Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 152 of 322
Found at i:49787383 original size:46 final size:45
Alignment explanation
Indices: 49787203--49787469 Score: 193
Period size: 47 Copynumber: 5.7 Consensus size: 45
49787193 ACTTGTGTGA
* * * *
49787203 GCTAGTGTAAGACATGTCTGGGACATGTATCAGCCAC-ATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGA-GATGA-T
* * * * * *
49787249 GCCAGTGTAAGACCATGTCCGGGACATGGCATCGGCATTGAGACGAGT
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCGAGATGA-T
49787297 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATGTAT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATG-AT
* * *
49787343 GCTAGTGTAATACATGTCTGGGACATGCTTC-GGCTACGAGATGAT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCT-CGAGATGAT
* * *
49787388 AG-TCAGAGTAAGACCATGTCTGGGACATGGCATC-GACTTGAGAT-AT
1 -GCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCGAGATGAT
* * *
49787434 GAGTCAGTGTAAGACCATGTTTAGGACATGGCATCA
1 G-CT-AGTGTAAGA-CATGTCTGGGACAT-GCATCA
49787470 AAACCTTTCC
Statistics
Matches: 182, Mismatches: 27, Indels: 22
0.79 0.12 0.10
Matches are distributed among these distances:
45 7 0.04
46 71 0.39
47 75 0.41
48 28 0.15
49 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.25
Consensus pattern (45 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATGAT
Found at i:49787461 original size:140 final size:141
Alignment explanation
Indices: 49787203--49787469 Score: 339
Period size: 140 Copynumber: 1.9 Consensus size: 141
49787193 ACTTGTGTGA
* *
49787203 GCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATTATGAGAGCCAGTGTAAGACCATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATGATGAGAGCCAGAGTAAGACCATGTC
* *
49787268 CGGGACATGGCATCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACAT-GCATCAGCC
66 CGGGACATGGCATCGACATTGAGACGAGTGCTAGTGTAAGACATGTCTAGGACATGGCATCAGCC
49787332 TCGAGATGTAT
131 TCGAGATGTAT
* * * * *
49787343 GCTAGTGTAATACATGTCTGGGACATGCT-TCGGCTACGA-GATGATAGTCAGAGTAAGACCATG
1 GCTAGTGTAAGACATGTCTGGGACATG-TATCAGCCAC-ATGATGAGAGCCAGAGTAAGACCATG
* * *
49787406 TCTGGGACATGGCATCGAC-TTGAGATATGAGT-C-AGTGTAAGACCATGTTTAGGACATGGCAT
64 TCCGGGACATGGCATCGACATTGAG--ACGAGTGCTAGTGTAAGA-CATGTCTAGGACATGGCAT
49787468 CA
126 CA
49787470 AAACCTTTCC
Statistics
Matches: 109, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
139 14 0.13
140 82 0.75
141 13 0.12
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.25
Consensus pattern (141 bp):
GCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATGATGAGAGCCAGAGTAAGACCATGTC
CGGGACATGGCATCGACATTGAGACGAGTGCTAGTGTAAGACATGTCTAGGACATGGCATCAGCC
TCGAGATGTAT
Found at i:49788954 original size:48 final size:48
Alignment explanation
Indices: 49788880--49788973 Score: 161
Period size: 48 Copynumber: 2.0 Consensus size: 48
49788870 CCACACGCTC
* *
49788880 GTGTAGGTGGGCCGTGTTGACTCACACGCTCGTGTGACTTGGGGCACG
1 GTGTAGGGGGGCCGTGTTGACACACACGCTCGTGTGACTTGGGGCACG
*
49788928 GTGTAGGGGGGCCGTGTTGACACACACGCTCGTGTGGCTTGGGGCA
1 GTGTAGGGGGGCCGTGTTGACACACACGCTCGTGTGACTTGGGGCA
49788974 TGCCCATGCC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.13, C:0.22, G:0.41, T:0.23
Consensus pattern (48 bp):
GTGTAGGGGGGCCGTGTTGACACACACGCTCGTGTGACTTGGGGCACG
Found at i:49789566 original size:37 final size:37
Alignment explanation
Indices: 49789502--49789575 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
49789492 TTACAAGCCA
49789502 AAATCATTATAAGCCACATCTCATGGCTACAT-ACAAC
1 AAATCATTATAAGCCACATCTCATGGCTA-ATCACAAC
*
49789539 AAATCATTATAAGCCA-ATACAT-TTGGCTAATCACAAC
1 AAATCATTATAAGCCACAT-C-TCATGGCTAATCACAAC
49789576 GACATCGATC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
36 4 0.12
37 28 0.85
38 1 0.03
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (37 bp):
AAATCATTATAAGCCACATCTCATGGCTAATCACAAC
Found at i:49794324 original size:13 final size:13
Alignment explanation
Indices: 49794306--49794334 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
49794296 ATTCAATTAC
49794306 AACAACAATAATA
1 AACAACAATAATA
49794319 AACAACAATAATA
1 AACAACAATAATA
49794332 AAC
1 AAC
49794335 TCATATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (13 bp):
AACAACAATAATA
Found at i:49795220 original size:15 final size:16
Alignment explanation
Indices: 49795197--49795237 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
49795187 TTCCTCTTTT
*
49795197 AATATAAAATAAA-AA
1 AATAAAAAATAAATAA
49795212 AATAAAAAATAAATAA
1 AATAAAAAATAAATAA
49795228 ATATAAAAAA
1 A-ATAAAAAA
49795238 AAACTCACAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.52
16 3 0.13
17 8 0.35
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
AATAAAAAATAAATAA
Found at i:49796690 original size:13 final size:14
Alignment explanation
Indices: 49796659--49796690 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
49796649 AGTGTATTTC
49796659 ATTT-ATTAAATGA
1 ATTTAATTAAATGA
49796672 ATTTAATTAAAT-A
1 ATTTAATTAAATGA
49796685 ATTTAA
1 ATTTAA
49796691 AGTAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
ATTTAATTAAATGA
Found at i:49796874 original size:23 final size:22
Alignment explanation
Indices: 49796824--49796874 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
49796814 TAGAATTTGA
49796824 ATTTTATATTTTTATTTTTAGG
1 ATTTTATATTTTTATTTTTAGG
*
49796846 AATTTAGT-TTTTCTATTGTTTA-G
1 ATTTTA-TATTTT-TATT-TTTAGG
49796869 ATTTTA
1 ATTTTA
49796875 AAATTCAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
22 9 0.38
23 11 0.46
24 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.65
Consensus pattern (22 bp):
ATTTTATATTTTTATTTTTAGG
Found at i:49797438 original size:13 final size:13
Alignment explanation
Indices: 49797404--49797442 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
49797394 ATTAAATTAT
49797404 TAAAAAATAAAAA
1 TAAAAAATAAAAA
* * *
49797417 TATATAATAACAA
1 TAAAAAATAAAAA
49797430 TAAAAAATAAAAA
1 TAAAAAATAAAAA
49797443 AAACTTTTGC
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (13 bp):
TAAAAAATAAAAA
Found at i:49797942 original size:13 final size:13
Alignment explanation
Indices: 49797924--49797948 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49797914 TATAAGTTCA
49797924 ATTATTAATATAC
1 ATTATTAATATAC
49797937 ATTATTAATATA
1 ATTATTAATATA
49797949 TATAACTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTATTAATATAC
Found at i:49804634 original size:26 final size:26
Alignment explanation
Indices: 49804603--49804710 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
49804593 TGAAATGCCC
*
49804603 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
49804629 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
49804655 ATCATAGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
49804681 ATCATGGAACATTTTCCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
49804707 ATCA
1 ATCA
49804711 ATTTGTACCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:49807865 original size:16 final size:16
Alignment explanation
Indices: 49807844--49807877 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
49807834 AGGTGTATAA
49807844 AAATATATAAATAAAT
1 AAATATATAAATAAAT
*
49807860 AAATATATAATTAAAT
1 AAATATATAAATAAAT
49807876 AA
1 AA
49807878 CAATAATGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATATATAAATAAAT
Found at i:49807907 original size:5 final size:5
Alignment explanation
Indices: 49807891--49807930 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
49807881 TAATGAGGAC
*
49807891 AAAAT AACAT AAAAT AAAAT -AAAT AAAAT -AAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
49807931 TAAAAAGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 8 0.26
5 23 0.74
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:49807916 original size:14 final size:14
Alignment explanation
Indices: 49807891--49807935 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
49807881 TAATGAGGAC
49807891 AAAATAACATAAAAT
1 AAAATAA-ATAAAAT
49807906 AAAATAAATAAAAT
1 AAAATAAATAAAAT
*
49807920 -AAATAAA-ATAAT
1 AAAATAAATAAAAT
49807932 AAAA
1 AAAA
49807936 AGGAATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 4 0.14
13 10 0.36
14 7 0.25
15 7 0.25
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (14 bp):
AAAATAAATAAAAT
Found at i:49807936 original size:9 final size:9
Alignment explanation
Indices: 49807892--49807935 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
49807882 AATGAGGACA
*
49807892 AAATAACAT
1 AAATAAAAT
49807901 AAAATAAAAT
1 -AAATAAAAT
49807911 AAATAAAAT
1 AAATAAAAT
49807920 AAATAAAAT
1 AAATAAAAT
49807929 -AATAAAA
1 AAATAAAA
49807936 AGGAATAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
8 7 0.21
9 18 0.55
10 8 0.24
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:49809842 original size:44 final size:44
Alignment explanation
Indices: 49809556--49810257 Score: 469
Period size: 44 Copynumber: 15.8 Consensus size: 44
49809546 TACAATCTGT
* * ** * * *
49809556 TCCACTACAACTTCAGGGAAATAAGATTCACTATCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATT-TGTAACTTCAATCTAC
* ** * **
49809601 TCCACTGCAACTTCAGGGAGATAAGACTAATAACTTCAACCTGT
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTAC
* * * * *
49809645 TCTATTGCAACTTCAGGGAGATAAGGTTTG---CTAT-GATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTAACT-TCAATCTAC
* * * *
49809686 TCTACTGCAACTTCAGAGAGATAAGATCTATAATTTATAGCTTCAATCTAT
1 TCCACTGCAACTTCAGGGAGATAAGA--T-T--TGTA-A-CTTCAATCTAC
** * * ** * *
49809737 TCCACTATAACTTCAGGGAAATAAGATTCGCTATTTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TAACTTCAATCTAC
* * * * * *
49809782 TTCACTGCAATTTTAGGGAGATAAGACTTGTAACTTCAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTAC
* * * * * *
49809826 TCCACTACAACTTTAGGGAGATAAGGTTTATAGCTTTAATCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTAC
* * * * * * * *
49809870 TCTACTACAACTTCAGAGAGATAAAATTTTCTATCTTCGATCTTC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTTGTAACTTCAATCTAC
* * * *
49809915 TCCACCGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTAC
* * * * *
49809959 TCCACTACAACTTTAGGGAGATAA-AGTTTATAGCTTTAATCTAC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTTGTAACTTCAATCTAC
* * * * * *
49810003 TCTAATGCAACTTCAGAGAGATAAGATTTTCTATCTTCGATCTAC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTTGTAACTTCAATCTAC
* * * *
49810048 TCCACTGCAACTTCAGGGAGATAGGACTTGTAACTTCAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTAC
* * * * * *
49810092 TCCACAGCAACTTCAGGGAGATAAGGTTTATAGCTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTAC
* * ** *
49810136 TCTACTGCAACTTCAGAGAGATAAGATTTGCTATGTTCATTCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TAACTTCAATCTAC
* * * *
49810181 TCCACTACAATTTTAGGGAGATAAGACTTGTAACTTCAATCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTAC
* *
49810225 TTCATTGCAACTTCAGGGAGATAAGATTTGTAA
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTAA
49810258 TTTGTAGCTT
Statistics
Matches: 499, Mismatches: 141, Indels: 35
0.74 0.21 0.05
Matches are distributed among these distances:
41 29 0.06
42 1 0.00
43 2 0.00
44 276 0.55
45 158 0.32
46 1 0.00
47 2 0.00
48 1 0.00
49 1 0.00
50 1 0.00
51 27 0.05
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTAC
Found at i:49809844 original size:89 final size:88
Alignment explanation
Indices: 49809552--49810346 Score: 330
Period size: 89 Copynumber: 8.8 Consensus size: 88
49809542 TAGCTACAAT
* *
49809552 CTGTTCCACTACAACTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTGCAACTTCAG
1 CTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTAT-TTCAGTCTGCTTCACTGCAACTTCAG
*
49809617 GGAGATAAGACTAATAACTTCAAC
65 GGAGATAAGACTTATAACTTCAAC
* * * * * * *
49809641 CTGTTCTATTGCAACTTCAGGGAGATAAGGTTTGCTA--TGA-TCTGC-TCTACTGCAACTTCAG
1 CTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATTTCAGTCTGCTTC-ACTGCAACTTCAG
* *
49809702 AGAGATAAGATCTATAATTTATAGCTTCAAT
65 GGAGATAAGA-CT-T-A--TA-A-CTTCAAC
* * * *
49809733 CTATTCCACTATAACTTCAGGGAAATAAGATTCGCTATTTTCAGTCTGCTTCACTGCAATTTTAG
1 CTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTA-TTTCAGTCTGCTTCACTGCAACTTCAG
*
49809798 GGAGATAAGACTTGTAACTTCAAC
65 GGAGATAAGACTTATAACTTCAAC
* * * * ** * * *
49809822 CTGCTCCACTACAACTTTAGGGAGATAAGGTT-TATAGCTTT-AATCTAC-TCTACTACAACTTC
1 CTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTA--TTTCAGTCTGCTTC-ACTGCAACTTC
* * * * * * *
49809884 AGAGAGATAAAATTTTCTATCTTCGAT
63 AGGGAGATAAGA-CTTATAACTTCAAC
** * * ** * * *
49809911 CT-TCTCCACCGCAACTTCAGGGAGATAAGACTT-G-TAACTTCAACCTGCTCCACTACAACTTT
1 CTGT-TCCACTACAACTTCAGGGAAATAAGA-TTCGCT-ATTTCAGTCTGCTTCACTGCAACTTC
* * * *
49809973 AGGGAGATAA-AGTTTATAGCTTTAAT
63 AGGGAGATAAGA-CTTATAACTTCAAC
** * * * * * ** * *
49809999 CTACTCTAATGCAACTTCAGAGAGATAAGATTTTCTATCTTC-GATCTACTCCACTGCAACTTCA
1 CTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTAT-TTCAG-TCTGCTTCACTGCAACTTCA
* *
49810063 GGGAGATAGGACTTGTAACTTCAAC
64 GGGAGATAAGACTTATAACTTCAAC
* * * ** *
49810088 CTGCTCCAC-AGCAACTTCAGGGAGATAAGGTT-TATAGCTTT-AATCTGC-TCTACTGCAACTT
1 CTGTTCCACTA-CAACTTCAGGGAAATAAGATTCGCTA--TTTCAGTCTGCTTC-ACTGCAACTT
* * * ** **
49810149 CAGAGAGATAAGATTTGCTATGTTCATT
62 CAGGGAGATAAGACTT-ATAACTTCAAC
** * * * * * * *
49810177 CTACTCCACTACAATTTTAGGGAGATAAGACTT-G-TAACTTCAATCTACTTCATTGCAACTTCA
1 CTGTTCCACTACAACTTCAGGGAAATAAGA-TTCGCT-ATTTCAGTCTGCTTCACTGCAACTTCA
* * * *
49810240 GGGAGATAAGATTTGTAATTTGTAGCTTTAAT
64 GGGAGATAAGA-CT-T-A----TAACTTCAAC
* * * * *
49810272 CTGTTCCACTATAGCTTCAGAGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTACAACTTCAG
1 CTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTAT-TTCAGTCTGCTTCACTGCAACTTCAG
*
49810337 AGAGATAAGA
65 GGAGATAAGA
49810347 TTCGCCATGA
Statistics
Matches: 529, Mismatches: 130, Indels: 87
0.71 0.17 0.12
Matches are distributed among these distances:
84 1 0.00
85 27 0.05
86 4 0.01
87 5 0.01
88 96 0.18
89 245 0.46
90 17 0.03
91 4 0.01
92 35 0.07
94 3 0.01
95 34 0.06
96 56 0.11
97 2 0.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (88 bp):
CTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATTTCAGTCTGCTTCACTGCAACTTCAGG
GAGATAAGACTTATAACTTCAAC
Found at i:49809846 original size:181 final size:184
Alignment explanation
Indices: 49809497--49810346 Score: 546
Period size: 177 Copynumber: 4.7 Consensus size: 184
49809487 TCTATGTCTT
* * * * * * *
49809497 TAATTTGCTCCACTGTAACTTTAGGGAGATAAGATATCTAATTTATAGCTACAATCTGTTCCACT
1 TAATCTGCTCTACTGCAACTTCAGAGAGATAAGATATATAATTTATAGCTACAATCTATTCCACT
49809562 ACAACTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
66 ACAACTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
* * * *
49809627 CTAATAACTTCAACCTGTTCTATTGCAACTTCAGGGAGATAAGG-TT-T-GCTA
131 CTAATAACTTCAACCTGCTCCACTACAACTTCAGGGAGATAAGGTTTATAGCTA
* * *
49809678 TGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATAATTTATAGCTTCAATCTATTCCACT
1 TAATCTGCTCTACTGCAACTTCAGAGAGATAAGATATATAATTTATAGCTACAATCTATTCCACT
* * * * * *
49809743 ATAACTTCAGGGAAATAAGATTCGCTATTTTCAGTCTGCTTCACTGCAATTTTAGGGAGATAAGA
66 ACAACTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
** * *
49809808 CTTGTAACTTCAACCTGCTCCACTACAACTTTAGGGAGATAAGGTTTATAGCTT
131 CTAATAACTTCAACCTGCTCCACTACAACTTCAGGGAGATAAGGTTTATAGCTA
* * * *
49809862 TAATCTACTCTACTACAACTTCAGAGAGATAA-A-AT-T--TTCTAT--CTTCGATCT-TCTCCA
1 TAATCTGCTCTACTGCAACTTCAGAGAGATAAGATATATAATT-TATAGCTACAATCTAT-TCCA
** * * * ** * *
49809919 CCGCAACTTCAGGGAGATAAGACTT--GTAACTTCAACCTGCTCCACTACAACTTTAGGGAGATA
64 CTACAACTTCAGGGAAATAAGA-TTCACTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATA
* * * * * * * * * * * * *
49809982 A-AGTTTATAGCTTTAATCTACTCTAATGCAACTTCAGAGAGATAAGATTTTCTATCT-
128 AGA-CTAATAACTTCAACCTGCTCCACTACAACTTCAGGGAGATAAG-GTTTATAGCTA
* * * * * * * * * **
49810039 TCGATCTACTCCACTGCAACTTCAGGGAGAT-AG-GA-CT--TGTA-A-CTTCAACCTGCTCCAC
1 T-AATCTGCTCTACTGCAACTTCAGAGAGATAAGATATATAATTTATAGCTACAATCTATTCCAC
* * * * * * * *
49810097 -AGCAACTTCAGGGAGATAAGGTTTA-TAGCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAA
65 TA-CAACTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
* ** ** ** * * * ** * *
49810160 GATTTGCTATGTTCATTCTACTCCACTACAATTTTAGGGAGATAAGACTTGTAACT-
129 GA-CTAATAACTTCAACCTGCTCCACTACAACTTCAGGGAGATAAGGTTTATAGCTA
* * * * * * ** *
49810216 TCAATCTACT-TCATTGCAACTTCAGGGAGATAAGATTTGTAATTTGTAGCTTTAATCTGTTCCA
1 T-AATCTGCTCT-ACTGCAACTTCAGAGAGATAAGATATATAATTTATAGCTACAATCTATTCCA
* * * * * *
49810280 CTATAGCTTCAGAGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTACAACTTCAGAGAGATAA
64 CTACAACTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
49810345 GA
129 GA
49810347 TTCGCCATGA
Statistics
Matches: 529, Mismatches: 112, Indels: 52
0.76 0.16 0.08
Matches are distributed among these distances:
176 3 0.01
177 162 0.31
178 99 0.19
179 4 0.01
180 4 0.01
181 152 0.29
182 5 0.01
183 3 0.01
184 61 0.12
185 36 0.07
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (184 bp):
TAATCTGCTCTACTGCAACTTCAGAGAGATAAGATATATAATTTATAGCTACAATCTATTCCACT
ACAACTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
CTAATAACTTCAACCTGCTCCACTACAACTTCAGGGAGATAAGGTTTATAGCTA
Found at i:49809882 original size:133 final size:133
Alignment explanation
Indices: 49809719--49810346 Score: 731
Period size: 133 Copynumber: 4.7 Consensus size: 133
49809709 AGATCTATAA
* * * * * * * * * *
49809719 TTTATAGCTTCAATCTATTCCACTATAACTTCAGGGAAATAAGATTCGCTATTTTCAGTCTGCTT
1 TTTATAGCTTTAATCTACTCTACTACAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTACTC
* * *
49809784 CACTGCAATTTTAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTACAACTTTAGGGAGATA
66 CACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTACAACTTCAGGGAGATA
49809849 AGG
131 AGG
* * *
49809852 TTTATAGCTTTAATCTACTCTACTACAACTTCAGAGAGATAAAATTTTCTATCTTC-GATCTTCT
1 TTTATAGCTTTAATCTACTCTACTACAACTTCAGAGAGATAAGATTTGCTATCTTCAG-TCTACT
* *
49809916 CCACCGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTACAACTTTAGGGAGAT
65 CCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTACAACTTCAGGGAGAT
*
49809981 AAAG
130 AAGG
* * *
49809985 TTTATAGCTTTAATCTACTCTAATGCAACTTCAGAGAGATAAGATTTTCTATCTTC-GATCTACT
1 TTTATAGCTTTAATCTACTCTACTACAACTTCAGAGAGATAAGATTTGCTATCTTCAG-TCTACT
*
49810049 CCACTGCAACTTCAGGGAGATAGGACTTGTAACTTCAACCTGCTCCAC-AGCAACTTCAGGGAGA
65 CCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTA-CAACTTCAGGGAGA
49810113 TAAGG
129 TAAGG
* * * *
49810118 TTTATAGCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATGTTCATTCTACTC
1 TTTATAGCTTTAATCTACTCTACTACAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTACTC
* * * * * * * *
49810183 CACTACAATTTTAGGGAGATAAGACTTGTAACTTCAATCTACTTCATTGCAACTTCAGGGAGATA
66 CACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTACAACTTCAGGGAGATA
49810248 AGATTTG
131 AG----G
* ** * * * * * *
49810255 TAATTTGTAGCTTTAATCTGTTCCACTATAGCTTCAGAGAAATAAGATTCGCTATCTTCAGTCTG
1 ---TTTATAGCTTTAATCTACTCTACTACAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTA
* *
49810320 CTCCACTACAACTTCAGAGAGATAAGA
63 CTCCACTGCAACTTCAGGGAGATAAGA
49810347 TTCGCCATGA
Statistics
Matches: 432, Mismatches: 52, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
132 2 0.00
133 354 0.82
137 1 0.00
140 75 0.17
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (133 bp):
TTTATAGCTTTAATCTACTCTACTACAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTACTC
CACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTACAACTTCAGGGAGATA
AGG
Found at i:49812922 original size:34 final size:34
Alignment explanation
Indices: 49812874--49812971 Score: 178
Period size: 34 Copynumber: 2.9 Consensus size: 34
49812864 GACTTTATAG
49812874 ATCTTCTCTGTTGACCCCTCTTCTGAGGCGATAA
1 ATCTTCTCTGTTGACCCCTCTTCTGAGGCGATAA
* *
49812908 ATCTTCTCTATTGACCCCTCTTCTGAGGCGATAG
1 ATCTTCTCTGTTGACCCCTCTTCTGAGGCGATAA
49812942 ATCTTCTCTGTTGACCCCTCTTCTGAGGCG
1 ATCTTCTCTGTTGACCCCTCTTCTGAGGCG
49812972 CATACGTTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 61 1.00
ACGTcount: A:0.15, C:0.31, G:0.18, T:0.36
Consensus pattern (34 bp):
ATCTTCTCTGTTGACCCCTCTTCTGAGGCGATAA
Found at i:49822471 original size:16 final size:16
Alignment explanation
Indices: 49822450--49822484 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
49822440 AGGTGTGTAA
49822450 AAATATATAAATAAAT
1 AAATATATAAATAAAT
*
49822466 AAATATATAATTAAAT
1 AAATATATAAATAAAT
49822482 AAA
1 AAA
49822485 AATAATGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATATATAAATAAAT
Found at i:49835894 original size:21 final size:21
Alignment explanation
Indices: 49835862--49835974 Score: 145
Period size: 21 Copynumber: 5.4 Consensus size: 21
49835852 GTACATCATT
*
49835862 AACAGAAACTCGTAAGAGTTG
1 AACAGAAACTCATAAGAGTTG
* * * *
49835883 AATAGAAGCTCGTAAGAGCTG
1 AACAGAAACTCATAAGAGTTG
49835904 AACAGAAACTCATAAGAGTTG
1 AACAGAAACTCATAAGAGTTG
49835925 AACAGAAACTCATAAGAGTTG
1 AACAGAAACTCATAAGAGTTG
* * * *
49835946 AACAGAAGCTCATGAGAGCTA
1 AACAGAAACTCATAAGAGTTG
49835967 AACAGAAA
1 AACAGAAA
49835975 GTAAAACATG
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 80 1.00
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (21 bp):
AACAGAAACTCATAAGAGTTG
Found at i:49837105 original size:16 final size:16
Alignment explanation
Indices: 49837068--49837110 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
49837058 AGCAAGTGCA
**
49837068 CCTTTTTTAATTTGGT
1 CCTTTTTTAATTCAGT
*
49837084 CTTTTTTTAATTCAGT
1 CCTTTTTTAATTCAGT
49837100 CC-TTTTTAATT
1 CCTTTTTTAATT
49837111 AATTAACTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.16, C:0.14, G:0.07, T:0.63
Consensus pattern (16 bp):
CCTTTTTTAATTCAGT
Found at i:49848341 original size:22 final size:22
Alignment explanation
Indices: 49848289--49848333 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
49848279 AATAAGTGAT
*
49848289 AAAAGTAACATATTTTAATCTC
1 AAAAGTAATATATTTTAATCTC
49848311 AAAAGTAATATATTTTAATCTC
1 AAAAGTAATATATTTTAATCTC
49848333 A
1 A
49848334 TTCTTAATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (22 bp):
AAAAGTAATATATTTTAATCTC
Found at i:49858167 original size:25 final size:25
Alignment explanation
Indices: 49858121--49858199 Score: 95
Period size: 25 Copynumber: 3.2 Consensus size: 25
49858111 CACTACAGTC
* * *
49858121 TCAGTATACACTATCTAGAGTATTT
1 TCAGAATATACTATCTACAGTATTT
* * * *
49858146 TCATAGTATACTACCTACAGTAGTT
1 TCAGAATATACTATCTACAGTATTT
49858171 TCAGAATATACTATCTACAGTATTT
1 TCAGAATATACTATCTACAGTATTT
49858196 TCAG
1 TCAG
49858200 TTTAAACTTA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (25 bp):
TCAGAATATACTATCTACAGTATTT
Found at i:49868006 original size:17 final size:17
Alignment explanation
Indices: 49867984--49868019 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
49867974 GTTTTTGTGT
*
49867984 TGTGCAAATGAGAAAGA
1 TGTGCAAATAAGAAAGA
49868001 TGTGCAAATAAGAAAGA
1 TGTGCAAATAAGAAAGA
49868018 TG
1 TG
49868020 ATGATTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.28, T:0.19
Consensus pattern (17 bp):
TGTGCAAATAAGAAAGA
Found at i:49868500 original size:15 final size:15
Alignment explanation
Indices: 49868480--49868512 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
49868470 TATTACTTGA
49868480 TAGGTGCAGTTGCCT
1 TAGGTGCAGTTGCCT
*
49868495 TAGGTGCGGTTGCCT
1 TAGGTGCAGTTGCCT
49868510 TAG
1 TAG
49868513 TCAGATTTTT
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:0.12, C:0.18, G:0.36, T:0.33
Consensus pattern (15 bp):
TAGGTGCAGTTGCCT
Found at i:49869908 original size:25 final size:23
Alignment explanation
Indices: 49869859--49869910 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
49869849 TTGGTCATTA
*
49869859 AATAACTTACTAAATTAAGTATC
1 AATAACTTACTAAAATAAGTATC
*
49869882 AATAACTTACTAAAAATAATTACTC
1 AATAACTTACT-AAAATAAGTA-TC
49869907 AATA
1 AATA
49869911 TCAATAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.44
24 8 0.32
25 6 0.24
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (23 bp):
AATAACTTACTAAAATAAGTATC
Found at i:49870217 original size:72 final size:72
Alignment explanation
Indices: 49870133--49870279 Score: 285
Period size: 72 Copynumber: 2.0 Consensus size: 72
49870123 TTTTATAATT
*
49870133 TTTACAATTTAGTCCCTAATCAATTAACCCATTAATTGAATTATTTTTTCTCAAAAACACTTTAT
1 TTTACAACTTAGTCCCTAATCAATTAACCCATTAATTGAATTATTTTTTCTCAAAAACACTTTAT
49870198 CTAATCA
66 CTAATCA
49870205 TTTACAACTTAGTCCCTAATCAATTAACCCATTAATTGAATTATTTTTTCTCAAAAACACTTTAT
1 TTTACAACTTAGTCCCTAATCAATTAACCCATTAATTGAATTATTTTTTCTCAAAAACACTTTAT
49870270 CTAATCA
66 CTAATCA
49870277 TTT
1 TTT
49870280 TAGGCTACTA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (72 bp):
TTTACAACTTAGTCCCTAATCAATTAACCCATTAATTGAATTATTTTTTCTCAAAAACACTTTAT
CTAATCA
Found at i:49880246 original size:33 final size:33
Alignment explanation
Indices: 49880209--49880286 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
49880199 TGGCCCTGCC
* *
49880209 ATGGTCTTA-CACTCAT-AGTGCCATAACCTAGTT
1 ATGGTCTTATCA-TCATGA-TGCCATAACCCAGCT
*
49880242 ATGGTCTTATCATCATGATGCCATAGCCCAGCT
1 ATGGTCTTATCATCATGATGCCATAACCCAGCT
49880275 ATGGTCTT-TCAT
1 ATGGTCTTATCAT
49880287 GAATAATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
32 4 0.10
33 33 0.82
34 3 0.08
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (33 bp):
ATGGTCTTATCATCATGATGCCATAACCCAGCT
Found at i:49880337 original size:103 final size:101
Alignment explanation
Indices: 49880189--49880421 Score: 270
Period size: 103 Copynumber: 2.3 Consensus size: 101
49880179 GTCTTACACG
* ** * *
49880189 AATATTGCCATGGCCCTGCCATGGTCTTACACTCATAGTGCCATAACCTAGTTATGGTCTTATCA
1 AATATTGCCATGGTCCAACCATGGTCTTACACTCACAGTGCCATAACCTAATTATGGTCTTATCA
** *
49880254 -TCATGATGCCATAGCCCAGCTATGGTCTTTCATGAATA
66 CT-AAAATGCCATAGCCCAGCTATGGTCTTACAT--ATA
* ** * * * *
49880292 ATTATTGCCATGGTCCAACCATGGTCTTACGTTCACGGTGTCATAACTTAATTATGGTCTTTTCA
1 AATATTGCCATGGTCCAACCATGGTCTTACACTCACAGTGCCATAACCTAATTATGGTCTTATCA
*
49880357 CTAAAATGCCATAGCCCAGCTATGGTCTTACATTTA
66 CTAAAATGCCATAGCCCAGCTATGGTCTTACATATA
**
49880393 AACGTTGCCATGGTCCAACCATGGTCTTA
1 AATATTGCCATGGTCCAACCATGGTCTTA
49880422 TCTATCAACT
Statistics
Matches: 110, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
101 28 0.25
103 81 0.74
104 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.33
Consensus pattern (101 bp):
AATATTGCCATGGTCCAACCATGGTCTTACACTCACAGTGCCATAACCTAATTATGGTCTTATCA
CTAAAATGCCATAGCCCAGCTATGGTCTTACATATA
Found at i:49886583 original size:13 final size:13
Alignment explanation
Indices: 49886565--49886594 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
49886555 AAAAATAATT
49886565 CACACGGTTTGGA
1 CACACGGTTTGGA
49886578 CACACGGTTTGGA
1 CACACGGTTTGGA
49886591 CACA
1 CACA
49886595 TGAGTGTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (13 bp):
CACACGGTTTGGA
Found at i:49887261 original size:17 final size:17
Alignment explanation
Indices: 49887208--49887254 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
49887198 TTTTGAATTA
* *
49887208 TTTATATTTTATTTGGT
1 TTTATGTTTTATTTAGT
49887225 TTTATGTTTTATTTAGT
1 TTTATGTTTTATTTAGT
49887242 TTTAT-TTTTATTT
1 TTTATGTTTTATTT
49887255 TTATTTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 8 0.29
17 20 0.71
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTATGTTTTATTTAGT
Found at i:49890522 original size:16 final size:16
Alignment explanation
Indices: 49890485--49890526 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
49890475 ATCAATAAAA
*
49890485 AATAT-AATTTTAATT
1 AATATAAATATTAATT
* *
49890500 AACATAAATATTATTT
1 AATATAAATATTAATT
49890516 AATATAAATAT
1 AATATAAATAT
49890527 AAATAACTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATAAATATTAATT
Found at i:49892067 original size:24 final size:24
Alignment explanation
Indices: 49892039--49892088 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
49892029 ATCATGTAAG
49892039 ATTAAAAAAATAAAGAGCCTTTTT
1 ATTAAAAAAATAAAGAGCCTTTTT
49892063 ATTAAAAAAATAAAGAGCCTTTTT
1 ATTAAAAAAATAAAGAGCCTTTTT
49892087 AT
1 AT
49892089 CATTCATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (24 bp):
ATTAAAAAAATAAAGAGCCTTTTT
Found at i:49894738 original size:18 final size:18
Alignment explanation
Indices: 49894717--49894756 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
49894707 ATTCAGGTAA
49894717 AATCGAAAAAATTCAGTT
1 AATCGAAAAAATTCAGTT
** *
49894735 AATCGACCAAATTCGGTT
1 AATCGAAAAAATTCAGTT
49894753 AATC
1 AATC
49894757 AGTCGGTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (18 bp):
AATCGAAAAAATTCAGTT
Found at i:49894944 original size:16 final size:16
Alignment explanation
Indices: 49894923--49894975 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
49894913 ATCCACCCAG
*
49894923 ACCCAATCTAATATAA
1 ACCCAATATAATATAA
*
49894939 ACCCAATATAA-ACTCA
1 ACCCAATATAATA-TAA
*
49894955 ATCCAATAT-ATATAA
1 ACCCAATATAATATAA
49894970 ACCCAA
1 ACCCAA
49894976 GTACCCAACC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
15 9 0.30
16 21 0.70
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (16 bp):
ACCCAATATAATATAA
Found at i:49900150 original size:23 final size:22
Alignment explanation
Indices: 49900099--49900150 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
49900089 CCTCGTCTTT
*
49900099 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
49900121 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
49900144 TTCTTTT
1 TTCTTTT
49900151 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:49905205 original size:43 final size:43
Alignment explanation
Indices: 49905156--49905288 Score: 185
Period size: 43 Copynumber: 3.1 Consensus size: 43
49905146 AGGTTATATT
* * **
49905156 TTTAGCGGCGTTTTTGCGAGAAGCACCGCTAAAGGTAGTGGTC
1 TTTAGCGGCGTTTTTGAGAAAAGCACCGCTAAAGGTCTTGGTC
* * *
49905199 TTTAGCGGCATTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTTTGAGAAAAGCACCGCTAAAGGTCTTGGTC
* *
49905242 TTTAGCGGCGTTTTTGGGAAAAGCACCCCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTTTGAGAAAAGCACCGCTAAAGGTCTTGGTC
49905285 TTTA
1 TTTA
49905289 ACGACATTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 78 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTTTGAGAAAAGCACCGCTAAAGGTCTTGGTC
Found at i:49905267 original size:86 final size:86
Alignment explanation
Indices: 49905156--49905318 Score: 229
Period size: 86 Copynumber: 1.9 Consensus size: 86
49905146 AGGTTATATT
* * * * *
49905156 TTTAGCGGCGTTTTTGCGAGAAGCACCGCTAAAGGTAGTGGTCTTTAGCGGCATTTGT-GAGAAA
1 TTTAGCGGCGTTTTTGCGAAAAGCACCCCTAAAGGTAGTGGTCTTTAACGACATTT-TAGAAAAA
*
49905220 AGCGCCGCTAAAGGTCTTGGTC
65 AACGCCGCTAAAGGTCTTGGTC
* **
49905242 TTTAGCGGCGTTTTTGGGAAAAGCACCCCTAAAGGTCTTGGTCTTTAACGACATTTTAGAAAAAA
1 TTTAGCGGCGTTTTTGCGAAAAGCACCCCTAAAGGTAGTGGTCTTTAACGACATTTTAGAAAAAA
49905307 ACGCCGCTAAAG
66 ACGCCGCTAAAG
49905319 TTAGCGACGT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
85 1 0.01
86 66 0.99
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (86 bp):
TTTAGCGGCGTTTTTGCGAAAAGCACCCCTAAAGGTAGTGGTCTTTAACGACATTTTAGAAAAAA
ACGCCGCTAAAGGTCTTGGTC
Found at i:49905317 original size:43 final size:42
Alignment explanation
Indices: 49905156--49905318 Score: 164
Period size: 43 Copynumber: 3.8 Consensus size: 42
49905146 AGGTTATATT
* * * * **
49905156 TTTAGCGGCGTTTTTGCGAGAAGCACCGCTAAAGGTAGTGGTC
1 TTTAGCGGC-ATTTTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
49905199 TTTAGCGGCATTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCATTT-TGAGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * *
49905242 TTTAGCGGCGTTTTTGGGAAAAGCACCCCTAAAGGTCTTGGTC
1 TTTAGCGGC-ATTTTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * *
49905285 TTTAACGACATTTTAGAAAAAAACGCCGCTAAAG
1 TTTAGCGGCATTTT-GAGAAAAGCGCCGCTAAAG
49905319 TTAGCGACGT
Statistics
Matches: 99, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
42 7 0.07
43 89 0.90
44 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (42 bp):
TTTAGCGGCATTTTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:49908339 original size:28 final size:28
Alignment explanation
Indices: 49908307--49908363 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
49908297 CAAAAACACC
49908307 TGATCAGCTGTAGAGTACTCAATATCCT
1 TGATCAGCTGTAGAGTACTCAATATCCT
*
49908335 TGATCAGCTGTAGAGTATTCAATATCCT
1 TGATCAGCTGTAGAGTACTCAATATCCT
49908363 T
1 T
49908364 TCTTTTTAAA
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:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (28 bp):
TGATCAGCTGTAGAGTACTCAATATCCT
Found at i:49911560 original size:9 final size:9
Alignment explanation
Indices: 49911546--49911574 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
49911536 TAAATAACAC
49911546 ATTTTTTTA
1 ATTTTTTTA
49911555 A-TTTTTTA
1 ATTTTTTTA
49911563 ATTTTTTTA
1 ATTTTTTTA
49911572 ATT
1 ATT
49911575 ATAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:49912193 original size:20 final size:20
Alignment explanation
Indices: 49912168--49912207 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
49912158 AACCAACCTT
49912168 GGGTTATTGGGTTGGGTTTA
1 GGGTTATTGGGTTGGGTTTA
*
49912188 GGGTTATTGGGTTGTGTTTA
1 GGGTTATTGGGTTGGGTTTA
49912208 TAAAGTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.42, T:0.47
Consensus pattern (20 bp):
GGGTTATTGGGTTGGGTTTA
Found at i:49915406 original size:13 final size:13
Alignment explanation
Indices: 49915388--49915419 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
49915378 GTATGTTTGT
49915388 AAAAAAATTGAAA
1 AAAAAAATTGAAA
49915401 AAAAAAATTGAAA
1 AAAAAAATTGAAA
49915414 AAAAAA
1 AAAAAA
49915420 GAAACAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (13 bp):
AAAAAAATTGAAA
Found at i:49925423 original size:5 final size:5
Alignment explanation
Indices: 49925413--49925439 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
49925403 ACCCTCAAGC
49925413 AAACA AAACA AAACA AAACA AAACA AA
1 AAACA AAACA AAACA AAACA AAACA AA
49925440 CTAAATAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:49926925 original size:20 final size:20
Alignment explanation
Indices: 49926894--49927059 Score: 131
Period size: 20 Copynumber: 8.2 Consensus size: 20
49926884 CATTAATGTA
*
49926894 AAACAGGGGCACAGATGTGC
1 AAACAAGGGCACAGATGTGC
** *
49926914 AGTCAAGGGCACCA-AAGTGC
1 AAACAAGGGCA-CAGATGTGC
*
49926934 AAAAAAGGGACACAGATGTGC
1 AAACAAGGG-CACAGATGTGC
* * *
49926955 AAGCAGGGGCACCGATGTGC
1 AAACAAGGGCACAGATGTGC
** *
49926975 AAACAAGGGTGCAGATATGC
1 AAACAAGGGCACAGATGTGC
*
49926995 AAACAGGGGCACAGATGTGC
1 AAACAAGGGCACAGATGTGC
* * *
49927015 AAATAAAGGTATC-GATGTGC
1 AAACAAGGGCA-CAGATGTGC
*
49927035 AAACAGGGGCATCA-ATGTGC
1 AAACAAGGGCA-CAGATGTGC
49927055 AAACA
1 AAACA
49927060 TAAATAATTG
Statistics
Matches: 111, Mismatches: 30, Indels: 10
0.74 0.20 0.07
Matches are distributed among these distances:
20 95 0.86
21 16 0.14
ACGTcount: A:0.38, C:0.19, G:0.31, T:0.13
Consensus pattern (20 bp):
AAACAAGGGCACAGATGTGC
Found at i:49926952 original size:41 final size:41
Alignment explanation
Indices: 49926893--49926983 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
49926883 TCATTAATGT
* *
49926893 AAAACAGGGGCACAGATGTGC-AGTCAAGGGCACCAAAGTGC
1 AAAAAAGGGACACAGATGTGCAAG-CAAGGGCACCAAAGTGC
* * *
49926934 AAAAAAGGGACACAGATGTGCAAGCAGGGGCACCGATGTGC
1 AAAAAAGGGACACAGATGTGCAAGCAAGGGCACCAAAGTGC
*
49926975 AAACAAGGG
1 AAAAAAGGG
49926984 TGCAGATATG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 41 0.95
42 2 0.05
ACGTcount: A:0.38, C:0.20, G:0.33, T:0.09
Consensus pattern (41 bp):
AAAAAAGGGACACAGATGTGCAAGCAAGGGCACCAAAGTGC
Found at i:49927002 original size:40 final size:41
Alignment explanation
Indices: 49926905--49927059 Score: 145
Period size: 40 Copynumber: 3.8 Consensus size: 41
49926895 AACAGGGGCA
** * * * * *
49926905 CAGATGTGCAGTCAAGGGCACCAAAGTGCAAA-AAAGGGACA
1 CAGATGTGCAAACAGGGGCACCGATGTGCAAACAAAGGTA-G
* *
49926946 CAGATGTGCAAGCAGGGGCACCGATGTGCAAACAAGGGT-G
1 CAGATGTGCAAACAGGGGCACCGATGTGCAAACAAAGGTAG
* * * *
49926986 CAGATATGCAAACAGGGGCACAGATGTGCAAATAAAGGTAT
1 CAGATGTGCAAACAGGGGCACCGATGTGCAAACAAAGGTAG
* *
49927027 C-GATGTGCAAACAGGGGCATCAATGTGCAAACA
1 CAGATGTGCAAACAGGGGCACCGATGTGCAAACA
49927060 TAAATAATTG
Statistics
Matches: 93, Mismatches: 19, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
40 61 0.66
41 28 0.30
42 4 0.04
ACGTcount: A:0.37, C:0.19, G:0.30, T:0.14
Consensus pattern (41 bp):
CAGATGTGCAAACAGGGGCACCGATGTGCAAACAAAGGTAG
Found at i:49928414 original size:28 final size:28
Alignment explanation
Indices: 49928381--49928506 Score: 189
Period size: 28 Copynumber: 4.5 Consensus size: 28
49928371 TGACTTTCGA
49928381 CACTAAGTGTGCGAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* *
49928409 TACTAAGTGTGCTAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
*
49928437 CACTAAGTGTGCGAGTTTAATGGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * **
49928465 CACTAAGTGTGCGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
49928493 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
49928507 ACTTATTAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 88 1.00
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:49929253 original size:23 final size:23
Alignment explanation
Indices: 49929224--49929420 Score: 171
Period size: 23 Copynumber: 8.5 Consensus size: 23
49929214 TGATACTTAA
*
49929224 ATGCTGCCCAATTTCTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
* * *
49929247 ATACTGCTCAATTTGTTGCATAT
1 ATGCTGCCCAATTTGTTGTATAT
* * * *
49929270 ATGTTGTCCAATTTTTATGCT-TAA
1 ATGCTGCCCAATTTGT-TG-TATAT
* * *
49929294 ATGCTGCTCAATTTGGTATATAT
1 ATGCTGCCCAATTTGTTGTATAT
49929317 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
* * * * *
49929340 AAGCTGTCCAATTTTGGTGTAAAA
1 ATGCTGCCCAA-TTTGTTGTATAT
* *
49929364 ATACTGCTCAATTTGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
* *
49929387 GTGCTGCCCAAATTGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
*
49929410 ATGCTGTCCAA
1 ATGCTGCCCAA
49929421 ATTTTGGTGT
Statistics
Matches: 131, Mismatches: 39, Indels: 8
0.74 0.22 0.04
Matches are distributed among these distances:
22 1 0.01
23 99 0.76
24 31 0.24
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.42
Consensus pattern (23 bp):
ATGCTGCCCAATTTGTTGTATAT
Found at i:49929316 original size:70 final size:70
Alignment explanation
Indices: 49929210--49929426 Score: 265
Period size: 70 Copynumber: 3.1 Consensus size: 70
49929200 TGTTCATGTT
* * * * * * *
49929210 ATTTTGATACTTAAATGCTGCCCAATTTCTTGTATATATACTGCTCAATTTGTTGCATATATGTT
1 ATTTTGATGCTTAAATGCTGCTCAATTTGTTGTATATATGCTGCCCAATTTGTTGTATATATGCT
49929275 GTCCA
66 GTCCA
* * * *
49929280 ATTTTTATGCTTAAATGCTGCTCAATTTGGTATATATATGCTGCCCAATTTGTTGTATATAAGCT
1 ATTTTGATGCTTAAATGCTGCTCAATTTGTTGTATATATGCTGCCCAATTTGTTGTATATATGCT
49929345 GTCCA
66 GTCCA
* * * * *
49929350 ATTTTGGTG-TAAAAATACTGCTCAATTTGTTGTATATGTGCTGCCCAAATTGTTGTATATATGC
1 ATTTTGATGCT-TAAATGCTGCTCAATTTGTTGTATATATGCTGCCCAATTTGTTGTATATATGC
49929414 TGTCCAA
65 TGTCC-A
49929421 ATTTTG
1 ATTTTG
49929427 GTGTGAAAAT
Statistics
Matches: 125, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
69 1 0.01
70 117 0.94
71 7 0.06
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (70 bp):
ATTTTGATGCTTAAATGCTGCTCAATTTGTTGTATATATGCTGCCCAATTTGTTGTATATATGCT
GTCCA
Found at i:49929424 original size:47 final size:45
Alignment explanation
Indices: 49929224--49929420 Score: 153
Period size: 47 Copynumber: 4.2 Consensus size: 45
49929214 TGATACTTAA
* * * * *
49929224 ATGCTGCCCAATTTCTTGTATATATACTGCTCAATTTGTTGCATAT
1 ATGCTG-CCAATTTGTTGTATATATGCTGCCCAATTTGGTGTATAT
* * * * *
49929270 ATGTTGTCCAATTTTTATGCT-TAAATGCTGCTCAATTTGGTATATAT
1 ATGCTG-CCAATTTGT-TG-TATATATGCTGCCCAATTTGGTGTATAT
* * * *
49929317 ATGCTGCCCAATTTGTTGTATATAAGCTGTCCAATTTTGGTGTAAAA
1 ATGCTG-CCAATTTGTTGTATATATGCTGCCCAA-TTTGGTGTATAT
* * * *
49929364 ATACTGCTCAATTTGTTGTATATGTGCTGCCCAAATTGTTGTATAT
1 ATGCTGC-CAATTTGTTGTATATATGCTGCCCAATTTGGTGTATAT
49929410 ATGCTGTCCAA
1 ATGCTG-CCAA
49929421 ATTTTGGTGT
Statistics
Matches: 118, Mismatches: 27, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
45 1 0.01
46 42 0.36
47 74 0.63
48 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.42
Consensus pattern (45 bp):
ATGCTGCCAATTTGTTGTATATATGCTGCCCAATTTGGTGTATAT
Found at i:49929441 original size:25 final size:25
Alignment explanation
Indices: 49929305--49929471 Score: 83
Period size: 23 Copynumber: 7.0 Consensus size: 25
49929295 TGCTGCTCAA
* *
49929305 TTTGGTATATATATGCTG-CCCAAT
1 TTTGGTATATAAATGCTGTCCAAAT
*
49929329 TTGTTGTATAT-AA-GCTGTCC-AAT
1 TT-TGGTATATAAATGCTGTCCAAAT
* * *
49929352 TTTGGTGTAAAAATACTG-CTC-AAT
1 TTTGGTATATAAATGCTGTC-CAAAT
* * *
49929376 TTGTTGTATAT--GTGCTGCCCAAAT
1 TT-TGGTATATAAATGCTGTCCAAAT
49929400 TGTT-GTATAT--ATGCTGTCCAAAT
1 T-TTGGTATATAAATGCTGTCCAAAT
* * *
49929423 TTTGGTGTGA-AAATGCTGT-C-TAG
1 TTTGGTAT-ATAAATGCTGTCCAAAT
49929446 TTTGGTATATAAATGCTGTCCAAAT
1 TTTGGTATATAAATGCTGTCCAAAT
49929471 T
1 T
49929472 GATGTATGAG
Statistics
Matches: 108, Mismatches: 19, Indels: 31
0.68 0.12 0.20
Matches are distributed among these distances:
22 8 0.07
23 55 0.51
24 23 0.21
25 22 0.20
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.41
Consensus pattern (25 bp):
TTTGGTATATAAATGCTGTCCAAAT
Found at i:49929469 original size:71 final size:70
Alignment explanation
Indices: 49929222--49929478 Score: 257
Period size: 70 Copynumber: 3.7 Consensus size: 70
49929212 TTTGATACTT
* ** * * * * * * * **
49929222 AAATGCTGCCCAATTTCTTGTATATATACTGCTCAATTTGTTGCATATATGTTGTCCAATTTTTA
1 AAATGCTGCTCAATTTGGTATATATATGCTGCCCAAATTGTTGTATATAAGCTGTCCAATTTTGG
*
49929287 TGCT-T
66 TG-TAA
*
49929292 AAATGCTGCTCAATTTGGTATATATATGCTGCCCAATTTGTTGTATATAAGCTGTCCAATTTTGG
1 AAATGCTGCTCAATTTGGTATATATATGCTGCCCAAATTGTTGTATATAAGCTGTCCAATTTTGG
49929357 TGTAA
66 TGTAA
* * * * *
49929362 AAATACTGCTCAATTTGTTGTATATGTGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTG
1 AAATGCTGCTCAATTTGGTATATATATGCTGCCCAAATTGTTGTATATAAGCTGTCC-AATTTTG
*
49929427 GTGTGA
65 GTGTAA
* * * *
49929433 AAATGCTG-TCTAGTTTGGTATATAAATGCTGTCCAAATTGATGTAT
1 AAATGCTGCTC-AATTTGGTATATATATGCTGCCCAAATTGTTGTAT
49929479 GAGGGCTGTC
Statistics
Matches: 157, Mismatches: 27, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
69 1 0.01
70 109 0.69
71 47 0.30
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (70 bp):
AAATGCTGCTCAATTTGGTATATATATGCTGCCCAAATTGTTGTATATAAGCTGTCCAATTTTGG
TGTAA
Found at i:49932639 original size:5 final size:5
Alignment explanation
Indices: 49932629--49932657 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
49932619 GTAAGAAGAT
49932629 GGAAG GGAAG GGAAG GGAAG GGAAG GGAA
1 GGAAG GGAAG GGAAG GGAAG GGAAG GGAA
49932658 CGTAAAAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (5 bp):
GGAAG
Found at i:49934423 original size:22 final size:22
Alignment explanation
Indices: 49934377--49934419 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
49934367 TTTCGAAATT
49934377 TAAAACATTTTGATAATTTAAA
1 TAAAACATTTTGATAATTTAAA
49934399 TAAAACATTTTGA-AATTTAAA
1 TAAAACATTTTGATAATTTAAA
49934420 ATAATCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (22 bp):
TAAAACATTTTGATAATTTAAA
Found at i:49935813 original size:31 final size:31
Alignment explanation
Indices: 49935762--49935827 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
49935752 AACAACACAG
49935762 TGACTTAAATAAAAACTTTTGAATAGTCCAA
1 TGACTTAAATAAAAACTTTTGAATAGTCCAA
* * * *
49935793 TGACTTGAATGAAAATTTTTGAATAGTTCAA
1 TGACTTAAATAAAAACTTTTGAATAGTCCAA
49935824 TGAC
1 TGAC
49935828 CAACTTATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.35
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTGAATAGTCCAA
Found at i:49936082 original size:6 final size:6
Alignment explanation
Indices: 49936071--49936108 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
49936061 AAGTATAATC
49936071 TTGTAA TTGTAA TTGTAA TTGTAA TTGTAA TTGTAA TT
1 TTGTAA TTGTAA TTGTAA TTGTAA TTGTAA TTGTAA TT
49936109 ATATTTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53
Consensus pattern (6 bp):
TTGTAA
Found at i:49942692 original size:73 final size:73
Alignment explanation
Indices: 49942573--49942720 Score: 269
Period size: 73 Copynumber: 2.0 Consensus size: 73
49942563 CACGAGCTCA
* *
49942573 ATTTACAGAAATAGGGTTCCGATATCTCATTTTTTTTAAATCATTTGACTTTGGGACTGAACCAC
1 ATTTACAGAAATAGGGGTCCGATATCTCATTTTTTTTAAATCATTTGACTTTGGGAATGAACCAC
49942638 TTATACTT
66 TTATACTT
*
49942646 ATTTACAGAAATAGGGGTCCGATATCTCATTTTTTTTAAATCATTTGACTTTGGGAATGAACTAC
1 ATTTACAGAAATAGGGGTCCGATATCTCATTTTTTTTAAATCATTTGACTTTGGGAATGAACCAC
49942711 TTATACTT
66 TTATACTT
49942719 AT
1 AT
49942721 CTATTTGTTC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (73 bp):
ATTTACAGAAATAGGGGTCCGATATCTCATTTTTTTTAAATCATTTGACTTTGGGAATGAACCAC
TTATACTT
Found at i:49948342 original size:75 final size:75
Alignment explanation
Indices: 49948218--49948414 Score: 252
Period size: 75 Copynumber: 2.6 Consensus size: 75
49948208 TATCGTATTT
* * * *
49948218 TTTTGCCATCAATTTCCTTGTCTTTGTTTT-TTTATTTTGTTTATTTGATTGTTTAATTGTCATC
1 TTTTGCCATCAATTCCCTTTTCTTTGTTTTGTTTATTTTATTTATTTGATTGTTTAATTATCATC
** *
49948282 ATTGTCTCTA
66 ATTACCTATA
* * *
49948292 TTTTGCCATTACTTCCCTTTTCTTTGTTTTGTTTATTTTCTTTATTTGATTGTTTAATTATCATC
1 TTTTGCCATCAATTCCCTTTTCTTTGTTTTGTTTATTTTATTTATTTGATTGTTTAATTATCATC
* *
49948357 GTTACCTATG
66 ATTACCTATA
* *
49948367 TTTTGCCATCAAATCCCTTTTCTTTCTTTTGTTTATTTTTATTTATTT
1 TTTTGCCATCAATTCCCTTTTCTTTGTTTTGTTTA-TTTTATTTATTT
49948415 TATTTTATTT
Statistics
Matches: 105, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
74 26 0.25
75 68 0.65
76 11 0.10
ACGTcount: A:0.15, C:0.15, G:0.09, T:0.61
Consensus pattern (75 bp):
TTTTGCCATCAATTCCCTTTTCTTTGTTTTGTTTATTTTATTTATTTGATTGTTTAATTATCATC
ATTACCTATA
Found at i:49948418 original size:5 final size:5
Alignment explanation
Indices: 49948398--49948436 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
49948388 CTTTCTTTTG
49948398 TTTAT TTT-T ATTTAT TTTAT TTTAT TTTAT TTTAGT TTT
1 TTTAT TTTAT -TTTAT TTTAT TTTAT TTTAT TTTA-T TTT
49948437 CTGTTCAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
4 1 0.03
5 25 0.81
6 5 0.16
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:49958766 original size:6 final size:7
Alignment explanation
Indices: 49958739--49958772 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
49958729 ATTTTCTCCC
49958739 AAATG-A
1 AAATGAA
49958745 AAATGAA
1 AAATGAA
49958752 AAATGAA
1 AAATGAA
*
49958759 AAATAAA
1 AAATGAA
49958766 AAATGAA
1 AAATGAA
49958773 TTTATGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (7 bp):
AAATGAA
Found at i:49965746 original size:17 final size:17
Alignment explanation
Indices: 49965711--49965749 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
49965701 TTAAGATAAT
*
49965711 TATTAAATTTTATTTAA
1 TATTAAATTTTATTAAA
49965728 TATTAAA-TTTATTAAAA
1 TATTAAATTTTATT-AAA
49965745 TATTA
1 TATTA
49965750 TTATTTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTAAATTTTATTAAA
Found at i:49969125 original size:66 final size:66
Alignment explanation
Indices: 49969007--49969144 Score: 201
Period size: 66 Copynumber: 2.1 Consensus size: 66
49968997 GTTGCACAAC
*
49969007 TAAT-GGAATTTGGATTCAAATTGCAGTCTAAGAAATCTGTTAAAAAAAGATTAGGTTTA-TTGG
1 TAATGGGAATTTGGATTCAAATTGAAGTCTAAGAAATCTGTTAAAAAAAGATTAGG-TTAGTTGG
49969070 GA
65 GA
* * *
49969072 TAATGGGAATTTGGATTGAAATTGAAGTCTAA-AAAGTCTGTTAAATAATGATTAGGTTAGTTGG
1 TAATGGGAATTTGGATTCAAATTGAAGTCTAAGAAA-TCTGTTAAAAAAAGATTAGGTTAGTTGG
49969136 GA
65 GA
49969138 TAATGGG
1 TAATGGG
49969145 CATGTCTTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
65 10 0.15
66 56 0.85
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (66 bp):
TAATGGGAATTTGGATTCAAATTGAAGTCTAAGAAATCTGTTAAAAAAAGATTAGGTTAGTTGGG
A
Found at i:49978613 original size:39 final size:38
Alignment explanation
Indices: 49978557--49978656 Score: 130
Period size: 39 Copynumber: 2.6 Consensus size: 38
49978547 CGAATATAAT
* * *
49978557 AATTATAATTATC-ATAATTATAATAATGTTTGAGTGAAA
1 AATTATAATTA-CAATAATTATAATAATATTCGA-TCAAA
* *
49978596 AATTACAATTACAATAATTATAATAATATTCGATCATA
1 AATTATAATTACAATAATTATAATAATATTCGATCAAA
49978634 AATTATAATTACAATAATTATAA
1 AATTATAATTACAATAATTATAA
49978657 CAAGGATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
38 26 0.48
39 28 0.52
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (38 bp):
AATTATAATTACAATAATTATAATAATATTCGATCAAA
Found at i:50005811 original size:16 final size:16
Alignment explanation
Indices: 50005790--50005831 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
50005780 CGTTTGGTTC
*
50005790 GCTGTAATGGAATAGA
1 GCTGTAATAGAATAGA
50005806 GCTGTAATAGAATAGA
1 GCTGTAATAGAATAGA
50005822 GGC-GTAATAG
1 -GCTGTAATAG
50005832 TAATTCAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 22 0.92
17 2 0.08
ACGTcount: A:0.38, C:0.07, G:0.31, T:0.24
Consensus pattern (16 bp):
GCTGTAATAGAATAGA
Found at i:50006178 original size:120 final size:120
Alignment explanation
Indices: 50006042--50006468 Score: 802
Period size: 120 Copynumber: 3.5 Consensus size: 120
50006032 TTATTCATAT
*
50006042 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
50006107 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
50006162 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
50006227 AAATATTCTTATATGAATTTACTAAAATCATAATATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCAT-A-ATATATAATACTATAAAATATAA
50006284 TTTAAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA-
1 TTT-AAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAT
*
50006348 TAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
65 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
50006404 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
50006469 TGATAGAACT
Statistics
Matches: 301, Mismatches: 2, Indels: 8
0.97 0.01 0.03
Matches are distributed among these distances:
119 60 0.20
120 122 0.41
121 2 0.01
122 57 0.19
123 60 0.20
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:50006307 original size:27 final size:27
Alignment explanation
Indices: 50006276--50006355 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 27
50006266 TAATACTATA
50006276 AAATATAATTTAAAAATAATTATTATT
1 AAATATAATTTAAAAATAATTATTATT
*
50006303 AAATATAATTTAATAAA-AATATATAATT
1 AAATATAATTTAA-AAATAAT-TATTATT
* * * *
50006331 TAATAAAATTCTTAATATAATTATT
1 AAATATAATT-TAAAAATAATTATT
50006356 CTTATATGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
27 16 0.37
28 22 0.51
29 5 0.12
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (27 bp):
AAATATAATTTAAAAATAATTATTATT
Found at i:50010918 original size:7 final size:7
Alignment explanation
Indices: 50010906--50010940 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
50010896 TATATATGAG
50010906 ATGTGAT
1 ATGTGAT
50010913 ATGTGAT
1 ATGTGAT
50010920 ATGTGAT
1 ATGTGAT
50010927 ATGTGAT
1 ATGTGAT
50010934 ATGTGAT
1 ATGTGAT
50010941 TTAAAAGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (7 bp):
ATGTGAT
Found at i:50010921 original size:21 final size:21
Alignment explanation
Indices: 50010897--50010940 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
50010887 GTTGTAATAT
50010897 ATATATGAGATGTGATATGTG
1 ATATATGAGATGTGATATGTG
* *
50010918 ATATGTGATATGTGATATGTG
1 ATATATGAGATGTGATATGTG
50010939 AT
1 AT
50010941 TTAAAAGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.27, T:0.41
Consensus pattern (21 bp):
ATATATGAGATGTGATATGTG
Found at i:50016368 original size:43 final size:44
Alignment explanation
Indices: 50016267--50016381 Score: 137
Period size: 43 Copynumber: 2.6 Consensus size: 44
50016257 TGAGTTATCG
* * *
50016267 TGTAAGACCACGTCTGGGACGTTGGCATGGATTTGAGATTTACA
1 TGTAAGACCATGTCTGAGACGTTGGCATAGATTTGAGATTTACA
* *
50016311 TGTAAGACCCTGTCTGAGACAG-TGGCATAGATATT-TGA-TTACA
1 TGTAAGACCATGTCTGAGAC-GTTGGCATAGAT-TTGAGATTTACA
*
50016354 TGTAAGACCATGTCTGGGACGTTGGCAT
1 TGTAAGACCATGTCTGAGACGTTGGCAT
50016382 TGTATGAGCT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
42 1 0.02
43 29 0.48
44 28 0.46
45 3 0.05
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (44 bp):
TGTAAGACCATGTCTGAGACGTTGGCATAGATTTGAGATTTACA
Found at i:50017481 original size:68 final size:68
Alignment explanation
Indices: 50017403--50017529 Score: 254
Period size: 68 Copynumber: 1.9 Consensus size: 68
50017393 TTTGTGGTGC
50017403 CAAATATATACATATATTATATTTGAATGTTTAGTCGTGTAAGTTCGATTGTTAAATGACTAAAC
1 CAAATATATACATATATTATATTTGAATGTTTAGTCGTGTAAGTTCGATTGTTAAATGACTAAAC
50017468 ATT
66 ATT
50017471 CAAATATATACATATATTATATTTGAATGTTTAGTCGTGTAAGTTCGATTGTTAAATGA
1 CAAATATATACATATATTATATTTGAATGTTTAGTCGTGTAAGTTCGATTGTTAAATGA
50017530 TAACTATTGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (68 bp):
CAAATATATACATATATTATATTTGAATGTTTAGTCGTGTAAGTTCGATTGTTAAATGACTAAAC
ATT
Found at i:50017812 original size:63 final size:63
Alignment explanation
Indices: 50017734--50017857 Score: 203
Period size: 63 Copynumber: 2.0 Consensus size: 63
50017724 TTGCTTTTAA
* *
50017734 GGAAAGATGTGTATTATACATATACATATACATCCATAATATGTTCGGCCAAGTTGCATTGAG
1 GGAAAGATGTCTATTATACATATACATATACATCCATAATATATTCGGCCAAGTTGCATTGAG
* * *
50017797 GGAAAGATGTCTATTATACATATACATGTACATCCATAATATATTCGGTCAGGTTGCATTG
1 GGAAAGATGTCTATTATACATATACATATACATCCATAATATATTCGGCCAAGTTGCATTG
50017858 TTACTAATGT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (63 bp):
GGAAAGATGTCTATTATACATATACATATACATCCATAATATATTCGGCCAAGTTGCATTGAG
Found at i:50028866 original size:28 final size:28
Alignment explanation
Indices: 50028825--50028888 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
50028815 ATTCCTGGGA
* *
50028825 TATTTTCTCAGAACTCATCTTGTCAAAAT
1 TATTTT-TCAGAACCCATCTCGTCAAAAT
50028854 TATTTTTCAGAACCCATCTCGTCAAAAT
1 TATTTTTCAGAACCCATCTCGTCAAAAT
*
50028882 CATTTTT
1 TATTTTT
50028889 TTCGAACCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 26 0.81
29 6 0.19
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.42
Consensus pattern (28 bp):
TATTTTTCAGAACCCATCTCGTCAAAAT
Found at i:50029025 original size:19 final size:18
Alignment explanation
Indices: 50028997--50029034 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
50028987 CTAAAACACT
50028997 AATTAAT-AAACACTTAAA
1 AATTAATAAAACAC-TAAA
50029015 AATTAAATAAAACACTAAA
1 AATT-AATAAAACACTAAA
50029034 A
1 A
50029035 CGCTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 8 0.44
20 6 0.33
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.24
Consensus pattern (18 bp):
AATTAATAAAACACTAAA
Found at i:50029062 original size:22 final size:22
Alignment explanation
Indices: 50029015--50029100 Score: 81
Period size: 22 Copynumber: 4.0 Consensus size: 22
50029005 AACACTTAAA
* *
50029015 AATTAAATAAAACACTAAAACGCT
1 AATTTAAT-AAACACT-AAACCCT
50029039 AATTTAATAAACACTAAACCCT
1 AATTTAATAAACACTAAACCCT
50029061 AA-TT-A-AAAC-CTTAAACCCT
1 AATTTAATAAACAC-TAAACCCT
* *
50029080 AATTTAATATACCCTAAACCC
1 AATTTAATAAACACTAAACCC
50029101 CTAAAAACGA
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
18 1 0.02
19 14 0.26
20 3 0.06
21 3 0.06
22 18 0.33
23 8 0.15
24 7 0.13
ACGTcount: A:0.50, C:0.23, G:0.01, T:0.26
Consensus pattern (22 bp):
AATTTAATAAACACTAAACCCT
Found at i:50029097 original size:41 final size:42
Alignment explanation
Indices: 50028980--50029100 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 42
50028970 TTATTTTTCC
* * *** *
50028980 TAAAACTCTAAAACACTAA-TTAATAAACACTTAAAAATTAAA
1 TAAAACACTAAAACCCTAATTTAATAAACAC-TAAACCCTAAT
*
50029022 TAAAACACTAAAACGCTAATTTAATAAACACTAAACCCTAAT
1 TAAAACACTAAAACCCTAATTTAATAAACACTAAACCCTAAT
* * *
50029064 TAAAAC-CTTAAACCCTAATTTAATATACCCTAAACCC
1 TAAAACACTAAAACCCTAATTTAATAAACACTAAACCC
50029101 CTAAAAACGA
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 27 0.40
42 30 0.44
43 11 0.16
ACGTcount: A:0.52, C:0.21, G:0.01, T:0.26
Consensus pattern (42 bp):
TAAAACACTAAAACCCTAATTTAATAAACACTAAACCCTAAT
Found at i:50029529 original size:19 final size:19
Alignment explanation
Indices: 50029505--50029550 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
50029495 GAAACTCCTC
50029505 TAATATATTAT-TATATAAA
1 TAATATATTATGTATAT-AA
50029524 TAATATATTATGTATATAA
1 TAATATATTATGTATATAA
50029543 TAATATAT
1 TAATATAT
50029551 AAATACATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TAATATATTATGTATATAA
Found at i:50029532 original size:16 final size:16
Alignment explanation
Indices: 50029513--50029555 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
50029503 TCTAATATAT
50029513 TATTATATAAATAATA
1 TATTATATAAATAATA
* *
50029529 TATTATGTATATAATA
1 TATTATATAAATAATA
50029545 -A-TATATAAATA
1 TATTATATAAATA
50029556 CATTTAAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 8 0.35
15 1 0.04
16 14 0.61
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
TATTATATAAATAATA
Found at i:50029795 original size:2 final size:2
Alignment explanation
Indices: 50029784--50029812 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
50029774 GTCATAACCT
50029784 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
50029813 ATGTTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:50031475 original size:19 final size:18
Alignment explanation
Indices: 50031447--50031483 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
50031437 AAAAAAAGAG
50031447 AAATAGTAAATTATCAGAA
1 AAATAGTAAATTA-CAGAA
*
50031466 AAATATTAAATTACAGAA
1 AAATAGTAAATTACAGAA
50031484 TTAAAGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.27
Consensus pattern (18 bp):
AAATAGTAAATTACAGAA
Found at i:50041862 original size:31 final size:31
Alignment explanation
Indices: 50041826--50041884 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
50041816 AAAATATATA
* * *
50041826 TTTTATACTTTTTTAATTTTTTGAAAATACC
1 TTTTATAATTTTTTAAGTTTTTCAAAATACC
*
50041857 TTTTATAATTTTTTGAGTTTTTCAAAAT
1 TTTTATAATTTTTTAAGTTTTTCAAAAT
50041885 TTAAAAACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (31 bp):
TTTTATAATTTTTTAAGTTTTTCAAAATACC
Found at i:50042912 original size:19 final size:19
Alignment explanation
Indices: 50042864--50042900 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
50042854 TAAATATTAT
*
50042864 AATTAATTATAAATTAAAA
1 AATTAATTATAAAATAAAA
50042883 AATTAATTATAAAATAAA
1 AATTAATTATAAAATAAA
50042901 TAATAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATTATAAAATAAAA
Found at i:50044374 original size:23 final size:24
Alignment explanation
Indices: 50044334--50044378 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
50044324 GAAATACTTG
50044334 AGGATTCAATAAGTAATTAAACTA
1 AGGATTCAATAAGTAATTAAACTA
50044358 AGGATCTCAA-AA-TAATTAAAC
1 AGGAT-TCAATAAGTAATTAAAC
50044379 CATTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.45
24 7 0.35
25 4 0.20
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (24 bp):
AGGATTCAATAAGTAATTAAACTA
Found at i:50048123 original size:50 final size:49
Alignment explanation
Indices: 50048060--50048204 Score: 139
Period size: 50 Copynumber: 2.9 Consensus size: 49
50048050 TCTTGAGAAA
* *
50048060 ATTGTCTCTATAGTTGCGACATTCCATTGATGAAGTTACGACATCAAGCT
1 ATTGTCTCCATAGTTGCGACATTCC-TTGATGAAGTCACGACATCAAGCT
* * * * * * *
50048110 GTTGTCTCCATAGTCGTGACATTCCCT-ACTAAAGTCGCAACATCAAGCT
1 ATTGTCTCCATAGTTGCGACATTCCTTGA-TGAAGTCACGACATCAAGCT
* * * *
50048159 ACTGTCTCCATAGTTGCAATATTCCCTTGTTGAAGTCACGACATCA
1 ATTGTCTCCATAGTTGCGACATT-CCTTGATGAAGTCACGACATCA
50048205 TGATATTGCT
Statistics
Matches: 72, Mismatches: 20, Indels: 6
0.73 0.20 0.06
Matches are distributed among these distances:
48 1 0.01
49 34 0.47
50 37 0.51
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (49 bp):
ATTGTCTCCATAGTTGCGACATTCCTTGATGAAGTCACGACATCAAGCT
Found at i:50053032 original size:45 final size:45
Alignment explanation
Indices: 50052968--50053054 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
50052958 CAGAGACTCA
* *
50052968 GTGGATTCAACACATAGCAACCACCTTATTAATCAATGATGTCCG
1 GTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTCCG
* * *
50053013 GTGGAATCAGCACATAGCAACTACTTTACTAATCAATGATGT
1 GTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGT
50053055 TTGGTTCACA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (45 bp):
GTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTCCG
Found at i:50053120 original size:51 final size:52
Alignment explanation
Indices: 50053065--50053200 Score: 206
Period size: 50 Copynumber: 2.7 Consensus size: 52
50053055 TTGGTTCACA
50053065 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATT-CGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCCGATACACG
** * *
50053116 TAGTAGCCTGCACATAGTACTACACATACGACC--TATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCCGATACACG
*
50053166 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAT
50053201 CACTTTCACT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
49 6 0.08
50 38 0.51
51 31 0.41
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (52 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCCGATACACG
Found at i:50057127 original size:23 final size:23
Alignment explanation
Indices: 50057101--50057153 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
50057091 ATAAGTGTCA
*
50057101 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
*
50057124 CACTGAAATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
50057147 CACTGAT
1 CACTGAT
50057154 CAATAACACT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCAAAGCTAC
Found at i:50058312 original size:51 final size:52
Alignment explanation
Indices: 50058247--50058368 Score: 171
Period size: 51 Copynumber: 2.4 Consensus size: 52
50058237 GCATGGACTG
* *
50058247 TGTGTAGGCCACTATGTGAAAGT-GAA-AGTGATGGTCACGTGTGTAGTACTA
1 TGTGTAGGCTACTATGTGAAA-TCGAATAGTGATGGTCACATGTGTAGTACTA
*
50058298 TGTGTAGGCTACTATGTG-TATCGAATAGTGATGGTCACATGTGTAGTACTA
1 TGTGTAGGCTACTATGTGAAATCGAATAGTGATGGTCACATGTGTAGTACTA
50058349 TGTG-ACGGCTACTATGTGAA
1 TGTGTA-GGCTACTATGTGAA
50058369 CCGGTATCAT
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
49 1 0.02
50 5 0.08
51 57 0.90
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.32
Consensus pattern (52 bp):
TGTGTAGGCTACTATGTGAAATCGAATAGTGATGGTCACATGTGTAGTACTA
Found at i:50058440 original size:46 final size:43
Alignment explanation
Indices: 50058368--50058466 Score: 110
Period size: 46 Copynumber: 2.2 Consensus size: 43
50058358 TACTATGTGA
* *
50058368 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTACTGAAT-CC
* *
50058411 ACCGGATATCATTGATTACAAATGGTGGTTGCTGTGTACTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTACTGAATCC
50058457 ACCGTGTATC
1 ACCG-GTATC
50058467 TGTTATTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 5 0.11
44 11 0.23
45 2 0.04
46 26 0.55
47 3 0.06
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTACTGAATCC
Found at i:50058611 original size:16 final size:16
Alignment explanation
Indices: 50058590--50058621 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
50058580 TGATTGAAAG
*
50058590 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
50058606 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
50058622 GCAACAAAAT
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:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:50063363 original size:46 final size:46
Alignment explanation
Indices: 50063313--50063436 Score: 203
Period size: 46 Copynumber: 2.7 Consensus size: 46
50063303 AATACAAACC
*
50063313 AAGATAATTTTATTAATATATGCTAATGGAATAATAAATGAATTTT
1 AAGATAATTTTATTAATATATACTAATGGAATAATAAATGAATTTT
* *
50063359 AAGATAATTTTATTAATATATACTAATGGAACAATAAATGAGTTTT
1 AAGATAATTTTATTAATATATACTAATGGAATAATAAATGAATTTT
* *
50063405 AAGATAATTTTGTTAATATATACTGATGGAAT
1 AAGATAATTTTATTAATATATACTAATGGAAT
50063437 TTTTATAAGA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.40
Consensus pattern (46 bp):
AAGATAATTTTATTAATATATACTAATGGAATAATAAATGAATTTT
Found at i:50071195 original size:27 final size:26
Alignment explanation
Indices: 50071161--50071218 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
50071151 TCTCATCCTT
50071161 ATTTTACCCCTCAACAAAATTTTGATG
1 ATTTTACCCCT-AACAAAATTTTGATG
***
50071188 ATTTTACCCCTGGTAAAATTTTGATG
1 ATTTTACCCCTAACAAAATTTTGATG
50071214 ATTTT
1 ATTTT
50071219 GCCCTTGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.43
Consensus pattern (26 bp):
ATTTTACCCCTAACAAAATTTTGATG
Found at i:50071212 original size:26 final size:26
Alignment explanation
Indices: 50071176--50071234 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
50071166 ACCCCTCAAC
50071176 AAAATTTTGATGATTTTACCCCTGGT
1 AAAATTTTGATGATTTTACCCCTGGT
* *
50071202 AAAATTTTGATGATTTTGCCCTTGGT
1 AAAATTTTGATGATTTTACCCCTGGT
50071228 AAAATTT
1 AAAATTT
50071235 CGAGAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (26 bp):
AAAATTTTGATGATTTTACCCCTGGT
Found at i:50074773 original size:18 final size:17
Alignment explanation
Indices: 50074750--50074789 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
50074740 TCTCTTTTTG
50074750 TTCTTTTTCATTCTCTTT
1 TTCTTTTTCATT-TCTTT
*
50074768 TTCTTTTTTGATTTCTTT
1 TTC-TTTTTCATTTCTTT
50074786 TTCT
1 TTCT
50074790 GTCTTTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 11 0.55
19 8 0.40
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.75
Consensus pattern (17 bp):
TTCTTTTTCATTTCTTT
Found at i:50079871 original size:14 final size:13
Alignment explanation
Indices: 50079853--50079894 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
50079843 TATAGGCTTT
*
50079853 TATATATTTTTAA
1 TATATATTTTAAA
50079866 T-TATATTTTAAAA
1 TATATATTTT-AAA
*
50079879 TATATATTTTATA
1 TATATATTTTAAA
50079892 TAT
1 TAT
50079895 TTTAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.32
13 9 0.36
14 8 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATATTTTAAA
Found at i:50079897 original size:23 final size:26
Alignment explanation
Indices: 50079853--50079903 Score: 81
Period size: 23 Copynumber: 2.1 Consensus size: 26
50079843 TATAGGCTTT
50079853 TATATATTTTTAATTATATTTTAAAA
1 TATATATTTTTAATTATATTTTAAAA
50079879 TATATA-TTTT-A-TATATTTTAAAA
1 TATATATTTTTAATTATATTTTAAAA
50079902 TA
1 TA
50079904 ATAATAACCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 14 0.56
24 1 0.04
25 4 0.16
26 6 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TATATATTTTTAATTATATTTTAAAA
Found at i:50081172 original size:17 final size:17
Alignment explanation
Indices: 50081150--50081185 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
50081140 GTATGTATTC
50081150 AAACTACATGTGAGGTG
1 AAACTACATGTGAGGTG
50081167 AAACTACATGTGAGGTG
1 AAACTACATGTGAGGTG
50081184 AA
1 AA
50081186 GTCCAGCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.28, T:0.22
Consensus pattern (17 bp):
AAACTACATGTGAGGTG
Found at i:50098774 original size:41 final size:41
Alignment explanation
Indices: 50098729--50098827 Score: 171
Period size: 41 Copynumber: 2.4 Consensus size: 41
50098719 TTTTTGAATC
*
50098729 AATGAAAGGGTTGAAAAGGATGTTATCCGAAAAGGATATCA
1 AATGAAAAGGTTGAAAAGGATGTTATCCGAAAAGGATATCA
*
50098770 AATGAAAAGGTTGAAAAGGATGTTATCCGGAAAGGATATCA
1 AATGAAAAGGTTGAAAAGGATGTTATCCGAAAAGGATATCA
*
50098811 AATGAAAAGGTCGAAAA
1 AATGAAAAGGTTGAAAA
50098828 TGATAGAAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.46, C:0.07, G:0.26, T:0.20
Consensus pattern (41 bp):
AATGAAAAGGTTGAAAAGGATGTTATCCGAAAAGGATATCA
Found at i:50100561 original size:20 final size:21
Alignment explanation
Indices: 50100522--50100563 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
50100512 GTGACCCTTG
50100522 TTTTCAAGTTTTTTTCCAAAA
1 TTTTCAAGTTTTTTTCCAAAA
50100543 TTTTCAA-TTTTGTTT-CAAAA
1 TTTTCAAGTTTT-TTTCCAAAA
50100563 T
1 T
50100564 GATCCCAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTTCAAGTTTTTTTCCAAAA
Found at i:50107105 original size:17 final size:17
Alignment explanation
Indices: 50107068--50107107 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
50107058 TGTGTTCTAG
* **
50107068 TAGCTAAAGATATTCCG
1 TAGCTAAAGATAGTCAA
50107085 TAGCTAAAGATAGTCAA
1 TAGCTAAAGATAGTCAA
50107102 TAGCTA
1 TAGCTA
50107108 TGGAACCTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (17 bp):
TAGCTAAAGATAGTCAA
Found at i:50109944 original size:40 final size:40
Alignment explanation
Indices: 50109899--50110130 Score: 315
Period size: 40 Copynumber: 5.8 Consensus size: 40
50109889 ATAACCACAA
* * *
50109899 GCACAATTGCCTTCGGGTCTTAACCCGGGTATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
50109939 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
50109979 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* * * *
50110019 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
50110059 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* *
50110099 GCACAATTGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
50110131 CATTCAAATG
Statistics
Matches: 169, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 4 0.02
40 158 0.93
41 7 0.04
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:50109983 original size:80 final size:80
Alignment explanation
Indices: 50109899--50110130 Score: 358
Period size: 80 Copynumber: 2.9 Consensus size: 80
50109889 ATAACCACAA
* * * * * *
50109899 GCACAATTGCCTTCGGGTCTTAACCCGGGT-ATATCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTAGCACAATTGCCTTCGGGTCTTAGC
*
50109963 CCGGATATATCAACTC
65 CCGGATATAGCAACTC
*
50109979 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCC
*
50110044 CGGGTATAGCAACTC
66 CGGATATAGCAACTC
*
50110059 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCC
50110124 CGGATAT
66 CGGATAT
50110131 CATTCAAATG
Statistics
Matches: 139, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
80 135 0.97
81 4 0.03
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCC
CGGATATAGCAACTC
Found at i:50110103 original size:120 final size:120
Alignment explanation
Indices: 50109870--50110129 Score: 407
Period size: 120 Copynumber: 2.2 Consensus size: 120
50109860 ACCCAAGTTT
* * * *
50109870 CTTCGGAATTTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGTATATC
1 CTTCGGGACTTAGCCCGGATAAAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGC
* *
50109934 AACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGC
66 AACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAAATCAACTAGCACAAATGC
* * *
50109989 CTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGC
1 CTTCGGGACTTAGCCCGGATAAAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGC
*
50110054 AACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTAGCACAATTGC
66 AACTCGCACAAATGCCTTCGGGTCTTAGCCCGGAT-AAATCAACTAGCACAAATGC
50110109 CTTCGGGACTTAGCCCGGATA
1 CTTCGGGACTTAGCCCGGATA
50110130 TCATTCAAAT
Statistics
Matches: 128, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
119 10 0.08
120 114 0.89
121 4 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (120 bp):
CTTCGGGACTTAGCCCGGATAAAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGC
AACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAAATCAACTAGCACAAATGC
Found at i:50122326 original size:27 final size:27
Alignment explanation
Indices: 50122285--50122336 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
50122275 ACAAGTGAGG
50122285 AAAAAGAGAAAGAGAATGAAAAAGAGC
1 AAAAAGAGAAAGAGAATGAAAAAGAGC
** *
50122312 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAGAAAGAGAATGAAAAAGA
50122337 AATTGAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.63, C:0.02, G:0.27, T:0.08
Consensus pattern (27 bp):
AAAAAGAGAAAGAGAATGAAAAAGAGC
Found at i:50130928 original size:33 final size:32
Alignment explanation
Indices: 50130890--50130998 Score: 116
Period size: 33 Copynumber: 3.3 Consensus size: 32
50130880 AGATTAATTT
50130890 ATATTTTATGTATTATTATATTAAATTATTTAA
1 ATATTTTATGTATTATTATATTAAATT-TTTAA
* * *
50130923 ATATTTCATGTATCATTATATTAAATTTTTTAG
1 ATATTTTATGTATTATTATATTAAA-TTTTTAA
*
50130956 ATATCATTTAT-TATTA-TAT-TTAAGTTTTTAAA
1 ATAT--TTTATGTATTATTATATTAAATTTTT-AA
50130988 ATATTTTATGT
1 ATATTTTATGT
50130999 TTCATTAATT
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
30 5 0.08
31 6 0.09
32 9 0.14
33 34 0.53
34 6 0.09
35 4 0.06
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.57
Consensus pattern (32 bp):
ATATTTTATGTATTATTATATTAAATTTTTAA
Found at i:50135312 original size:23 final size:23
Alignment explanation
Indices: 50135267--50135312 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
50135257 TTTTTTTTTA
50135267 TTTTTATAAATTTTAAAATAATT
1 TTTTTATAAATTTTAAAATAATT
* *
50135290 TTTTTCTAATTTTCTAAAA-AATT
1 TTTTTATAAATTT-TAAAATAATT
50135313 AACTCATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTTATAAATTTTAAAATAATT
Found at i:50139522 original size:21 final size:21
Alignment explanation
Indices: 50139496--50139543 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
50139486 GTTGATGTCT
*
50139496 TTTTTTACTGTTTTCTTGCTG
1 TTTTTTACTGTTTTCTTGCTA
* *
50139517 TTTTTTATTGTTTTGTTGCTA
1 TTTTTTACTGTTTTCTTGCTA
50139538 TTTTTT
1 TTTTTT
50139544 TGTTTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.06, C:0.08, G:0.12, T:0.73
Consensus pattern (21 bp):
TTTTTTACTGTTTTCTTGCTA
Found at i:50141131 original size:33 final size:33
Alignment explanation
Indices: 50141092--50141156 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
50141082 ATATAGCCAA
50141092 TAAAATTTTAAGAAGGAAATATTTTAAATATTT
1 TAAAATTTTAAGAAGGAAATATTTTAAATATTT
*
50141125 TAAAATTTTAATAAGGAAATATTTTAAATATT
1 TAAAATTTTAAGAAGGAAATATTTTAAATATT
50141157 GCTGCAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (33 bp):
TAAAATTTTAAGAAGGAAATATTTTAAATATTT
Found at i:50141134 original size:8 final size:9
Alignment explanation
Indices: 50141108--50141156 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
50141098 TTTAAGAAGG
50141108 AAATATTTT
1 AAATATTTT
50141117 AAATATTTT
1 AAATATTTT
50141126 AAA-ATTTT
1 AAATATTTT
***
50141134 -AATA-AGG
1 AAATATTTT
50141141 AAATATTTT
1 AAATATTTT
50141150 AAATATT
1 AAATATT
50141157 GCTGCAAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
7 2 0.06
8 10 0.32
9 19 0.61
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (9 bp):
AAATATTTT
Found at i:50141148 original size:16 final size:16
Alignment explanation
Indices: 50141096--50141151 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
50141086 AGCCAATAAA
*
50141096 ATTTTAAGAAGGAAAT
1 ATTTTAATAAGGAAAT
***
50141112 ATTTTAAATATTTTAAA-
1 ATTTT-AATA-AGGAAAT
50141129 ATTTTAATAAGGAAAT
1 ATTTTAATAAGGAAAT
50141145 ATTTTAA
1 ATTTTAA
50141152 ATATTGCTGC
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
15 3 0.10
16 16 0.53
17 8 0.27
18 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (16 bp):
ATTTTAATAAGGAAAT
Found at i:50142114 original size:23 final size:22
Alignment explanation
Indices: 50142070--50142116 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 22
50142060 TTAACAATTG
50142070 AAATTAAATTTTAAAATTTAAAA
1 AAATTAAATTTTAAAA-TTAAAA
50142093 AAATTAAATTCTTGAAAA-TAAAA
1 AAATTAAATT-TT-AAAATTAAAA
50142116 A
1 A
50142117 TACATACACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 16 0.73
24 2 0.09
25 4 0.18
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
AAATTAAATTTTAAAATTAAAA
Found at i:50145234 original size:44 final size:44
Alignment explanation
Indices: 50145141--50145235 Score: 113
Period size: 44 Copynumber: 2.1 Consensus size: 44
50145131 ATAAAGTCGT
* *
50145141 AATGGAATAGAGGTGTAATAGCAATTTAATTGTTTGGTTGAATCT
1 AATGGAATAGAGGCGTAATAGCAATTT-ATTGTTTGGTTGAATCG
* *
50145186 AATGGAATAGAGGCGTAATAG-TATTCT-TGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGCAATT-TAT-TGTTTGGTTGAATCG
50145230 AATGGA
1 AATGGA
50145236 GGTATAATAG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 21 0.48
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGCAATTTATTGTTTGGTTGAATCG
Found at i:50145524 original size:102 final size:102
Alignment explanation
Indices: 50145410--50145629 Score: 395
Period size: 102 Copynumber: 2.2 Consensus size: 102
50145400 TAATAAAAAT
* * *
50145410 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTATGATATAAATTTACTAAAATCATAATATAT
*
50145475 AATACTATAAAATGTAATTTAACATAATTATTATTAA
66 AATACTATAAAATATAATTTAACATAATTATTATTAA
50145512 ATATAATTTAATAAAATTCTTAATATTAAATATTATGATATAAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTATGATATAAATTTACTAAAATCATAATATAT
*
50145577 AATGCTATAAAATATAATTTAACATAATTATTATTAA
66 AATACTATAAAATATAATTTAACATAATTATTATTAA
50145614 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
50145630 ATATATAATT
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 113 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (102 bp):
ATATAATTTAATAAAATTCTTAATATTAAATATTATGATATAAATTTACTAAAATCATAATATAT
AATACTATAAAATATAATTTAACATAATTATTATTAA
Found at i:50145529 original size:26 final size:26
Alignment explanation
Indices: 50145477--50145629 Score: 77
Period size: 26 Copynumber: 6.0 Consensus size: 26
50145467 TAATATATAA
* * * *
50145477 TACTATAAAATGTAATTTAACATAAT
1 TACTATTAAATATAATTTAATAAAAT
*
50145503 TATTATTAAATATAATTTAATAAAATTCT
1 TACTATTAAATATAATTTAATAAAA---T
* * * *
50145532 TAATATTAAATATTA-TGATATAAATT
1 TACTATTAAATATAATTTA-ATAAAAT
*
50145558 TACTA--AAATCATAA--T-ATATAA-
1 TACTATTAAAT-ATAATTTAATAAAAT
* * * *
50145579 TGCTATAAAATATAATTTAACATAAT
1 TACTATTAAATATAATTTAATAAAAT
*
50145605 TATTATTAAATATAATTTAATAAAA
1 TACTATTAAATATAATTTAATAAAA
50145630 ATATATAATT
Statistics
Matches: 95, Mismatches: 21, Indels: 22
0.69 0.15 0.16
Matches are distributed among these distances:
21 4 0.04
22 8 0.08
23 4 0.04
24 5 0.05
25 8 0.08
26 45 0.47
28 2 0.02
29 19 0.20
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (26 bp):
TACTATTAAATATAATTTAATAAAAT
Found at i:50146643 original size:18 final size:17
Alignment explanation
Indices: 50146583--50146643 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 17
50146573 ACCTCTTCGT
*
50146583 CTTCATCCTCGGAATCA
1 CTTCATCCTCAGAATCA
*
50146600 TCTTCATCAC-CAGAACCA
1 -CTTCATC-CTCAGAATCA
50146618 CTTCCATCCTCAGAATCA
1 CTT-CATCCTCAGAATCA
50146636 CTATCATC
1 CT-TCATC
50146644 ATCATCGTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 4 0.11
18 30 0.83
19 2 0.06
ACGTcount: A:0.28, C:0.38, G:0.07, T:0.28
Consensus pattern (17 bp):
CTTCATCCTCAGAATCA
Found at i:50148243 original size:13 final size:13
Alignment explanation
Indices: 50148225--50148254 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
50148215 CCAAGGGGTT
*
50148225 AACAAGGAAATCA
1 AACAAGAAAATCA
50148238 AACAAGAAAATCA
1 AACAAGAAAATCA
50148251 AACA
1 AACA
50148255 TGCAATACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.17, G:0.10, T:0.07
Consensus pattern (13 bp):
AACAAGAAAATCA
Found at i:50151662 original size:17 final size:18
Alignment explanation
Indices: 50151629--50151664 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
50151619 TAAAATAAAA
50151629 TTATAAAATTAAATAATT
1 TTATAAAATTAAATAATT
*
50151647 TTATTAAATT-AATAATT
1 TTATAAAATTAAATAATT
50151664 T
1 T
50151665 ATAGGTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATAAAATTAAATAATT
Found at i:50151710 original size:28 final size:29
Alignment explanation
Indices: 50151679--50151739 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
50151669 GTATGTTTAA
50151679 TAATATT-AAAAATTATAACATTTGATT-T
1 TAATATTGAAAAATTATAA-ATTTGATTAT
** *
50151707 TAATATTGTTAAATTTTAAATTTGATTAT
1 TAATATTGAAAAATTATAAATTTGATTAT
50151736 TAAT
1 TAAT
50151740 TTAGTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (29 bp):
TAATATTGAAAAATTATAAATTTGATTAT
Done.