 TAATAAAAATAAAA
1 TAAT-AAAATAAAA
*
17526493 TAAATAAAGTAAAA
1 T-AATAAAATAAAA
17526507 TAAT
1 TAAT
17526511 TTAAAATACT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 3 0.10
14 21 0.72
15 5 0.17
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (13 bp):
TAATAAAATAAAA
Found at i:17529243 original size:14 final size:13
Alignment explanation
Indices: 17529207--17529246 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
17529197 TTAAATCGTA
17529207 ATTTTAGTAAAAT
1 ATTTTAGTAAAAT
17529220 ATTTTAGTAAAACT
1 ATTTTAGTAAAA-T
* *
17529234 TTTTTTGTAAAAT
1 ATTTTAGTAAAAT
17529247 CGAGGGTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (13 bp):
ATTTTAGTAAAAT
Found at i:17537653 original size:34 final size:34
Alignment explanation
Indices: 17537610--17537714 Score: 149
Period size: 34 Copynumber: 3.1 Consensus size: 34
17537600 CATGGCATTC
17537610 ATAGAGATAAGTCCGCTGGGACAGTAAACACGAA
1 ATAGAGATAAGTCCGCTGGGACAGTAAACACGAA
** * *
17537644 ATAGAGATAAGT-CTATCGGGATAGTAAACACAAA
1 ATAGAGATAAGTCCGCT-GGGACAGTAAACACGAA
*
17537678 ATAGAGATAAGTCCGCTGGGACAATAAACACGAA
1 ATAGAGATAAGTCCGCTGGGACAGTAAACACGAA
17537712 ATA
1 ATA
17537715 TATATAAATC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
33 2 0.03
34 56 0.93
35 2 0.03
ACGTcount: A:0.45, C:0.15, G:0.23, T:0.17
Consensus pattern (34 bp):
ATAGAGATAAGTCCGCTGGGACAGTAAACACGAA
Found at i:17537736 original size:68 final size:68
Alignment explanation
Indices: 17537610--17537737 Score: 175
Period size: 68 Copynumber: 1.9 Consensus size: 68
17537600 CATGGCATTC
* * * * ***
17537610 ATAGAGATAAGTCCGCTGGGACAGTAAACACGAAATAGAGATAAGTCTATCGGGATAGTAAACAC
1 ATAGAGATAAGTCCGCTGGGACAATAAACACGAAATAGAGATAAATCCACCAAAATAGTAAACAC
17537675 AAA
66 AAA
* *
17537678 ATAGAGATAAGTCCGCTGGGACAATAAACACGAAATATATATAAATCCACCAAAATAGTA
1 ATAGAGATAAGTCCGCTGGGACAATAAACACGAAATAGAGATAAATCCACCAAAATAGTA
17537738 GATATGGAAC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
68 51 1.00
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.19
Consensus pattern (68 bp):
ATAGAGATAAGTCCGCTGGGACAATAAACACGAAATAGAGATAAATCCACCAAAATAGTAAACAC
AAA
Found at i:17539832 original size:18 final size:18
Alignment explanation
Indices: 17539809--17539848 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
17539799 AAATCAAGAT
* *
17539809 AATGATTTTGAAATGGCA
1 AATGATATTGAAATAGCA
17539827 AATGATATTGAAATAGCA
1 AATGATATTGAAATAGCA
17539845 AATG
1 AATG
17539849 TTATGGAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
AATGATATTGAAATAGCA
Found at i:17541071 original size:18 final size:17
Alignment explanation
Indices: 17541026--17541071 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 17
17541016 AATGCCAAAA
17541026 TGGTATCGATATTTATT
1 TGGTATCGATATTTATT
17541043 TGGTATCGATATTTATT
1 TGGTATCGATATTTATT
*
17541060 TGAGTATTGATA
1 TG-GTATCGATA
17541072 CTTTTTCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.26, C:0.04, G:0.20, T:0.50
Consensus pattern (17 bp):
TGGTATCGATATTTATT
Found at i:17542275 original size:36 final size:36
Alignment explanation
Indices: 17542235--17542306 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
17542225 ATGACAATTC
*
17542235 TTTTCT-TTCTATTA-TATTAGTATTTTCTATTCTATT
1 TTTTCTATTCTATTAGTATTAG-A-TTACTATTCTATT
17542271 TTTTCTATTCTATTAGTATTAGATTACTATTCTATT
1 TTTTCTATTCTATTAGTATTAGATTACTATTCTATT
17542307 CTATTATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
36 18 0.55
37 9 0.27
38 6 0.18
ACGTcount: A:0.22, C:0.11, G:0.04, T:0.62
Consensus pattern (36 bp):
TTTTCTATTCTATTAGTATTAGATTACTATTCTATT
Found at i:17542276 original size:14 final size:14
Alignment explanation
Indices: 17542257--17542284 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17542247 TATATTAGTA
17542257 TTTTCTATTCTATT
1 TTTTCTATTCTATT
17542271 TTTTCTATTCTATT
1 TTTTCTATTCTATT
17542285 AGTATTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:17542292 original size:6 final size:6
Alignment explanation
Indices: 17542281--17542356 Score: 53
Period size: 5 Copynumber: 14.2 Consensus size: 6
17542271 TTTTCTATTC
* * * *
17542281 TATTAG TATTAG -ATTAC TATT-C TATT-C TATTAT TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
17542326 --TTAG -ATTAG -ATTAG -ATTAG -ATTAG TATTAG T
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG T
17542357 TAGTGATCCC
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
4 4 0.06
5 33 0.52
6 26 0.41
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (6 bp):
TATTAG
Found at i:17542336 original size:5 final size:5
Alignment explanation
Indices: 17542315--17542359 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
17542305 TTCTATTATT
17542315 ATTAG TATTAG -TTAG ATTAG ATTAG ATTAG ATTAG TATTAG -TTAG
1 ATTAG -ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG -ATTAG ATTAG
17542360 TGATCCCGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 8 0.22
5 19 0.51
6 10 0.27
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (5 bp):
ATTAG
Found at i:17545385 original size:15 final size:15
Alignment explanation
Indices: 17545365--17545395 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17545355 ATGATTATAT
17545365 TTTTAGAATATTTTA
1 TTTTAGAATATTTTA
*
17545380 TTTTAGAATGTTTTA
1 TTTTAGAATATTTTA
17545395 T
1 T
17545396 AGTCGTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (15 bp):
TTTTAGAATATTTTA
Found at i:17545706 original size:26 final size:27
Alignment explanation
Indices: 17545644--17545707 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
17545634 TTTATCGAGG
* * *
17545644 TTATTAGTGTATCGATAAATGAATATT
1 TTATTAATTTATCGATAAATGAATACT
*
17545671 TTATTAATTTATCGATAAATTAAT-CT
1 TTATTAATTTATCGATAAATGAATACT
17545697 TTATTAATTTA
1 TTATTAATTTA
17545708 GAGAATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 12 0.36
27 21 0.64
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.50
Consensus pattern (27 bp):
TTATTAATTTATCGATAAATGAATACT
Found at i:17546948 original size:15 final size:15
Alignment explanation
Indices: 17546928--17546956 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17546918 TAACCAAGAT
17546928 TATTAATTTATCGAA
1 TATTAATTTATCGAA
17546943 TATTAATTTATCGA
1 TATTAATTTATCGA
17546957 GGTTTTACTA
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:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (15 bp):
TATTAATTTATCGAA
Found at i:17547997 original size:25 final size:26
Alignment explanation
Indices: 17547956--17548006 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
17547946 AGTTGTAGAG
17547956 AGAAAATTCTCTAAAGAGATTATTTT
1 AGAAAATTCTCTAAAGAGATTATTTT
* *
17547982 AGAAAATT-TCTAAAGATATTTTTTT
1 AGAAAATTCTCTAAAGAGATTATTTT
17548007 GATTTACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (26 bp):
AGAAAATTCTCTAAAGAGATTATTTT
Found at i:17549420 original size:58 final size:58
Alignment explanation
Indices: 17549343--17549518 Score: 194
Period size: 58 Copynumber: 3.0 Consensus size: 58
17549333 GTAAGATAAA
* * *
17549343 CCTTAGCGGACTTCGCAACACTAGATAGTCTTAACGAACATCCTCTTCATTTTTTAGT
1 CCTTAGCGGACTTCCCAACACTAGATAGTCCTAACGAACATCCTCTTCATTTGTTAGT
* * * * *
17549401 CCTTGGCGGACTTCCCAACACTAGATAGTCCTAACGGATATCCTTCTT-ATTCGATAGT
1 CCTTAGCGGACTTCCCAACACTAGATAGTCCTAACGAACATCC-TCTTCATTTGTTAGT
* * * * * *
17549459 CTTTAGCGTATTTCCCAACACTAAATATTCCT-ACTAGACATCCTCTTCATTTGTTAGT
1 CCTTAGCGGACTTCCCAACACTAGATAGTCCTAACGA-ACATCCTCTTCATTTGTTAGT
17549517 CC
1 CC
17549519 CTGGCAAACT
Statistics
Matches: 95, Mismatches: 20, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
57 6 0.06
58 85 0.89
59 4 0.04
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (58 bp):
CCTTAGCGGACTTCCCAACACTAGATAGTCCTAACGAACATCCTCTTCATTTGTTAGT
Found at i:17550063 original size:35 final size:35
Alignment explanation
Indices: 17550019--17550094 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 35
17550009 GATAAGTAAG
* ** * *
17550019 TAGACCATTTTCATGGTGTCACTTCGCAGAGCCAA
1 TAGATCATTTTCATCATGTCACTCCACAGAGCCAA
* *
17550054 TAGATCATTTTCATCATGTCACTCCATAGAGCCAG
1 TAGATCATTTTCATCATGTCACTCCACAGAGCCAA
17550089 TAGATC
1 TAGATC
17550095 GTTTCCACGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (35 bp):
TAGATCATTTTCATCATGTCACTCCACAGAGCCAA
Found at i:17550108 original size:35 final size:35
Alignment explanation
Indices: 17550046--17550133 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 35
17550036 GTCACTTCGC
* * *
17550046 AGAGCCAATAGATCATTTTCATCATGTCACTCCAT
1 AGAGCCAGTAGATCGTTTCCATCATGTCACTCCAT
* *
17550081 AGAGCCAGTAGATCGTTTCCA-CGATGTCATTCTAT
1 AGAGCCAGTAGATCGTTTCCATC-ATGTCACTCCAT
* *
17550116 AGATCAAGTAGATCGTTT
1 AGAGCCAGTAGATCGTTT
17550134 ATTCAATCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 1 0.02
35 44 0.98
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32
Consensus pattern (35 bp):
AGAGCCAGTAGATCGTTTCCATCATGTCACTCCAT
Found at i:17553178 original size:38 final size:38
Alignment explanation
Indices: 17553101--17553237 Score: 125
Period size: 38 Copynumber: 3.6 Consensus size: 38
17553091 GTGAAAGGGA
** *
17553101 TCAACTGGTCCTTC-AGGGCAACACCGTGATAGCAATAT
1 TCAACTGGTCCTTCGA-GGCAACACCGTGACGGCAGTAT
**
17553139 TCAACTGGTCCTTCGAGGCAACACCGTGACGGTGGTAT
1 TCAACTGGTCCTTCGAGGCAACACCGTGACGGCAGTAT
* * * ** * *
17553177 TCAACTAGTCTTTCAAGGTGACACTGTGACGACAGTAT
1 TCAACTGGTCCTTCGAGGCAACACCGTGACGGCAGTAT
* *
17553215 TCGACT-GTCCTTCGAGGAAACAC
1 TCAACTGGTCCTTCGAGGCAACAC
17553238 TATGATAACG
Statistics
Matches: 79, Mismatches: 19, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
37 13 0.16
38 65 0.82
39 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (38 bp):
TCAACTGGTCCTTCGAGGCAACACCGTGACGGCAGTAT
Found at i:17553252 original size:37 final size:38
Alignment explanation
Indices: 17553197--17553299 Score: 102
Period size: 38 Copynumber: 2.7 Consensus size: 38
17553187 TTTCAAGGTG
* * * *
17553197 ACACTGTGACGACAGTATTCGACT-GTCCTTC-GAGGAA
1 ACACTATGACAACGGTATTCGAATGGTCCTTCAG-GGAA
* *
17553234 ACACTATGATAACGGTATTTGAATGGTCCTTCAGGGAA
1 ACACTATGACAACGGTATTCGAATGGTCCTTCAGGGAA
* * *
17553272 ACACTGTGACAACGATATTCAAATGGTC
1 ACACTATGACAACGGTATTCGAATGGTC
17553300 ATTCGGGGTA
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
37 18 0.34
38 34 0.64
39 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.26
Consensus pattern (38 bp):
ACACTATGACAACGGTATTCGAATGGTCCTTCAGGGAA
Found at i:17561051 original size:12 final size:12
Alignment explanation
Indices: 17561034--17561059 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17561024 ATAAAGCTTT
17561034 AATTAAGTAGTA
1 AATTAAGTAGTA
17561046 AATTAAGTAGTA
1 AATTAAGTAGTA
17561058 AA
1 AA
17561060 ATATGTACCA
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:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (12 bp):
AATTAAGTAGTA
Found at i:17562255 original size:28 final size:25
Alignment explanation
Indices: 17562183--17562255 Score: 74
Period size: 28 Copynumber: 2.7 Consensus size: 25
17562173 TATATTATGT
* *
17562183 AATTTATATTATATGAAAATTAAAT
1 AATTTATATTATATTAAAATTAAAA
*
17562208 AATTTATATTATGTTATAAACATTAAAA
1 AATTTATATTAT-AT-TAAA-ATTAAAA
17562236 AATTTAATACTTATATTAAA
1 AATTT-ATA-TTATATTAAA
17562256 GTACTTTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 12 0.31
26 1 0.03
27 3 0.08
28 15 0.38
29 4 0.10
30 4 0.10
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (25 bp):
AATTTATATTATATTAAAATTAAAA
Found at i:17562691 original size:3 final size:3
Alignment explanation
Indices: 17562672--17562712 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
17562662 TAATGGTTAG
* *
17562672 ATA ATA AAA ATA A-A ATA ATA ATA ATA ATA ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17562713 TGGACGATCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:17562853 original size:17 final size:17
Alignment explanation
Indices: 17562831--17562864 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17562821 TATTGATACC
*
17562831 ATACATGAGCCTTGCCT
1 ATACATGAACCTTGCCT
17562848 ATACATGAACCTTGCCT
1 ATACATGAACCTTGCCT
17562865 GAGTTTGGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (17 bp):
ATACATGAACCTTGCCT
Found at i:17567397 original size:36 final size:35
Alignment explanation
Indices: 17567357--17567434 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 35
17567347 ACTCTTTTTT
*
17567357 TTGGTGTGTTTCAGTTGGACTAGCTCTTCA-GAGCCA
1 TTGGTGTGTTTCAGATGGACTAGCTCTT-ATGAG-CA
** *
17567393 TTGGTGTGTTTTGGATGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCAGATGGACTAGCTCTTATGAGCA
17567428 TTGGTGT
1 TTGGTGT
17567435 ATGGCCTGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 10 0.27
36 27 0.73
ACGTcount: A:0.15, C:0.13, G:0.31, T:0.41
Consensus pattern (35 bp):
TTGGTGTGTTTCAGATGGACTAGCTCTTATGAGCA
Found at i:17573922 original size:572 final size:573
Alignment explanation
Indices: 17571513--17576100 Score: 8851
Period size: 573 Copynumber: 8.0 Consensus size: 573
17571503 TTAGATATTT
*
17571513 AATTAAAGAAAAAGTACGAAATTGAAAAAGGTGCAAAACTTAGTAATTATTACATTTAAAAGATG
1 AATTAAAGAAAAAGTACTAAATTGAAAAAGGTGCAAAACTTAGTAATTATTACATTTAAAAGATG
17571578 AAATAGCTTAATTACTAAAAGAGGAAGGACTTAAGTAACAATTAGGCCTTATGTAATGAGGTTGG
66 AAATAGCTTAATTACTAAAAGAGGAAGGACTTAAGTAACAATTAGGCCTTATGTAATGAGGTTGG
17571643 ACGGCAATTGATATTAAAATGTTAGAATAATATATGCTTAATGGCAAAATTGTAAATAAATCTAA
131 ACGGCAATTGATATTAAAATGTTAGAATAATATATGCTTAATGGCAAAATTGTAAATAAATCTAA
17571708 AGTAAAATAAAACAAATTGAAAGAAATAAGCTTTTATTCTTCATAATTTGACTTCATCTTTGCCT
196 AGTAAAATAAAACAAATTGAAAGAAATAAGCTTTTATTCTTCATAATTTGACTTCATCTTTGCCT
17571773 AAAATCCATGGAAGAATAGCTTGGAGAATCGGCTAGACTTAATACCTTGCATGTAAATGAATTTC
261 AAAATCCATGGAAGAATAGCTTGGAGAATCGGCTAGACTTAATACCTTGCATGTAAATGAATTTC
* * *
17571838 ATATATGTTTCTTGTAATTTTTATGATTTTGAGATTATTGCAACTACGTCCAGCTAGCCCGTACC
326 ATATATGTTTCTTGTAATTTTTATGTTTTTGAGATCATTGCAACTACGTCCAGCTAGCCCATACC
17571903 TTCGTTTTTGAATCTGTTAAAAATTTTAGAAGTTGCCGTTGATGAATCTTGAA-TTTTTTTTATG
391 TTCGTTTTTGAATCTGTTAAAAATTTTAGAAGTTGCCGTTGATGAATCTTGAATTTTTTTTTATG
17571967 ATAACCATGTCTTTGAAGCTTTAGTTGTGTTGTTTGATGATTTTGTAAAGTGATTTTTGTTAGAT
456 ATAACCATGTCTTTGAAGCTTTAGTTGTGTTGTTTGATGATTTTGTAAAGTGATTTTTGTTAGAT
* *
17572032 TTTGATTTTAGTATTAAATCGTGAAAATGTCAAAATTTTAGGGTTTGATAGTG
521 TTTGATTTTAGTATTAAACCGTGAAAATGTCAAAATTTTAGGGTTTGATAATG
17572085 AATTAAAGAAAAAGTACTAAATTGAAAAAGGTGCAAAACTTAGTAATTATTACATTTAAAAGATG
1 AATTAAAGAAAAAGTACTAAATTGAAAAAGGTGCAAAACTTAGTAATTATTACATTTAAAAGATG
17572150 AAATAGCTTAATTACTAAAAGAGGAAGGACTTAAGTAACAATTAGGCCTTATGTAATGAGGTTGG
66 AAATAGCTTAATTACTAAAAGAGGAAGGACTTAAGTAACAATTAGGCCTTATGTAATGAGGTTGG
17572215 ACGGCAATTGATATTAAAATGTTAGAATAATATATGCTTAATGGCAAAATTGTAAATAAATCTAA
131 ACGGCAATTGATATTAAAATGTTAGAATAATATATGCTTAATGGCAAAATTGTAAATAAATCTAA
17572280 AGTAAAATAAAACAAATTGAAAGAAATAAGCTTTTATTCTTCATAATTTGACTTCATCTTTGCCT
196 AGTAAAATAAAACAAATTGAAAGAAATAAGCTTTTATTCTTCATAATTTGACTTCATCTTTGCCT
17572345 AAAATCCATGGAAGAATAGCTTGGAGAATCGGCTAGACTTAATACCTTGCATGTAAATGAATTTC
261 AAAATCCATGGAAGAATAGCTTGGAGAATCGGCTAGACTTAATACCTTGCATGTAAATGAATTTC
17572410 ATATATGTTTCTTGTAATTTTTATGTTTTTGAGATCATTGCAACTACGTCCAGCTAGCCCATACC
326 ATATATGTTTCTTGTAATTTTTATGTTTTTGAGATCATTGCAACTACGTCCAGCTAGCCCATACC
17572475 TTCGTTTTTGAATCTGTTAAAAATTTTAGAAGTTGCCGTTGATGAATCTTGAATTTTTTTATTAT
391 TTCGTTTTTGAATCTGTTAAAAATTTTAGAAGTTGCCGTTGATGAATCTTGAATTTTTTT-TTAT
17572540 GATAACCATGTCTTTGAAGCTTTAGTTGTGTTGTTTGATGATTTTGTAAAGTGATTTTTGTTAGA
455 GATAACCATGTCTTTGAAGCTTTAGTTGTGTTGTTTGATGATTTTGTAAAGTGATTTTTGTTAGA
17572605 TTTTGATTTTAGTATTAAACCGTGAAAATGTCAAAATTTTAGGGTTTGATAATG
520 TTTTGATTTTAGTATTAAACCGTGAAAATGTCAAAATTTTAGGGTTTGATAATG
* *
17572659 AATTAAAGAAAAAGTACTAAATTGAAAAAGGTGCAAAAGTTAATAATTATTACATTTAAAAGATG
1 AATTAAAGAAAAAGTACTAAATTGAAAAAGGTGCAAAACTTAGTAATTATTACATTTAAAAGATG
17572724 AAATAGCTTAATTACTAAAAGAGGAAGGACTTAAGTAACAATTAGGCCTTATGTAATGAGGTTGG
66 AAATAGCTTAATTACTAAAAGAGGAAGGACTTAAGTAACAATTAGGCCTTATGTAATGAGGTTGG
17572789 ACGGCAATTGATATTAAAATGTTAGAATAATATATGCTTAATGGCAAAATTGTAAATAAATCTAA
131 ACGGCAATTGATATTAAAATGTTAGAATAATATATGCTTAATGGCAAAATTGTAAATAAATCTAA
17572854 AGTAAAAT-AAACAAATTGAAAGAAATAAGCTTTTATTCTTCATAATTTGACTTCATCTTTGCCT
196 AGTAAAATAAAACAAATTGAAAGAAATAAGCTTTTATTCTTCATAATTTGACTTCATCTTTGCCT
17572918 AAAATCCATGGAAGAATAGCTTGGAGAATCGGCTAGACTTAATACCTTGCATGTAAATGAATTTC
261 AAAATCCATGGAAGAATAGCTTGGAGAATCGGCTAGACTTAATACCTTGCATGTAAATGAATTTC
* *
17572983 ATATATGTTTCTTGTAATTTTTATGTTTTTGAGATTATTGCAACTACGTCCAGCTAGCCCGTACC
326 ATATATGTTTCTTGTAATTTTTATGTTTTTGAGATCATTGCAACTACGTCCAGCTAGCCCATACC
17573048 TTCGTTTTTGAATCTGTTAAAAATTTTAGAAGTTGCCGTTGATGAATCTTGAATTTTTTTTTTAT
391 TTCGTTTTTGAATCTGTTAAAAATTTTAGAAGTTGCCGTTGATGAATCTTGAA-TTTTTTTTTAT
17573113 GATAACCATGTCTTTGAAGCTTTAGTTGTGTTGTTTGATGATTTTGTAAAGTGATTTTTGTTAGA
455 GATAACCATGTCTTTGAAGCTTTAGTTGTGTTGTTTGATGATTTTGTAAAGTGATTTTTGTTAGA
17573178 TTTTGATTTTAGTATTAAACCGTGAAAATGTCAAAATTTTAGGGTTTGATAATG
520 TTTTGATTTTAGTATTAAACCGTGAAAATGTCAAAATTTTAGGGTTTGATAATG
17573232 AATTAAAGAAAAAGTACTAAATTGAAAAAGGTGCAAAACTTAGTAATTATTACATTTAAAAGATG
1 AATTAAAGAAAAAGTACTAAATTGAAAAAGGTGCAAAACTTAGTAATTATTACATTTAAAAGATG
17573297 AAATAGCTTAATTACTAAAAGAGGAAGGACTTAAGTAACAATTAGGCCTTATGTAATGAGGTTGG
66 AAATAGCTTAATTACTAAAAGAGGAAGGACTTAAGTAACAATTAGGCCTTATGTAATGAGGTTGG
17573362 ACGGCAATTGATATTAAAATGTTAGAATAATATATGCTTAATGGCAAAATTGTAAATAAATCTAA
131 ACGGCAATTGATATTAAAATGTTAGAATAATATATGCTTAATGGCAAAATTGTAAATAAATCTAA
17573427 AGTAAAATAAAACAAATTGAAAGAAATAAGCTTTTATTCTTCATAATTTGACTTCATCTTTGCCT
196 AGTAAAATAAAACAAATTGAAAGAAATAAGCTTTTATTCTTCATAATTTGACTTCATCTTTGCCT
17573492 AAAATCCATGGAAGAATAGCTTGGAGAATCGGCTAGACTTAATACCTTGCATGTAAATGAATTTC
261 AAAATCCATGGAAGAATAGCTTGGAGAATCGGCTAGACTTAATACCTTGCATGTAAATGAATTTC
* * *
17573557 ATATATGTTTCTTGTAATTTTTATGATTTTGAGATTATTGCAACTACGTCCAGCTAGCCCGTACC
326 ATATATGTTTCTTGTAATTTTTATGTTTTTGAGATCATTGCAACTACGTCCAGCTAGCCCATACC
17573622 TTCGTTTTTGAATCTGTTAAAAATTTTAGAAGTTGCCGTTGATGAATCTTGAA-TTTTTTTTATG
391 TTCGTTTTTGAATCTGTTAAAAATTTTAGAAGTTGCCGTTGATGAATCTTGAATTTTTTTTTATG
17573686 ATAACCATGTCTTTGAAGCTTTAGTTGTGTTGTTTGATGATTTTGTAAAGTGATTTTTGTTAGAT
456 ATAACCATGTCTTTGAAGCTTTAGTTGTGTTGTTTGATGATTTTGTAAAGTGATTTTTGTTAGAT
* *
17573751 TTTGATTTTAGTATTAAATCGTGAAAATGTCAAAATTTTAGGGTTTGATAGTG
521 TTTGATTTTAGTATTAAACCGTGAAAATGTCAAAATTTTAGGGTTTGATAATG
17573804 AATTAAAGAAAAAGTACTAAATTGAAAAAGGTGCAAAACTTAGTAATTATTACATTTAAAAGATG
1 AATTAAAGAAAAAGTACTAAATTGAAAAAGGTGCAAAACTTAGTAATTATTACATTTAAAAGATG
17573869 AAATAGCTTAATTACTAAAAGAGGAAGGACTTAAGTAACAATTAGGCCTTATGTAATGAGGTTGG
66 AAATAGCTTAATTACTAAAAGAGGAAGGACTTAAGTAACAATTAGGCCTTATGTAATGAGGTTGG
17573934 ACGGCAATTGATATTAAAATGTTAGAATAATATATGCTTAATGGCAAAATTGTAAATAAATCTAA
131 ACGGCAATTGATATTAAAATGTTAGAATAATATATGCTTAATGGCAAAATTGTAAATAAATCTAA
17573999 AGTAAAATAAAACAAATTGAAAGAAATAAGCTTTTATTCTTCATAATTTGACTTCATCTTTGCCT
196 AGTAAAATAAAACAAATTGAAAGAAATAAGCTTTTATTCTTCATAATTTGACTTCATCTTTGCCT
17574064 AAAATCCATGGAAGAATAGCTTGGAGAATCGGCTAGACTTAATACCTTGCATGTAAATGAATTTC
261 AAAATCCATGGAAGAATAGCTTGGAGAATCGGCTAGACTTAATACCTTGCATGTAAATGAATTTC
17574129 ATATATGTTTCTTGTAATTTTTATGTTTTTGAGATCATTGCAACTACGTCCAGCTAGCCCATACC
326 ATATATGTTTCTTGTAATTTTTATGTTTTTGAGATCATTGCAACTACGTCCAGCTAGCCCATACC
17574194 TTCGTTTTTGAATCTGTTAAAAATTTTAGAAGTTGCCGTTGATGAATCTTGAATTTTTTTATTAT
391 TTCGTTTTTGAATCTGTTAAAAATTTTAGAAGTTGCCGTTGATGAATCTTGAATTTTTTT-TTAT
17574259 GATAACCATGTCTTTGAAGCTTTAGTTGTGTTGTTTGATGATTTTGTAAAGTGATTTTTGTTAGA
455 GATAACCATGTCTTTGAAGCTTTAGTTGTGTTGTTTGATGATTTTGTAAAGTGATTTTTGTTAGA
17574324 TTTTGATTTTAGTATTAAACCGTGAAAATGTCAAAATTTTAGGGTTTGATAATG
520 TTTTGATTTTAGTATTAAACCGTGAAAATGTCAAAATTTTAGGGTTTGATAATG
* *
17574378 AATTAAAGAAAAAGTACTAAATTGAAAAAGGTGCAAAAGTTAATAATTATTACATTTAAAAGATG
1 AATTAAAGAAAAAGTACTAAATTGAAAAAGGTGCAAAACTTAGTAATTATTACATTTAAAAGATG
17574443 AAATAGCTTAATTACTAAAAGAGGAAGGACTTAAGTAACAATTAGGCCTTATGTAATGAGGTTGG
66 AAATAGCTTAATTACTAAAAGAGGAAGGACTTAAGTAACAATTAGGCCTTATGTAATGAGGTTGG
17574508 ACGGCAATTGATATTAAAATGTTAGAATAATATATGCTTAATGGCAAAATTGTAAATAAATCTAA
131 ACGGCAATTGATATTAAAATGTTAGAATAATATATGCTTAATGGCAAAATTGTAAATAAATCTAA
17574573 AGTAAAATAAAACAAATTGAAAGAAATAAGCTTTTATTCTTCATAATTTGACTTCATCTTTGCCT
196 AGTAAAATAAAACAAATTGAAAGAAATAAGCTTTTATTCTTCATAATTTGACTTCATCTTTGCCT
17574638 AAAATCCATGGAAGAATAGCTTGGAGAATCGGCTAGACTTAATACCTTGCATGTAAATGAATTTC
261 AAAATCCATGGAAGAATAGCTTGGAGAATCGGCTAGACTTAATACCTTGCATGTAAATGAATTTC
* *
17574703 ATATATGTTTCTTGTAATTTTTATGTTTTTGAGATTATTGCAACTACGTCCAGCTAGCCCGTACC
326 ATATATGTTTCTTGTAATTTTTATGTTTTTGAGATCATTGCAACTACGTCCAGCTAGCCCATACC
17574768 TTCGTTTTTGAATCTGTTAAAAATTTTAGAAGTTGCCGTTGATGAATCTTGAATTTTTTTTTATG
391 TTCGTTTTTGAATCTGTTAAAAATTTTAGAAGTTGCCGTTGATGAATCTTGAATTTTTTTTTATG
17574833 ATAACCATGTCTTTGAAGCTTTAGTTGTGTTGTTTGATGATTTTGTAAAGTGATTTTTGTTAGAT
456 ATAACCATGTCTTTGAAGCTTTAGTTGTGTTGTTTGATGATTTTGTAAAGTGATTTTTGTTAGAT
17574898 TTTGATTTTAGTATTAAACCGTGAAAATGTCAAAATTTTAGGGTTTGATAATG
521 TTTGATTTTAGTATTAAACCGTGAAAATGTCAAAATTTTAGGGTTTGATAATG
17574951 AATTAAAGAAAAAGTACTAAATTGAAAAAGGTGCAAAACTTAGTAATTATTACATTTAAAAGATG
1 AATTAAAGAAAAAGTACTAAATTGAAAAAGGTGCAAAACTTAGTAATTATTACATTTAAAAGATG
17575016 AAATAGCTTAATTACTAAAAGAGGAAGGACTTAAGTAACAATTAGGCCTTATGTAATGAGGTTGG
66 AAATAGCTTAATTACTAAAAGAGGAAGGACTTAAGTAACAATTAGGCCTTATGTAATGAGGTTGG
*
17575081 ACGGCAATTGATATTAAAATGTTAGAATAATATATGCTTAATGGAAAAATTGTAAATAAATCTAA
131 ACGGCAATTGATATTAAAATGTTAGAATAATATATGCTTAATGGCAAAATTGTAAATAAATCTAA
17575146 AGTAAAATAAAACAAATTGAAAGAAATAAGCTTTTATTCTTCATAATTTGACTTCATCTTTGCCT
196 AGTAAAATAAAACAAATTGAAAGAAATAAGCTTTTATTCTTCATAATTTGACTTCATCTTTGCCT
17575211 AAAATCCATGGAAGAATAGCTTGGAGAATCGGCTAGACTTAATACCTTGCATGTAAATGAATTTC
261 AAAATCCATGGAAGAATAGCTTGGAGAATCGGCTAGACTTAATACCTTGCATGTAAATGAATTTC
*
17575276 ATATATGTTTCTTGTAATTTTTATGTTTTTGAGATCATTGCAACTACGTCCAGCTAGCCCAAACC
326 ATATATGTTTCTTGTAATTTTTATGTTTTTGAGATCATTGCAACTACGTCCAGCTAGCCCATACC
*
17575341 TTCGTTTTTGAATCTGTTAAAAATTTTAGAAGTTGCCATTGATGAATCTTGAATTTTTTTTTATG
391 TTCGTTTTTGAATCTGTTAAAAATTTTAGAAGTTGCCGTTGATGAATCTTGAATTTTTTTTTATG
17575406 ATAACCATGTCTTTGAAGCTTTAGTTGTGTTGTTTGATGATTTTGTAAAGTGATTTTTGTTAGAT
456 ATAACCATGTCTTTGAAGCTTTAGTTGTGTTGTTTGATGATTTTGTAAAGTGATTTTTGTTAGAT
*
17575471 TTTGATTTTAGTATTAAATCGTGAAAATGTCAAAATTTTAGGGTTTGATAATG
521 TTTGATTTTAGTATTAAACCGTGAAAATGTCAAAATTTTAGGGTTTGATAATG
17575524 AATTAAAGAAAAAGTACTAAATTGAAAAAGGTGCAAAACTTAGTAATTATTACATTTAAAAGATG
1 AATTAAAGAAAAAGTACTAAATTGAAAAAGGTGCAAAACTTAGTAATTATTACATTTAAAAGATG
17575589 AAATAGCTTAATTACTAAAAGAGGAAGGACTTAAGTAACAATTAGGCCTTAT-TGAATGAGGTTG
66 AAATAGCTTAATTACTAAAAGAGGAAGGACTTAAGTAACAATTAGGCCTTATGT-AATGAGGTTG
17575653 GACGGCAATTGATATTAAAATGTTAGAATAATATATGCTTAATGGCAAAATTGTAAATAAATCTA
130 GACGGCAATTGATATTAAAATGTTAGAATAATATATGCTTAATGGCAAAATTGTAAATAAATCTA
17575718 AAGTAAAATAAAACAAATTGAAAGAAATAAGCTTTTATTCTTCATAATTTGACTTCATCTTTGCC
195 AAGTAAAATAAAACAAATTGAAAGAAATAAGCTTTTATTCTTCATAATTTGACTTCATCTTTGCC
17575783 TAAAATCCATGGAAGAATAGCTTGGAGAATCGGCTAGACTTAATACCTTGCATGTAAATGAATTT
260 TAAAATCCATGGAAGAATAGCTTGGAGAATCGGCTAGACTTAATACCTTGCATGTAAATGAATTT
*
17575848 CATATATGTTTCTTGTAATTTTTATGTTTTTGAGATCATTGCAACTACGTCCAGCTAGCCCAAAC
325 CATATATGTTTCTTGTAATTTTTATGTTTTTGAGATCATTGCAACTACGTCCAGCTAGCCCATAC
*
17575913 CTTCGTTTTTGAATCTGTTAAAAATTTTAGAAGTTGCCGTTGATGAATCTTAAATTTTTTTTTAT
390 CTTCGTTTTTGAATCTGTTAAAAATTTTAGAAGTTGCCGTTGATGAATCTTGAATTTTTTTTTAT
*
17575978 GATAACCATGTCTTTGAAGCTTTAGTTGTGTTGTTTGATGATTTTGTAACGTGATTTTTGTTAGA
455 GATAACCATGTCTTTGAAGCTTTAGTTGTGTTGTTTGATGATTTTGTAAAGTGATTTTTGTTAGA
* * *
17576043 TTTTGATTTTAGTATTAAATCATGAAAATGTCAAAATTTTAGGGTTTGATAGTG
520 TTTTGATTTTAGTATTAAACCGTGAAAATGTCAAAATTTTAGGGTTTGATAATG
17576097 AATT
1 AATT
17576101 TGATGTTCAT
Statistics
Matches: 3971, Mismatches: 38, Indels: 13
0.99 0.01 0.00
Matches are distributed among these distances:
572 1007 0.25
573 1830 0.46
574 1134 0.29
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (573 bp):
AATTAAAGAAAAAGTACTAAATTGAAAAAGGTGCAAAACTTAGTAATTATTACATTTAAAAGATG
AAATAGCTTAATTACTAAAAGAGGAAGGACTTAAGTAACAATTAGGCCTTATGTAATGAGGTTGG
ACGGCAATTGATATTAAAATGTTAGAATAATATATGCTTAATGGCAAAATTGTAAATAAATCTAA
AGTAAAATAAAACAAATTGAAAGAAATAAGCTTTTATTCTTCATAATTTGACTTCATCTTTGCCT
AAAATCCATGGAAGAATAGCTTGGAGAATCGGCTAGACTTAATACCTTGCATGTAAATGAATTTC
ATATATGTTTCTTGTAATTTTTATGTTTTTGAGATCATTGCAACTACGTCCAGCTAGCCCATACC
TTCGTTTTTGAATCTGTTAAAAATTTTAGAAGTTGCCGTTGATGAATCTTGAATTTTTTTTTATG
ATAACCATGTCTTTGAAGCTTTAGTTGTGTTGTTTGATGATTTTGTAAAGTGATTTTTGTTAGAT
TTTGATTTTAGTATTAAACCGTGAAAATGTCAAAATTTTAGGGTTTGATAATG
Found at i:17588252 original size:15 final size:14
Alignment explanation
Indices: 17588217--17588246 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
17588207 ATTTTGTTCC
17588217 AAAATTTCAAAAAT
1 AAAATTTCAAAAAT
17588231 AAAATTTCAAAAAT
1 AAAATTTCAAAAAT
17588245 AA
1 AA
17588247 TTATTTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATTTCAAAAAT
Found at i:17588366 original size:18 final size:18
Alignment explanation
Indices: 17588324--17588366 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
17588314 CTAGTTTTGA
* *
17588324 AATTATTTATTAATTTTTT
1 AATT-TTTATGAATTTTCT
*
17588343 ATTTTTTATGAATTTTCT
1 AATTTTTATGAATTTTCT
17588361 AATTTT
1 AATTTT
17588367 ATAAAACAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
AATTTTTATGAATTTTCT
Found at i:17590319 original size:17 final size:16
Alignment explanation
Indices: 17590274--17590310 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
17590264 TTTTTATAAT
17590274 ATTTTAAAAAAATGAC
1 ATTTTAAAAAAATGAC
17590290 ATTTTAAAAAAATGAC
1 ATTTTAAAAAAATGAC
17590306 ATTTT
1 ATTTT
17590311 TTTAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTTTAAAAAAATGAC
Found at i:17596516 original size:20 final size:21
Alignment explanation
Indices: 17596479--17596519 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
17596469 TATATAATCA
17596479 TTATTTTCATAATCTATATAT
1 TTATTTTCATAATCTATATAT
17596500 TTATTTT-ATAA-CTTATATAT
1 TTATTTTCATAATC-TATATAT
17596520 GTACATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.05
20 11 0.58
21 7 0.37
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTTCATAATCTATATAT
Found at i:17608992 original size:45 final size:44
Alignment explanation
Indices: 17608910--17609335 Score: 334
Period size: 45 Copynumber: 9.6 Consensus size: 44
17608900 GGATTGGAGT
* *
17608910 AAGCAAGTCTAATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAAGA
1 AAGCAAGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA
** * * * *
17608955 TGGCAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCC
1 AAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-A
* * * * *
17609001 AA-TAA-TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAG-
1 AAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGA
** * * *
17609042 GTG-ATAGATCTTATCTCTCTGAAGTTGCAGTAGG-GTAGA-T--CA
1 AAGCA-AG-TCTTATCTCCCTGAAGTTGCAGT-GGAGCAGACTAAGA
* * *
17609084 CATCAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGA
1 AAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGA
* * * *
17609129 AAGCAGGTCTTATCTCCCTGAGGTTGCAATGGAGCAGGCCTAAGA
1 AAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA-GACTAAGA
** *
17609174 AAGCAAGTCTTATCTCTTTGAAGTTGCAGTGGAGCAGACCCAAGA
1 AAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAGA
* * * * * *
17609219 AAGCGATTTTTATCTCCCTAAAGTTACAGTAGAGCAGACTAAGA
1 AAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGA
*
17609263 AAGCAAGTCTTATCTCCCT-AAGGTTGTAGTGGAGCAGACTCAAGA
1 AAGCAAGTCTTATCTCCCTGAA-GTTGCAGTGGAGCAGACT-AAGA
*
17609308 AAGCAAGTCTTATCTCCCTAAAGTTGCA
1 AAGCAAGTCTTATCTCCCTGAAGTTGCA
17609336 ATGGTGTAAT
Statistics
Matches: 304, Mismatches: 57, Indels: 40
0.76 0.14 0.10
Matches are distributed among these distances:
40 2 0.01
41 27 0.09
42 3 0.01
43 7 0.02
44 89 0.29
45 168 0.55
46 8 0.03
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (44 bp):
AAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGA
Found at i:17609057 original size:44 final size:44
Alignment explanation
Indices: 17608960--17609165 Score: 145
Period size: 44 Copynumber: 4.7 Consensus size: 44
17608950 GAAGATGGCA
*
17608960 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * * ***
17609004 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATT-AAGGTGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * * * *
17609047 AGATCTTATCTCTCTGAAGTTGCAGTAGG-GTAGATCACA-TC-A-
1 A-ATCTTATCTCCCTGAAGTTGCAGT-GGAGCAGATTAAAGCCAAT
** * * * *
17609089 GGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAG-AAAGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA-T
* * *
17609133 AGGTCTTATCTCCCTGAGGTTGCAATGGAGCAG
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAG
17609166 GCCTAAGAAA
Statistics
Matches: 125, Mismatches: 28, Indels: 17
0.74 0.16 0.10
Matches are distributed among these distances:
40 2 0.02
41 27 0.22
42 1 0.01
43 7 0.06
44 56 0.45
45 32 0.26
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
Found at i:17609307 original size:89 final size:89
Alignment explanation
Indices: 17609090--17609337 Score: 329
Period size: 89 Copynumber: 2.8 Consensus size: 89
17609080 ATCACATCAG
* * *
17609090 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAGGTCTTATCTCCCTGAGGTTG
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA-GTCTTATCTCCCTAAAGTTA
* *
17609155 CAATGGAGCAGGCCTAAGAAAGCAA
65 CAATAGAGCAGGACTAAGAAAGCAA
** * * *
17609180 GTCTTATCTCTTTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCGATTTTTATCTCCCTAAAGTTA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGC-AGTCTTATCTCCCTAAAGTTA
*
17609245 CAGTAGAGCA-GACTAAGAAAGCAA
65 CAATAGAGCAGGACTAAGAAAGCAA
*
17609269 GTCTTATCTCCCT-AAGGTTGTAGTGGAGCAGACTCAAGAAAGCAAGTCTTATCTCCCTAAAGTT
1 GTCTTATCTCCCTGAA-GTTGCAGTGGAGCAGACTCAAGAAAGC-AGTCTTATCTCCCTAAAGTT
*
17609333 GCAAT
64 ACAAT
17609338 GGTGTAATGA
Statistics
Matches: 136, Mismatches: 20, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
88 2 0.01
89 70 0.51
90 63 0.46
91 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (89 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAGTCTTATCTCCCTAAAGTTAC
AATAGAGCAGGACTAAGAAAGCAA
Found at i:17609334 original size:134 final size:135
Alignment explanation
Indices: 17609093--17609335 Score: 364
Period size: 134 Copynumber: 1.8 Consensus size: 135
17609083 ACATCAGGTC
* * * * *
17609093 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAGGTCTTATCTCCCTGAGGTTGCAA
1 TTATCTCCCTAAAGTTACAGTAGAGCAGACTCAAGAAAGCAAGTCTTATCTCCCTAAGGTTGCAA
* ** *
17609158 TGGAGCAGGCCTAAGAAAGCAAGTCTTATCTCTTTGAAGTTGCAGTGGAGCAGACCCAAGAAAGC
66 TGGAGCAGACCTAAGAAAGCAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACCCAAGAAAGC
17609223 GATTT
131 GATTT
* *
17609228 TTATCTCCCTAAAGTTACAGTAGAGCAGACT-AAGAAAGCAAGTCTTATCTCCCTAAGGTTGTAG
1 TTATCTCCCTAAAGTTACAGTAGAGCAGACTCAAGAAAGCAAGTCTTATCTCCCTAAGGTTGCAA
17609292 TGGAGCAGA-CTCAAGAAAGCAAGTCTTATCTCCCTAAAGTTGCA
66 TGGAGCAGACCT-AAGAAAGCAAGTCTTATCTCCCTAAAGTTGCA
17609336 ATGGTGTAAT
Statistics
Matches: 96, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
133 2 0.02
134 66 0.69
135 28 0.29
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (135 bp):
TTATCTCCCTAAAGTTACAGTAGAGCAGACTCAAGAAAGCAAGTCTTATCTCCCTAAGGTTGCAA
TGGAGCAGACCTAAGAAAGCAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACCCAAGAAAGC
GATTT
Found at i:17609661 original size:14 final size:14
Alignment explanation
Indices: 17609644--17609689 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
17609634 TAAAAAAATG
17609644 TTATTAAATTATTA
1 TTATTAAATTATTA
*
17609658 TTATTAAATTAGTA
1 TTATTAAATTATTA
17609672 TTATTAAATTATTA
1 TTATTAAATTATTA
17609686 TTAT
1 TTAT
17609690 ATTTTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TTATTAAATTATTA
Found at i:17609824 original size:3 final size:3
Alignment explanation
Indices: 17609818--17609846 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
17609808 TATTAAAATA
17609818 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
17609847 ACTAGGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:17611035 original size:23 final size:22
Alignment explanation
Indices: 17611008--17611092 Score: 95
Period size: 21 Copynumber: 4.0 Consensus size: 22
17610998 GGCTTTGCCG
* *
17611008 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACCTCATGTGTCGT-T
*
17611031 ATCAGGCACCTCGTGTGTCG-T
1 ATCAGGCACCTCATGTGTCGTT
*
17611052 ATCAGGCACCTCGTGTGTCGTT
1 ATCAGGCACCTCATGTGTCGTT
*
17611074 -TCAGGCA-CTTATGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
17611093 ATACTGATCA
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.18
21 28 0.50
22 1 0.02
23 17 0.30
ACGTcount: A:0.16, C:0.24, G:0.26, T:0.34
Consensus pattern (22 bp):
ATCAGGCACCTCATGTGTCGTT
Found at i:17611054 original size:21 final size:21
Alignment explanation
Indices: 17611021--17611094 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
17611011 AGGCACTTTA
17611021 TGTGTCGTATATCAGGCACCTCG
1 TGTGTCG--TATCAGGCACCTCG
17611044 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
* **
17611065 TGTGTCGTTTCAGGCA-CTTA
1 TGTGTCGTATCAGGCACCTCG
17611085 TGTGTCGTAT
1 TGTGTCGTAT
17611095 ACTGATCAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
20 11 0.23
21 29 0.62
23 7 0.15
ACGTcount: A:0.15, C:0.23, G:0.27, T:0.35
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:17611772 original size:9 final size:9
Alignment explanation
Indices: 17611758--17611785 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
17611748 GAATATGAAA
17611758 TGAATTGGT
1 TGAATTGGT
17611767 TGAATTGGT
1 TGAATTGGT
17611776 TGAATTGGT
1 TGAATTGGT
17611785 T
1 T
17611786 ATGTTTGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.46
Consensus pattern (9 bp):
TGAATTGGT
Found at i:17618593 original size:20 final size:21
Alignment explanation
Indices: 17618556--17618596 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
17618546 TATATAATCA
17618556 TTATTTTCATAATCTATATAT
1 TTATTTTCATAATCTATATAT
17618577 TTATTTT-ATAA-CTTATATAT
1 TTATTTTCATAATC-TATATAT
17618597 GTACATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.05
20 11 0.58
21 7 0.37
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTTCATAATCTATATAT
Found at i:17620952 original size:16 final size:16
Alignment explanation
Indices: 17620919--17620964 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
17620909 AATTCAAATC
17620919 TAAA-TTTAAATTAATT
1 TAAATTTTAAA-TAATT
17620935 TAAATTTTAAAT-ATT
1 TAAATTTTAAATAATT
*
17620950 TTAATTTTCAAATAA
1 TAAATTTT-AAATAA
17620965 AAAATTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 10 0.38
16 9 0.35
17 7 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAATTTTAAATAATT
Found at i:17629179 original size:44 final size:44
Alignment explanation
Indices: 17629105--17629243 Score: 135
Period size: 45 Copynumber: 3.2 Consensus size: 44
17629095 CATTGGAATA
* *
17629105 ATAA-CAA-ATACACGGTGG-ATCAGCACATAGC-ATCACCCTT-
1 ATAATCAATATACTCGGTGGAATCAGCACATAGCAACCA-CCTTC
* *
17629145 ATAGTCAATGATACTCGGTGGAATTAGCACATAGCAACCACCTTC
1 ATAATCAAT-ATACTCGGTGGAATCAGCACATAGCAACCACCTTC
* * * * *
17629190 ATAATCAATAGTACTCGGTGGAATCAACACACAACAACCACTTTT
1 ATAATCAATA-TACTCGGTGGAATCAGCACATAGCAACCACCTTC
17629235 ATAATCAAT
1 ATAATCAAT
17629244 GGTACCCGGT
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
40 3 0.04
41 3 0.04
43 10 0.12
44 17 0.21
45 48 0.59
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (44 bp):
ATAATCAATATACTCGGTGGAATCAGCACATAGCAACCACCTTC
Found at i:17636586 original size:33 final size:33
Alignment explanation
Indices: 17636549--17636619 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
17636539 GAAGTCCAAG
17636549 GAGCTTGCTCTTGAAGCCTCCAAGAAA-GCCGAT
1 GAGCTTGCTCTTGAAGCCTCCAA-AAAGGCCGAT
*
17636582 GAGCTTGCTCTTGAAGCTTCCAAAAAGGCCGAT
1 GAGCTTGCTCTTGAAGCCTCCAAAAAGGCCGAT
17636615 GAGCT
1 GAGCT
17636620 CAAAGTCGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 3 0.08
33 33 0.92
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (33 bp):
GAGCTTGCTCTTGAAGCCTCCAAAAAGGCCGAT
Found at i:17638062 original size:6 final size:6
Alignment explanation
Indices: 17638051--17638080 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
17638041 ATTATTCAGA
17638051 TGATGG TGATGG TGATGG TGATGG TGATGG
1 TGATGG TGATGG TGATGG TGATGG TGATGG
17638081 GAGCTTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
TGATGG
Found at i:17638838 original size:123 final size:126
Alignment explanation
Indices: 17638685--17638940 Score: 351
Period size: 127 Copynumber: 2.0 Consensus size: 126
17638675 TGCATTACTA
* * *
17638685 TTTTATATCATATCATGTGACATG-ACTT-TTTTTAATAAAATATTTTATTTTTATATAATTAAT
1 TTTTATATCATATCATATGACATGAATTTATTTTTAATAAAATA-TTTAATTTTATATAATTAAT
* * * * *
17638748 ATAAATAATCATTATTAGTAGATATGT-AAATGTATAAAATATTTTAAAATATTCTTTAGT-
65 ATAAATAACCATTATTAGGAGATAAGTAAAATATATAAAATATTTTAAAATATTCATTAGTG
17638808 TTTTATATCATATCATATAGACAT-AATTTTTTATTTTTAATAAAATATTTAATTTTATATAATT
1 TTTTATATCATATCATAT-GACATGAA---TTTATTTTTAATAAAATATTTAATTTTATATAATT
*
17638872 AATATAAATAACCATTATTAGGAGATAAGTAAAATATATAATATATTTTAAAATATTCATTAGTG
62 AATATAAATAACCATTATTAGGAGATAAGTAAAATATATAAAATATTTTAAAATATTCATTAGTG
17638937 TTTT
1 TTTT
17638941 TTGAAACAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
123 17 0.15
124 6 0.05
127 45 0.39
128 44 0.38
129 4 0.03
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (126 bp):
TTTTATATCATATCATATGACATGAATTTATTTTTAATAAAATATTTAATTTTATATAATTAATA
TAAATAACCATTATTAGGAGATAAGTAAAATATATAAAATATTTTAAAATATTCATTAGTG
Found at i:17642610 original size:3 final size:3
Alignment explanation
Indices: 17642602--17642630 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
17642592 GAATGGAAAT
17642602 ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17642631 TTCGGGTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:17657809 original size:28 final size:28
Alignment explanation
Indices: 17657777--17657833 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
17657767 CATATTCGCT
17657777 TACATCTATTGTCAAAAGAGTCATTTAA
1 TACATCTATTGTCAAAAGAGTCATTTAA
*
17657805 TACATCTATTGTCAAAAGCGTCATTTAA
1 TACATCTATTGTCAAAAGAGTCATTTAA
17657833 T
1 T
17657834 TAATTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (28 bp):
TACATCTATTGTCAAAAGAGTCATTTAA
Found at i:17660807 original size:17 final size:16
Alignment explanation
Indices: 17660785--17660848 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 16
17660775 GTATTCCTTC
17660785 TTTCTTTATTTTTTTCT
1 TTTCTTT-TTTTTTTCT
17660802 TTTCTTTCTTTTTCTTCCT
1 TTTCTTT-TTTTT-TT-CT
*
17660821 GTTTCTCTTTTCTTTTTAT
1 -TTTCT-TTTT-TTTTTCT
17660840 TTTCTTTTT
1 TTTCTTTTT
17660849 GATTGCATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
17 16 0.40
18 7 0.17
19 3 0.08
20 9 0.22
21 5 0.12
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTCTTTTTTTTTTCT
Found at i:17661079 original size:63 final size:63
Alignment explanation
Indices: 17661012--17661180 Score: 214
Period size: 63 Copynumber: 2.7 Consensus size: 63
17661002 GACTCATTGC
* *
17661012 TTGCCACTATAGATCACACGGGCTAGAGACACGGGCGTGTGTCCAGGTCGTGTGACTT-ACGGT
1 TTGCCACTATAGATCACACGGGCCAGAGACACGGGCGTGTGTCCAGGTCGTATGA-TTCACGGT
* * * *
17661075 TTGCCACTATTGATCACATGGGCCAGAGACACGGGCGTGTGTCCAGGTTGTATGATTCACTGT
1 TTGCCACTATAGATCACACGGGCCAGAGACACGGGCGTGTGTCCAGGTCGTATGATTCACGGT
* * * * * *
17661138 TGGCCACTATAAATCATACGAGCCAGAGACACAGGCATGTGTC
1 TTGCCACTATAGATCACACGGGCCAGAGACACGGGCGTGTGTC
17661181 TAGGCAGTGT
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
62 2 0.02
63 89 0.98
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (63 bp):
TTGCCACTATAGATCACACGGGCCAGAGACACGGGCGTGTGTCCAGGTCGTATGATTCACGGT
Found at i:17662444 original size:23 final size:24
Alignment explanation
Indices: 17662417--17662462 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
17662407 AGCTTGTTTT
*
17662417 TTTAATATTT-ATGTTATA-AAATA
1 TTTAAT-TTTGATGTGATATAAATA
17662440 TTTAATTTTGATGTGATATAAAT
1 TTTAATTTTGATGTGATATAAAT
17662463 GACATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 13 0.65
24 4 0.20
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (24 bp):
TTTAATTTTGATGTGATATAAATA
Found at i:17662977 original size:10 final size:10
Alignment explanation
Indices: 17662948--17662980 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
17662938 GCGAATTAAT
17662948 TTTCTTATGA
1 TTTCTTATGA
*
17662958 TATC-TATGA
1 TTTCTTATGA
17662967 TTTCTTATGA
1 TTTCTTATGA
17662977 TTTC
1 TTTC
17662981 AGAATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (10 bp):
TTTCTTATGA
Found at i:17663123 original size:13 final size:13
Alignment explanation
Indices: 17663088--17663125 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
17663078 GATATATTTG
*
17663088 TAATTTGAAAGCT
1 TAATTTGAAAACT
17663101 TAAGTTTGAAAACT
1 TAA-TTTGAAAACT
17663115 TAATTTGAAAA
1 TAATTTGAAAA
17663126 TTTGGAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (13 bp):
TAATTTGAAAACT
Found at i:17663163 original size:29 final size:27
Alignment explanation
Indices: 17663089--17663163 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 27
17663079 ATATATTTGT
* * * *
17663089 AATTTGAAAGCTTAAGTTTGAAAACTT
1 AATTTGAAAACTTAAATTTAAAAACTA
*
17663116 AATTTGAAAATTTGGAAATTTAAAAACTA
1 AATTTGAAAACTT--AAATTTAAAAACTA
17663145 AATTTTTGAAAACTTAAAT
1 AA--TTTGAAAACTTAAAT
17663164 GTCTTGAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 11 0.29
29 17 0.45
31 10 0.26
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (27 bp):
AATTTGAAAACTTAAATTTAAAAACTA
Found at i:17663426 original size:35 final size:34
Alignment explanation
Indices: 17663382--17663645 Score: 315
Period size: 35 Copynumber: 7.8 Consensus size: 34
17663372 TTCACTTGTC
* * *
17663382 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCAC-CATTA
* * *
17663417 TTCTGTTGCAGGGAATCTTTCCTGTTCA-CATCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACCATTA
*
17663450 -TTTCTTGCAGGGAATCTCTCCTGTTCACACATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCAC-CATTA
17663484 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCAC-CATTA
* *
17663519 TTTTGTTGCAGGGAATCTTTCCTGTTCA-CATCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACCATTA
* * *
17663552 -TTTCTTGCAGGGAATCTCTCATGTTCACGTATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCAC-CATTA
*
17663586 TTTTGTTGCAGGGAATCTCTCCTGTTCA-CATCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACCATTA
* *
17663619 -TTTCTTGTAGGGAATCTCTCCTGTTCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCA
17663646 TGTATTATTT
Statistics
Matches: 201, Mismatches: 22, Indels: 15
0.84 0.09 0.06
Matches are distributed among these distances:
32 73 0.36
33 11 0.05
34 7 0.03
35 110 0.55
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (34 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACCATTA
Found at i:17663563 original size:102 final size:102
Alignment explanation
Indices: 17663382--17663645 Score: 401
Period size: 102 Copynumber: 2.6 Consensus size: 102
17663372 TTCACTTGTC
* * * * *
17663382 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTCTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
*
17663447 TCATTTCTTGCAGGGAATCTCTCCTGTTCACACATTA
66 TCATTTCTTGCAGGGAATCTCTCATGTTCACACATTA
17663484 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
**
17663549 TCATTTCTTGCAGGGAATCTCTCATGTTCACGTATTA
66 TCATTTCTTGCAGGGAATCTCTCATGTTCACACATTA
* *
17663586 TTTTGTTGCAGGGAATCTCTCCTGTTCACATCATT-TCTTG-T--AGGGAATCTCTCCTGTTCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACA-CATTATTTTGTTGCAGGGAATCTTTCCTGTTCA
17663646 TGTATTATTT
Statistics
Matches: 151, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
99 18 0.12
101 1 0.01
102 128 0.85
103 4 0.03
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (102 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
TCATTTCTTGCAGGGAATCTCTCATGTTCACACATTA
Found at i:17663651 original size:67 final size:68
Alignment explanation
Indices: 17663382--17663655 Score: 310
Period size: 67 Copynumber: 4.0 Consensus size: 68
17663372 TTCACTTGTC
* * * *
17663382 TTTTCTTGCAGGGAATATTTCCTGTTCAC-GCATTATTCTGTTGCAGGGAATCTTTCCTGTTCA-
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACATCATTA-TC--TTGCAGGGAATCTCTCCTGTTCAC
*
17663445 -CATCA
63 GCATTA
*
17663450 -TTTCTTGCAGGGAATCTCTCCTGTTCACA-CATTATTTTGTTGCAGGGAATCTCTCCTGTTCAC
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACATCATTA---TCTTGCAGGGAATCTCTCCTGTTCAC
*
17663513 ACATTA
63 GCATTA
* * * *
17663519 TTTTGTTGCAGGGAATCTTTCCTGTTCACATCATT-TCTTGCAGGGAATCTCTCATGTTCACGTA
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACATCATTATCTTGCAGGGAATCTCTCCTGTTCACGCA
17663583 TTA
66 TTA
* * * *
17663586 TTTTGTTGCAGGGAATCTCTCCTGTTCACATCATT-TCTTGTAGGGAATCTCTCCTGTTCATGTA
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACATCATTATCTTGCAGGGAATCTCTCCTGTTCACGCA
17663650 TTA
66 TTA
17663653 TTT
1 TTT
17663656 CTTTTTGGAC
Statistics
Matches: 184, Mismatches: 15, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
67 147 0.80
69 6 0.03
70 27 0.15
71 4 0.02
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (68 bp):
TTTTCTTGCAGGGAATCTCTCCTGTTCACATCATTATCTTGCAGGGAATCTCTCCTGTTCACGCA
TTA
Found at i:17666495 original size:20 final size:22
Alignment explanation
Indices: 17666458--17666501 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
17666448 GAGCAAATTG
17666458 TTGATTCTATTTCTTTTTG-AT
1 TTGATTCTATTTCTTTTTGTAT
17666479 TTGA-TCTA-TTCTTTTTTGTAT
1 TTGATTCTATTTC-TTTTTGTAT
17666500 TT
1 TT
17666502 TCTTTTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 3 0.14
20 10 0.48
21 8 0.38
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.68
Consensus pattern (22 bp):
TTGATTCTATTTCTTTTTGTAT
Found at i:17678129 original size:233 final size:238
Alignment explanation
Indices: 17677788--17678224 Score: 632
Period size: 233 Copynumber: 1.8 Consensus size: 238
17677778 GGCGTTTTGT
* * *
17677788 TTAAAGCGCCGCAAAATATCTTTACTAAAACGCGTAGTTTTAATTTTGATGTATACTAATATTAG
1 TTAAAACGCCGCAAAATATCTTAACTAAAACGCATAGTTTTAATTTT-ATGTATA-TAATATTAG
* * *
17677853 TGACGCTTACAAGAAAACGCCGTTAAAGAATATCTTTAGCGGCGATTTAGACGAAGCGCCGCAAC
64 TGACGCTTACAAGAAAACGCCGTTAAAGAATAGCATTAGCGGCGATTTAGACGAAGCGCCGCAAA
* * * * * * *
17677918 TTATCTTAAGAAAACGCAGTGTTTGGTCTTAAGCCATGTTACATTTAGTGGCGCTTATGGGAAAA
129 GTACCTTAACAAAACGCAGTGTTTCGTCTGAAGCCATGTTACATTTAGTGGCGCTTATAGCAAAA
17677983 CGCCGCAAAAAATCTCGATGTATACTTCAATTAGTGGCGCTGACG
194 CGCCGCAAAAAATCTCGATGTATACTTCAATTAGTGGCGCTGACG
*
17678028 TTAAAACGCCGCAAAATATCTTAACTAAAATGCATAGTTTTAA-TTT-TG-AT-T-ATATTAGTG
1 TTAAAACGCCGCAAAATATCTTAACTAAAACGCATAGTTTTAATTTTATGTATATAATATTAGTG
* * * * *
17678088 GCGCTTACTAGAAAACGCCGTTATAGAATAGCATTAGCGGCGCTTTAGCCGAAGCGCCGCAAAGT
66 ACGCTTACAAGAAAACGCCGTTAAAGAATAGCATTAGCGGCGATTTAGACGAAGCGCCGCAAAGT
**
17678153 ACCTTAACAAAACGCAGTGTTTCGTCTGAAGTTATGTTACATTTAGTGGCGCTTATAGCAAAACG
131 ACCTTAACAAAACGCAGTGTTTCGTCTGAAGCCATGTTACATTTAGTGGCGCTTATAGCAAAACG
17678218 CCGCAAA
196 CCGCAAA
17678225 CTATCTGAAC
Statistics
Matches: 176, Mismatches: 21, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
233 129 0.73
234 1 0.01
236 2 0.01
237 2 0.01
239 3 0.02
240 39 0.22
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (238 bp):
TTAAAACGCCGCAAAATATCTTAACTAAAACGCATAGTTTTAATTTTATGTATATAATATTAGTG
ACGCTTACAAGAAAACGCCGTTAAAGAATAGCATTAGCGGCGATTTAGACGAAGCGCCGCAAAGT
ACCTTAACAAAACGCAGTGTTTCGTCTGAAGCCATGTTACATTTAGTGGCGCTTATAGCAAAACG
CCGCAAAAAATCTCGATGTATACTTCAATTAGTGGCGCTGACG
Found at i:17678485 original size:189 final size:189
Alignment explanation
Indices: 17678081--17678473 Score: 612
Period size: 189 Copynumber: 2.1 Consensus size: 189
17678071 TTTTGATTAT
* *
17678081 ATTAGTGGCGCTTACTAGAAAACGCCGTTATAGAATAGCATTAGCGGCGCTTTAGCCGAAGCGCC
1 ATTAGTGGCGCTTACTAGAAAACGCCGTTAAAGAATAGCATTAGCGGCGCTTTAGCCAAAGCGCC
*
17678146 GCAAAGTACCTTAACAAAACGCAGTGTTTCGTCTGAAGTTATGTTACATTTAGTGGCGCTTATAG
66 GCAAAGTACCTTAACAAAACGCAGTGTTTCGTCTGAAGCTATGTTACATTTAGTGGCGCTTATAG
*
17678211 CAAAACGCCGCAAACTATCTGAACCAAAACACACCATTTTGGTCTCGATGTATACTTCA
131 CAAAACGCCGCAAAATATCTGAACCAAAACACACCATTTTGGTCTCGATGTATACTTCA
* * **
17678270 ATTAGTGGCGCTTACTAGAAAACGCCGTTAAAGAATA-TATTTAGCGGCGCTTTGGGTAAAGCGC
1 ATTAGTGGCGCTTACTAGAAAACGCCGTTAAAGAATAGCA-TTAGCGGCGCTTTAGCCAAAGCGC
* * *
17678334 CGCAACGTATCTTAACAAAACGCAGTGGTTT-GTCTTAAGCTATGTTACATTTAGTGGCGCTTAT
65 CGCAAAGTACCTTAACAAAACGCAGT-GTTTCGTCTGAAGCTATGTTACATTTAGTGGCGCTTAT
* * *
17678398 ATG-AAAACGCCGCAAAATATCTGAACCAAAACGCACCGTTTTGGTCTCGATGTATACTTTA
129 A-GCAAAACGCCGCAAAATATCTGAACCAAAACACACCATTTTGGTCTCGATGTATACTTCA
17678459 ATTAGTGGCGCTTAC
1 ATTAGTGGCGCTTAC
17678474 GTTCAAACGC
Statistics
Matches: 187, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
188 1 0.01
189 181 0.97
190 5 0.03
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (189 bp):
ATTAGTGGCGCTTACTAGAAAACGCCGTTAAAGAATAGCATTAGCGGCGCTTTAGCCAAAGCGCC
GCAAAGTACCTTAACAAAACGCAGTGTTTCGTCTGAAGCTATGTTACATTTAGTGGCGCTTATAG
CAAAACGCCGCAAAATATCTGAACCAAAACACACCATTTTGGTCTCGATGTATACTTCA
Found at i:17679090 original size:21 final size:21
Alignment explanation
Indices: 17679072--17679126 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
17679062 TAAGGTTTGT
17679072 AGTTTAGGGTTTAAAGTTTAA
1 AGTTTAGGGTTTAAAGTTTAA
* *
17679093 AGGTTACGGGTTTAAAGTATAA
1 AGTTTA-GGGTTTAAAGTTTAA
*
17679115 AGGTTACGGGTT
1 AGTTTA-GGGTT
17679127 AAACTTAGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 5 0.16
22 26 0.84
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (21 bp):
AGTTTAGGGTTTAAAGTTTAA
Found at i:17679103 original size:22 final size:22
Alignment explanation
Indices: 17679078--17679126 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
17679068 TTGTAGTTTA
*
17679078 GGGTTTAAAGTTTAAAGGTTAC
1 GGGTTTAAAGTATAAAGGTTAC
17679100 GGGTTTAAAGTATAAAGGTTAC
1 GGGTTTAAAGTATAAAGGTTAC
17679122 GGGTT
1 GGGTT
17679127 AAACTTAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.35
Consensus pattern (22 bp):
GGGTTTAAAGTATAAAGGTTAC
Found at i:17679709 original size:24 final size:24
Alignment explanation
Indices: 17679666--17679719 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
17679656 TTCATTCCCT
*
17679666 AATTTCCCATTTCATATTCCCCCC
1 AATTCCCCATTTCATATTCCCCCC
17679690 AATTCCCCGATTTCAT-TTCCCCCC
1 AATTCCCC-ATTTCATATTCCCCCC
17679714 AATTCC
1 AATTCC
17679720 TATTCCCCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.20, C:0.43, G:0.02, T:0.35
Consensus pattern (24 bp):
AATTCCCCATTTCATATTCCCCCC
Found at i:17681131 original size:15 final size:15
Alignment explanation
Indices: 17681107--17681139 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
17681097 AAGGTTTCTA
*
17681107 TATTAGTATTAAATT
1 TATTACTATTAAATT
17681122 TATTACTATTAAATT
1 TATTACTATTAAATT
17681137 TAT
1 TAT
17681140 AAAAAATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (15 bp):
TATTACTATTAAATT
Found at i:17681156 original size:93 final size:92
Alignment explanation
Indices: 17681041--17681349 Score: 386
Period size: 93 Copynumber: 3.4 Consensus size: 92
17681031 TAATGATAAC
*
17681041 ATTTCTAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAACTTATAAGGTTTCT
1 ATTTATAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAA-TTATAAGGTTTCT
17681106 ATATTAGTATTAAATTTATTACTATTAA
65 ATATTAGTATTAAATTTATTACTATTAA
* * * * * *
17681134 ATTTATAAAAAATTCTAAATATTGTTTTAATATCTATATTAGTATTATAAA-TAT--TGTTT-TA
1 ATTTATAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAATTATAAGGTTTCT-
* * * *
17681195 ATATAACCTATAAAATTTA--A--A--AG
65 ATATTA-GTATTAAATTTATTACTATTAA
* *
17681218 TTTTCTAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAATTTATAAGGTTTCT
1 ATTTATAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAA-TTATAAGGTTTCT
17681283 ATATTAGTATTAAATTTATTACTATTAA
65 ATATTAGTATTAAATTTATTACTATTAA
*
17681311 ATTTATAAATAATTCTAAATATTGTTTTAATATCTATAT
1 ATTTATAAATAATTATAAATATTGTTTTAATATCTATAT
17681350 TAGTATTATA
Statistics
Matches: 177, Mismatches: 26, Indels: 26
0.77 0.11 0.11
Matches are distributed among these distances:
84 45 0.25
86 4 0.02
87 10 0.06
88 11 0.06
89 11 0.06
90 10 0.06
91 4 0.02
93 82 0.46
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (92 bp):
ATTTATAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAATTATAAGGTTTCTA
TATTAGTATTAAATTTATTACTATTAA
Found at i:17681236 original size:21 final size:21
Alignment explanation
Indices: 17681208--17681269 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
17681198 TAACCTATAA
17681208 AATT-TAAAAGTTTTCTAAAT
1 AATTATAAAAGTTTTCTAAAT
*
17681228 AATTATAAATA-TTGTT-TTAAT
1 AATTATAAA-AGTT-TTCTAAAT
*
17681249 -ATCTATATAAGTTTTCTAAAT
1 AAT-TATAAAAGTTTTCTAAAT
17681270 TTATAAGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
20 9 0.27
21 21 0.64
22 3 0.09
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (21 bp):
AATTATAAAAGTTTTCTAAAT
Found at i:17681287 original size:177 final size:177
Alignment explanation
Indices: 17681042--17681427 Score: 754
Period size: 177 Copynumber: 2.2 Consensus size: 177
17681032 AATGATAACA
17681042 TTTCTAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAACTTATAAGGTTTCTA
1 TTTCTAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAACTTATAAGGTTTCTA
17681107 TATTAGTATTAAATTTATTACTATTAAATTTATAAAAAATTCTAAATATTGTTTTAATATCTATA
66 TATTAGTATTAAATTTATTACTATTAAATTTATAAAAAATTCTAAATATTGTTTTAATATCTATA
17681172 TTAGTATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGT
131 TTAGTATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGT
*
17681219 TTTCTAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAATTTATAAGGTTTCTA
1 TTTCTAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAACTTATAAGGTTTCTA
*
17681284 TATTAGTATTAAATTTATTACTATTAAATTTATAAATAATTCTAAATATTGTTTTAATATCTATA
66 TATTAGTATTAAATTTATTACTATTAAATTTATAAAAAATTCTAAATATTGTTTTAATATCTATA
17681349 TTAGTATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGT
131 TTAGTATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGT
17681396 TTTCTAAATAATTATAAATATTGTTTTAATAT
1 TTTCTAAATAATTATAAATATTGTTTTAATAT
17681428 TAAATTTATT
Statistics
Matches: 207, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
177 207 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (177 bp):
TTTCTAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAACTTATAAGGTTTCTA
TATTAGTATTAAATTTATTACTATTAAATTTATAAAAAATTCTAAATATTGTTTTAATATCTATA
TTAGTATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGT
Found at i:17681308 original size:15 final size:15
Alignment explanation
Indices: 17681284--17681316 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
17681274 AAGGTTTCTA
*
17681284 TATTAGTATTAAATT
1 TATTACTATTAAATT
17681299 TATTACTATTAAATT
1 TATTACTATTAAATT
17681314 TAT
1 TAT
17681317 AAATAATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (15 bp):
TATTACTATTAAATT
Found at i:17681463 original size:17 final size:17
Alignment explanation
Indices: 17681408--17681464 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
17681398 TCTAAATAAT
17681408 TATAAATATTGTTTTAA
1 TATAAATATTGTTTTAA
* * *
17681425 TATTAAAT-TTATTAGTAT
1 TA-TAAATATTGTT-TTAA
17681443 TATAAATATTGTTTTAA
1 TATAAATATTGTTTTAA
17681460 TATAA
1 TATAA
17681465 CCTATAAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
17 18 0.58
18 13 0.42
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
TATAAATATTGTTTTAA
Found at i:17681477 original size:177 final size:175
Alignment explanation
Indices: 17681042--17681477 Score: 637
Period size: 177 Copynumber: 2.5 Consensus size: 175
17681032 AATGATAACA
* *
17681042 TTTCTAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAACTTATAAGGTTTCTA
1 TTTCTAAATAATTATAAATATTGTTTTAATATCTATATAAGTATTATAAA-TTAT-AGGTTTCTA
* * *
17681107 TATTAGTATTAAATTTATTACTATTAAATTTATAAAAAATTCTAAATATTGTTTTAATATCTATA
64 TATAACTATAAAATTTATTACTATTAAATTTATAAAAAATTCTAAATATTGTTTTAATATCTATA
17681172 TTAGTATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGT
129 TTAGTATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGT
* *
17681219 TTTCTAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAATTTATAAGGTTTCTA
1 TTTCTAAATAATTATAAATATTGTTTTAATATCTATATAAGTATTATAAA-TTAT-AGGTTTCTA
* * * *
17681284 TATTAGTATTAAATTTATTACTATTAAATTTATAAATAATTCTAAATATTGTTTTAATATCTATA
64 TATAACTATAAAATTTATTACTATTAAATTTATAAAAAATTCTAAATATTGTTTTAATATCTATA
17681349 TTAGTATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGT
129 TTAGTATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGT
* *
17681396 TTTCTAAATAATTATAAATATTGTTTTAATAT-TAAATTTATTAGTATTATAAA-TAT-TGTTT-
1 TTTCTAAATAATTATAAATATTGTTTTAATATCT--A--TATAAGTATTATAAATTATAGGTTTC
17681457 TAATATAACCTATAAAATTTA
62 T-ATATAA-CTATAAAATTTA
17681478 AAAGTTTTCT
Statistics
Matches: 244, Mismatches: 9, Indels: 12
0.92 0.03 0.05
Matches are distributed among these distances:
175 1 0.00
176 10 0.04
177 217 0.89
178 4 0.02
180 12 0.05
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (175 bp):
TTTCTAAATAATTATAAATATTGTTTTAATATCTATATAAGTATTATAAATTATAGGTTTCTATA
TAACTATAAAATTTATTACTATTAAATTTATAAAAAATTCTAAATATTGTTTTAATATCTATATT
AGTATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGT
Found at i:17681531 original size:87 final size:84
Alignment explanation
Indices: 17681139--17681514 Score: 470
Period size: 87 Copynumber: 4.3 Consensus size: 84
17681129 ATTAAATTTA
* *
17681139 TAAAAAATTCTAAATATTGTTTTAATATCTATATTAGTATTATAAATATTGTTTTAATATAACCT
1 TAAATAATTATAAATATTGTTTTAATATCTATATTAGTATTATAAATATTGTTTTAATATAACCT
17681204 ATAAAATTTAAAAGTTTTC
66 ATAAAATTTAAAAGTTTTC
* * * *
17681223 TAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAATTTATAAGGTTTCT-ATAT
1 TAAATAATTATAAATATTGTTTTAATATCTATATTAGTATTATAAA--TAT--TGTTT-TAATAT
* * * ** *
17681287 TA-GTATTAAATTTATTACTATTAAATTTA
61 AACCTATAAAATTTA--A--A--AGTTTTC
*
17681316 TAAATAATTCTAAATATTGTTTTAATATCTATATTAGTATTATAAATATTGTTTTAATATAACCT
1 TAAATAATTATAAATATTGTTTTAATATCTATATTAGTATTATAAATATTGTTTTAATATAACCT
17681381 ATAAAATTTAAAAGTTTTC
66 ATAAAATTTAAAAGTTTTC
17681400 TAAATAATTATAAATATTGTTTTAATAT-TAAATTTATTAGTATTATAAATATTGTTTTAATATA
1 TAAATAATTATAAATATTGTTTTAATATCT--A--TATTAGTATTATAAATATTGTTTTAATATA
17681464 ACCTATAAAATTTAAAAGTTTTC
62 ACCTATAAAATTTAAAAGTTTTC
*
17681487 TAAATAATTATAAATATTGTTTAAATAT
1 TAAATAATTATAAATATTGTTTTAATAT
17681515 TAAATTTATT
Statistics
Matches: 250, Mismatches: 25, Indels: 31
0.82 0.08 0.10
Matches are distributed among these distances:
83 1 0.00
84 72 0.29
85 1 0.00
86 4 0.02
87 90 0.36
88 11 0.04
89 11 0.04
90 10 0.04
91 4 0.02
93 46 0.18
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (84 bp):
TAAATAATTATAAATATTGTTTTAATATCTATATTAGTATTATAAATATTGTTTTAATATAACCT
ATAAAATTTAAAAGTTTTC
Found at i:17681752 original size:9 final size:9
Alignment explanation
Indices: 17681725--17681995 Score: 184
Period size: 9 Copynumber: 32.1 Consensus size: 9
17681715 AATAATACAC
17681725 ACTTACATA
1 ACTTACATA
* *
17681734 AATTAAATA
1 ACTTACATA
*
17681743 AGTTACATA
1 ACTTACATA
*
17681752 A--TACACA
1 ACTTACATA
*
17681759 AATTACATA
1 ACTTACATA
17681768 ACTTACATA
1 ACTTACATA
17681777 A--TACATA
1 ACTTACATA
*
17681784 ATTTACATA
1 ACTTACATA
*
17681793 A--TACACA
1 ACTTACATA
*
17681800 ACTGACATA
1 ACTTACATA
17681809 ACTTACATA
1 ACTTACATA
17681818 A--TACATA
1 ACTTACATA
** *
17681825 TTTTACATC
1 ACTTACATA
17681834 ACTTACATA
1 ACTTACATA
*
17681843 A--GACATA
1 ACTTACATA
17681850 ACTTACATA
1 ACTTACATA
* *
17681859 AGTTTCATA
1 ACTTACATA
*
17681868 A--TACACA
1 ACTTACATA
*
17681875 ACTAACATA
1 ACTTACATA
17681884 ACTTACATA
1 ACTTACATA
*
17681893 A--TACACA
1 ACTTACATA
17681900 ACTTACATA
1 ACTTACATA
*
17681909 AC-CATCATA
1 ACTTA-CATA
*
17681918 A--TACACA
1 ACTTACATA
17681925 ACTTACATA
1 ACTTACATA
* *
17681934 AGTTTCATA
1 ACTTACATA
*
17681943 A--TACACA
1 ACTTACATA
17681950 ACTTACATA
1 ACTTACATA
*
17681959 GCTTACATA
1 ACTTACATA
*
17681968 ACTTACACA
1 ACTTACATA
17681977 ACTTACATA
1 ACTTACATA
17681986 ACTTACATA
1 ACTTACATA
17681995 A
1 A
17681996 TAAATAAGTT
Statistics
Matches: 203, Mismatches: 40, Indels: 38
0.72 0.14 0.14
Matches are distributed among these distances:
7 51 0.25
8 2 0.01
9 150 0.74
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (9 bp):
ACTTACATA
Found at i:17681789 original size:25 final size:24
Alignment explanation
Indices: 17681704--17681894 Score: 102
Period size: 25 Copynumber: 7.6 Consensus size: 24
17681694 ATCCTACATT
* *
17681704 ATAAATTACATAATAATACACACTTAC
1 ATAAATTACATAAT--TACATA-ATAC
*
17681731 ATAAATTAAATAAGTTACATAATAC
1 ATAAATTACATAA-TTACATAATAC
*
17681756 ACAAATTACATAACTTACATAATAC
1 ATAAATTACATAA-TTACATAATAC
* *
17681781 ATAATTTACATAA-TACACAACTGAC
1 ATAAATTACATAATTACATAA-T-AC
* *
17681806 ATAACTTACATAA-TACATATTTTAC
1 ATAAATTACATAATTACATA--ATAC
* * *
17681831 ATCACTTACATAA-GACATAACTTAC
1 ATAAATTACATAATTACATAA--TAC
* * *
17681856 ATAAGTTTCATAA-TACACAACTAAC
1 ATAAATTACATAATTACATAA-T-AC
*
17681881 ATAACTTACATAAT
1 ATAAATTACATAAT
17681895 ACACAACTTA
Statistics
Matches: 132, Mismatches: 23, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
23 6 0.05
24 2 0.02
25 105 0.80
26 6 0.05
27 12 0.09
28 1 0.01
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (24 bp):
ATAAATTACATAATTACATAATAC
Found at i:17681795 original size:41 final size:41
Alignment explanation
Indices: 17681725--17681934 Score: 165
Period size: 41 Copynumber: 5.2 Consensus size: 41
17681715 AATAATACAC
* *
17681725 ACTTACATAAATTAAATAAGTTACATAATACACAAATTACATA
1 ACTTACAT-AA-TACATAATTTACATAATACACAAATTACATA
* *
17681768 ACTTACATAATACATAATTTACATAATACACAACTGACATA
1 ACTTACATAATACATAATTTACATAATACACAAATTACATA
*
17681809 ACTTACATAATACATATTTTAC---AT-CAC---TTACATA
1 ACTTACATAATACATAATTTACATAATACACAAATTACATA
* * *
17681843 A--GACATAACTTACATAAGTTT-CATAATACACAACTAACATA
1 ACTTACATAA--TACATAA-TTTACATAATACACAAATTACATA
* * * *
17681884 ACTTACATAATACACAACTTACATAA-CCATCATAA-TACACA
1 ACTTACATAATACATAATTTACATAATACA-CA-AATTACATA
17681925 ACTTACATAA
1 ACTTACATAA
17681935 GTTTCATAAT
Statistics
Matches: 136, Mismatches: 16, Indels: 32
0.74 0.09 0.17
Matches are distributed among these distances:
32 6 0.04
34 14 0.10
35 3 0.02
37 5 0.04
38 5 0.04
40 4 0.03
41 82 0.60
42 3 0.02
43 14 0.10
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.30
Consensus pattern (41 bp):
ACTTACATAATACATAATTTACATAATACACAAATTACATA
Found at i:17681895 original size:25 final size:25
Alignment explanation
Indices: 17681778--17681997 Score: 271
Period size: 25 Copynumber: 8.7 Consensus size: 25
17681768 ACTTACATAA
*
17681778 TACATAATTTACATAATACACAACT
1 TACATAACTTACATAATACACAACT
* * **
17681803 GACATAACTTACATAATACATATTT
1 TACATAACTTACATAATACACAACT
* * *
17681828 TACATCACTTACATAAGACATAACT
1 TACATAACTTACATAATACACAACT
* *
17681853 TACATAAGTTTCATAATACACAACT
1 TACATAACTTACATAATACACAACT
*
17681878 AACATAACTTACATAATACACAACT
1 TACATAACTTACATAATACACAACT
*
17681903 TACATAAC-CATCATAATACACAACT
1 TACATAACTTA-CATAATACACAACT
* *
17681928 TACATAAGTTTCATAATACACAACT
1 TACATAACTTACATAATACACAACT
*
17681953 TACATAGCTTACATAACTTACACAACT
1 TACATAACTTACATAA--TACACAACT
17681980 TACATAACTTACATAATA
1 TACATAACTTACATAATA
17681998 AATAAGTTAT
Statistics
Matches: 164, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
24 1 0.01
25 139 0.85
27 24 0.15
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.30
Consensus pattern (25 bp):
TACATAACTTACATAATACACAACT
Found at i:17687529 original size:12 final size:12
Alignment explanation
Indices: 17687509--17687560 Score: 95
Period size: 12 Copynumber: 4.3 Consensus size: 12
17687499 AGTAGAGGCC
17687509 GCAGCGAGAGAA
1 GCAGCGAGAGAA
*
17687521 GCAGGGAGAGAA
1 GCAGCGAGAGAA
17687533 GCAGCGAGAGAA
1 GCAGCGAGAGAA
17687545 GCAGCGAGAGAA
1 GCAGCGAGAGAA
17687557 GCAG
1 GCAG
17687561 AGGTTCAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.40, C:0.15, G:0.44, T:0.00
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:17688117 original size:85 final size:85
Alignment explanation
Indices: 17687981--17688143 Score: 199
Period size: 85 Copynumber: 1.9 Consensus size: 85
17687971 TTTGTGAAAT
* * * *
17687981 AAGCGCCGCTAAAGAACACTACTTTTAGCGGCGTTTTTGAACAAGCCCCGCTATAGAACATTACT
1 AAGCGCCGCTAAAAAACACTACTTTTAGCGGCGTTTTTGAACAAGCACCGCTAAAGAACATGA-T
17688046 -TTTAGAGGCGTTTTCCTCAA
65 ATTTAGAGGCGTTTTCCTCAA
**
17688066 AAGCGCCGCTAAAAAACA-TGAAC-TTTAGCGGCGTTTTT-TCCTAAGCACCGCTAAAGAACATG
1 AAGCGCCGCTAAAAAACACT--ACTTTTAGCGGCGTTTTTGAAC-AAGCACCGCTAAAGAACATG
*
17688128 ATATTTAGCGGCGTTT
63 ATATTTAGAGGCGTTT
17688144 ATTTCTAAGT
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
84 3 0.04
85 62 0.93
86 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (85 bp):
AAGCGCCGCTAAAAAACACTACTTTTAGCGGCGTTTTTGAACAAGCACCGCTAAAGAACATGATA
TTTAGAGGCGTTTTCCTCAA
Found at i:17688273 original size:42 final size:42
Alignment explanation
Indices: 17687979--17688284 Score: 276
Period size: 42 Copynumber: 7.2 Consensus size: 42
17687969 CATTTGTGAA
**
17687979 ATAAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCGTTTTTGA
1 ATAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTTTT
* * * * * * *
17688021 ACAAGCCCCGCTATAGAACATTA-CTTTTAGAGGCGTTTTCCTC
1 ATAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTT-TTT
* * * *
17688064 AAAAGCGCCGCTAAAAAACATGAACTTTAGCGGCGTTTTTTC
1 ATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
* * * *
17688106 CTAAGCACCGCTAAAGAACATGATATTTAGCGGCGTTTATTT
1 ATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
* * ** * *
17688148 CTAAGTGCCGCTAAAGATTATGTTCTTTAGCGGCGTTTATTT
1 ATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
* * * **
17688190 GTAAGCGCCACTAAAGAACATGATCTTTAACGGCGCATTTTT
1 ATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
*
17688232 ATAACCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
1 ATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
17688274 ATGTAAGCGCC
1 A--TAAGCGCC
17688285 ACAAAAGTTA
Statistics
Matches: 214, Mismatches: 45, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
41 1 0.00
42 174 0.81
43 31 0.14
44 8 0.04
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (42 bp):
ATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
Found at i:17692108 original size:37 final size:38
Alignment explanation
Indices: 17692067--17692140 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 38
17692057 GTTGTTCAAC
*
17692067 TCGAAAAAAAGAAATA-AA-AAATTTAATAACAAAGAAA
1 TCGAAAAAAAGAAA-AGAAGAAATTTAAGAACAAAGAAA
** *
17692104 TCGAAAGGAAGAAAAGAAGAAATTTGAGAACAAAGAA
1 TCGAAAAAAAGAAAAGAAGAAATTTAAGAACAAAGAA
17692141 CAAATAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
36 1 0.03
37 14 0.45
38 16 0.52
ACGTcount: A:0.65, C:0.05, G:0.16, T:0.14
Consensus pattern (38 bp):
TCGAAAAAAAGAAAAGAAGAAATTTAAGAACAAAGAAA
Found at i:17692153 original size:7 final size:7
Alignment explanation
Indices: 17692143--17692184 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
17692133 ACAAAGAACA
17692143 AATAAAT
1 AATAAAT
17692150 AATAAAT
1 AATAAAT
17692157 AATAAAT
1 AATAAAT
*
17692164 AAT-CAT
1 AATAAAT
17692170 AAATAAAT
1 -AATAAAT
*
17692178 AAGAAAT
1 AATAAAT
17692185 GGAAATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 2 0.07
7 26 0.87
8 2 0.07
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (7 bp):
AATAAAT
Found at i:17702369 original size:29 final size:30
Alignment explanation
Indices: 17702318--17702382 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 30
17702308 TCACTAGATC
17702318 CTTTTT-CATTTTTATTTTAATTTT-CTTTT
1 CTTTTTACATTTTTATTTTAATTTTGC-TTT
*
17702347 CTTTTTACCTTTTTATTTT-ATTTTGCTTT
1 CTTTTTACATTTTTATTTTAATTTTGCTTT
17702376 CTTTTTA
1 CTTTTTA
17702383 TTGTTGCAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 21 0.64
30 12 0.36
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.74
Consensus pattern (30 bp):
CTTTTTACATTTTTATTTTAATTTTGCTTT
Found at i:17720458 original size:23 final size:26
Alignment explanation
Indices: 17720431--17720486 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
17720421 AAACAAATAC
17720431 TCATATTTATA-TA-ATTAAAAAAT-
1 TCATATTTATACTAGATTAAAAAATG
*
17720454 TCATATTTTATACTAGATTAAAATATG
1 TCATA-TTTATACTAGATTAAAAAATG
17720481 TCATAT
1 TCATAT
17720487 GTCCCTATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 5 0.18
24 6 0.21
25 2 0.07
26 10 0.36
27 5 0.18
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (26 bp):
TCATATTTATACTAGATTAAAAAATG
Found at i:17720712 original size:20 final size:20
Alignment explanation
Indices: 17720687--17720728 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
17720677 TTTATTTAAA
17720687 AATTACACATCAACAAAATT
1 AATTACACATCAACAAAATT
17720707 AATTACACATCAACAAAATT
1 AATTACACATCAACAAAATT
17720727 AA
1 AA
17720729 CAATGTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.57, C:0.19, G:0.00, T:0.24
Consensus pattern (20 bp):
AATTACACATCAACAAAATT
Done.