Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 42 of 168
Found at i:11515359 original size:125 final size:125
Alignment explanation
Indices: 11515110--11515399 Score: 447
Period size: 125 Copynumber: 2.3 Consensus size: 125
11515100 TCAGGCCAAA
* * *
11515110 CAGGAGCTACTGTAGCAAAAGCGCGTCCACATGGGAGCTTCTTTCAGTATTTTTGCTGACAAAGC
1 CAGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
* *
11515175 ATCCTGTTTAAAACGTTTTTATACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTT
66 ATCCTGCTTAAAACGTTTTTACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTT
* *
11515235 CAGGAGCTACTGTAGCAAAAGTGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGC
1 CAGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
* * * *
11515300 ATCCTGCTTAAAGCGTTTTTGACACTATTTTCTCAGAAACGTCTTCTCGAAATTATTTTTT
66 ATCCTGCTTAAAACGTTTTT-ACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTT
* *
11515361 CAGGA-CTACTGTAGTAAAAGAGCATCCACGTGGGAGCTT
1 CAGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
11515400 TTTTAAATTA
Statistics
Matches: 151, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
125 110 0.73
126 41 0.27
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (125 bp):
CAGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
ATCCTGCTTAAAACGTTTTTACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTT
Found at i:11515585 original size:96 final size:94
Alignment explanation
Indices: 11515436--11515774 Score: 378
Period size: 97 Copynumber: 3.6 Consensus size: 94
11515426 AGTAACCCTA
* *
11515436 AACCCCAAACCCTAATTTATTTGAGTTTTTCCTTAAAAACCCTAAACCCTAAACTCTAATCTATT
1 AACCCTAAACCCTAATTTATTTGA-TTTTTCCTTAAAAACCCTAAACACTAAAC-CTAATCTA-T
11515501 TTTTTAAAAATTTATAATTAATTTACTCAAGT
63 TTTTTAAAAATTTATAATTAATTTACTCAAGT
* * *
11515533 AACCCTAAACCCGAATTTATTTGATTTTTCCTTAAAAACCCTTAACATTAAACCCTAATCTAAAT
1 AACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAA-CCTAATCT--AT
* *
11515598 TTTTTAAAATTTTTTAATTAATTTACTCAAGT
63 TTTTTAAAAATTTATAATTAATTTACTCAAGT
* * * * * *
11515630 AACCCTAAACCCTAATTTAATTAATTTTT-CTTTAAAACCCATAAACACAAAACCTAATCCAATT
1 AACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCC-TAAACACTAAACCTAATCTATTT
* * * * *
11515694 TTGAAAAATTTATAATTAATCTAATTAAGA
65 TTTAAAAATTTATAATTAATTTACTCAAGT
* * * * *
11515724 AACCCTAAACTCTTATTTATTT-ATTTTTTTCTTTAAAACCTTAAAC-CTAAA
1 AACCCTAAACCCTAATTTATTTGA-TTTTTCCTTAAAAACCCTAAACACTAAA
11515775 AACCCCAAAA
Statistics
Matches: 208, Mismatches: 28, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
93 5 0.02
94 55 0.26
95 10 0.05
96 49 0.24
97 88 0.42
98 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.39
Consensus pattern (94 bp):
AACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCTAATCTATTTT
TTAAAAATTTATAATTAATTTACTCAAGT
Found at i:11515820 original size:33 final size:35
Alignment explanation
Indices: 11515760--11515824 Score: 107
Period size: 33 Copynumber: 1.9 Consensus size: 35
11515750 TTTTCTTTAA
*
11515760 AACCTTAAACCTAAAAACCCCAAAACCCTAACCCT
1 AACCCTAAACCTAAAAACCCCAAAACCCTAACCCT
11515795 AACCCTAAACC-AAAAA-CCCAAAACCCTAAC
1 AACCCTAAACCTAAAAACCCCAAAACCCTAAC
11515825 TAGTAGGAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 14 0.48
34 5 0.17
35 10 0.34
ACGTcount: A:0.49, C:0.40, G:0.00, T:0.11
Consensus pattern (35 bp):
AACCCTAAACCTAAAAACCCCAAAACCCTAACCCT
Found at i:11518479 original size:22 final size:22
Alignment explanation
Indices: 11518454--11518500 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
11518444 ACTCAAAAAC
11518454 ATGTTTATAGATAAATTTCCTA
1 ATGTTTATAGATAAATTTCCTA
11518476 ATGTTTATAGATAAATTTCCTA
1 ATGTTTATAGATAAATTTCCTA
11518498 ATG
1 ATG
11518501 GTCACATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.45
Consensus pattern (22 bp):
ATGTTTATAGATAAATTTCCTA
Found at i:11519750 original size:18 final size:18
Alignment explanation
Indices: 11519727--11519787 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
11519717 AGATGATGAT
11519727 GAAGATGCAATCGAGGAA
1 GAAGATGCAATCGAGGAA
* *
11519745 GAAGATGTAGAT-AAGGAA
1 GAAGATGCA-ATCGAGGAA
* * *
11519763 GAAGATACGACCGAGGAA
1 GAAGATGCAATCGAGGAA
11519781 GAAGATG
1 GAAGATG
11519788 TATGTGAGGA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 1 0.03
18 30 0.91
19 2 0.06
ACGTcount: A:0.46, C:0.08, G:0.34, T:0.11
Consensus pattern (18 bp):
GAAGATGCAATCGAGGAA
Found at i:11526879 original size:25 final size:25
Alignment explanation
Indices: 11526844--11526912 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 25
11526834 GTTTCGACCC
* *
11526844 ACAGCTGGTGAGAGCATACCGATTT
1 ACAGCTCGTGAGAGCATACCAATTT
* *
11526869 ACAGCTTGTGAGAGCATATCAATTT
1 ACAGCTCGTGAGAGCATACCAATTT
*
11526894 ACAGCTCGTGTGAGCATAC
1 ACAGCTCGTGAGAGCATAC
11526913 TTGTACAAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (25 bp):
ACAGCTCGTGAGAGCATACCAATTT
Found at i:11532086 original size:7 final size:7
Alignment explanation
Indices: 11532074--11532098 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
11532064 CATTTATACT
11532074 TTTTAAA
1 TTTTAAA
11532081 TTTTAAA
1 TTTTAAA
11532088 TTTTAAA
1 TTTTAAA
11532095 TTTT
1 TTTT
11532099 GTTATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:11532143 original size:25 final size:26
Alignment explanation
Indices: 11532095--11532143 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
11532085 AAATTTTAAA
*
11532095 TTTTGTTATATATTTATATACATAAG
1 TTTTGTTATATATATATATACATAAG
*
11532121 TTTTTTTATA-ATATATATACATA
1 TTTTGTTATATATATATATACATA
11532144 TACATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (26 bp):
TTTTGTTATATATATATATACATAAG
Found at i:11532226 original size:13 final size:15
Alignment explanation
Indices: 11532187--11532227 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
11532177 GTATATGCTT
11532187 TACATATATATTTATA
1 TACATATAT-TTTATA
11532203 TACATATATTTTATA
1 TACATATATTTTATA
11532218 TA-ATA-ATTTT
1 TACATATATTTT
11532228 GAAATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.20
14 3 0.12
15 8 0.32
16 9 0.36
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (15 bp):
TACATATATTTTATA
Found at i:11532691 original size:109 final size:109
Alignment explanation
Indices: 11532500--11532951 Score: 757
Period size: 109 Copynumber: 4.2 Consensus size: 109
11532490 TATGCATACT
* * *
11532500 AATATCCTTTAAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCAAGAAAACGTGCC
1 AATATCCTTTTAAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
*
11532565 CAAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
*
11532609 AATATCCTTTTAAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAATGTGCC
1 AATATCCTTTTAAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
* * *
11532674 CTAATGTGCTAGGTTTCGATTTTTCTCATTCAACCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
* * *
11532718 AATATCCTTTCAAAAATTTCAAAATTAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
1 AATATCCTTTTAAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
11532783 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
11532827 AATATCCTTTTAAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
1 AATATCCTTTTAAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
* *
11532892 CTAATGTGTTGGGTTTCG--GTTTCTCGTTCGACCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
*
11532934 AATATCCTTCT-AAATTTT
1 AATATCCTTTTAAAATTTT
11532952 AATCCATGTC
Statistics
Matches: 322, Mismatches: 21, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
106 7 0.02
107 33 0.10
109 282 0.88
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (109 bp):
AATATCCTTTTAAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
Found at i:11539550 original size:2 final size:2
Alignment explanation
Indices: 11539543--11539567 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11539533 GCAAAAATTC
11539543 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11539568 CACTAATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11540285 original size:64 final size:63
Alignment explanation
Indices: 11540166--11540346 Score: 246
Period size: 64 Copynumber: 2.9 Consensus size: 63
11540156 GCAAACAAAC
*
11540166 ATTCGAACCACATATGTA-T-AATTTACA-ACATTAAAATTCAGCTCAACGAA-TTTGTAACCTA
1 ATTCGAACCACATATGTATTAAAATT-CATACATT-AAATTCAGCTCAA-GAACTTTGTAACCTA
11540227 T
63 T
*
11540228 ATTCGAACCACATATGTATGTAAAATTCATACATTAAATTCAGCTCAAAAACTTTGTAACCTAT
1 ATTCGAACCACATATGTAT-TAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
*
11540292 ATTTGAACCACATATGTATATAAAATTCATACATTAAATAT-AGCTCAAGAACTTT
1 ATTCGAACCACATATGTAT-TAAAATTCATACATTAAAT-TCAGCTCAAGAACTTT
11540347 AAATATATAT
Statistics
Matches: 108, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
62 18 0.17
63 2 0.02
64 78 0.72
65 10 0.09
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (63 bp):
ATTCGAACCACATATGTATTAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
Found at i:11540445 original size:61 final size:60
Alignment explanation
Indices: 11540375--11540488 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 60
11540365 CATATGGGCA
* * *
11540375 TATATATATAATTCATAA-TATT-ATGTTCAACTCAAAGAACTTATATCATACATTAAAACTT
1 TATACATATAATTCATAACT-TTAAT-TTCAACTC-AAGAAATTAAATCATACATTAAAACTT
*
11540436 TATACATATAATTCATAACTTTAATTTCAACTCAAGAAATTAAATCTTACATT
1 TATACATATAATTCATAACTTTAATTTCAACTCAAGAAATTAAATCATACATT
11540489 CGAACTACTT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
60 17 0.36
61 27 0.57
62 3 0.06
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (60 bp):
TATACATATAATTCATAACTTTAATTTCAACTCAAGAAATTAAATCATACATTAAAACTT
Found at i:11541448 original size:28 final size:28
Alignment explanation
Indices: 11541415--11541471 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
11541405 ATGTTGTTTT
11541415 TTTATTATAATAA-CTTTATAATATATTA
1 TTTATTATAATAACCTTTATAAT-TATTA
*
11541443 TTTATTATTATAACCTTTATAATTATTA
1 TTTATTATAATAACCTTTATAATTATTA
11541471 T
1 T
11541472 AAAAACTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTATTATAATAACCTTTATAATTATTA
Found at i:11541682 original size:14 final size:15
Alignment explanation
Indices: 11541663--11541691 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
11541653 TCACGAAACT
11541663 TTCACACAT-ATAAA
1 TTCACACATAATAAA
11541677 TTCACACATAATAAA
1 TTCACACATAATAAA
11541692 CACAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:11547745 original size:44 final size:43
Alignment explanation
Indices: 11547695--11547933 Score: 152
Period size: 44 Copynumber: 5.5 Consensus size: 43
11547685 TCCTACCTCC
* *
11547695 CTGAAGTTGCAGTGGAGCGGATTAAAAACACAGACCTTATCTCT
1 CTGAAGTTGCAGTAGAGCAGATTAAAAAC-CAGACCTTATCTCT
*** * *
11547739 CTGAAGTTGCAGTAGAGCAGA-TCGCATCCAG-TCTTATCTCT
1 CTGAAGTTGCAGTAGAGCAGATTAAAAACCAGACCTTATCTCT
* * **
11547780 CTGCAGTTGCAGTGGAGCAGACAGAAGAAACCA-ATCC-TATCTC-
1 CTGAAGTTGCAGTAGAGCAGA-TTAA-AAACCAGA-CCTTATCTCT
* * * *
11547823 CTTGAAGTTACAGTAGAGCGGATTAAAAAAACCACAGATCTCATCTCT
1 C-TGAAGTTGCAGTAGAGCAGATT--AAAAA-C-CAGACCTTATCTCT
* * * * *
11547871 CTGAAGTTGCAGTAGAGCAGA-T-CAAATCA-ATCTTAGCTCC
1 CTGAAGTTGCAGTAGAGCAGATTAAAAACCAGACCTTATCTCT
*
11547911 CTGAAGTTGCAGTGGAGCAGATT
1 CTGAAGTTGCAGTAGAGCAGATT
11547934 GAAGATACAA
Statistics
Matches: 150, Mismatches: 31, Indels: 31
0.71 0.15 0.15
Matches are distributed among these distances:
40 28 0.19
41 31 0.21
42 3 0.02
43 7 0.05
44 48 0.32
45 4 0.03
46 4 0.03
47 24 0.16
48 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (43 bp):
CTGAAGTTGCAGTAGAGCAGATTAAAAACCAGACCTTATCTCT
Found at i:11547929 original size:40 final size:44
Alignment explanation
Indices: 11547871--11547975 Score: 130
Period size: 44 Copynumber: 2.5 Consensus size: 44
11547861 TCTCATCTCT
*
11547871 CTGAAGTTGCAGTAGAGCAGA-TCAA-AT-CAA-TCTTAGC-TCC
1 CTGAAGTTGCAGTGGAGCAGATTCAAGATACAAGTCTTA-CTTCC
*
11547911 CTGAAGTTGCAGTGGAGCAGATTGAAGATACAAGTCTTACTTCC
1 CTGAAGTTGCAGTGGAGCAGATTCAAGATACAAGTCTTACTTCC
* *
11547955 CTGAGGTTGTAGTGGAGCAGA
1 CTGAAGTTGCAGTGGAGCAGA
11547976 CTAAAACCAC
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
40 20 0.36
41 3 0.05
42 2 0.04
43 4 0.07
44 27 0.48
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAGCAGATTCAAGATACAAGTCTTACTTCC
Found at i:11547981 original size:131 final size:130
Alignment explanation
Indices: 11547672--11547931 Score: 371
Period size: 129 Copynumber: 2.0 Consensus size: 130
11547662 GTTAATTAGG
* * *
11547672 CAGAAGAAACCAATCCTACCTCCCTGAAGTTGCAGTGGAGCGGAT-TAAAAACACAGACCTTATC
1 CAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATAAAAAAACACAGACCTCATC
** * * * *
11547736 TCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCTCTGCAGTTGCAGTGGAGCAGA
66 TCTCTGAAGTTGCAGTAGAGCAGATCAAATCCAATCTTAGCTCCCTGAAGTTGCAGTGGAGCAGA
* * * *
11547801 CAGAAGAAACCAATCCTATCTCCTTGAAGTTACAGTAGAGCGGATTAAAAAAACCACAGATCTCA
1 CAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGA-TAAAAAAA-CACAGACCTCA
11547866 TCTCTCTGAAGTTGCAGTAGAGCAGATCAAAT-CAATCTTAGCTCCCTGAAGTTGCAGTGGAGCA
64 TCTCTCTGAAGTTGCAGTAGAGCAGATCAAATCCAATCTTAGCTCCCTGAAGTTGCAGTGGAGCA
11547930 GA
129 GA
11547932 TTGAAGATAC
Statistics
Matches: 115, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
129 40 0.35
130 1 0.01
131 35 0.30
132 39 0.34
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (130 bp):
CAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATAAAAAAACACAGACCTCATC
TCTCTGAAGTTGCAGTAGAGCAGATCAAATCCAATCTTAGCTCCCTGAAGTTGCAGTGGAGCAGA
Found at i:11549652 original size:27 final size:27
Alignment explanation
Indices: 11549622--11549676 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
11549612 TACATGAGTT
11549622 TTTTTATA-ATATATATACATATACATA
1 TTTTTATACAT-TATATACATATACATA
* *
11549649 TTTTTATACATTGTCTACATATACATA
1 TTTTTATACATTATATACATATACATA
11549676 T
1 T
11549677 ATACCTATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (27 bp):
TTTTTATACATTATATACATATACATA
Found at i:11549893 original size:13 final size:15
Alignment explanation
Indices: 11549858--11549894 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
11549848 TATGCTTACT
11549858 TATATATTTATATACA
1 TATAT-TTTATATACA
11549874 TATATTTTATATA-A
1 TATATTTTATATACA
11549888 TA-ATTTT
1 TATATTTT
11549895 GAAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.24
14 3 0.14
15 8 0.38
16 5 0.24
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATTTTATATACA
Found at i:11549955 original size:2 final size:2
Alignment explanation
Indices: 11549942--11549973 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
11549932 AATTTTATGA
*
11549942 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11549974 CTTTTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11550374 original size:109 final size:109
Alignment explanation
Indices: 11550183--11550521 Score: 565
Period size: 109 Copynumber: 3.1 Consensus size: 109
11550173 TACGCATACT
* * *
11550183 AATATCCTTTAAAAAATTTCAAAAAAAGGCAATGTTTTACATTTGGAAATTCGAGAAAACGTGCC
1 AATATCCTTTAAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
* * *
11550248 CAAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAACCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
* *
11550292 AATATCCTTTCAAAAATTTCAAAATAAGGCAGTGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
1 AATATCCTTTAAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
11550357 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
* *
11550401 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCC
1 AATATCCTTTAAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
11550466 CTAATGTGCTGGGTTTCGA--TTTCTCGTTCGACCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
11550508 AATATCCTTCTAAA
1 AATATCCTT-TAAA
11550522 TTTTAATCCA
Statistics
Matches: 217, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
107 32 0.15
108 3 0.01
109 182 0.84
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (109 bp):
AATATCCTTTAAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
Found at i:11550914 original size:11 final size:11
Alignment explanation
Indices: 11550898--11550922 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11550888 GTTGCCTATT
11550898 TTAGCCTTATA
1 TTAGCCTTATA
11550909 TTAGCCTTATA
1 TTAGCCTTATA
11550920 TTA
1 TTA
11550923 CTTTAATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (11 bp):
TTAGCCTTATA
Found at i:11556551 original size:3 final size:3
Alignment explanation
Indices: 11556545--11556570 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11556535 AAAAATGATG
11556545 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
11556571 TTTCATTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:11557370 original size:20 final size:20
Alignment explanation
Indices: 11557345--11557384 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
11557335 ACAATTTAAA
11557345 TTTTTTTCT-TTTAACTTTCC
1 TTTTTTT-TATTTAACTTTCC
*
11557365 TTTTTTTTATTTTACTTTCC
1 TTTTTTTTATTTAACTTTCC
11557385 ATCCTCTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTTTTATTTAACTTTCC
Found at i:11557371 original size:21 final size:20
Alignment explanation
Indices: 11557345--11557384 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
11557335 ACAATTTAAA
*
11557345 TTTTTTTCTTTTAACTTTCCT
1 TTTTTTTATTTT-ACTTTCCT
11557366 TTTTTTTATTTTACTTTCC
1 TTTTTTTATTTTACTTTCC
11557385 ATCCTCTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTTTATTTTACTTTCCT
Found at i:11563771 original size:29 final size:29
Alignment explanation
Indices: 11563738--11563796 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
11563728 AAAAAGTAAA
11563738 GCAATTATTGCAACTATATACATAAAGTT
1 GCAATTATTGCAACTATATACATAAAGTT
11563767 GCAATTATTGCAACTATATACATAAAGTT
1 GCAATTATTGCAACTATATACATAAAGTT
11563796 G
1 G
11563797 TAATATTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.34
Consensus pattern (29 bp):
GCAATTATTGCAACTATATACATAAAGTT
Found at i:11569128 original size:20 final size:20
Alignment explanation
Indices: 11569092--11569133 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
11569082 TTAAAGTAGT
11569092 AATTAGTAAATAAAAGA-AA
1 AATTAGTAAATAAAAGACAA
**
11569111 AATTAAGTAAATTGAAGACAA
1 AATT-AGTAAATAAAAGACAA
11569132 AA
1 AA
11569134 GAAAGATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
20 11 0.58
21 4 0.21
ACGTcount: A:0.64, C:0.02, G:0.12, T:0.21
Consensus pattern (20 bp):
AATTAGTAAATAAAAGACAA
Found at i:11579993 original size:100 final size:95
Alignment explanation
Indices: 11579807--11580222 Score: 292
Period size: 94 Copynumber: 4.5 Consensus size: 95
11579797 AAAACCAAAA
* * * *
11579807 TTTTCGTCACACTATTTTAATTTACCTATTTGATAATT-----TAGCACACCCCCTCCCTTACAC
1 TTTTCATCATACTCTTTAAATTTACCTATTTGATAATTGAGCATAGCACACCCCCT-CCTTACAC
*
11579867 TCTTTGTTTAACA-AAATGGCCAAAAAATGGAAC
65 TCTTTG-TT-ACATAAATGG-CAAAAAATGGAAT
11579900 TTTTCATCATACTCTTTAAATTTACCTATTTGATAATTGAGCAATGAGCACACCCCCTCCATTAC
1 TTTTCATCATACTCTTTAAATTTACCTATTTGATAATTGAGC-AT-AGCACACCCCCTCC-TTAC
11579965 ACTCTTTGTGTAGCATAAATGGTCAAAAAAACT-GAAT
63 ACTCTTTGT-TA-CATAAATGG-C-AAAAAA-TGGAAT
* * *
11580002 TTTTCATCAAGACTCTTTAAATTTACTTATTTGGTAATT-----TAGCACACCCCCTTCCTTACA
1 TTTTCATC-ATACTCTTTAAATTTACCTATTTGATAATTGAGCATAGCACACCCCC-TCCTTACA
* *
11580062 TTCTTTATT---T-AA---C-AAAAATGGAAT
64 CTCTTTGTTACATAAATGGCAAAAAATGGAAT
* * *
11580086 TTTTCATCATACACTTTAAATTTACCTATTTGATAATTGAGC--A-CAC-CCCTC-CCTTTCACT
1 TTTTCATCATACTCTTTAAATTTACCTATTTGATAATTGAGCATAGCACACCCCCTCCTTACACT
** *
11580146 CATTAT-TTAACATAAATGATAAAAAAAACT-AAAT
66 C-TT-TGTT-ACATAAATG--GCAAAAAA-TGGAAT
* * *
11580180 TTTTCATCAAACTCTTTTAATTTATCTATTTGATAATTGAGCA
1 TTTTCATCATACTCTTTAAATTTACCTATTTGATAATTGAGCA
11580223 CACATCTTCC
Statistics
Matches: 264, Mismatches: 24, Indels: 68
0.74 0.07 0.19
Matches are distributed among these distances:
82 8 0.03
83 31 0.12
84 22 0.08
85 3 0.01
86 2 0.01
87 1 0.00
88 2 0.01
90 2 0.01
91 1 0.00
93 34 0.13
94 46 0.17
95 2 0.01
96 22 0.08
97 4 0.02
99 5 0.02
100 27 0.10
101 7 0.03
102 17 0.06
103 28 0.11
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (95 bp):
TTTTCATCATACTCTTTAAATTTACCTATTTGATAATTGAGCATAGCACACCCCCTCCTTACACT
CTTTGTTACATAAATGGCAAAAAATGGAAT
Found at i:11580131 original size:83 final size:83
Alignment explanation
Indices: 11579998--11580163 Score: 226
Period size: 83 Copynumber: 2.0 Consensus size: 83
11579988 CAAAAAAACT
* * * * * *
11579998 GAATTTTTCATCAAGACTCTTTAAATTTACTTATTTGGTAATTTAGCACACCCCCTTCCTTACAT
1 GAATTTTTCATCAAGACACTTTAAATTTACCTATTTGATAATTGAGCACA-CCCCTCCCTTACAC
*
11580063 TCTTTATTTAACAAAAATG
65 TCATTATTTAACAAAAATG
* *
11580082 GAATTTTTCATC-ATACACTTTAAATTTACCTATTTGATAATTGAGCACACCCCTCCCTTTCACT
1 GAATTTTTCATCAAGACACTTTAAATTTACCTATTTGATAATTGAGCACACCCCTCCCTTACACT
*
11580146 CATTATTTAACATAAATG
66 CATTATTTAACAAAAATG
11580164 ATAAAAAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
82 28 0.39
83 32 0.44
84 12 0.17
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (83 bp):
GAATTTTTCATCAAGACACTTTAAATTTACCTATTTGATAATTGAGCACACCCCTCCCTTACACT
CATTATTTAACAAAAATG
Found at i:11580265 original size:94 final size:94
Alignment explanation
Indices: 11580083--11580265 Score: 242
Period size: 94 Copynumber: 1.9 Consensus size: 94
11580073 ACAAAAATGG
* * *
11580083 AATTTTTCATCATACACTTTAAATTTACCTATTTGATAATTGAGCACACCCCTCCCTTTCACTCA
1 AATTTTTCATCAAACACTTTAAATTTACCTATTTGATAATTGAGCACACACCTCCCTTACACTCA
11580148 TTATTTAACATAAATGATAAAAAAAACTA
66 TTATTTAACATAAATGATAAAAAAAACTA
* * * * * * *
11580177 AATTTTTCATCAAACTCTTTTAATTTATCTATTTGATAATTGAGCACACATCTTCCTTAACCCTT
1 AATTTTTCATCAAACACTTTAAATTTACCTATTTGATAATTGAGCACACACCTCCCTT-ACACTC
*
11580242 TTTATTTAACATAAAT-AGTAAAAA
65 ATTATTTAACATAAATGA-TAAAAA
11580266 TACCCAATAT
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
94 52 0.68
95 24 0.32
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.39
Consensus pattern (94 bp):
AATTTTTCATCAAACACTTTAAATTTACCTATTTGATAATTGAGCACACACCTCCCTTACACTCA
TTATTTAACATAAATGATAAAAAAAACTA
Found at i:11580279 original size:94 final size:94
Alignment explanation
Indices: 11580087--11580291 Score: 225
Period size: 94 Copynumber: 2.2 Consensus size: 94
11580077 AAATGGAATT
* * * * *
11580087 TTTCATCATACACTTTAAATTTACCTATTTGATAATTGAGCACACCCCTCCCTTTCACTCATTAT
1 TTTCATCAAACTCTTTTAATTTACCTATTTGATAATTGAGCACACACCTCCCTTACACTCATTAT
* *
11580152 TTAACATAAATGATAAAAAAAACTAAATT
66 TTAACATAAATGATAAAAAAAACCAAATA
* * * * **
11580181 TTTCATCAAACTCTTTTAATTTATCTATTTGATAATTGAGCACACATCTTCCTTAACCCTTTTTA
1 TTTCATCAAACTCTTTTAATTTACCTATTTGATAATTGAGCACACACCTCCCTT-ACACTCATTA
* *
11580246 TTTAACATAAAT-AGT-AAAAATACCCAATA
65 TTTAACATAAATGA-TAAAAAAAACCAAATA
* *
11580275 TTTCATCACACTTTTTT
1 TTTCATCAAACTCTTTT
11580292 TTTGGTGAAA
Statistics
Matches: 92, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
94 73 0.79
95 19 0.21
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (94 bp):
TTTCATCAAACTCTTTTAATTTACCTATTTGATAATTGAGCACACACCTCCCTTACACTCATTAT
TTAACATAAATGATAAAAAAAACCAAATA
Found at i:11584820 original size:11 final size:10
Alignment explanation
Indices: 11584795--11584828 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
11584785 ACTACGATAG
11584795 TAATTTCCAT
1 TAATTTCCAT
11584805 TAATTTCCAGT
1 TAATTTCCA-T
11584816 TAATTTCCAT
1 TAATTTCCAT
11584826 TAA
1 TAA
11584829 CTCGAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.32, C:0.18, G:0.03, T:0.47
Consensus pattern (10 bp):
TAATTTCCAT
Found at i:11592762 original size:25 final size:26
Alignment explanation
Indices: 11592734--11592793 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 26
11592724 AAGTATTATA
*
11592734 CAGAGAA-CATAAATGTGCTAATAAT
1 CAGAGAAGCACAAATGTGCTAATAAT
** *
11592759 CAGA-AAGCACCGATGTGCTAATGAT
1 CAGAGAAGCACAAATGTGCTAATAAT
11592784 CAGAG-AGCAC
1 CAGAGAAGCAC
11592794 GCTAAACTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 2 0.07
25 27 0.93
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (26 bp):
CAGAGAAGCACAAATGTGCTAATAAT
Found at i:11593821 original size:50 final size:50
Alignment explanation
Indices: 11593746--11594230 Score: 562
Period size: 50 Copynumber: 9.6 Consensus size: 50
11593736 TTTCCTATAC
* * ** *
11593746 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * ***
11593796 TGCCCATGCCATGTCCTAGACATGGTCTTATGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
11593846 TGCCAACGCCGTGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
***
11593896 TGCCAACATCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
11593946 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
11593996 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
11594046 TCCCCAATGCCATGTCCCAGACATGGTCTTATATGGGACATCTCATCTCGG
1 T-GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * * * **
11594097 TGCCAACGCCATGTCCTAGATATGGTTTTACATGAGACCTCTCATAATTTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GG
* * * * *
11594153 TGCCAATGCCATGTCCTAGACATGGTCTTACACT-GG--CTCACATATTGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA-TGGGACCTCTCATCTCGG
* *
11594201 TGTCGATGCCATGTCCCAGACATGGTCTTA
1 TGCCAATGCCATGTCCCAGACATGGTCTTA
11594231 TACGAGATCG
Statistics
Matches: 377, Mismatches: 50, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
48 28 0.07
50 261 0.69
51 49 0.13
53 4 0.01
54 4 0.01
56 30 0.08
57 1 0.00
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:11597395 original size:16 final size:17
Alignment explanation
Indices: 11597374--11597407 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
11597364 TCGGGTTTAG
11597374 AAAATT-ATTTAATTAA
1 AAAATTAATTTAATTAA
*
11597390 AAAATTAATTTATTTAA
1 AAAATTAATTTAATTAA
11597407 A
1 A
11597408 TTAATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATTAATTTAATTAA
Found at i:11597402 original size:21 final size:23
Alignment explanation
Indices: 11597378--11597427 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
11597368 GTTTAGAAAA
*
11597378 TTATTT-AATTAAAAAATTA-AT
1 TTATTTAAATTAAAAAATAATAT
*
11597399 TTATTTAAATTAATAAATAATAT
1 TTATTTAAATTAAAAAATAATAT
11597422 TTATTT
1 TTATTT
11597428 TGAAAAGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.24
22 11 0.44
23 8 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATTTAAATTAAAAAATAATAT
Found at i:11597406 original size:17 final size:16
Alignment explanation
Indices: 11597369--11597407 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
11597359 TAGAATCGGG
*
11597369 TTTAGAAAATTATTTA
1 TTTAAAAAATTATTTA
*
11597385 ATTAAAAAATTAATTTA
1 TTTAAAAAATT-ATTTA
11597402 TTTAAA
1 TTTAAA
11597408 TTAATAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
TTTAAAAAATTATTTA
Found at i:11600331 original size:44 final size:43
Alignment explanation
Indices: 11600221--11600349 Score: 134
Period size: 43 Copynumber: 3.0 Consensus size: 43
11600211 AGCTAGTATA
* *
11600221 ATGCCAACGTCCCAGACGAGGTTTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGACGAGGTCTTACATGTAATCAAATATCG
* * * *
11600264 ATGCCACTATCCCAGACAAGGTCTTACATGTAAATCTCAA-ATCG
1 ATGCCAATGTCCCAGACGAGGTCTTACATGT-AATC-AAATATCG
* * * * *
11600308 ATGCCAATGTCCCAGGCGTGGTCTTACACGAAATCACATATC
1 ATGCCAATGTCCCAGACGAGGTCTTACATGTAATCAAATATC
11600350 AGAATCCCAT
Statistics
Matches: 68, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
42 1 0.01
43 33 0.49
44 32 0.47
45 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGAGGTCTTACATGTAATCAAATATCG
Found at i:11605945 original size:40 final size:39
Alignment explanation
Indices: 11605890--11606068 Score: 177
Period size: 40 Copynumber: 4.5 Consensus size: 39
11605880 TTTTCCAAGC
*
11605890 TGTGTATCAGAAAAGCTCCCATGTGAGTTTATGGATAAGT
1 TGTGTATCAGAAAAGCTCCC-TGTGAGCTTATGGATAAGT
* **
11605930 TGTGTATCAGCAAAGCTCTCCTGTGAGCTTATGGATAAAC
1 TGTGTATCAGAAAAGCTC-CCTGTGAGCTTATGGATAAGT
* *
11605970 TGTGTATCAGTAAAGTTCCTCTGTGAGCTTATGGATAAGT
1 TGTGTATCAGAAAAGCTCC-CTGTGAGCTTATGGATAAGT
* * *
11606010 TGTGTATCA-ACACAA-CTTCCTTGTGAGC-TAAGGACAAGT
1 TGTGTATCAGA-A-AAGC-TCCCTGTGAGCTTATGGATAAGT
*
11606049 TGTGTGTCA-AAGAAGCTCCC
1 TGTGTATCAGAA-AAGCTCCC
11606069 CACGTGAGCT
Statistics
Matches: 117, Mismatches: 16, Indels: 14
0.80 0.11 0.10
Matches are distributed among these distances:
38 6 0.05
39 20 0.17
40 84 0.72
41 7 0.06
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (39 bp):
TGTGTATCAGAAAAGCTCCCTGTGAGCTTATGGATAAGT
Found at i:11606076 original size:80 final size:81
Alignment explanation
Indices: 11605885--11606080 Score: 224
Period size: 80 Copynumber: 2.5 Consensus size: 81
11605875 AATAATTTTC
* *
11605885 CAAGCTGTGTATCAGAAAAGCT-CCCATGTGAGTTTATGGATAAGTTGTGTATCAGCAAAGCTCT
1 CAAGCTGTGTATCAGAAAAGCTCCCCATGTGAGCTTATGGATAAGTTGTGTATCAACAAAGCTCT
*
11605949 CCTGTGAGCTTATGGA
66 CCTGTGAGCTTAAGGA
* * * * *
11605965 TAAACTGTGTATCAGTAAAGTTCCTC-TGTGAGCTTATGGATAAGTTGTGTATCAACACAA-CT-
1 CAAGCTGTGTATCAGAAAAGCTCCCCATGTGAGCTTATGGATAAGTTGTGTATCAACA-AAGCTC
11606027 TCCTTGTGAGC-TAAGGA
65 TCC-TGTGAGCTTAAGGA
* * *
11606044 CAAGTTGTGTGTCA-AAGAAGCTCCCCACGTGAGCTTA
1 CAAGCTGTGTATCAGAA-AAGCTCCCCATGTGAGCTTA
11606081 AGTGATGAAG
Statistics
Matches: 95, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
78 1 0.01
79 25 0.26
80 65 0.68
81 4 0.04
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (81 bp):
CAAGCTGTGTATCAGAAAAGCTCCCCATGTGAGCTTATGGATAAGTTGTGTATCAACAAAGCTCT
CCTGTGAGCTTAAGGA
Found at i:11608888 original size:21 final size:21
Alignment explanation
Indices: 11608858--11608906 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
11608848 ATGTCCCAGG
* *
11608858 GGCGACGATGGGCAAACCTTA
1 GGCGATGATGGGCAAACCTCA
11608879 GGCGATGATGGGCAAACCTCA
1 GGCGATGATGGGCAAACCTCA
11608900 GGCGATG
1 GGCGATG
11608907 CTAAGTTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.22, G:0.37, T:0.14
Consensus pattern (21 bp):
GGCGATGATGGGCAAACCTCA
Found at i:11609657 original size:20 final size:20
Alignment explanation
Indices: 11609596--11609650 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
11609586 CTACAATGTT
11609596 TAAATGAACTTACTAATTTC
1 TAAATGAACTTACTAATTTC
11609616 TAAATGAACTTACTAATTTC
1 TAAATGAACTTACTAATTTC
11609636 TAAATGAACTTACTA
1 TAAATGAACTTACTA
11609651 GTGTCTATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAATGAACTTACTAATTTC
Found at i:11613282 original size:43 final size:43
Alignment explanation
Indices: 11613234--11613320 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
11613224 CCATGAAAAC
11613234 TTTTAGCCTATTATAGAATCTTAAATGGCTACTCAAAGACAAG
1 TTTTAGCCTATTATAGAATCTTAAATGGCTACTCAAAGACAAG
* *
11613277 TTTTAGCCTTTTATAGAATCTTAAATGGCTACTCAAAGGCAAG
1 TTTTAGCCTATTATAGAATCTTAAATGGCTACTCAAAGACAAG
11613320 T
1 T
11613321 AGGAATTTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (43 bp):
TTTTAGCCTATTATAGAATCTTAAATGGCTACTCAAAGACAAG
Found at i:11618416 original size:18 final size:17
Alignment explanation
Indices: 11618376--11618424 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
11618366 AAAACACTAA
11618376 AAATTTATTTTAAAAAT
1 AAATTTATTTTAAAAAT
11618393 AAATTTATTTT-AAAA-
1 AAATTTATTTTAAAAAT
*
11618408 AAA-GTATTTTAAAAAT
1 AAATTTATTTTAAAAAT
11618424 A
1 A
11618425 TTTTAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 6 0.21
15 7 0.24
16 5 0.17
17 11 0.38
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
AAATTTATTTTAAAAAT
Found at i:11628423 original size:18 final size:17
Alignment explanation
Indices: 11628396--11628452 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
11628386 TACTTCATTT
11628396 TTTTTA-ATTTTATGAA
1 TTTTTATATTTTATGAA
*
11628412 CTTTTTATATTTTTTG-A
1 -TTTTTATATTTTATGAA
11628429 TTTTTAAATATTTTAT-AA
1 TTTTT--ATATTTTATGAA
11628447 TTTTTA
1 TTTTTA
11628453 AATTATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 6 0.18
17 7 0.21
18 21 0.62
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (17 bp):
TTTTTATATTTTATGAA
Found at i:11628453 original size:18 final size:18
Alignment explanation
Indices: 11628418--11628461 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
11628408 TGAACTTTTT
* *
11628418 ATATTTTTTGATTTTTAA
1 ATATTTTATAATTTTTAA
11628436 ATATTTTATAATTTTTAA
1 ATATTTTATAATTTTTAA
11628454 ATTATTTT
1 A-TATTTT
11628462 TTGATGTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
ATATTTTATAATTTTTAA
Found at i:11637642 original size:26 final size:25
Alignment explanation
Indices: 11637598--11637742 Score: 109
Period size: 25 Copynumber: 5.8 Consensus size: 25
11637588 AGCTCTTATA
11637598 AGCTTCCCGATTATATGGCTCTTCGTG
1 AGCTTCCCG-TTAT-TGGCTCTTCGTG
*
11637625 AGCTTCCCGTTAATTGGCTCTTTGTG
1 AGCTTCCCGTT-ATTGGCTCTTCGTG
* * *
11637651 AGCTTCCCGATA-TGGCTC-GCTTG
1 AGCTTCCCGTTATTGGCTCTTCGTG
* * * *
11637674 AACTTCCCGATATATGGCTATCCG-G
1 AGCTTCCCGTTAT-TGGCTCTTCGTG
* *
11637699 AGCTCCCCGATTAATGGCTCTTCG-G
1 AGCTTCCCG-TTATTGGCTCTTCGTG
* *
11637724 AGCTACCCGTTATAGGCTC
1 AGCTTCCCGTTATTGGCTC
11637743 GCACGAGCTT
Statistics
Matches: 95, Mismatches: 18, Indels: 13
0.75 0.14 0.10
Matches are distributed among these distances:
23 13 0.14
24 14 0.15
25 31 0.33
26 26 0.27
27 11 0.12
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.32
Consensus pattern (25 bp):
AGCTTCCCGTTATTGGCTCTTCGTG
Found at i:11637754 original size:74 final size:76
Alignment explanation
Indices: 11637598--11637754 Score: 187
Period size: 74 Copynumber: 2.1 Consensus size: 76
11637588 AGCTCTTATA
* * * * *
11637598 AGCTTCCCGATTATATGGCTCTTCGTGAGCTTCCCGTTAATTGGCTCTTTGTGAGCTTCCCGATA
1 AGCTTCCCGATTATATGGCTATCCGTGAGCTCCCCGTTAATTGGCTCTTCGTGAGCTACCCGATA
**
11637663 TGGCTCGCTTG
66 TGGCTCGCACG
* *
11637674 AACTTCCCGA-TATATGGCTATCCG-GAGCTCCCCGATTAA-TGGCTCTTCG-GAGCTACCCGTT
1 AGCTTCCCGATTATATGGCTATCCGTGAGCTCCCCG-TTAATTGGCTCTTCGTGAGCTACCCGAT
11637735 ATAGGCTCGCACG
65 AT-GGCTCGCACG
11637748 AGCTTCC
1 AGCTTCC
11637755 TGAATATTGC
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
73 12 0.17
74 32 0.46
75 16 0.23
76 9 0.13
ACGTcount: A:0.17, C:0.29, G:0.23, T:0.31
Consensus pattern (76 bp):
AGCTTCCCGATTATATGGCTATCCGTGAGCTCCCCGTTAATTGGCTCTTCGTGAGCTACCCGATA
TGGCTCGCACG
Found at i:11641171 original size:15 final size:16
Alignment explanation
Indices: 11641151--11641180 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11641141 CCAATACAAA
11641151 AGAATAAGAT-TTAAG
1 AGAATAAGATGTTAAG
11641166 AGAATAAGATGTTAA
1 AGAATAAGATGTTAA
11641181 ATAAGATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (16 bp):
AGAATAAGATGTTAAG
Found at i:11642311 original size:21 final size:20
Alignment explanation
Indices: 11642287--11642341 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
11642277 AAACATAGGG
11642287 TTTTACAGGAAATTAAC-TGGA
1 TTTTACAGGAAA--AACTTGGA
* *
11642308 TTTTATAGGAAAAACTTGGG
1 TTTTACAGGAAAAACTTGGA
11642328 TCTTTACAGGAAAA
1 T-TTTACAGGAAAA
11642342 GTCATTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 3 0.10
20 4 0.14
21 22 0.76
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (20 bp):
TTTTACAGGAAAAACTTGGA
Found at i:11642385 original size:16 final size:17
Alignment explanation
Indices: 11642353--11642388 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11642343 TCATTTTATC
11642353 TTTTTAATTTTCTTAAA
1 TTTTTAATTTTCTTAAA
* *
11642370 TTTTTTATTTTCTAAAA
1 TTTTTAATTTTCTTAAA
11642387 TT
1 TT
11642389 AATTTTAAAC
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:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTAATTTTCTTAAA
Found at i:11645187 original size:2 final size:2
Alignment explanation
Indices: 11645167--11645204 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
11645157 ACATATTATC
*
11645167 AT AT GT AT A- AT ACT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
11645205 TATTTTCACA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11651722 original size:9 final size:9
Alignment explanation
Indices: 11651708--11651839 Score: 61
Period size: 10 Copynumber: 13.7 Consensus size: 9
11651698 ATACAAATAA
11651708 ATAAAAATT
1 ATAAAAATT
11651717 ATAAAAATT
1 ATAAAAATT
**
11651726 ATTAAATTTT
1 A-TAAAAATT
*
11651736 AATAAAAAAT
1 -ATAAAAATT
11651746 ATAAAAGAATAT
1 AT-AAA-AAT-T
* *
11651758 TTAAAACTT
1 ATAAAAATT
*
11651767 ATTATAAATT
1 A-TAAAAATT
*
11651777 AGAACAAAATT
1 A-TA-AAAATT
*
11651788 ATAAAAATC
1 ATAAAAATT
11651797 ATAAAAAATT
1 AT-AAAAATT
**
11651807 A-AAATTTT
1 ATAAAAATT
11651815 ATAAAAATCT
1 ATAAAAAT-T
11651825 -TAAAAATTT
1 ATAAAAA-TT
11651834 ATAAAA
1 ATAAAA
11651840 TATAGAAAAA
Statistics
Matches: 90, Mismatches: 21, Indels: 23
0.67 0.16 0.17
Matches are distributed among these distances:
8 6 0.07
9 31 0.34
10 39 0.43
11 12 0.13
12 2 0.02
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:11651731 original size:19 final size:19
Alignment explanation
Indices: 11651690--11651839 Score: 74
Period size: 20 Copynumber: 7.7 Consensus size: 19
11651680 GACATGTGGC
* * *
11651690 AAAAATTGATACAAATAAAT
1 AAAAATT-ATAAAAATTATT
11651710 AAAAATTATAAAAATTATT
1 AAAAATTATAAAAATTATT
** * *
11651729 AAATTTTAATAAAAAATATA
1 AAAAATT-ATAAAAATTATT
* *
11651749 AAAGAATATTTAAAACTTATT
1 AAA-AAT-TATAAAAATTATT
* *
11651770 ATAAATTAGAACAAAATTA-T
1 AAAAATTA-TA-AAAATTATT
*
11651790 AAAAATCATAAAAA--ATT
1 AAAAATTATAAAAATTATT
* *
11651807 AAAATTTTATAAAAA-TCTT
1 AAAA-ATTATAAAAATTATT
11651826 AAAAATTTATAAAA
1 AAAAA-TTATAAAA
11651840 TATAGAAAAA
Statistics
Matches: 97, Mismatches: 24, Indels: 19
0.69 0.17 0.14
Matches are distributed among these distances:
16 1 0.01
17 5 0.05
18 12 0.12
19 30 0.31
20 31 0.32
21 17 0.18
22 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAATTATAAAAATTATT
Found at i:11651818 original size:18 final size:19
Alignment explanation
Indices: 11651690--11651839 Score: 69
Period size: 19 Copynumber: 7.7 Consensus size: 19
11651680 GACATGTGGC
* * *
11651690 AAAAATTGATACAAATAAAT
1 AAAAATTTATAAAAAT-ATT
11651710 AAAAA-TTATAAAAATTATT
1 AAAAATTTATAAAAA-TATT
* *
11651729 -AAATTTTAATAAAAAATATA
1 AAAAATTT-AT-AAAAATATT
*
11651749 AAAGAATATT-TAAAACTTATT
1 AAA-AAT-TTATAAAA-ATATT
* *
11651770 ATAAA-TTAGAACAAA-ATT
1 AAAAATTTATAA-AAATATT
* *
11651788 ATAAAAATCATAAAAA-ATT
1 A-AAAATTTATAAAAATATT
* *
11651807 AAAATTTTATAAAAATCTT
1 AAAAATTTATAAAAATATT
11651826 AAAAATTTATAAAA
1 AAAAATTTATAAAA
11651840 TATAGAAAAA
Statistics
Matches: 98, Mismatches: 19, Indels: 27
0.68 0.13 0.19
Matches are distributed among these distances:
18 20 0.20
19 38 0.39
20 23 0.23
21 13 0.13
22 2 0.02
23 2 0.02
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAATTTATAAAAATATT
Found at i:11651934 original size:20 final size:20
Alignment explanation
Indices: 11651874--11651938 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 20
11651864 TATAAAGTTT
* * *
11651874 TATAAAGTTT-TAAGAAAAT
1 TATAAAATTTGTAAAAAAAA
* *
11651893 TATAAAATATGT-AAAGAAA
1 TATAAAATTTGTAAAAAAAA
11651912 TATAAAATTTGTAAAAAAAA
1 TATAAAATTTGTAAAAAAAA
11651932 TATAAAA
1 TATAAAA
11651939 ATTACTATAC
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 23 0.62
20 14 0.38
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (20 bp):
TATAAAATTTGTAAAAAAAA
Found at i:11652175 original size:28 final size:28
Alignment explanation
Indices: 11652144--11652200 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
11652134 TTTTTTTCTA
11652144 ATTTTTAGTAAATTTCAAAT-ATTTTTAT
1 ATTTTTAGTAAATTT-AAATAATTTTTAT
* *
11652172 ATTTTTATTAAATTTTAATAATTTTTAT
1 ATTTTTAGTAAATTTAAATAATTTTTAT
11652200 A
1 A
11652201 ACTTTTATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
ATTTTTAGTAAATTTAAATAATTTTTAT
Found at i:11652206 original size:19 final size:19
Alignment explanation
Indices: 11652172--11652218 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
11652162 ATATTTTTAT
11652172 ATTTTTATTAAATTTTAATA
1 ATTTTTA-TAAATTTTAATA
* * *
11652192 ATTTTTATAACTTTTATTG
1 ATTTTTATAAATTTTAATA
11652211 ATTTTTAT
1 ATTTTTAT
11652219 TTTTTATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTTATAAATTTTAATA
Found at i:11652231 original size:9 final size:9
Alignment explanation
Indices: 11652136--11652232 Score: 65
Period size: 9 Copynumber: 10.6 Consensus size: 9
11652126 ATTTTATATT
*
11652136 TTTTTCTAA
1 TTTTTATAA
11652145 TTTTTAGTAA
1 TTTTTA-TAA
* * *
11652155 ATTTCAAATA
1 TTTTTATA-A
11652165 TTTTTAT-A
1 TTTTTATAA
11652173 TTTTTATTAAA
1 TTTTTA-T-AA
*
11652184 TTTTAATAA
1 TTTTTATAA
11652193 TTTTTATAA
1 TTTTTATAA
* *
11652202 CTTTTATTGA
1 TTTTTA-TAA
11652212 TTTTTAT--
1 TTTTTATAA
11652219 TTTTTATAA
1 TTTTTATAA
11652228 TTTTT
1 TTTTT
11652233 TGTCACATGT
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
7 7 0.10
8 7 0.10
9 28 0.41
10 20 0.29
11 6 0.09
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:11652520 original size:90 final size:90
Alignment explanation
Indices: 11652365--11652715 Score: 374
Period size: 90 Copynumber: 3.9 Consensus size: 90
11652355 AGATCAACAA
* * * * * *
11652365 TTTGACAGATCAAGTACCCAATTGAGTGCCCAAAAAAAAGTAAGGGCTTAATTGCTTTTTTTGAA
1 TTTGAAAGTTCAAGTACCCAATTGAGTG-CAAAAAAAAAGCAGGGGCTTAATGGCTTTTTTTG-A
* * *
11652430 AAAATTTTGAGGGCCTTTTTGATTCAT
64 AAAAGTTTGAGGGCATTTTTGATGCAT
* * * * *
11652457 TTTGAAAGTTTAAGTACCCAATTAAGTG-TAAAAAAAAGCAGGGGTTTAATGGCTTTTATTGAAA
1 TTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAATGGCTTTTTTTGAAA
11652521 AAGTTTGAGGGCATTTTTGATGCAT
66 AAGTTTGAGGGCATTTTTGATGCAT
* * *
11652546 TTTGAAAGTTCAAGTTCCCAATTGAGTGAAAAAAAAAAGCAGAGGCTTAATGGCTTTTTTTGAAA
1 TTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAATGGCTTTTTTTGAAA
* *
11652611 AAGTTTAAGGGTCGTTTTT-ATGCATT
66 AAGTTTGAGGG-CATTTTTGATGCA-T
* * * * * *
11652637 TTTAAAAGTTCAAGTACCTAATTGAGTGGAAAAAAAAA--A-GAGTTTAATTGCTTTTTTT-AAG
1 TTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAATGGCTTTTTTTGAA-
*
11652698 AAAGTTTGGGGGC-TTTTT
65 AAAGTTTGAGGGCATTTTT
11652716 ACACCCTGAA
Statistics
Matches: 223, Mismatches: 32, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
86 5 0.02
87 3 0.01
88 25 0.11
89 51 0.23
90 74 0.33
91 41 0.18
92 24 0.11
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.36
Consensus pattern (90 bp):
TTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAATGGCTTTTTTTGAAA
AAGTTTGAGGGCATTTTTGATGCAT
Found at i:11653163 original size:23 final size:23
Alignment explanation
Indices: 11653115--11653157 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
11653105 TTTCGAAAAG
*
11653115 TTTTATTATTAATCATTTAGTCA
1 TTTTATTATTAATCATTTAATCA
*
11653138 TTTTATTATT-ATTATTTAAT
1 TTTTATTATTAATCATTTAAT
11653158 GGATTTGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTTATTATTAATCATTTAATCA
Found at i:11663479 original size:45 final size:44
Alignment explanation
Indices: 11663430--11663522 Score: 132
Period size: 45 Copynumber: 2.1 Consensus size: 44
11663420 ATTAATAGTA
11663430 TTTATCATGATGCCATAACATATTTCAACTATAATCTTACTCATT
1 TTTATCATGATGCCATAACATATTTCAACTATAATCTTACTC-TT
* * * **
11663475 TTTATCATGATGCCATAACATCTTTTAGCTATGGTCTTACTCTT
1 TTTATCATGATGCCATAACATATTTCAACTATAATCTTACTCTT
11663519 TTTA
1 TTTA
11663523 GGCGTATAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 6 0.14
45 37 0.86
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.45
Consensus pattern (44 bp):
TTTATCATGATGCCATAACATATTTCAACTATAATCTTACTCTT
Found at i:11673801 original size:45 final size:45
Alignment explanation
Indices: 11673737--11673830 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
11673727 AATAGATACT
* * *
11673737 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
*
11673782 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
11673827 CGGT
1 CGGT
11673831 TCACATAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:11673894 original size:51 final size:50
Alignment explanation
Indices: 11673827--11674022 Score: 205
Period size: 51 Copynumber: 3.9 Consensus size: 50
11673817 CAATGATGTT
* * *
11673827 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATC
* * * *
11673878 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATC
* ** * * * * * *
11673929 TGGTATGCATAGCAGCCTGCACATAGTACTACATATGCGACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TC
*
11673979 CGGTACACGTAGTAGCCTGCACATAGTACTACACACATGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
11674023 CACTTCAACT
Statistics
Matches: 113, Mismatches: 29, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
49 2 0.02
50 36 0.32
51 73 0.65
52 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCATC
Found at i:11674041 original size:101 final size:100
Alignment explanation
Indices: 11673833--11674018 Score: 257
Period size: 101 Copynumber: 1.8 Consensus size: 100
11673823 TGTTCGGTTC
* *
11673833 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTGC
1 ACATAGCAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTGC
* * *
11673898 ACATAGTACTACACACGTGATCGAAACTATCTGGTAT
65 ACATAGTACTACACACATGATCCAAACTAACT-GTAT
* * * *
11673935 GCATAGCAGCCTGCACATAGTACTACATATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGC
1 ACATAGCAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTGC
11673999 ACATAGTACTACACACATGA
65 ACATAGTACTACACACATGA
11674019 CCATCACTTC
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
100 4 0.05
101 40 0.53
102 32 0.42
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (100 bp):
ACATAGCAGCCTGCACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACATGATCCAAACTAACTGTAT
Found at i:11689414 original size:31 final size:31
Alignment explanation
Indices: 11689376--11689437 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
11689366 AGGCAAATTA
11689376 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
11689407 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
11689438 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:11702687 original size:15 final size:15
Alignment explanation
Indices: 11702667--11702697 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11702657 CGATTGAGGT
11702667 TGTGGTAGGAGGATG
1 TGTGGTAGGAGGATG
11702682 TGTGGTAGGAGGATG
1 TGTGGTAGGAGGATG
11702697 T
1 T
11702698 TTAGACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.52, T:0.29
Consensus pattern (15 bp):
TGTGGTAGGAGGATG
Found at i:11704441 original size:33 final size:33
Alignment explanation
Indices: 11704400--11704496 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 33
11704390 GCGTCCACAG
*
11704400 AGTAAGTTCGTTGGGGCAGTAAACAGGGAATAA
1 AGTAAGTTCGTTGGGACAGTAAACAGGGAATAA
* * ** *
11704433 AGTAAGTTCATTGGGATAGTAAACATAGAATAG
1 AGTAAGTTCGTTGGGACAGTAAACAGGGAATAA
11704466 AGTAAGTTCGTTGGGACAGTAAACACGGGAA
1 AGTAAGTTCGTTGGGACAGTAAACA-GGGAA
11704497 GTCTACTGGG
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
33 50 0.94
34 3 0.06
ACGTcount: A:0.38, C:0.09, G:0.30, T:0.23
Consensus pattern (33 bp):
AGTAAGTTCGTTGGGACAGTAAACAGGGAATAA
Found at i:11709468 original size:19 final size:19
Alignment explanation
Indices: 11709444--11709481 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
11709434 GAGTGTAAGT
11709444 TCGAACAAATCGAATCAAA
1 TCGAACAAATCGAATCAAA
11709463 TCGAACAAATCGAATCAAA
1 TCGAACAAATCGAATCAAA
11709482 CACATGAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.21, G:0.11, T:0.16
Consensus pattern (19 bp):
TCGAACAAATCGAATCAAA
Found at i:11709471 original size:9 final size:10
Alignment explanation
Indices: 11709444--11709481 Score: 62
Period size: 9 Copynumber: 4.0 Consensus size: 10
11709434 GAGTGTAAGT
11709444 TCGAA-CAAA
1 TCGAATCAAA
11709453 TCGAATCAAA
1 TCGAATCAAA
11709463 TCGAA-CAAA
1 TCGAATCAAA
11709472 TCGAATCAAA
1 TCGAATCAAA
11709482 CACATGAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 14 0.52
10 13 0.48
ACGTcount: A:0.53, C:0.21, G:0.11, T:0.16
Consensus pattern (10 bp):
TCGAATCAAA
Found at i:11716902 original size:24 final size:23
Alignment explanation
Indices: 11716875--11716924 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 23
11716865 ATAATAAATG
11716875 AATTCTACACATAAAAAAAAAACA
1 AATTCTACACAT-AAAAAAAAACA
*
11716899 AATTCTACACATAAAAAATAACA
1 AATTCTACACATAAAAAAAAACA
11716922 AAT
1 AAT
11716925 AAAAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (23 bp):
AATTCTACACATAAAAAAAAACA
Found at i:11718597 original size:7 final size:7
Alignment explanation
Indices: 11718585--11718632 Score: 96
Period size: 7 Copynumber: 6.9 Consensus size: 7
11718575 CATAGAATTG
11718585 AATCATT
1 AATCATT
11718592 AATCATT
1 AATCATT
11718599 AATCATT
1 AATCATT
11718606 AATCATT
1 AATCATT
11718613 AATCATT
1 AATCATT
11718620 AATCATT
1 AATCATT
11718627 AATCAT
1 AATCAT
11718633 CAATGTTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (7 bp):
AATCATT
Found at i:11726203 original size:22 final size:21
Alignment explanation
Indices: 11726177--11726218 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
11726167 AAGAATTTTT
*
11726177 TTTAATTTTCCTATTATTATTA
1 TTTAATTTTACTATT-TTATTA
11726199 TTTAATTTTACTATTTTATT
1 TTTAATTTTACTATTTTATT
11726219 TTATTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTAATTTTACTATTTTATTA
Found at i:11727182 original size:29 final size:32
Alignment explanation
Indices: 11727134--11727193 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 32
11727124 AATTTTGTGC
11727134 AGGAATACAATTTGGGGCTAAATAGAAGAAAA
1 AGGAATACAATTTGGGGCTAAATAGAAGAAAA
* *
11727166 AGGAA-ACAA-TT-GGGCTAGATTGAAGAAA
1 AGGAATACAATTTGGGGCTAAATAGAAGAAA
11727194 GAAGCAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 15 0.58
30 2 0.08
31 4 0.15
32 5 0.19
ACGTcount: A:0.48, C:0.07, G:0.27, T:0.18
Consensus pattern (32 bp):
AGGAATACAATTTGGGGCTAAATAGAAGAAAA
Found at i:11732139 original size:28 final size:30
Alignment explanation
Indices: 11732108--11732165 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
11732098 TTTGGTCTAA
*
11732108 TGTGCA-TTTTATATATG-AACTTTGATTT
1 TGTGCAGTTTTATACATGAAACTTTGATTT
* *
11732136 TGTGCAGTTTTGTACATGAAATTTTGATTT
1 TGTGCAGTTTTATACATGAAACTTTGATTT
11732166 GATCCAATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.24
29 9 0.36
30 10 0.40
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.52
Consensus pattern (30 bp):
TGTGCAGTTTTATACATGAAACTTTGATTT
Found at i:11732258 original size:23 final size:23
Alignment explanation
Indices: 11732217--11732262 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
11732207 CCTTTTATAT
11732217 TTATATATTATATAAATAAATAA
1 TTATATATTATATAAATAAATAA
*
11732240 TTATAT-TTATCTAATATAAATAA
1 TTATATATTATATAA-ATAAATAA
11732263 ATTGGTGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TTATATATTATATAAATAAATAA
Found at i:11732264 original size:27 final size:28
Alignment explanation
Indices: 11732211--11732264 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
11732201 ATACATCCTT
11732211 TTATATTTATATATTATATAAATAAATAA
1 TTATATTTATATA-TATATAAATAAATAA
*
11732240 TTATATTTATCTA-ATATAAATAAAT
1 TTATATTTATATATATATAAATAAAT
11732265 TGGTGTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 12 0.50
29 12 0.50
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
TTATATTTATATATATATAAATAAATAA
Found at i:11737405 original size:27 final size:27
Alignment explanation
Indices: 11737370--11737433 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
11737360 GGATCACTAT
*
11737370 AAATTATCCATA-AAAATACAACCATC
1 AAATTATCCATACAAAATAAAACCATC
*
11737396 AAAATGATCCA-ACAAAATAAAACCATC
1 -AAATTATCCATACAAAATAAAACCATC
11737423 AAATTATCCAT
1 AAATTATCCAT
11737434 CGTATCTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 10 0.31
27 22 0.69
ACGTcount: A:0.55, C:0.22, G:0.02, T:0.22
Consensus pattern (27 bp):
AAATTATCCATACAAAATAAAACCATC
Found at i:11741559 original size:32 final size:32
Alignment explanation
Indices: 11741491--11741559 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
11741481 TTTTCATCAA
* * **
11741491 CCATGTAATGCCAATGAGAGGATATCATTTAC
1 CCATATAATGCCAATGAAAGGATATCATGCAC
*
11741523 CCATATAATGCCAATGAAAGGATATCATGCAT
1 CCATATAATGCCAATGAAAGGATATCATGCAC
11741555 CCATA
1 CCATA
11741560 GCATAAACAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (32 bp):
CCATATAATGCCAATGAAAGGATATCATGCAC
Found at i:11742097 original size:26 final size:26
Alignment explanation
Indices: 11742038--11742103 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
11742028 CCTGTACATA
11742038 TATGCTCACACGAGCTATGAAATAAG
1 TATGCTCACACGAGCTATGAAATAAG
* **
11742064 TATGCTCAAACGAGCTATGAAATGGG
1 TATGCTCACACGAGCTATGAAATAAG
11742090 TTAT-CTCACACGAG
1 -TATGCTCACACGAG
11742104 TTGTGGAGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 32 0.91
27 3 0.09
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (26 bp):
TATGCTCACACGAGCTATGAAATAAG
Found at i:11745819 original size:36 final size:35
Alignment explanation
Indices: 11745779--11745900 Score: 86
Period size: 36 Copynumber: 3.2 Consensus size: 35
11745769 TCACATATTG
11745779 AGCATGCCCTATTCTAAAATTCTGATTTGCATGATA
1 AGCATGCCCTATTCTAAAATTCTGATTTGCATG-TA
* *
11745815 AGCATG-CC-ATTATGAAAATATATAAGATCTTATTCGCATGTTA
1 AGCATGCCCTATTCT-AAAAT-TCT--GA---T-TT-GCATG-TA
* *
11745858 AGCATGCCATATTCTAAAAATCTGATTTGCATGTAA
1 AGCATGCCCTATTCTAAAATTCTGATTTGCATGT-A
11745894 AGCATGC
1 AGCATGC
11745901 TACTGAAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 24
0.68 0.07 0.24
Matches are distributed among these distances:
34 4 0.06
35 8 0.12
36 21 0.31
37 2 0.03
38 3 0.04
41 3 0.04
42 2 0.03
43 15 0.22
44 5 0.07
45 4 0.06
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (35 bp):
AGCATGCCCTATTCTAAAATTCTGATTTGCATGTA
Found at i:11749619 original size:20 final size:20
Alignment explanation
Indices: 11749576--11749619 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
11749566 ATGTTTATTC
* *
11749576 AATTTAGTCCAAATCCTTCC
1 AATTTAGTCCAAAGCCTTCA
11749596 AATTTAGTCCTAAAGCCTT-A
1 AATTTAGTCC-AAAGCCTTCA
11749616 AATT
1 AATT
11749620 ATTTAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.36
Consensus pattern (20 bp):
AATTTAGTCCAAAGCCTTCA
Found at i:11752549 original size:12 final size:12
Alignment explanation
Indices: 11752532--11752564 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
11752522 CGCGCCACAT
11752532 GGTCGTGTGGTA
1 GGTCGTGTGGTA
11752544 GGTCGTGTGGTA
1 GGTCGTGTGGTA
*
11752556 GGTCATGTG
1 GGTCGTGTG
11752565 CCAGATCGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.09, G:0.48, T:0.33
Consensus pattern (12 bp):
GGTCGTGTGGTA
Found at i:11757207 original size:27 final size:27
Alignment explanation
Indices: 11757156--11757207 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
11757146 ATCCGACATC
* *
11757156 CTTACCATCTTTCAAGTTCTCAAATAG
1 CTTACCATCTTTCAAGTCCTAAAATAG
11757183 CTTACC-TCTTTCAAGTCCTGAAAAT
1 CTTACCATCTTTCAAGTCCT-AAAAT
11757208 CCAAATCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.37
Consensus pattern (27 bp):
CTTACCATCTTTCAAGTCCTAAAATAG
Found at i:11762797 original size:24 final size:25
Alignment explanation
Indices: 11762744--11762807 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
11762734 ATTTTTATTT
* *
11762744 TTATTTTTTTAACTTTTATATGTAA
1 TTATTTTTTTAAATTATATATGTAA
11762769 TTATTTTTTTAAATATATATATGTATA
1 TTATTTTTTTAAAT-TATATATGTA-A
11762796 TTTATTTATTTT
1 -TTATTT-TTTT
11762808 TATGTACATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 13 0.39
26 9 0.27
27 1 0.03
28 6 0.18
29 4 0.12
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.66
Consensus pattern (25 bp):
TTATTTTTTTAAATTATATATGTAA
Found at i:11766392 original size:98 final size:98
Alignment explanation
Indices: 11766223--11766419 Score: 376
Period size: 98 Copynumber: 2.0 Consensus size: 98
11766213 GTGTAATAAA
11766223 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
* *
11766288 CCTCTAAAATCCCTAACTTGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
11766321 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
11766386 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
11766419 A
1 A
11766420 TTATTTAAAA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:11767460 original size:23 final size:22
Alignment explanation
Indices: 11767434--11767478 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
11767424 AATTACATTT
*
11767434 CAAAACATTTTAAAAAAAAAAAC
1 CAAAAC-TTTCAAAAAAAAAAAC
*
11767457 CAAATCTTTCAAAAAAAAAAAC
1 CAAAACTTTCAAAAAAAAAAAC
11767479 TCTCTCAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.67, C:0.16, G:0.00, T:0.18
Consensus pattern (22 bp):
CAAAACTTTCAAAAAAAAAAAC
Found at i:11768583 original size:44 final size:44
Alignment explanation
Indices: 11768534--11768849 Score: 134
Period size: 44 Copynumber: 7.2 Consensus size: 44
11768524 AATATTCACC
*
11768534 GTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
1 GTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
* * * * * * * * **
11768578 ATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAG-GCT-TG
1 GTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
* * * *
11768620 GTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAAAGATAAGAT-TCGCC
1 GT--CTTCAATCTGC-T-CCACTACTGCTTAGG-GAGATAAGATCT-ACA
* *
11768666 GTCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTACA
1 GTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
* * * * * * * * **
11768710 ATCTTCAACCTTCTCCGCTGCTGCTTAGAGAGACAAG-GCT-TG
1 GTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
* * * *
11768752 GTGGCTTAAATCTGCTTCCCACTAC--CTT-GGAAAGATAAGAT-TCGCC
1 GT--CTTCAATCTGC-T-CCACTACTGCTTAGG-GAGATAAGATCT-ACA
* *
11768798 GTCTTCGATCTTCTCCACTACTGCTTAGGGAGATAAGATCTACA
1 GTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
*
11768842 ATCTTCAA
1 GTCTTCAA
11768850 CCTTCTCTGC
Statistics
Matches: 188, Mismatches: 60, Indels: 48
0.64 0.20 0.16
Matches are distributed among these distances:
42 15 0.08
43 10 0.05
44 141 0.75
45 9 0.05
46 13 0.07
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (44 bp):
GTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
Found at i:11768607 original size:132 final size:132
Alignment explanation
Indices: 11768448--11769205 Score: 1224
Period size: 132 Copynumber: 5.8 Consensus size: 132
11768438 AGACTTGTAG
* * *
11768448 CTTCAACCTTTTCTGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTTAATCTGCTTCCCACTAT
1 CTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
* *
11768513 CTTGGAAAGATAATATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
66 CTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
11768578 AT
131 AT
11768580 CTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
1 CTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
*
11768645 CTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTACA
66 CTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
11768710 AT
131 AT
* * *
11768712 CTTCAACCTTCTCCGCTGCTGCTTAGAGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAC
1 CTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
*
11768777 CTTGGAAAGATAAGATTCGCCGTCTTCGATCTTCTCCACTACTGCTTAGGGAGATAAGATCTACA
66 CTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
11768842 AT
131 AT
* * * *
11768844 CTTCAACCTTCTCTGCTGCTGCTCAGGGAAACAAGGCTTGGTGGCCTAAATCTACTTCCCACTAT
1 CTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
* * * * *
11768909 CTTGGATAGATAAAACTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATA
66 CTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
11768974 AT
131 AT
* *
11768976 CTTCAACCTTCTCCGCTGATGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTACTTCCCACTAT
1 CTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
*
11769041 CTTGGAAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT---
66 CTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
11769103 A-
131 AT
* * * *
11769104 --T-AACCTTCTTCGCTACTGCTCGGGGAGACAAGGCTTGGTGGCTTAAATCGGCTTCCCACTAT
1 CTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
*
11769166 CTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACT
66 CTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACT
11769206 GTAACTTCAG
Statistics
Matches: 585, Mismatches: 41, Indels: 7
0.92 0.06 0.01
Matches are distributed among these distances:
125 93 0.16
126 1 0.00
129 1 0.00
132 490 0.84
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (132 bp):
CTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
CTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
AT
Found at i:11780726 original size:98 final size:98
Alignment explanation
Indices: 11780557--11780753 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
11780547 GTGCAATAAA
*
11780557 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTACGGTACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTACGGCACGATT
* *
11780622 CCTCTAAAATCCCAAACTTGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGAAATATTTCCTTT
* * *
11780655 ACTTTCAAAGAACATCCACTTATCCAAGATTTAAGAAATCATACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTACGGCACGATT
11780720 CCTCTAAAATCCCAAACTCGAAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGAAATATTTCCTTT
11780753 A
1 A
11780754 TTATTTTTAA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.37, C:0.25, G:0.09, T:0.29
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTACGGCACGATT
CCTCTAAAATCCCAAACTCGAAATATTTCCTTT
Found at i:11791719 original size:75 final size:75
Alignment explanation
Indices: 11791570--11791729 Score: 214
Period size: 75 Copynumber: 2.1 Consensus size: 75
11791560 GGATCGAGTT
* * *
11791570 AACCGACAGTATTGAATGTGAGCCCAGCTCTAGCTGGATAAACCAACAATGTTTGCGCCCAATGC
1 AACCGACAATATTAAATGTGAGCCCAGCTCTAGCTGGATAAACCAACAATGTTTGCGCCCAACGC
* *
11791635 TGGTTGGATA
66 TAGTCGGATA
* * ** *
11791645 TAA-CGACAATATTAAATGTGAGCCCAGCTCTAGTTGGATGAACCAACGGTGTTTGCGCCCAGCG
1 -AACCGACAATATTAAATGTGAGCCCAGCTCTAGCTGGATAAACCAACAATGTTTGCGCCCAACG
11791709 CTAGTCGGATA
65 CTAGTCGGATA
11791720 AACCGACAAT
1 AACCGACAAT
11791730 TGTGTGCCCA
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
74 2 0.03
75 69 0.95
76 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (75 bp):
AACCGACAATATTAAATGTGAGCCCAGCTCTAGCTGGATAAACCAACAATGTTTGCGCCCAACGC
TAGTCGGATA
Found at i:11795776 original size:20 final size:20
Alignment explanation
Indices: 11795726--11795776 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 20
11795716 ACATAGAAAT
11795726 TAAATAAAAA-AACTAAAGC
1 TAAATAAAAATAACTAAAGC
11795745 -AAA-AATAAATAAC-AAAGTC
1 TAAATAA-AAATAACTAAAG-C
11795764 TAAATAAAAATAA
1 TAAATAAAAATAA
11795777 GAACATCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
17 2 0.07
18 10 0.37
19 4 0.15
20 9 0.33
21 2 0.07
ACGTcount: A:0.71, C:0.08, G:0.04, T:0.18
Consensus pattern (20 bp):
TAAATAAAAATAACTAAAGC
Found at i:11797503 original size:7 final size:7
Alignment explanation
Indices: 11797491--11797533 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
11797481 ATACCACTAG
11797491 TATGTGA
1 TATGTGA
11797498 TATGTGA
1 TATGTGA
11797505 TATGTGA
1 TATGTGA
11797512 TATGTGA
1 TATGTGA
* *
11797519 TTTATGA
1 TATGTGA
*
11797526 GATGTGA
1 TATGTGA
11797533 T
1 T
11797534 GATGAAGAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (7 bp):
TATGTGA
Found at i:11801444 original size:83 final size:82
Alignment explanation
Indices: 11801293--11801449 Score: 194
Period size: 83 Copynumber: 1.9 Consensus size: 82
11801283 GGCCACGTAT
* * * * *
11801293 GGAGGGAACAAGCCAACTTCCTTGCTTAAAATAGCAAAGGAAGACCCATTCTTCCTCACATCATG
1 GGAGGAAACAAGCCAACTTCCTTGCTTAAAATAGCAAAGGAAGAACCACTCTTCCTCACAACAAG
11801358 GGACGACATCACAAGGG
66 GGACGACATCACAAGGG
* *
11801375 GGAGGAAACCAAGCTAACTTCCTTGC-TAAAATTAGC-AAGGAAGCAATCACTCTTCCATCA-AA
1 GGAGGAAA-CAAGCCAACTTCCTTGCTTAAAA-TAGCAAAGGAAG-AACCACTCTTCC-TCACAA
11801437 CAAGGGACGACAT
62 CAAGGGACGACAT
11801450 ATACATGTAG
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
82 19 0.30
83 42 0.66
84 3 0.05
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (82 bp):
GGAGGAAACAAGCCAACTTCCTTGCTTAAAATAGCAAAGGAAGAACCACTCTTCCTCACAACAAG
GGACGACATCACAAGGG
Found at i:11807016 original size:32 final size:32
Alignment explanation
Indices: 11806970--11807031 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
11806960 ATGGGGTAGG
11806970 ATTTGGGAAAACAATGCCCTATAGGAAATTTT
1 ATTTGGGAAAACAATGCCCTATAGGAAATTTT
*
11807002 ATTTGGGAACACAATGCCCTATAGGAAATT
1 ATTTGGGAAAACAATGCCCTATAGGAAATT
11807032 ATACTTAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (32 bp):
ATTTGGGAAAACAATGCCCTATAGGAAATTTT
Found at i:11812262 original size:27 final size:27
Alignment explanation
Indices: 11812226--11812301 Score: 136
Period size: 26 Copynumber: 2.9 Consensus size: 27
11812216 GAATAAAAAG
11812226 GGGGTTGCTAAGTGCTGATTCCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
11812253 GGGGTTGCTAAGTGCTGATT-CCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
*
11812279 GGGGTTGCTAAGTGTTGATTCCC
1 GGGGTTGCTAAGTGCTGATTCCC
11812302 TGAATCTTTG
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
26 25 0.53
27 22 0.47
ACGTcount: A:0.17, C:0.22, G:0.32, T:0.29
Consensus pattern (27 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:11812390 original size:27 final size:27
Alignment explanation
Indices: 11812354--11812456 Score: 197
Period size: 27 Copynumber: 3.8 Consensus size: 27
11812344 AAATGTGAAG
*
11812354 GGGGTTGCTAAGTGCTAATTCCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
11812381 GGGGTTGCTAAGTGCTGATTCCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
11812408 GGGGTTGCTAAGTGCTGATTCCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
11812435 GGGGTTGCTAAGTGCTGATTCC
1 GGGGTTGCTAAGTGCTGATTCC
11812457 ACCGTATCTT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
27 75 1.00
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.27
Consensus pattern (27 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:11812484 original size:96 final size:99
Alignment explanation
Indices: 11812379--11812600 Score: 335
Period size: 96 Copynumber: 2.3 Consensus size: 99
11812369 TAATTCCCCC
11812379 AAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATT-CCC-CCA-AGG-GGT
1 AAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCACCATAGGTGGT
11812440 TGCTAAGTGCTGATTCCACCGTATCTTAAATGTGA
66 TGCTAAGTGCTGATTCCACCGTATC-TAAATGTGA
* * * *
11812475 AGGGGGTTGCTAAGTGTTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGAACCATTGGTG
1 AAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCC--ACCATAGGTG
* *
11812540 GTTGCTAAGTGCTGATTCCACCGTATCTGAGTGTGA
64 GTTGCTAAGTGCTGATTCCACCGTATCTAAATGTGA
11812576 AAGGGGTTGCTAAGTGCTGATTCCC
1 AAGGGGTTGCTAAGTGCTGATTCCC
11812601 TGAATCATTG
Statistics
Matches: 112, Mismatches: 8, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
96 46 0.41
97 3 0.03
100 3 0.03
101 32 0.29
102 28 0.25
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (99 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCACCATAGGTGGT
TGCTAAGTGCTGATTCCACCGTATCTAAATGTGA
Found at i:11812489 original size:123 final size:125
Alignment explanation
Indices: 11812223--11812527 Score: 499
Period size: 123 Copynumber: 2.4 Consensus size: 125
11812213 ATTGAATAAA
11812223 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATT-CCCCAAGGGGTTGC
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGC
* **
11812287 TAAGTGTTGATTCCCTGAATCTTTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
66 TAAGTGCTGATTCCCCCAA----TGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
*
11812351 AAGGGGGTTGCTAAGTGCTAATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGC
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGC
11812416 TAAGTGCTGATTCCCCCAA-GG-GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
66 TAAGTGCTGATTCCCCCAATGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
* *
11812474 AAGGGGGTTGCTAAGTGTTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCC
11812528 GAACCATTGG
Statistics
Matches: 169, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
123 88 0.52
124 2 0.01
128 49 0.29
129 30 0.18
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (125 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGC
TAAGTGCTGATTCCCCCAATGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
Found at i:11812548 original size:33 final size:33
Alignment explanation
Indices: 11812506--11812637 Score: 120
Period size: 33 Copynumber: 3.7 Consensus size: 33
11812496 TCCCCCAAGG
*
11812506 GGTTGCTAAGTGTTGATTCCCCGAACCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAACCATTGGT
* * *
11812539 GGTTGCTAAGTGCTGATTCCACCGTATCTGAGTGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-AAC-CA-T-TG---GT
* *
11812580 GGTTGCTAAGTGCTGATTCCCTGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAACCATTGGT
*
11812613 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
11812638 TAACGGATAA
Statistics
Matches: 79, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
33 39 0.49
34 6 0.08
35 2 0.03
36 3 0.04
37 2 0.03
38 3 0.04
39 1 0.01
40 2 0.03
41 21 0.27
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAACCATTGGT
Found at i:11814408 original size:19 final size:19
Alignment explanation
Indices: 11814375--11814414 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
11814365 TCTAAAAATC
*
11814375 AATAAATAATATTTTGGAA
1 AATAAATAATATTTTAGAA
11814394 AATAAA-AATATTTTTAGAA
1 AATAAATAATA-TTTTAGAA
11814413 AA
1 AA
11814415 ATTAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (19 bp):
AATAAATAATATTTTAGAA
Found at i:11820867 original size:26 final size:26
Alignment explanation
Indices: 11820808--11820870 Score: 92
Period size: 25 Copynumber: 2.5 Consensus size: 26
11820798 AAATTGAACA
**
11820808 AAATAAAAAAAATCTATATTAGTATT
1 AAATAAAAAAAATCTATATTAAAATT
*
11820834 AAATAAAAATAAT-TATATTAAAATT
1 AAATAAAAAAAATCTATATTAAAATT
11820859 AAATAAAAAAAA
1 AAATAAAAAAAA
11820871 AACCTCTTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
25 21 0.64
26 12 0.36
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (26 bp):
AAATAAAAAAAATCTATATTAAAATT
Found at i:11821279 original size:20 final size:22
Alignment explanation
Indices: 11821244--11821283 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
11821234 TATAAATATA
11821244 AATATAAATATTTTTATTTATT
1 AATATAAATATTTTTATTTATT
11821266 AATAT-AAT-TTTTTATTTA
1 AATATAAATATTTTTATTTA
11821284 ATTAGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 3 0.17
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
AATATAAATATTTTTATTTATT
Found at i:11825574 original size:109 final size:105
Alignment explanation
Indices: 11825373--11825586 Score: 277
Period size: 109 Copynumber: 2.0 Consensus size: 105
11825363 TTTTAAAACA
* * ***
11825373 AGGTCCAATTCCAAAACTTATCCCTCTTTTATGAAAATTGTTTAGTTGATCCCTCTATTGTCTTT
1 AGGTCCAATTACAAAACTTATCCCTCTTTCATGAAAATTGAGAAGTTGATCCCTCTATTGTCTTT
*
11825438 TTTACTAAATGCTCTAATTACAAAATTTATCCCTTTACTT
66 TTTACTAAATGCTCTAATTACAAAATTTATCCCTCTACTT
* * *
11825478 AGGTCCAATTATAAATA-TTATCCCTCTAGTTCATGAAAATTGAGAAGTTGATCCCTTTATTGTT
1 AGGTCCAATTACAAA-ACTTATCCCTCT--TTCATGAAAATTGAGAAGTTGATCCCTCTATTGTC
* *
11825542 TTGGTTTTACTAAATGTTCTAATTCCAAAATTTATCCCTCTACTT
63 TT--TTTTACTAAATGCTCTAATTACAAAATTTATCCCTCTACTT
11825587 TATGAAAATT
Statistics
Matches: 93, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
105 23 0.25
106 1 0.01
107 31 0.33
109 38 0.41
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.43
Consensus pattern (105 bp):
AGGTCCAATTACAAAACTTATCCCTCTTTCATGAAAATTGAGAAGTTGATCCCTCTATTGTCTTT
TTTACTAAATGCTCTAATTACAAAATTTATCCCTCTACTT
Found at i:11825610 original size:109 final size:107
Alignment explanation
Indices: 11825416--11825611 Score: 243
Period size: 109 Copynumber: 1.8 Consensus size: 107
11825406 AAAATTGTTT
*
11825416 AGTTGATCCCTCTATTGTCTTTTTTACTAAATGCTCTAATTACAAAATTTATCCCTTTACTTAGG
1 AGTTGATCCCTCTATTGTCTTTTTTACTAAATGCTCTAATTACAAAATTTATCCCTCTACTTAGG
** * *
11825481 TCCAATTATAAATATTATCCCTCTAGTTCATGAAAATTGAGA
66 TAAAATTAGAAATATAATCCCTCTAGTTCATGAAAATTGAGA
* * * *
11825523 AGTTGATCCCTTTATTGTTTTGGTTTTACTAAATGTTCTAATTCCAAAATTTATCCCTCTACTTT
1 AGTTGATCCCTCTATTGTCTT--TTTTACTAAATGCTCTAATTACAAAATTTATCCCTCTAC-TT
* *
11825588 ATG-AAAATTGAGAAGT-TAATCCCT
63 AGGTAAAATT-AGAAATATAATCCCT
11825612 TTATTGTTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
107 19 0.26
109 47 0.64
110 8 0.11
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (107 bp):
AGTTGATCCCTCTATTGTCTTTTTTACTAAATGCTCTAATTACAAAATTTATCCCTCTACTTAGG
TAAAATTAGAAATATAATCCCTCTAGTTCATGAAAATTGAGA
Found at i:11825627 original size:78 final size:77
Alignment explanation
Indices: 11825490--11825705 Score: 342
Period size: 78 Copynumber: 2.8 Consensus size: 77
11825480 GTCCAATTAT
* * *
11825490 AAATATTATCCCTCTAGTTCATGAAAATTGAGAAGTTGATCCCTTTATTGTTTTGGTTTTACTAA
1 AAAT-TTATCCCTCTACTTTATGAAAATTGAGAAGTT-ATCCCTTTATTGTTTTTGTTTTACTAA
11825555 ATGTTCTAATTCCA
64 ATGTTCTAATTCCA
*
11825569 AAATTTATCCCTCTACTTTATGAAAATTGAGAAGTTAATCCCTTTATTGTTTTTGTTTTACTGAA
1 AAATTTATCCCTCTACTTTATGAAAATTGAGAAGTT-ATCCCTTTATTGTTTTTGTTTTACTAAA
11825634 TGTTCTAATTCCA
65 TGTTCTAATTCCA
* *
11825647 AAATTTATCCCTCTACTTTATGAAAATTGAGAAGTTAGCCTCTTTATTGTTTTTTTTTT
1 AAATTTATCCCTCTACTTTATGAAAATTGAGAAGTTATCC-CTTTATTGTTTTTGTTTT
11825706 TAAAACTAAA
Statistics
Matches: 129, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
77 3 0.02
78 122 0.95
79 4 0.03
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (77 bp):
AAATTTATCCCTCTACTTTATGAAAATTGAGAAGTTATCCCTTTATTGTTTTTGTTTTACTAAAT
GTTCTAATTCCA
Found at i:11826017 original size:112 final size:115
Alignment explanation
Indices: 11825645--11826062 Score: 530
Period size: 113 Copynumber: 3.6 Consensus size: 115
11825635 GTTCTAATTC
* * ** *
11825645 CAAAATTTATCCCTCTACTTTATGAAAATTGAGAAGTT-AGCCTCTTTATTGTTTTTTTTTTTAA
1 CAAAATTGATCCCTCTACTTTATGAAAATTGAAAAGTTAATACTCTATATTG---TTTTTTTT--
*
11825709 AACTAAATGCTCAAGTTGTTATTTCTCCTTTTTC-TTCCAAAACAATGTCTAACTA
61 -ACTAAATGCTCAAGTTGTTATTTCTCCTTTTTCTTTTCAAAACAATGTCTAACTA
*
11825764 CAAAATTGGTCCCTCTACTTTATGAAAATTGAAAAGTTAATAC-CTATATTG-TTTTTTTACTAA
1 CAAAATTGATCCCTCTACTTTATGAAAATTGAAAAGTTAATACTCTATATTGTTTTTTTTACTAA
* *
11825827 A-GCTCAAGTTGTTGTTTCTCCTTTTTTTTTTTCAAAACAATGTCTAACTA
66 ATGCTCAAGTTGTTATTTCTCC-TTTTTCTTTTCAAAACAATGTCTAACTA
* *
11825877 CAAAATTGGTCCCTCTACTTTATGAAAATTGAAAAGTTAGTAC-CTATATTG-TTTTTTTACTAA
1 CAAAATTGATCCCTCTACTTTATGAAAATTGAAAAGTTAATACTCTATATTGTTTTTTTTACTAA
* **
11825940 ATGCTCAAGTTGTTATTTCT-CTTCTTCTTTTCAAAACAATGTCTAAGAA
66 ATGCTCAAGTTGTTATTTCTCCTTTTTCTTTTCAAAACAATGTCTAACTA
* * *
11825989 CATAATCGATCCCTCTACTTTATGAAAATTGAGAAGTTAATACTTCTAT-TGTGTTTTTTTTACT
1 CAAAATTGATCCCTCTACTTTATGAAAATTGAAAAGTTAATAC-TCTATAT-TGTTTTTTTTACT
*
11826053 AAATGTTCAA
64 AAATGCTCAA
11826063 ATTGGGGCGA
Statistics
Matches: 270, Mismatches: 21, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
111 19 0.07
112 73 0.27
113 85 0.31
114 23 0.09
115 26 0.10
119 42 0.16
120 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (115 bp):
CAAAATTGATCCCTCTACTTTATGAAAATTGAAAAGTTAATACTCTATATTGTTTTTTTTACTAA
ATGCTCAAGTTGTTATTTCTCCTTTTTCTTTTCAAAACAATGTCTAACTA
Found at i:11827050 original size:2 final size:2
Alignment explanation
Indices: 11827043--11827079 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11827033 ATCTTAAGGA
11827043 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11827080 ACTAATAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11827441 original size:2 final size:2
Alignment explanation
Indices: 11827434--11827462 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11827424 ACGGATTGAT
11827434 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11827463 TAAAATATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11828625 original size:14 final size:15
Alignment explanation
Indices: 11828601--11828630 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
11828591 GCCTGGGCCC
11828601 AAATAAATAAATCAA
1 AAATAAATAAATCAA
11828616 AAAT-AATAAATCAA
1 AAATAAATAAATCAA
11828630 A
1 A
11828631 TAAAATTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATAAATAAATCAA
Found at i:11829686 original size:3 final size:3
Alignment explanation
Indices: 11829680--11829714 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
11829670 TTTTAAAAAA
*
11829680 ATT ATT ATT ATT ATT ATT ATT GTCT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT A
11829715 GCGTAAGTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.93
4 2 0.07
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:11839008 original size:44 final size:44
Alignment explanation
Indices: 11838870--11839509 Score: 315
Period size: 44 Copynumber: 14.7 Consensus size: 44
11838860 CCGCAAATCC
* * *
11838870 TATCTCCCTGAAGTTGCAGTGGAG-TGTATTGAAGATAACAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAG-ATT-AAAATAACAGATCT
* * * ** *
11838915 TATCCCCCTGAAGTTGCAATGGGGCAGACTGATTAAAGCCAATA-ATCT
1 TATCTCCCTGAAGTTGC-A-GTGG-AG-CAGATTAAA-ATAACAGATCT
* * *
11838963 TATCTCCTTGAAGTTGCAGCGGAGCGGATTAAAATAACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCT
** * * *
11839007 TATCTCTTTGAAGTTGCAG-AGAGCAGA-T--CACAACTAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAAC-AGATCT
* * * **
11839047 TATC-CCCTTGAAGTTGCAGTGGGGCAGACTGAAGATGGC-GAATCT
1 TATCTCCC-TGAAGTTGCAGTGGAGCAGA-TTAAAATAACAG-ATCT
* * ** *
11839092 TATCTCACTGAAGTTGCAGTAGAGCAGATTAAAGCCAATA-ATGC-
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATAACAGAT-CT
* * *
11839136 TATCTCCCTGAAGTTGCAGCGGAGCGGATTAAAATGACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCT
** * * **
11839180 TATCTTTCTGAAGTTGCAG-AGACCAGATT---GCAACTAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAAC-AGATCT
* * * * * **
11839220 TATCCCCCTGAAGTTGCAGTGGGGTAGACTGAAGATGGC-GAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAATAACAG-ATCT
** * *
11839265 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATAACAGATCT
* *
11839309 TATCTCCCTGAAGTTGCAGCGGAGC-GAATTAAAATGACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAATAACAGATCT
* * *** *
11839353 TATCTCTCTGAAGTTGCAGTAGAGCAGA-TCGCAT-CCAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCT
* * *
11839394 TATCTCCCTGAAGTTGCAGTGGAACAGA-CAGAAGA-AACCA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTA-AA-ATAA-CAGATCT
* * * *
11839438 TATCTCCTTAAAGTTGCAGTGGAGCGGATTAAAATTACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCT
** * *
11839482 TATCTCTATGAA-TTGCAATAGAGCAGAT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAT
11839510 CGCATCAAAC
Statistics
Matches: 440, Mismatches: 112, Indels: 88
0.69 0.17 0.14
Matches are distributed among these distances:
39 1 0.00
40 43 0.10
41 42 0.10
42 5 0.01
43 44 0.10
44 188 0.43
45 77 0.17
46 6 0.01
47 4 0.01
48 22 0.05
49 6 0.01
50 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCT
Found at i:11839140 original size:129 final size:130
Alignment explanation
Indices: 11838911--11839154 Score: 282
Period size: 129 Copynumber: 1.9 Consensus size: 130
11838901 AAGATAACAG
*
11838911 GTCTTATCCCCCTGAAGTTGCAATGGGGCAGACTGATTAAAGCCAATAATCTTATCTCCTTGAAG
1 GTCTTATCCCCCTGAAGTTGCAATGGGGCAGACTGA-TAAAGCC-AGAATCTTATCTCCTTGAAG
* * * **
11838976 TTGCAGCGGAGCGGATTAAAATAACAGATCTTATCTCTTTGAAGTTGCAGAGAGCAGATCACAAC
64 TTGCAGCAGAGCAGATTAAAACAACAGATCTTATCTCCCTGAAGTTGCAGAGAGCAGATCACAAC
11839041 TA
129 TA
* * * *
11839043 GTCTTATCCCCTTGAAGTTGCAGTGGGGCAGACTGA-AGATGGC-GAATCTTATCTCAC-TGAAG
1 GTCTTATCCCCCTGAAGTTGCAATGGGGCAGACTGATA-AAGCCAGAATCTTATCTC-CTTGAAG
* * *
11839105 TTGCAGTAGAGCAGATTAAAGCCAATA-ATGC-TATCTCCCTGAAGTTGCAG
64 TTGCAGCAGAGCAGATTAAA-ACAACAGAT-CTTATCTCCCTGAAGTTGCAG
11839155 CGGAGCGGAT
Statistics
Matches: 95, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
129 52 0.55
130 6 0.06
131 3 0.03
132 34 0.36
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (130 bp):
GTCTTATCCCCCTGAAGTTGCAATGGGGCAGACTGATAAAGCCAGAATCTTATCTCCTTGAAGTT
GCAGCAGAGCAGATTAAAACAACAGATCTTATCTCCCTGAAGTTGCAGAGAGCAGATCACAACTA
Found at i:11839395 original size:129 final size:128
Alignment explanation
Indices: 11839262--11839515 Score: 368
Period size: 129 Copynumber: 2.0 Consensus size: 128
11839252 AGATGGCGAA
* * * * *
11839262 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA-AAGCCAA-TAATCCTATCTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGA-CAGAAG-AAACCAATCCTATCTCCCTAAAGTTG
* *
11839325 CAGCGGAGCGAATTAAAATGACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCA
64 CAGCGGAGCGAATTAAAATGACAGATCTTATCTCTATGAA-TTGCAATAGAGCAGATCGCATCCA
11839390 G
128 G
*
11839391 TCTTATCTCCCTGAAGTTGCAGTGGAACAGACAGAAGAAACCAATCCTATCTCCTTAAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCA
* * *
11839456 GTGGAGCGGATTAAAATTACAGATCTTATCTCTATGAATTGCAATAGAGCAGATCGCATC
66 GCGGAGCGAATTAAAATGACAGATCTTATCTCTATGAATTGCAATAGAGCAGATCGCATC
11839516 AAACCTCAGT
Statistics
Matches: 112, Mismatches: 11, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
128 24 0.21
129 88 0.79
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (128 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAACAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCA
GCGGAGCGAATTAAAATGACAGATCTTATCTCTATGAATTGCAATAGAGCAGATCGCATCCAG
Found at i:11839444 original size:173 final size:172
Alignment explanation
Indices: 11838912--11839470 Score: 787
Period size: 173 Copynumber: 3.2 Consensus size: 172
11838902 AGATAACAGG
* * * * *
11838912 TCTTATCCCCCTGAAGTTGCAATGGGGCAGACTGATTAAAGCCAATAATCTTATCTCCTTGAAGT
1 TCTTATCTCCCTGAAGTTGC-A-GTGG-AG-CAGATTAAAGCCAATAATCCTATCTCCCTGAAGT
* * *
11838977 TGCAGCGGAGCGGATTAAAATAACAGATCTTATCTCTTTGAAGTTGCAGAGAGCAGATCACAACT
62 TGCAGCGGAGCGGATTAAAATGACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCAACT
11839042 AGTCTTATCCCCTTGAAGTTGCAGTGGGGCAGACTGAAGATGGCGAA
127 AGTCTTATCCCC-TGAAGTTGCAGTGGGGCAGACTGAAGATGGCGAA
* * *
11839089 TCTTATCTCACTGAAGTTGCAGTAGAGCAGATTAAAGCCAATAATGCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCA
* * *
11839154 GCGGAGCGGATTAAAATGACAGATCTTATCTTTCTGAAGTTGCAGAGACCAGATTGCAACTAGTC
66 GCGGAGCGGATTAAAATGACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCAACTAGTC
*
11839219 TTATCCCCCTGAAGTTGCAGTGGGGTAGACTGAAGATGGCGAA
131 TTAT-CCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCGAA
11839262 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCA
* * *
11839327 GCGGAGCGAATTAAAATGACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGT
66 GCGGAGCGGATTAAAATGACAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCGCAACTAGT
** * ** *
11839392 CTTATCTCCCTGAAGTTGCAGTGGAACAGACAGAAGA-AACCAA
130 CTTATC-CCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCGAA
* * * *
11839435 TCCTATCTCCTTAAAGTTGCAGTGGAGCGGATTAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
11839471 ATTACAGATC
Statistics
Matches: 344, Mismatches: 35, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
173 271 0.79
174 52 0.15
175 2 0.01
176 1 0.00
177 18 0.05
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (172 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCA
GCGGAGCGGATTAAAATGACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCAACTAGTC
TTATCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCGAA
Found at i:11841011 original size:18 final size:18
Alignment explanation
Indices: 11840988--11841022 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
11840978 TTCTTTTTTA
11840988 TATGTAATT-TTATTCTAC
1 TATGT-ATTATTATTCTAC
11841006 TATGTATTATTATTCTA
1 TATGTATTATTATTCTA
11841023 GTTTTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.57
Consensus pattern (18 bp):
TATGTATTATTATTCTAC
Found at i:11844715 original size:26 final size:26
Alignment explanation
Indices: 11844678--11844744 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
11844668 GTGGATTCTC
11844678 CACAGCTCGTGTGAGTAGGCCCATTT
1 CACAGCTCGTGTGAGTAGGCCCATTT
* *
11844704 CACAGCTTGTGTAAGTAGGCCCATTT
1 CACAGCTCGTGTGAGTAGGCCCATTT
11844730 CACAGCTCGTGTGAG
1 CACAGCTCGTGTGAG
11844745 CATTGATGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (26 bp):
CACAGCTCGTGTGAGTAGGCCCATTT
Found at i:11853171 original size:49 final size:50
Alignment explanation
Indices: 11853056--11853179 Score: 133
Period size: 49 Copynumber: 2.5 Consensus size: 50
11853046 TATCCCAGAT
* ** * ** *
11853056 ATGGTCTTACATGGGAGTTCTCATATTGGTGCACATGCCATGTCCTAGGC
1 ATGGTCTTACGTGGGACCTCTCATATCGGTGCACAACCCATGTCCTAGAC
* * * *
11853106 ATGGTCTAATGGGGGACCTCTCATCTCGGTGC-CAACCCATGTCCTAGAC
1 ATGGTCTTACGTGGGACCTCTCATATCGGTGCACAACCCATGTCCTAGAC
*
11853155 ATGGTCTTACGTGGGACCTCCCATA
1 ATGGTCTTACGTGGGACCTCTCATA
11853180 ACCTCAATGA
Statistics
Matches: 58, Mismatches: 16, Indels: 1
0.77 0.21 0.01
Matches are distributed among these distances:
49 34 0.59
50 24 0.41
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.28
Consensus pattern (50 bp):
ATGGTCTTACGTGGGACCTCTCATATCGGTGCACAACCCATGTCCTAGAC
Found at i:11860487 original size:50 final size:50
Alignment explanation
Indices: 11860415--11860581 Score: 129
Period size: 50 Copynumber: 3.2 Consensus size: 50
11860405 TAACCCATAT
* ** * * **
11860415 ATGGTCTTACATGGGAGTTCTCATATTGGTG-CACATGCCATGTCCTAGGC
1 ATGGTCTTACAGGGGACCTCTCATATTGGTGCCA-ACGCCATGTCCCAGAA
* *
11860465 ATGGTCTTACGGGGGACCTCTCATCTTGGTGCCAACGCCATGTCCCAGAA
1 ATGGTCTTACAGGGGACCTCTCATATTGGTGCCAACGCCATGTCCCAGAA
** * * * *
11860515 ATGGTCTTACATAGGACTTCTCATAACCTCAATGATGCCAATGCCATGTCCCAGAC
1 ATGGTCTTACAGGGGACCTCTCAT-A--T---TGGTGCCAACGCCATGTCCCAGAA
11860571 ATGGTCTTACA
1 ATGGTCTTACA
11860582 TGAGATCTCT
Statistics
Matches: 93, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
50 58 0.62
51 2 0.02
53 1 0.01
56 32 0.34
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.28
Consensus pattern (50 bp):
ATGGTCTTACAGGGGACCTCTCATATTGGTGCCAACGCCATGTCCCAGAA
Done.