Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 125 of 163
Found at i:40242414 original size:3 final size:3
Alignment explanation
Indices: 40242406--40242607 Score: 381
Period size: 3 Copynumber: 67.7 Consensus size: 3
40242396 ATTCTCACAA
40242406 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
40242454 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
40242502 AAG AAG AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
40242549 AA- AGAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
40242594 AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AA
40242608 AAATATACGT
Statistics
Matches: 196, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
2 3 0.02
3 192 0.98
4 1 0.01
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40244793 original size:32 final size:32
Alignment explanation
Indices: 40244751--40244862 Score: 102
Period size: 34 Copynumber: 3.4 Consensus size: 32
40244741 ATAAAAATAT
*
40244751 ATAAACTAAATTCCAAATTTATAACTTAAGGA
1 ATAAAATAAATTCCAAATTTATAACTTAAGGA
* ** **
40244783 ATAAAATAAATTTAACC-TATTTA-AAAATAAAAA
1 ATAAAATAAA-TT--CCAAATTTATAACTTAAGGA
40244816 TATATAAACTAAATTCCAAATTTATAACTTAAGGA
1 -ATA-AAA-TAAATTCCAAATTTATAACTTAAGGA
40244851 ATAAAATAAATT
1 ATAAAATAAATT
40244863 TAACCTATTT
Statistics
Matches: 61, Mismatches: 11, Indels: 16
0.69 0.12 0.18
Matches are distributed among these distances:
32 15 0.25
33 13 0.21
34 16 0.26
35 13 0.21
36 4 0.07
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (32 bp):
ATAAAATAAATTCCAAATTTATAACTTAAGGA
Found at i:40244811 original size:68 final size:68
Alignment explanation
Indices: 40244736--40244876 Score: 282
Period size: 68 Copynumber: 2.1 Consensus size: 68
40244726 ACTAAATTCC
40244736 TAAAAATAAAAATATATAAACTAAATTCCAAATTTATAACTTAAGGAATAAAATAAATTTAACCT
1 TAAAAATAAAAATATATAAACTAAATTCCAAATTTATAACTTAAGGAATAAAATAAATTTAACCT
40244801 ATT
66 ATT
40244804 TAAAAATAAAAATATATAAACTAAATTCCAAATTTATAACTTAAGGAATAAAATAAATTTAACCT
1 TAAAAATAAAAATATATAAACTAAATTCCAAATTTATAACTTAAGGAATAAAATAAATTTAACCT
40244869 ATT
66 ATT
40244872 TAAAA
1 TAAAA
40244877 TTACAGTCTC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 73 1.00
ACGTcount: A:0.57, C:0.09, G:0.03, T:0.32
Consensus pattern (68 bp):
TAAAAATAAAAATATATAAACTAAATTCCAAATTTATAACTTAAGGAATAAAATAAATTTAACCT
ATT
Found at i:40244873 original size:34 final size:34
Alignment explanation
Indices: 40244767--40244873 Score: 105
Period size: 34 Copynumber: 3.1 Consensus size: 34
40244757 TAAATTCCAA
40244767 ATTTATAACTTAAGGAATAAAATAAATTTAACCT
1 ATTTATAACTTAAGGAATAAAATAAATTTAACCT
** ** *
40244801 ATTTA-AAAATAAAAATATATAAACTAAA-TT--CCAA
1 ATTTATAACTTAAGGA-ATA-AAA-TAAATTTAACC-T
40244835 ATTTATAACTTAAGGAATAAAATAAATTTAACCT
1 ATTTATAACTTAAGGAATAAAATAAATTTAACCT
40244869 ATTTA
1 ATTTA
40244874 AAATTACAGT
Statistics
Matches: 55, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
32 4 0.07
33 13 0.24
34 21 0.38
35 13 0.24
36 4 0.07
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (34 bp):
ATTTATAACTTAAGGAATAAAATAAATTTAACCT
Found at i:40246031 original size:25 final size:26
Alignment explanation
Indices: 40245991--40246040 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
40245981 CATATATTTA
40245991 AAATTTAGTCCTTTTA-TTTCTTAAG
1 AAATTTAGTCCTTTTACTTTCTTAAG
*
40246016 AAATTTAGTCAC-TTTACTTTGTTAA
1 AAATTTAGTC-CTTTTACTTTCTTAA
40246041 TATTCTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (26 bp):
AAATTTAGTCCTTTTACTTTCTTAAG
Found at i:40261044 original size:19 final size:19
Alignment explanation
Indices: 40261022--40261059 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40261012 AAAATATATG
40261022 ATTTAAATTTTTTATAAAT
1 ATTTAAATTTTTTATAAAT
* *
40261041 ATTTTAATTTTTTTTAAAT
1 ATTTAAATTTTTTATAAAT
40261060 TTTTGTTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTAAATTTTTTATAAAT
Found at i:40272737 original size:11 final size:11
Alignment explanation
Indices: 40272723--40272752 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
40272713 AAAATAAAAA
40272723 TAAAATTATTT
1 TAAAATTATTT
*
40272734 TAAAAGTATTT
1 TAAAATTATTT
40272745 TAAAATTA
1 TAAAATTA
40272753 AAAAATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:40286057 original size:49 final size:49
Alignment explanation
Indices: 40286004--40286107 Score: 138
Period size: 49 Copynumber: 2.1 Consensus size: 49
40285994 GTGGTTATAT
* * *
40286004 GGTCACATGTTGAAGTATAACTAGGG-CTCCCAGTTGACGGCGATTTTGC
1 GGTCACAAGTTGAAGTATAACTAGGGAC-CCCAGTTGACAGCGACTTTGC
* * *
40286053 GGTCACAAGTTGAAGTATAACTCGGGACCCTAGTTGACAGTGACTTTGC
1 GGTCACAAGTTGAAGTATAACTAGGGACCCCAGTTGACAGCGACTTTGC
40286102 GGTCAC
1 GGTCAC
40286108 GGGTTCAAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
49 47 0.98
50 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (49 bp):
GGTCACAAGTTGAAGTATAACTAGGGACCCCAGTTGACAGCGACTTTGC
Found at i:40287833 original size:10 final size:10
Alignment explanation
Indices: 40287815--40287849 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
40287805 ATTTATTAAA
40287815 ATTTAAAAAAT
1 ATTT-AAAAAT
40287826 ATTTAAAAAT
1 ATTTAAAAAT
40287836 ATTTAAAAAT
1 ATTTAAAAAT
40287846 ATTT
1 ATTT
40287850 TTAATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 20 0.83
11 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATTTAAAAAT
Found at i:40287859 original size:20 final size:18
Alignment explanation
Indices: 40287804--40287898 Score: 65
Period size: 20 Copynumber: 5.2 Consensus size: 18
40287794 GTATTTAATT
40287804 AATTTATTAAAATTTAAAA
1 AATTT-TTAAAATTTAAAA
*
40287823 AATATTTAAAAATATTTAAAA
1 AAT-TTT-TAAA-ATTTAAAA
* *
40287844 ATATTTTTAATAATTTTAAT
1 A-ATTTTTAA-AATTTAAAA
*
40287864 GATTTTT--AATTTAAAA
1 AATTTTTAAAATTTAAAA
40287880 AA--TTT-AAATTTAAAA
1 AATTTTTAAAATTTAAAA
40287895 AATT
1 AATT
40287899 AATTAAATGC
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
14 3 0.05
15 11 0.18
16 8 0.13
19 10 0.17
20 13 0.22
21 13 0.22
22 2 0.03
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (18 bp):
AATTTTTAAAATTTAAAA
Found at i:40295420 original size:1 final size:1
Alignment explanation
Indices: 40295414--40295440 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
40295404 TCCAATTTGC
40295414 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
40295441 TTAAACATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:40295589 original size:199 final size:199
Alignment explanation
Indices: 40295249--40295647 Score: 746
Period size: 199 Copynumber: 2.0 Consensus size: 199
40295239 TAGTAAAATG
40295249 TGTTTTGTGCTCATTGCCCTCTTCCTTGTCCTTTTCTCTTTATTTGCTACAACATTCTCAGTTAG
1 TGTTTTGTGCTCATTGCCCTCTTCCTTGTCCTTTTCTCTTTATTTGCTACAACATTCTCAGTTAG
40295314 TGTTCATAGCATAAAATAGCCTTTCAACTCAGGTTGATCTGGCTCTTAATATTTCTTACATAATA
66 TGTTCATAGCATAAAATAGCCTTTCAACTCAGGTTGATCTGGCTCTTAATATTTCTTACATAATA
*
40295379 TGGGGTTATGAACCT-CCGAGAATCCTCCAATTTGCAAAAAAAAAAAAAAAAAAAAAAAAAAATT
131 TGGGGTTATGAACCTCCCGAGAA-CCCCCAATTTGCAAAAAAAAAAAAAAAAAAAAAAAAAAATT
40295443 AAACA
195 AAACA
40295448 TGTTTTGTGCTCATTGCCCTCTTCCTTGTCCTTTTCTCTTTATTTGCTACAACATTCTCAGTTAG
1 TGTTTTGTGCTCATTGCCCTCTTCCTTGTCCTTTTCTCTTTATTTGCTACAACATTCTCAGTTAG
40295513 TGTTCATAGCATAAAATAGCCTTTCAACTCAGGTTGATCTGGCTCTTAATATTTCTTACATAATA
66 TGTTCATAGCATAAAATAGCCTTTCAACTCAGGTTGATCTGGCTCTTAATATTTCTTACATAATA
* * *
40295578 TGGGGTTATGAACCTCCCGAGAACCCCCAATTTGCAAAAAAAAAAAAAAAAAACAGAAAAAATTG
131 TGGGGTTATGAACCTCCCGAGAACCCCCAATTTGCAAAAAAAAAAAAAAAAAAAAAAAAAAATTA
40295643 AACA
196 AACA
40295647 T
1 T
40295648 ACCTATACTG
Statistics
Matches: 195, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
199 188 0.96
200 7 0.04
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (199 bp):
TGTTTTGTGCTCATTGCCCTCTTCCTTGTCCTTTTCTCTTTATTTGCTACAACATTCTCAGTTAG
TGTTCATAGCATAAAATAGCCTTTCAACTCAGGTTGATCTGGCTCTTAATATTTCTTACATAATA
TGGGGTTATGAACCTCCCGAGAACCCCCAATTTGCAAAAAAAAAAAAAAAAAAAAAAAAAAATTA
AACA
Found at i:40304261 original size:18 final size:20
Alignment explanation
Indices: 40304238--40304281 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
40304228 AGTTTTACTT
*
40304238 TTTAAAAATACAAA-AA-TA
1 TTTAAAAATAAAAATAATTA
40304256 TTTAAAAATAAAAATAATTA
1 TTTAAAAATAAAAATAATTA
40304276 TTTAAA
1 TTTAAA
40304282 TATTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.57
19 2 0.09
20 8 0.35
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
TTTAAAAATAAAAATAATTA
Found at i:40305291 original size:59 final size:59
Alignment explanation
Indices: 40305223--40305339 Score: 189
Period size: 59 Copynumber: 2.0 Consensus size: 59
40305213 ATGATTTAAT
* *
40305223 GAAGGAGTATTAAATTTAAACAATGTTAGTGATTACAATAAAAATTACTAAAACAAAAC
1 GAAGGAGTATTAAATTTAAACAACGTTAGTGATTACAATAAAAATAACTAAAACAAAAC
* * *
40305282 GAAGGAGTATTAAATTTCAATAACGTTAGTGATTACAATAAATATAACTAAAACAAAA
1 GAAGGAGTATTAAATTTAAACAACGTTAGTGATTACAATAAAAATAACTAAAACAAAA
40305340 ATATGTATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (59 bp):
GAAGGAGTATTAAATTTAAACAACGTTAGTGATTACAATAAAAATAACTAAAACAAAAC
Found at i:40316498 original size:17 final size:16
Alignment explanation
Indices: 40316476--40316518 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
40316466 AAATAGTCTA
*
40316476 AATTAAATTTGTTTATT
1 AATTAAATTT-TTAATT
40316493 AATTAAAATTTTTAATT
1 AATT-AAATTTTTAATT
*
40316510 CATTAAATT
1 AATTAAATT
40316519 GAATTTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 12 0.52
18 6 0.26
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (16 bp):
AATTAAATTTTTAATT
Found at i:40325568 original size:21 final size:20
Alignment explanation
Indices: 40325544--40325585 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
40325534 TGAGAAAAAA
40325544 AAATTTATGAGTTTAAAA-ATG
1 AAATTTAT-A-TTTAAAATATG
40325565 AAATTTATATTTAAAATATG
1 AAATTTATATTTAAAATATG
40325585 A
1 A
40325586 GTAAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 5 0.25
21 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (20 bp):
AAATTTATATTTAAAATATG
Found at i:40327009 original size:9 final size:9
Alignment explanation
Indices: 40326995--40327081 Score: 66
Period size: 9 Copynumber: 9.4 Consensus size: 9
40326985 NNNNNNNNNN
40326995 TTATGTAAG
1 TTATGTAAG
*
40327004 TTATGTAAC
1 TTATGTAAG
** * *
40327013 CCATTGAAAT
1 TTA-TGTAAG
*
40327023 TTATGTAGG
1 TTATGTAAG
40327032 TTATGTAAG
1 TTATGTAAG
40327041 TTATGTAAG
1 TTATGTAAG
* *
40327050 TTATTTAAT
1 TTATGTAAG
*
40327059 TTATGCAAG
1 TTATGTAAG
*
40327068 TTTATGTAAA
1 -TTATGTAAG
40327078 TTAT
1 TTAT
40327082 TTAATTTACT
Statistics
Matches: 58, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
9 46 0.79
10 12 0.21
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:40327081 original size:28 final size:27
Alignment explanation
Indices: 40327032--40327089 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
40327022 TTTATGTAGG
* *
40327032 TTATGTAAGTTATGTAAGTTATTTAAT
1 TTATGCAAGTTATGTAAATTATTTAAT
40327059 TTATGCAAGTTTATGTAAATTATTTAAT
1 TTATGCAAG-TTATGTAAATTATTTAAT
40327087 TTA
1 TTA
40327090 CTTTACGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (27 bp):
TTATGCAAGTTATGTAAATTATTTAAT
Found at i:40327094 original size:23 final size:25
Alignment explanation
Indices: 40327041--40327104 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 25
40327031 GTTATGTAAG
40327041 TTATGTAAGTTATTTAATTTATGCAAGT
1 TTATGTAAGTTATTTAATTTA-GC-A-T
*
40327069 TTATGTAAATTATTTAATTTA-C-T
1 TTATGTAAGTTATTTAATTTAGCAT
*
40327092 TTACGTAAGTTAT
1 TTATGTAAGTTAT
40327105 ATATTACGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 12 0.36
26 1 0.03
28 20 0.61
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.52
Consensus pattern (25 bp):
TTATGTAAGTTATTTAATTTAGCAT
Found at i:40336153 original size:17 final size:16
Alignment explanation
Indices: 40336120--40336160 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
40336110 ATATATTTTT
*
40336120 TATTTTTAATCAAATA
1 TATTTTTAATAAAATA
*
40336136 TATTTTTATTAAATATA
1 TATTTTTAATAAA-ATA
40336153 TATTTTTA
1 TATTTTTA
40336161 GACTTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTTTAATAAAATA
Found at i:40341752 original size:15 final size:17
Alignment explanation
Indices: 40341734--40341766 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
40341724 ATTAATCAAA
40341734 TATATTAA-ATT-ATTT
1 TATATTAAGATTAATTT
40341749 TATATTAAGATTAATTT
1 TATATTAAGATTAATTT
40341766 T
1 T
40341767 TTTATTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TATATTAAGATTAATTT
Found at i:40343621 original size:22 final size:21
Alignment explanation
Indices: 40343590--40343656 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
40343580 TAATGATTTC
40343590 TTTTA-AATTTTCAAAATTATT
1 TTTTATAATTTT-AAAATTATT
* *
40343611 TTTTATAATTTAAAAAATTATA
1 TTTTATAATTT-TAAAATTATT
* *
40343633 ATTTATGGATTTTAAAATT-TT
1 TTTTAT-AATTTTAAAATTATT
40343654 TTT
1 TTT
40343657 AAAATATTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
21 8 0.22
22 24 0.67
23 4 0.11
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTTATAATTTTAAAATTATT
Found at i:40345005 original size:22 final size:22
Alignment explanation
Indices: 40344954--40345009 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
40344944 TAAAATTATG
40344954 AAATTATAATTTAATACATAAT
1 AAATTATAATTTAATACATAAT
*
40344976 AAACTTATATTTTAAT-CTATGAA-
1 AAA-TTATAATTTAATAC-AT-AAT
40344999 AAATTATAATT
1 AAATTATAATT
40345010 AAATTTTGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 11 0.38
23 16 0.55
24 2 0.07
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATTATAATTTAATACATAAT
Found at i:40348252 original size:23 final size:23
Alignment explanation
Indices: 40348222--40348286 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
40348212 NNNNNNTATC
40348222 GAGCTGAAACGGTAAGCTCCGTA
1 GAGCTGAAACGGTAAGCTCCGTA
*
40348245 GAGCTGAAACGGTAAGCTCCGTC
1 GAGCTGAAACGGTAAGCTCCGTA
* *
40348268 GAGTTGAAACGGTAGGCTC
1 GAGCTGAAACGGTAAGCTC
40348287 ATACAAGCTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.22, G:0.32, T:0.18
Consensus pattern (23 bp):
GAGCTGAAACGGTAAGCTCCGTA
Found at i:40358668 original size:31 final size:32
Alignment explanation
Indices: 40358620--40358681 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
40358610 TTTTTTAAAG
*
40358620 TTAAATTCGACTCTCAAT-TTTTAATAAAGAA
1 TTAAATTCGACTCTCAATATTTTAAAAAAGAA
*
40358651 TTAAATTTGA-TCATCAATATTTTAAAAAAGA
1 TTAAATTCGACTC-TCAATATTTTAAAAAAGA
40358682 GTCCAAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 2 0.07
31 14 0.52
32 11 0.41
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (32 bp):
TTAAATTCGACTCTCAATATTTTAAAAAAGAA
Found at i:40359821 original size:25 final size:25
Alignment explanation
Indices: 40359786--40359861 Score: 89
Period size: 26 Copynumber: 3.0 Consensus size: 25
40359776 CGGCCTGGCC
* *
40359786 CATTTTTAAAATAAACATTAAAAAT
1 CATTTTAAAAATAAAAATTAAAAAT
* *
40359811 TATTTTAAAAATAAAAACTAAAAAAT
1 CATTTTAAAAATAAAAA-TTAAAAAT
* *
40359837 CATTTTAAAATTAAAAAATAAAAAT
1 CATTTTAAAAATAAAAATTAAAAAT
40359862 AAAAATATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 20 0.48
26 22 0.52
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (25 bp):
CATTTTAAAAATAAAAATTAAAAAT
Found at i:40360365 original size:16 final size:16
Alignment explanation
Indices: 40360344--40360379 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
40360334 AAGCATATAT
40360344 ATCAACTTTGATTTAG
1 ATCAACTTTGATTTAG
40360360 ATCAACTTTGATTTAG
1 ATCAACTTTGATTTAG
40360376 ATCA
1 ATCA
40360380 GATATCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (16 bp):
ATCAACTTTGATTTAG
Found at i:40360658 original size:29 final size:27
Alignment explanation
Indices: 40360586--40360659 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 27
40360576 ACCCAGTTTG
*
40360586 AATATATTATGTTATAAAAATATTATATT
1 AATAT-TTATGTTA-AATAATATTATATT
*
40360615 AATTATATATG-TAAATAATAATGTATATT
1 AA-TATTTATGTTAAATAAT-AT-TATATT
*
40360644 TATATTTATGTTAAAT
1 AATATTTATGTTAAAT
40360660 CACGTATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 5 0.14
28 11 0.30
29 18 0.49
30 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (27 bp):
AATATTTATGTTAAATAATATTATATT
Found at i:40364302 original size:40 final size:41
Alignment explanation
Indices: 40364258--40364355 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 41
40364248 ACAAAAAAGC
* **
40364258 GAGCATTAGCGGCGATTTAGCCA-AAGCGCAGCTAAAGGTA
1 GAGCATTAGCGGCGATTTACCCAGAAGCGCAGCTAAAAATA
* *
40364298 GAGCATCAGCGGCGATTT-CCCAGAAGCGCCGCTAAAAATA
1 GAGCATTAGCGGCGATTTACCCAGAAGCGCAGCTAAAAATA
* *
40364338 G-GAATTAGCGGCGTTTTA
1 GAGCATTAGCGGCGATTTA
40364356 TATAAAGCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 16 0.33
40 32 0.67
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (41 bp):
GAGCATTAGCGGCGATTTACCCAGAAGCGCAGCTAAAAATA
Found at i:40364551 original size:82 final size:82
Alignment explanation
Indices: 40364404--40364633 Score: 284
Period size: 82 Copynumber: 2.8 Consensus size: 82
40364394 TTTTGCGATT
* *
40364404 TTCTTTGGCCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATTCTCTGGCCTTTAGCGGCATTTT
1 TTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGGCCTTTAGCGGCATTTT
* * *
40364469 TATCTGAGCGCCGCTAA
66 TAACTGAGCGCCACGAA
* * * *
40364486 TTCTCTGGCCTTTGGCGGCGTTTTTATATAAGCGCCGCTAATGCTC-GGATCTTTAGCGGCGTTT
1 TTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGG-CCTTTAGCGGCATTT
40364550 TTAACTGAGCGCCACGAA
65 TTAACTGAGCGCCACGAA
* * * * ** *
40364568 TTCTCTTGTCTTTAGCGGCGTTTGTAGCTAAGCGCCGCTAATGCAT-TTACCTTTAGCGGCCTTT
1 TTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGC-TCTGGCCTTTAGCGGCATTT
40364632 TT
65 TT
40364634 GCAAAAGCGC
Statistics
Matches: 126, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
81 2 0.02
82 123 0.98
83 1 0.01
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.37
Consensus pattern (82 bp):
TTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGGCCTTTAGCGGCATTTT
TAACTGAGCGCCACGAA
Found at i:40364627 original size:41 final size:41
Alignment explanation
Indices: 40364404--40364609 Score: 261
Period size: 41 Copynumber: 5.0 Consensus size: 41
40364394 TTTTGCGATT
*
40364404 TTCTTTGGCCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAA
1 TTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAA
* *
40364445 TTCTCTGGCCTTTAGCGGCATTTTTATCTGAGCGCCGCTAA
1 TTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAA
* *
40364486 TTCTCTGGCCTTTGGCGGCGTTTTTATATAAGCGCCGCTAA
1 TTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAA
* * * * * *
40364527 TGCTC-GGATCTTTAGCGGCGTTTTTAACTGAGCGCCACGAA
1 TTCTCTGG-CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAA
* * * *
40364568 TTCTCTTGTCTTTAGCGGCGTTTGTAGCTAAGCGCCGCTAA
1 TTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAA
40364609 T
1 T
40364610 GCATTTACCT
Statistics
Matches: 141, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
40 2 0.01
41 138 0.98
42 1 0.01
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.36
Consensus pattern (41 bp):
TTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAA
Found at i:40364633 original size:123 final size:123
Alignment explanation
Indices: 40364413--40364650 Score: 298
Period size: 123 Copynumber: 1.9 Consensus size: 123
40364403 TTTCTTTGGC
* * * * * *
40364413 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATTCTCTGGCCTTTAGCGGCATTTTTATCTGAGC
1 CTTTAGCGGCGTTTTTAACTAAGCGCCACGAATTCTCTGGCCTTTAGCGGCATTTGTAGCTAAGC
* * * * * *
40364478 GCCGCTAATTCTCTGGCCTTTGGCGGCGTTTTTATATAAGCGCCGCTAATGCTCGGAT
66 GCCGCTAATGCTCTGACCTTTAGCGGCCTTTTTACAAAAGCGCCGCTAATGCTCGGAT
* * * *
40364536 CTTTAGCGGCGTTTTTAACTGAGCGCCACGAATTCTCTTGTCTTTAGCGGCGTTTGTAGCTAAGC
1 CTTTAGCGGCGTTTTTAACTAAGCGCCACGAATTCTCTGGCCTTTAGCGGCATTTGTAGCTAAGC
* *
40364601 GCCGCTAATGCAT-TTACCTTTAGCGGCCTTTTTGCAAAAGCGCCGCTAAT
66 GCCGCTAATGC-TCTGACCTTTAGCGGCCTTTTTACAAAAGCGCCGCTAAT
40364651 AGTAACAAAA
Statistics
Matches: 96, Mismatches: 18, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
123 95 0.99
124 1 0.01
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.34
Consensus pattern (123 bp):
CTTTAGCGGCGTTTTTAACTAAGCGCCACGAATTCTCTGGCCTTTAGCGGCATTTGTAGCTAAGC
GCCGCTAATGCTCTGACCTTTAGCGGCCTTTTTACAAAAGCGCCGCTAATGCTCGGAT
Found at i:40365191 original size:14 final size:14
Alignment explanation
Indices: 40365125--40365192 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
40365115 TACGGGGTAT
*
40365125 AGATTTAAGGTTTG
1 AGATTTAGGGTTTG
* *
40365139 GGATTTAAGG-TT-
1 AGATTTAGGGTTTG
*
40365151 A-ATTTAGGGGTTAG
1 AGATTTA-GGGTTTG
*
40365165 AGGTTTAAGGGTTTG
1 AGATTT-AGGGTTTG
40365180 AGATTTAGGGTTT
1 AGATTTAGGGTTT
40365193 CAACGGTCAT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
11 5 0.12
12 2 0.05
13 3 0.07
14 17 0.40
15 14 0.33
16 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (14 bp):
AGATTTAGGGTTTG
Found at i:40367834 original size:21 final size:21
Alignment explanation
Indices: 40367810--40367863 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
40367800 AGAGGCGGCT
*
40367810 GCGAGGGAAGCAAAGGCTACA
1 GCGAGAGAAGCAAAGGCTACA
*
40367831 GCGAGAGAAGCAGAGGCTACA
1 GCGAGAGAAGCAAAGGCTACA
* *
40367852 GAGAGAAAAGCA
1 GCGAGAGAAGCA
40367864 GCAAGAAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.43, C:0.17, G:0.37, T:0.04
Consensus pattern (21 bp):
GCGAGAGAAGCAAAGGCTACA
Found at i:40368571 original size:41 final size:43
Alignment explanation
Indices: 40368514--40368607 Score: 147
Period size: 41 Copynumber: 2.2 Consensus size: 43
40368504 NNNNNNNNNG
40368514 CCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTC-TAAGCA
1 CCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCGTAAGCA
*
40368555 CCGCTAAAGAACATGATTTTTAGCGGCGTTTTTTTCTGTAAGCA
1 CCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC-GTAAGCA
*
40368599 CCGCAAAAG
1 CCGCTAAAG
40368608 TTAGCGACAT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
41 27 0.56
42 7 0.15
44 14 0.29
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (43 bp):
CCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCGTAAGCA
Found at i:40371363 original size:189 final size:190
Alignment explanation
Indices: 40371152--40371530 Score: 751
Period size: 189 Copynumber: 2.0 Consensus size: 190
40371142 TATAGAAATA
40371152 TTAAATATATTTTTCTTATAGATTCTTTTACAGTAAAGTTGTAATGATTATAACGAAATTAGAAT
1 TTAAATATATTTTTCTTATAGATTCTTTTACAGTAAAGTTGTAATGATTATAACGAAATTAGAAT
40371217 TGAGTTGAAAAAAAATTTTAACTAGAAAATTAATTAATTAAAATTAATTTATGATGTTTATTTTG
66 TGAGTTGAAAAAAAATTTTAACTAGAAAATTAATTAATTAAAATTAATTTATGATGTTTATTTTG
40371282 GAAAAAAAAAAAACAATTATTGGGTTGAATTGAATTATAAAGTATTAGGTTAAAAGTCAG
131 GAAAAAAAAAAAACAATTATTGGGTTGAATTGAATTATAAAGTATTAGGTTAAAAGTCAG
40371342 TTAAATATA-TTTTCTTATAGATTCTTTTACAGTAAAGTTGTAATGATTATAACGAAATTAGAAT
1 TTAAATATATTTTTCTTATAGATTCTTTTACAGTAAAGTTGTAATGATTATAACGAAATTAGAAT
40371406 TGAGTTGAAAAAAAATTTTAACTAGAAAATTAATTAATTAAAATTAATTTATGATGTTTATTTTG
66 TGAGTTGAAAAAAAATTTTAACTAGAAAATTAATTAATTAAAATTAATTTATGATGTTTATTTTG
40371471 GAAAAAAAAAAAACAATTATTGGGTTGAATTGAATTATAAAGTATTAGGTTAAAAGTCAG
131 GAAAAAAAAAAAACAATTATTGGGTTGAATTGAATTATAAAGTATTAGGTTAAAAGTCAG
40371531 GAAGCACTTA
Statistics
Matches: 189, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
189 180 0.95
190 9 0.05
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.39
Consensus pattern (190 bp):
TTAAATATATTTTTCTTATAGATTCTTTTACAGTAAAGTTGTAATGATTATAACGAAATTAGAAT
TGAGTTGAAAAAAAATTTTAACTAGAAAATTAATTAATTAAAATTAATTTATGATGTTTATTTTG
GAAAAAAAAAAAACAATTATTGGGTTGAATTGAATTATAAAGTATTAGGTTAAAAGTCAG
Found at i:40383440 original size:2 final size:2
Alignment explanation
Indices: 40383427--40383462 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
40383417 AGGTTGTGAG
*
40383427 AT AT AT AC AT 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 AT AT
40383463 CTGTATGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:40401666 original size:94 final size:93
Alignment explanation
Indices: 40401543--40401722 Score: 229
Period size: 94 Copynumber: 1.9 Consensus size: 93
40401533 CAATTTACAT
* *
40401543 TAATTGAAGAAAACATCATAAGCCATCAATTTGGATTCCACTCCGTATGTGAAATATTGAAATTG
1 TAATTGAAGAAAACATCATAAGCCATCAATTTGGATTCCACTCCATATGTGAAATATTCAAA-TG
*
40401608 -TTTTTTGGACAGTTCATATTCCTTTTATAC
65 ATTTTTT-GACAGTT-AAATTCCTTTTATAC
* * * *** *
40401638 TAATTGAAG-AAACGTCATAAGCCGTCAATTTGTATTCTTTTGCATATGTGAAATATTCAAATGA
1 TAATTGAAGAAAACATCATAAGCCATCAATTTGGATTCCACTCCATATGTGAAATATTCAAATGA
40401702 TTTTTTGACAGTTAAATTCCT
66 TTTTTTGACAGTTAAATTCCT
40401723 ATCAATTGAT
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
92 7 0.09
93 9 0.12
94 49 0.66
95 9 0.12
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (93 bp):
TAATTGAAGAAAACATCATAAGCCATCAATTTGGATTCCACTCCATATGTGAAATATTCAAATGA
TTTTTTGACAGTTAAATTCCTTTTATAC
Found at i:40407540 original size:21 final size:19
Alignment explanation
Indices: 40407475--40407568 Score: 152
Period size: 19 Copynumber: 4.8 Consensus size: 19
40407465 AATTTTTGAG
40407475 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
40407494 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
40407513 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40407532 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
40407553 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
40407569 AGATATGATT
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
19 51 0.73
21 19 0.27
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40407550 original size:40 final size:38
Alignment explanation
Indices: 40407475--40407575 Score: 152
Period size: 40 Copynumber: 2.7 Consensus size: 38
40407465 AATTTTTGAG
40407475 GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
*
40407513 GATATGCAATCTTAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATG--ATATGCAATCCTAGATAT
*
40407553 GATATGTAATCTTAGA-A-GATATG
1 GATATGCAATCTTAGATATGATATG
40407576 ATTTTGTAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
36 5 0.08
38 21 0.36
39 1 0.02
40 32 0.54
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
Found at i:40407587 original size:23 final size:22
Alignment explanation
Indices: 40407507--40407591 Score: 81
Period size: 21 Copynumber: 4.0 Consensus size: 22
40407497 ATGCAATCCT
*
40407507 AGATATGATATGCAATCTTAG-
1 AGATATGATATGTAATCTTAGA
* *
40407528 ATATGAT-ATATGCAATCTT---
1 AGAT-ATGATATGTAATCTTAGA
40407547 AGATATGATATGTAATCTTAGA
1 AGATATGATATGTAATCTTAGA
*
40407569 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGTAATCTTAGA
40407592 GATTTAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.04
19 14 0.26
21 15 0.28
22 10 0.19
23 13 0.24
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (22 bp):
AGATATGATATGTAATCTTAGA
Found at i:40407601 original size:22 final size:23
Alignment explanation
Indices: 40407557--40407601 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40407547 AGATATGATA
*
40407557 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
40407580 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
40407602 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:40412914 original size:16 final size:15
Alignment explanation
Indices: 40412890--40412934 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
40412880 GTTCAGATTC
40412890 AAAAAAAAAAATAAA
1 AAAAAAAAAAATAAA
* *
40412905 GAACAAAAAAAACAAA
1 -AAAAAAAAAAATAAA
40412921 AAAAAAGAAAAATA
1 AAAAAA-AAAAATA
40412935 GAGAGGCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.87, C:0.04, G:0.04, T:0.04
Consensus pattern (15 bp):
AAAAAAAAAAATAAA
Found at i:40415692 original size:132 final size:132
Alignment explanation
Indices: 40415270--40416169 Score: 1630
Period size: 132 Copynumber: 6.8 Consensus size: 132
40415260 NNNNNNNNNN
40415270 AGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
1 AGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
*
40415335 TAGG-CAACAATGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
66 T-GGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
40415399 CGA
130 CGA
40415402 AGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAG-CAGTAATTCTACTTCCC
1 AGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
* *
40415466 TGGA-AACAGTGGAATAGATTGAATATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
66 TGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
40415530 GA
131 GA
40415532 AGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
1 AGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
40415597 TGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
66 TGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
40415662 GA
131 GA
40415664 AGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
1 AGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
40415729 TGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
66 TGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
40415794 GA
131 GA
40415796 AGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
1 AGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
40415861 TGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
66 TGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
40415926 GA
131 GA
40415928 AGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
1 AGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
*
40415993 TGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATC
66 TGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
40416058 GA
131 GA
* * * *
40416060 AGATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGTCAGTAATCCTA-TCTCC
1 AGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCC
* * * *
40416124 CTAGTCAGCAGTGGAATAGATTGAAGATTGTAAG-TCTTATCTCCCT
65 CTGGACAACAGTGGAATAGATTGAAGATT-TCAGATCTTATCTCCCT
40416170 GTAGTTGCAG
Statistics
Matches: 749, Mismatches: 14, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
130 108 0.14
131 40 0.05
132 598 0.80
133 3 0.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (132 bp):
AGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
TGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
GA
Found at i:40416147 original size:43 final size:44
Alignment explanation
Indices: 40416089--40416207 Score: 120
Period size: 43 Copynumber: 2.7 Consensus size: 44
40416079 CCTGTGGTTA
* *
40416089 CAGTGGAGTACATTGAAGTCAGTAA-TCCTATCTCCC-TAGTCAG
1 CAGTGGAATAGATTGAAGTCAGTAACTCCTATCTCCCGTAGT-AG
* * * *
40416132 CAGTGGAATAGATTGAAGAT-TGTAAGTCTTATCTCCCTGTAGTTG
1 CAGTGGAATAGATTGAAG-TCAGTAACTCCTATCTCCC-GTAGTAG
*
40416177 CAGTGGAATAGATTGAAG-CACTAACTCCTAT
1 CAGTGGAATAGATTGAAGTCAGTAACTCCTAT
40416208 ACTTTTGAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
43 20 0.32
44 19 0.31
45 19 0.31
46 4 0.06
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (44 bp):
CAGTGGAATAGATTGAAGTCAGTAACTCCTATCTCCCGTAGTAG
Found at i:40416446 original size:43 final size:42
Alignment explanation
Indices: 40416398--40416479 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 42
40416388 AATTTTTGAG
**
40416398 GATATGCAATCTTATTAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGAAGATATGAT-TATGCAATCTTAGATAT
* * *
40416441 GATATGTAATCTTAGAAGATATGATTTTGTAATCTTAGA
1 GATATGCAATCTTAGAAGATATGATTATGCAATCTTAGA
40416480 GATTTAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
42 12 0.35
43 22 0.65
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (42 bp):
GATATGCAATCTTAGAAGATATGATTATGCAATCTTAGATAT
Found at i:40416451 original size:19 final size:19
Alignment explanation
Indices: 40416412--40416479 Score: 64
Period size: 19 Copynumber: 3.3 Consensus size: 19
40416402 TGCAATCTTA
*
40416412 TTAGATATGATATATGCAATC
1 TTAGATATG--ATATGTAATC
40416433 TTAGATATGATATGTAATC
1 TTAGATATGATATGTAATC
*
40416452 TTAGAAGATATGATTTTGTAATC
1 TT---AGATATGA-TATGTAATC
40416475 TTAGA
1 TTAGA
40416480 GATTTAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
19 11 0.27
20 3 0.07
21 9 0.22
22 8 0.20
23 10 0.24
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.41
Consensus pattern (19 bp):
TTAGATATGATATGTAATC
Found at i:40416475 original size:23 final size:22
Alignment explanation
Indices: 40416435--40416479 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
40416425 ATGCAATCTT
40416435 AGATATGATATGTAATCTTAGA
1 AGATATGATATGTAATCTTAGA
*
40416457 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGTAATCTTAGA
40416480 GATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (22 bp):
AGATATGATATGTAATCTTAGA
Found at i:40416489 original size:22 final size:23
Alignment explanation
Indices: 40416445--40416489 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40416435 AGATATGATA
*
40416445 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
40416468 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
40416490 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:40427316 original size:90 final size:90
Alignment explanation
Indices: 40427163--40427339 Score: 309
Period size: 90 Copynumber: 2.0 Consensus size: 90
40427153 GTGCGTCAGC
* *
40427163 GTTCATAGATTGGGTTTAGGCCAAATTGGGTTTGGGTGTATGGTGTTAGCACCACCAGTAAAAAA
1 GTTCATAGATCGAGTTTAGGCCAAATTGGGTTTGGGTGTATGGTGTTAGCACCACCAGTAAAAAA
40427228 TGATGTATCCACTGGTGCAGTGAGT
66 TGATGTATCCACTGGTGCAGTGAGT
* *
40427253 GTTCATAGATCGAGTTTAGGCCAAATTTGGTTTGGGTGTATGGTGTTAGCACCATCAGTAAAAAA
1 GTTCATAGATCGAGTTTAGGCCAAATTGGGTTTGGGTGTATGGTGTTAGCACCACCAGTAAAAAA
*
40427318 TGATGTATCCATTGGTGCAGTG
66 TGATGTATCCACTGGTGCAGTG
40427340 TTCACTAACT
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (90 bp):
GTTCATAGATCGAGTTTAGGCCAAATTGGGTTTGGGTGTATGGTGTTAGCACCACCAGTAAAAAA
TGATGTATCCACTGGTGCAGTGAGT
Found at i:40430556 original size:21 final size:21
Alignment explanation
Indices: 40430532--40430573 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40430522 CTTTTTGTTC
*
40430532 AATTAATTATCGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
**
40430553 AATTTCTTAACGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
40430574 TACTTATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
AATTAATTAACGAAACTTTAA
Found at i:40434482 original size:20 final size:20
Alignment explanation
Indices: 40434448--40434485 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40434438 TGACCACTTC
40434448 GTAATAAAACAATAACATAA
1 GTAATAAAACAATAACATAA
40434468 GTAACTAAAAC-ATAACAT
1 GTAA-TAAAACAATAACAT
40434486 TTTAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.61, C:0.13, G:0.05, T:0.21
Consensus pattern (20 bp):
GTAATAAAACAATAACATAA
Found at i:40437332 original size:22 final size:22
Alignment explanation
Indices: 40437298--40437478 Score: 209
Period size: 22 Copynumber: 8.2 Consensus size: 22
40437288 AAGTAAAAAT
*
40437298 TGTTGATTAAATGCTGTCCAAA
1 TGTTGATTAAATGTTGTCCAAA
* * *
40437320 TATTGATTGAATGTTGTCCAAT
1 TGTTGATTAAATGTTGTCCAAA
* *
40437342 TGTTGATTAAATGCTGTTCAAA
1 TGTTGATTAAATGTTGTCCAAA
* * * *
40437364 TGTTGATTTAATGCTATCCAAT
1 TGTTGATTAAATGTTGTCCAAA
*
40437386 TGTTGATTGAATGTTGTCCAAA
1 TGTTGATTAAATGTTGTCCAAA
* * *
40437408 TGTTGATTGAATGTTGTCTAAT
1 TGTTGATTAAATGTTGTCCAAA
40437430 TGTTGATTAAATGTTGTCCAAA
1 TGTTGATTAAATGTTGTCCAAA
* **
40437452 TGTTAATTAAATGTTGTCTGAA
1 TGTTGATTAAATGTTGTCCAAA
40437474 TGTTG
1 TGTTG
40437479 GATAATTGCT
Statistics
Matches: 133, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 133 1.00
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (22 bp):
TGTTGATTAAATGTTGTCCAAA
Found at i:40437376 original size:11 final size:11
Alignment explanation
Indices: 40437298--40437467 Score: 75
Period size: 11 Copynumber: 15.5 Consensus size: 11
40437288 AAGTAAAAAT
40437298 TGTTGATTAAA
1 TGTTGATTAAA
* *
40437309 TGCTG-TCCAAA
1 TGTTGAT-TAAA
* *
40437320 TATTGATTGAA
1 TGTTGATTAAA
* *
40437331 TGTTG-TCCAAT
1 TGTTGAT-TAAA
40437342 TGTTGATTAAA
1 TGTTGATTAAA
*
40437353 TGCTG-TTCAAA
1 TGTTGATT-AAA
*
40437364 TGTTGATTTAA
1 TGTTGATTAAA
* * *
40437375 TGCT-ATCCAAT
1 TGTTGAT-TAAA
*
40437386 TGTTGATTGAA
1 TGTTGATTAAA
*
40437397 TGTTG-TCCAAA
1 TGTTGAT-TAAA
*
40437408 TGTTGATTGAA
1 TGTTGATTAAA
*
40437419 TGTTG-TCTAAT
1 TGTTGAT-TAAA
40437430 TGTTGATTAAA
1 TGTTGATTAAA
*
40437441 TGTTG-TCCAAA
1 TGTTGAT-TAAA
*
40437452 TGTTAATTAAA
1 TGTTGATTAAA
40437463 TGTTG
1 TGTTG
40437468 TCTGAATGTT
Statistics
Matches: 111, Mismatches: 34, Indels: 28
0.64 0.20 0.16
Matches are distributed among these distances:
10 9 0.08
11 93 0.84
12 9 0.08
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.44
Consensus pattern (11 bp):
TGTTGATTAAA
Found at i:40437475 original size:11 final size:11
Alignment explanation
Indices: 40437395--40437478 Score: 66
Period size: 11 Copynumber: 7.6 Consensus size: 11
40437385 TTGTTGATTG
*
40437395 AATGTTGTCCA
1 AATGTTGTCTA
*
40437406 AATGTTGAT-TG
1 AATGTTG-TCTA
40437417 AATGTTGTCTA
1 AATGTTGTCTA
*
40437428 ATTGTTGAT-TA
1 AATGTTG-TCTA
*
40437439 AATGTTGTCCA
1 AATGTTGTCTA
*
40437450 AATGTTAAT-TA
1 AATGTT-GTCTA
*
40437461 AATGTTGTCTG
1 AATGTTGTCTA
40437472 AATGTTG
1 AATGTTG
40437479 GATAATTGCT
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
10 3 0.05
11 51 0.89
12 3 0.05
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (11 bp):
AATGTTGTCTA
Found at i:40437478 original size:44 final size:44
Alignment explanation
Indices: 40437295--40437469 Score: 251
Period size: 44 Copynumber: 4.0 Consensus size: 44
40437285 TTGAAGTAAA
*
40437295 AATTGTTGATTAAATGCTGTCCAAATATTGATTGAATGTTGTCC
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGTTGTCC
* * * *
40437339 AATTGTTGATTAAATGCTGTTCAAATGTTGATTTAATGCTATCC
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGTTGTCC
* * *
40437383 AATTGTTGATTGAATGTTGTCCAAATGTTGATTGAATGTTGTCT
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGTTGTCC
* * *
40437427 AATTGTTGATTAAATGTTGTCCAAATGTTAATTAAATGTTGTC
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGTTGTC
40437470 TGAATGTTGG
Statistics
Matches: 116, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 116 1.00
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.43
Consensus pattern (44 bp):
AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGTTGTCC
Found at i:40442376 original size:32 final size:32
Alignment explanation
Indices: 40442335--40442398 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
40442325 TAGTACTCAA
40442335 GATCAATCATTGTCATGTAACTTTGTTTATCT
1 GATCAATCATTGTCATGTAACTTTGTTTATCT
40442367 GATCAATCATTGTCATGTAACTTTGTTTATCT
1 GATCAATCATTGTCATGTAACTTTGTTTATCT
40442399 ACATACTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (32 bp):
GATCAATCATTGTCATGTAACTTTGTTTATCT
Found at i:40447531 original size:13 final size:13
Alignment explanation
Indices: 40447513--40447537 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40447503 AGGTAAAATA
40447513 TTAAAAATATATT
1 TTAAAAATATATT
40447526 TTAAAAATATAT
1 TTAAAAATATAT
40447538 ATAATTAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAAAATATATT
Found at i:40453185 original size:25 final size:24
Alignment explanation
Indices: 40452999--40453189 Score: 84
Period size: 25 Copynumber: 7.6 Consensus size: 24
40452989 CCCAGATCTC
* * *
40452999 GCCACAAAGGCATTTCAGATAATTC
1 GCCACTAAGGC-TTTTAGATAATTT
** *
40453024 GCCAC-AAGAGCTTCCCAGATAACTTC
1 GCCACTAAG-GCTT-TTAGATAA-TTT
* *
40453050 GCCACTAAGGCTTTTCGAATAATAT
1 GCCACTAAGGCTTTTAG-ATAATTT
* *
40453075 GCCACAAAAGCTTTTTAGATAATTT
1 GCCACTAAGGC-TTTTAGATAATTT
* * *
40453100 GCTA-TAAAAGTTTCTTAGATAACTTT
1 GCCACT-AAGGCTT-TTAGATAA-TTT
* * **
40453126 TCCACTAAGGCTTTCT-GAATGATAC
1 GCCACTAAGGCTTT-TAG-ATAATTT
*
40453151 GCCACAAAGGCCTTTTAGATAATTT
1 GCCACTAAGG-CTTTTAGATAATTT
40453176 GCCACTAAGG-TTTT
1 GCCACTAAGGCTTTT
40453190 CCGAATAATA
Statistics
Matches: 126, Mismatches: 26, Indels: 30
0.69 0.14 0.16
Matches are distributed among these distances:
23 4 0.03
24 7 0.06
25 71 0.56
26 40 0.32
27 4 0.03
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Consensus pattern (24 bp):
GCCACTAAGGCTTTTAGATAATTT
Found at i:40453201 original size:50 final size:46
Alignment explanation
Indices: 40453114--40453225 Score: 125
Period size: 50 Copynumber: 2.3 Consensus size: 46
40453104 TAAAAGTTTC
* * *
40453114 TTAGATAACTTTTCCACTAAGGCTTTCTGAATGATACGCCACAAAGGCCTT
1 TTAGATAA-TTTGCCACTAAGGCTTTCCGAATAATACGCCAC----GCCTT
* *
40453165 TTAGATAATTTGCCACTAAGGTTTTCCGAATAATACGCTACGCCTT
1 TTAGATAATTTGCCACTAAGGCTTTCCGAATAATACGCCACGCCTT
*
40453211 TCAGATAATTTGCCA
1 TTAGATAATTTGCCA
40453226 AAAAGGCATA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
46 19 0.35
50 28 0.51
51 8 0.15
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (46 bp):
TTAGATAATTTGCCACTAAGGCTTTCCGAATAATACGCCACGCCTT
Found at i:40454246 original size:27 final size:24
Alignment explanation
Indices: 40454203--40454258 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 24
40454193 TATCTTAACG
*
40454203 AAGAAGAAGTGAACATTTAGGTTAGA
1 AAGAAGAAGTGAACATTGA-G-TAGA
*
40454229 AAGAAGAAATTGAACATTGAGTAGA
1 AAGAAG-AAGTGAACATTGAGTAGA
40454254 AAGAA
1 AAGAA
40454259 AAACTATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 9 0.33
26 7 0.26
27 11 0.41
ACGTcount: A:0.52, C:0.04, G:0.25, T:0.20
Consensus pattern (24 bp):
AAGAAGAAGTGAACATTGAGTAGA
Found at i:40456859 original size:44 final size:44
Alignment explanation
Indices: 40456805--40456891 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
40456795 AATTACCGCC
* *
40456805 AAACCTAAGCTTTATGGTTCCAATTTTATGACCAAAATGAAGCA
1 AAACATAAGCTTTATGATTCCAATTTTATGACCAAAATGAAGCA
*
40456849 AAACATAAGCTTTATGATTCCATTTTTATGACCAAAATGAAGC
1 AAACATAAGCTTTATGATTCCAATTTTATGACCAAAATGAAGC
40456892 GTACCAAGCG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (44 bp):
AAACATAAGCTTTATGATTCCAATTTTATGACCAAAATGAAGCA
Found at i:40462608 original size:3 final size:3
Alignment explanation
Indices: 40462600--40462626 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40462590 TATATAGTAT
40462600 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
40462627 ATTTTGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:40465429 original size:16 final size:16
Alignment explanation
Indices: 40465408--40465440 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
40465398 TTCGCTGTAT
40465408 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
40465424 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
40465440 T
1 T
40465441 AACAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.36, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:40465691 original size:16 final size:16
Alignment explanation
Indices: 40465654--40465695 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40465644 TTAATCATAT
*
40465654 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
40465670 TT-AAATATATTATAA
1 TTAAAATATATTATAA
40465685 TTAAAATATAT
1 TTAAAATATAT
40465696 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:40465702 original size:14 final size:15
Alignment explanation
Indices: 40465663--40465704 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40465653 TTTAAACATA
*
40465663 ATTATTATTAAATAT
1 ATTATAATTAAATAT
40465678 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
40465692 A-TATAATTTAATA
1 ATTATAATTAAATA
40465705 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:40465916 original size:24 final size:25
Alignment explanation
Indices: 40465870--40465917 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
40465860 TATGAATTTG
40465870 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
40465896 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
40465918 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:40465921 original size:92 final size:92
Alignment explanation
Indices: 40465825--40466053 Score: 236
Period size: 92 Copynumber: 2.5 Consensus size: 92
40465815 TGATTTAATA
* * *
40465825 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
40465887 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
40465917 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* *
40465982 ATTAAATATAATTTAAT-AGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* * *
40466007 ATAATTTCATAAAATTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 A-AATTTCAAAAAATTCATAATAAT-AAAT-TATATTATATGAATTTA
40466054 CTAAAATCAA
Statistics
Matches: 119, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
90 2 0.02
91 27 0.23
92 81 0.68
93 9 0.08
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:40467460 original size:11 final size:11
Alignment explanation
Indices: 40467446--40467472 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
40467436 AAAAATCAAT
40467446 ACAAAAGTTTC
1 ACAAAAGTTTC
40467457 ACAAAAGTTTC
1 ACAAAAGTTTC
40467468 ACAAA
1 ACAAA
40467473 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:40473335 original size:36 final size:38
Alignment explanation
Indices: 40473246--40473406 Score: 231
Period size: 37 Copynumber: 4.3 Consensus size: 38
40473236 GGTAGAAACT
*
40473246 GAGCAAATCGGCCGAAAAAGAAAAGAAAAGAAACAGAGG
1 GAGCAAATCGGCAGAAAAAGAAAAGAAAAGAAACA-AGG
* *
40473285 GAGCAAATCGGCAG-AAAAGAAAAGAAAATAAAC-TGG
1 GAGCAAATCGGCAGAAAAAGAAAAGAAAAGAAACAAGG
* * *
40473321 GAGCAAATCAGCAGAAAAAGAAAAGAAAATAAAC-TGG
1 GAGCAAATCGGCAGAAAAAGAAAAGAAAAGAAACAAGG
40473358 GAGCAAATCGGCAG-AAAAGAAAAGAAAAGAAACAAGG
1 GAGCAAATCGGCAGAAAAAGAAAAGAAAAGAAACAAGG
40473395 GAGCAAATCGGC
1 GAGCAAATCGGC
40473407 TGAAGCTATA
Statistics
Matches: 113, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
36 33 0.29
37 49 0.43
38 18 0.16
39 13 0.12
ACGTcount: A:0.56, C:0.12, G:0.26, T:0.06
Consensus pattern (38 bp):
GAGCAAATCGGCAGAAAAAGAAAAGAAAAGAAACAAGG
Found at i:40473374 original size:73 final size:75
Alignment explanation
Indices: 40473246--40473403 Score: 239
Period size: 73 Copynumber: 2.1 Consensus size: 75
40473236 GGTAGAAACT
* *
40473246 GAGCAAATCGGCCGAAAAAGAAAAGAAAAGAAACAGAGGGAGCAAATCGGCAGAAAAGAAAAGAA
1 GAGCAAATCAGCAGAAAAAGAAAAGAAAAGAAACA-AGGGAGCAAATCGGCAGAAAAGAAAAGAA
* *
40473311 AATAAAC-TGG
65 AAGAAACAAGG
* *
40473321 GAGCAAATCAGCAGAAAAAGAAAAGAAAATAAAC-TGGGAGCAAATCGGCAGAAAAGAAAAGAAA
1 GAGCAAATCAGCAGAAAAAGAAAAGAAAAGAAACAAGGGAGCAAATCGGCAGAAAAGAAAAGAAA
40473385 AGAAACAAGG
66 AGAAACAAGG
40473395 GAGCAAATC
1 GAGCAAATC
40473404 GGCTGAAGCT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
73 34 0.45
74 11 0.14
75 31 0.41
ACGTcount: A:0.57, C:0.12, G:0.25, T:0.06
Consensus pattern (75 bp):
GAGCAAATCAGCAGAAAAAGAAAAGAAAAGAAACAAGGGAGCAAATCGGCAGAAAAGAAAAGAAA
AGAAACAAGG
Found at i:40477543 original size:49 final size:50
Alignment explanation
Indices: 40477461--40477571 Score: 120
Period size: 49 Copynumber: 2.3 Consensus size: 50
40477451 GGAGCATGAA
*
40477461 ACTTGAACCCAT-GACCGCATAACCACCACCAACTAAGG-GCCCAAGTTAT
1 ACTTGAACCCGTGGACCGCATAACCACCACCAACT-AGGAGCCCAAGTTAT
* ** * *
40477510 ACTTGAACCCGTGGA-CGCATAACTACCGTCAACTGGGAGCCCTAGTTAT
1 ACTTGAACCCGTGGACCGCATAACCACCACCAACTAGGAGCCCAAGTTAT
* *
40477559 ACTTAAACTCGTG
1 ACTTGAACCCGTG
40477572 ATTGTATAAC
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
48 2 0.04
49 48 0.92
50 2 0.04
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.21
Consensus pattern (50 bp):
ACTTGAACCCGTGGACCGCATAACCACCACCAACTAGGAGCCCAAGTTAT
Found at i:40488182 original size:5 final size:5
Alignment explanation
Indices: 40488172--40488243 Score: 51
Period size: 5 Copynumber: 13.6 Consensus size: 5
40488162 CAAGCCACCC
*
40488172 ATTTT ATTTT ATTTT ATTTT -TTATT ATTTGTT ATATT A-TTT ATTTTT
1 ATTTT ATTTT ATTTT ATTTT ATT-TT A-TT-TT ATTTT ATTTT A-TTTT
40488219 ATTTT ACTAATTT -TTTT ATTTT ATT
1 ATTTT A-T--TTT ATTTT ATTTT ATT
40488244 ATTCTTATAC
Statistics
Matches: 55, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
4 8 0.15
5 32 0.58
6 7 0.13
7 5 0.09
8 3 0.05
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:40488243 original size:32 final size:32
Alignment explanation
Indices: 40488172--40488251 Score: 78
Period size: 32 Copynumber: 2.5 Consensus size: 32
40488162 CAAGCCACCC
*
40488172 ATTTTATTT-TATTTTATTTTTTATTATTTGTT
1 ATTTTATTTAT-TTTTATTTTTAATTATTTGTT
*
40488204 ATATTATTTATTTTTATTTTACTAATT-TTT-TT
1 ATTTTATTTATTTTTATTTT--TAATTATTTGTT
*
40488236 ATTTTA-TTATTCTTAT
1 ATTTTATTTATTTTTAT
40488252 ACTTAGATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
31 9 0.22
32 24 0.59
33 4 0.10
34 4 0.10
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.74
Consensus pattern (32 bp):
ATTTTATTTATTTTTATTTTTAATTATTTGTT
Found at i:40488246 original size:31 final size:29
Alignment explanation
Indices: 40488173--40488251 Score: 72
Period size: 31 Copynumber: 2.7 Consensus size: 29
40488163 AAGCCACCCA
*
40488173 TTTTATTTTATT-TTATT-TTTTATTATT
1 TTTTATTTTATTATTATTATTTTATAATT
* * *
40488200 TGTTATATTATTTATTTTTATTTTACTAATTT
1 TTTTATTTTA-TTATTATTATTTTA-TAA-TT
*
40488232 TTTTATTTTATTATTCTTAT
1 TTTTATTTTATTATTATTAT
40488252 ACTTAGATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
27 8 0.20
28 2 0.05
29 4 0.10
30 5 0.12
31 11 0.28
32 10 0.25
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.75
Consensus pattern (29 bp):
TTTTATTTTATTATTATTATTTTATAATT
Found at i:40503761 original size:21 final size:21
Alignment explanation
Indices: 40503735--40503775 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40503725 ATGTGAAATT
40503735 TGTTCTAACGGTCTCAAGACA
1 TGTTCTAACGGTCTCAAGACA
** *
40503756 TGTTCTTTCTGTCTCAAGAC
1 TGTTCTAACGGTCTCAAGAC
40503776 TCGGTGACCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (21 bp):
TGTTCTAACGGTCTCAAGACA
Found at i:40507330 original size:23 final size:21
Alignment explanation
Indices: 40507304--40507348 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
40507294 AATAATGATT
40507304 ATTATGTGTTCTATTTATTTTTA
1 ATTATGTGTT-T-TTTATTTTTA
*
40507327 ATTATTTGTTTTTTATTTTTA
1 ATTATGTGTTTTTTATTTTTA
40507348 A
1 A
40507349 ATCCACAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.52
22 1 0.05
23 9 0.43
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (21 bp):
ATTATGTGTTTTTTATTTTTA
Found at i:40510554 original size:34 final size:35
Alignment explanation
Indices: 40510510--40510576 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
40510500 CAGTAAAATA
*
40510510 TTTTCCGTAAAATGATTT-CAGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACAGGAAAATATTTTAC
* *
40510544 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACAGGAAAATATTTT
40510577 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACAGGAAAATATTTTAC
Found at i:40511612 original size:16 final size:16
Alignment explanation
Indices: 40511587--40511624 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
40511577 TCATAATTGA
*
40511587 TTTTTTTAG-ATTAAT
1 TTTTTTTAGAAATAAT
40511602 TTTTATTTAGAAATAAT
1 TTTT-TTTAGAAATAAT
40511619 TTTTTT
1 TTTTTT
40511625 AAATATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 4 0.20
16 7 0.35
17 9 0.45
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (16 bp):
TTTTTTTAGAAATAAT
Found at i:40513293 original size:31 final size:31
Alignment explanation
Indices: 40513245--40513325 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
40513235 TTGATATAAT
**
40513245 CCAAGTTTAGGGACCAAAATGGATTTAGTTG
1 CCAAGTTTAGGGACCAAAATGGACCTAGTTG
* * *
40513276 TCAATTTTAAGGACCAAAATGGACCTAGTTG
1 CCAAGTTTAGGGACCAAAATGGACCTAGTTG
*
40513307 CCAAGTTTAGGGGCCAAAA
1 CCAAGTTTAGGGACCAAAA
40513326 ATTATATTCT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (31 bp):
CCAAGTTTAGGGACCAAAATGGACCTAGTTG
Found at i:40514567 original size:12 final size:12
Alignment explanation
Indices: 40514532--40514569 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
40514522 TGTATTACAT
*
40514532 ATATTAAAATT-
1 ATATAAAAATTA
40514543 ATATAAAAA-TA
1 ATATAAAAATTA
40514554 ATATAAAAATTA
1 ATATAAAAATTA
40514566 ATAT
1 ATAT
40514570 GGGCGGGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 1 0.04
11 17 0.71
12 6 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATATAAAAATTA
Found at i:40516724 original size:13 final size:13
Alignment explanation
Indices: 40516706--40516732 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40516696 AGTTTGGCAA
40516706 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
40516719 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
40516732 T
1 T
40516733 TTGGTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:40528090 original size:20 final size:20
Alignment explanation
Indices: 40528041--40528092 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
40528031 ATATTTATTT
40528041 ATTATATTTTA-ATATTTAA
1 ATTATATTTTATATATTTAA
* *
40528060 AATATAGTTTATATATTTAA
1 ATTATATTTTATATATTTAA
*
40528080 ATTAAATTTTATA
1 ATTATATTTTATA
40528093 AATAATTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTATATTTTATATATTTAA
Found at i:40528577 original size:30 final size:30
Alignment explanation
Indices: 40528541--40528603 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
40528531 ACTTATTTTA
40528541 TTGTTAATTTTATTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* *
40528571 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
40528601 TTG
1 TTG
40528604 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:40529175 original size:24 final size:23
Alignment explanation
Indices: 40529148--40529198 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
40529138 ATTTTTACTC
40529148 TTAACAAAATTAATCTATTTATCT
1 TTAACAAAATTAATCTATTTAT-T
* *
40529172 TTAATAATATTAATCTATTTATT
1 TTAACAAAATTAATCTATTTATT
40529195 TTAA
1 TTAA
40529199 ATTAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAACAAAATTAATCTATTTATT
Found at i:40529261 original size:21 final size:22
Alignment explanation
Indices: 40529237--40529286 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
40529227 ATCGAAAATA
*
40529237 AATTTAAAATA-T-TTTATATGT
1 AATTTAAAATAGTATTTA-AAGT
*
40529258 AATTTTAAATAGTATTTAAAGT
1 AATTTAAAATAGTATTTAAAGT
40529280 AATTTAA
1 AATTTAA
40529287 TATTAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.42
22 10 0.42
23 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (22 bp):
AATTTAAAATAGTATTTAAAGT
Found at i:40531161 original size:30 final size:31
Alignment explanation
Indices: 40531114--40531180 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
40531104 TGGTATCTTA
40531114 TTTTAATTTCTTCAATTTCAATCATT-TACT
1 TTTTAATTTCTTCAATTTCAATCATTATACT
* * * *
40531144 TTTTAATTTGGTT-AATTTTAATCTTTATATT
1 TTTTAATTT-CTTCAATTTCAATCATTATACT
40531175 TTTTAA
1 TTTTAA
40531181 AATTTAGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.27, C:0.09, G:0.03, T:0.61
Consensus pattern (31 bp):
TTTTAATTTCTTCAATTTCAATCATTATACT
Found at i:40534229 original size:44 final size:43
Alignment explanation
Indices: 40534181--40534324 Score: 105
Period size: 44 Copynumber: 3.1 Consensus size: 43
40534171 AATCCATTGT
40534181 ACTGCAATTTCAGGGATATAATATTTTTAGTTTCATTTTGCTTC
1 ACTGCAATTT-AGGGATATAATATTTTTAGTTTCATTTTGCTTC
* *
40534225 ACTGC-ATCCTTAGGGAGATAATATTTGTTA-TTGT-AGTTTCAATCCATTC
1 ACTGCAAT--TTAGGGATATAATATTT-TTAGTT-TCA-TTT---TGC-TTC
* * * *
40534274 TACTGCAATTTTAGGGATGTAATATTTGTAGCTTCATTTTGCTCC
1 -ACTGCAA-TTTAGGGATATAATATTTTTAGTTTCATTTTGCTTC
40534319 ACTGCA
1 ACTGCA
40534325 TCCTTAAAGA
Statistics
Matches: 78, Mismatches: 8, Indels: 28
0.68 0.07 0.25
Matches are distributed among these distances:
43 2 0.03
44 28 0.36
45 11 0.14
46 2 0.03
48 2 0.03
49 9 0.12
50 22 0.28
51 1 0.01
52 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (43 bp):
ACTGCAATTTAGGGATATAATATTTTTAGTTTCATTTTGCTTC
Found at i:40534278 original size:94 final size:94
Alignment explanation
Indices: 40534142--40534343 Score: 305
Period size: 94 Copynumber: 2.1 Consensus size: 94
40534132 TTTCAACATC
* *
40534142 AAGGAGATAAGATTTGTTGTTATAGTTTCAATCCATTGTACTGCAATTTCAGGGATATAATATTT
1 AAGGAGATAAGATTTGTTATTATAGTTTCAATCCATTCTACTGCAATTTCAGGGATATAATATTT
* * *
40534207 TTAGTTTCATTTTGCTTCACTGCATCCTT
66 GTAGCTTCATTTTGCTCCACTGCATCCTT
* * * * *
40534236 AGGGAGATAATATTTGTTATTGTAGTTTCAATCCATTCTACTGCAATTTTAGGGATGTAATATTT
1 AAGGAGATAAGATTTGTTATTATAGTTTCAATCCATTCTACTGCAATTTCAGGGATATAATATTT
40534301 GTAGCTTCATTTTGCTCCACTGCATCCTT
66 GTAGCTTCATTTTGCTCCACTGCATCCTT
*
40534330 AAAGAGATAAGATT
1 AAGGAGATAAGATT
40534344 CGCCATGGTA
Statistics
Matches: 95, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (94 bp):
AAGGAGATAAGATTTGTTATTATAGTTTCAATCCATTCTACTGCAATTTCAGGGATATAATATTT
GTAGCTTCATTTTGCTCCACTGCATCCTT
Found at i:40534288 original size:50 final size:49
Alignment explanation
Indices: 40534144--40534302 Score: 138
Period size: 50 Copynumber: 3.3 Consensus size: 49
40534134 TCAACATCAA
* * * *
40534144 GGAGATAAGATTTGTTGTTATAGTTTCAATCCATTGTACTGCAATTTCAG
1 GGAGATAATATTTGTTATT-TAGTTTCAATCCATTCTACTGCAATTTTAG
* * *
40534194 GGATATAATATTT-TTAGTTTCA-TTT---TGC-TTC-ACTGC-ATCCTTAG
1 GGAGATAATATTTGTTA-TTT-AGTTTCAATCCATTCTACTGCAAT-TTTAG
40534238 GGAGATAATATTTGTTATTGTAGTTTCAATCCATTCTACTGCAATTTTAG
1 GGAGATAATATTTGTTATT-TAGTTTCAATCCATTCTACTGCAATTTTAG
40534288 GGATG-TAATATTTGT
1 GGA-GATAATATTTGT
40534303 AGCTTCATTT
Statistics
Matches: 86, Mismatches: 10, Indels: 26
0.70 0.08 0.21
Matches are distributed among these distances:
43 2 0.02
44 23 0.27
45 9 0.10
46 2 0.02
48 2 0.02
49 9 0.10
50 36 0.42
51 3 0.03
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (49 bp):
GGAGATAATATTTGTTATTTAGTTTCAATCCATTCTACTGCAATTTTAG
Found at i:40534395 original size:94 final size:94
Alignment explanation
Indices: 40534297--40534491 Score: 212
Period size: 94 Copynumber: 2.1 Consensus size: 94
40534287 GGGATGTAAT
* * * *
40534297 ATTTGTAGCTTCATTTTGCTCCACTGCATCCTTAAAG-AGATAAGATTCGCCATGGTAACTTCAA
1 ATTTGTAGCTTCATCTTGCTCCACTGCA-ACTTAAAGAAGATAAGATTCACCATGATAACTTCAA
* * * *
40534361 TCTAACCCACTGTAACTTTATGGGTATTGG
65 TCTAACCCACTGCAACTTCAGGGGTATAGG
* * * * * * * *
40534391 ATTTGTATCTTTATCTTGTTCCACTGCAACTTCAGGAAGATAAGATTCACCATTATAATTTCATT
1 ATTTGTAGCTTCATCTTGCTCCACTGCAACTTAAAGAAGATAAGATTCACCATGATAACTTCAAT
*
40534456 CTGACCCACTGCAACTTCAGGGGTATAGG
66 CTAACCCACTGCAACTTCAGGGGTATAGG
*
40534485 AATTGTA
1 ATTTGTA
40534492 TATTTAATCC
Statistics
Matches: 82, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
93 5 0.06
94 77 0.94
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (94 bp):
ATTTGTAGCTTCATCTTGCTCCACTGCAACTTAAAGAAGATAAGATTCACCATGATAACTTCAAT
CTAACCCACTGCAACTTCAGGGGTATAGG
Found at i:40534492 original size:94 final size:94
Alignment explanation
Indices: 40534334--40534516 Score: 224
Period size: 94 Copynumber: 1.9 Consensus size: 94
40534324 ATCCTTAAAG
* * * * * * *
40534334 AGATAAGATTCGCCATGGTAACTTCAATCTAACCCACTGTAACTTTATGGGTATTGGATTTGTAT
1 AGATAAGATTCACCATGATAACTTCAATCTAACCCACTGCAACTTCAGGGGTATAGGAATTGTAT
* * *
40534399 CTTT-ATCTTGTTCCACTGCAACTTCAGGA
66 ATTTAATC-CGATCCACTGCAACTTCAGGA
* * * *
40534428 AGATAAGATTCACCATTATAATTTCATTCTGACCCACTGCAACTTCAGGGGTATAGGAATTGTAT
1 AGATAAGATTCACCATGATAACTTCAATCTAACCCACTGCAACTTCAGGGGTATAGGAATTGTAT
40534493 ATTTAATCCGATCCACTGCAACTT
66 ATTTAATCCGATCCACTGCAACTT
40534517 TAAGGATATA
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
94 71 0.96
95 3 0.04
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (94 bp):
AGATAAGATTCACCATGATAACTTCAATCTAACCCACTGCAACTTCAGGGGTATAGGAATTGTAT
ATTTAATCCGATCCACTGCAACTTCAGGA
Found at i:40534527 original size:44 final size:44
Alignment explanation
Indices: 40534461--40534838 Score: 183
Period size: 44 Copynumber: 8.3 Consensus size: 44
40534451 TCATTCTGAC
* *
40534461 CCACTGCAACTTCAGGGGTATAGGAATTGTATATTTAATCCGAT
1 CCACTGCAACTTCAAGGATATAGGAATTGTATATTTAATCCGAT
* * ** * * *
40534505 CCACTGCAACTTTAAGGATATAGGATTTGTAGCTTCATAT-TGCT
1 CCACTGCAACTTCAAGGATATAGGAATTGTATATTTA-ATCCGAT
* * * * *
40534549 CCACTGCAACTTTCGA-GAGATAGGATTCACCATTGTA-ATTTCATTCCAAC
1 CCACTGCAAC-TTCAAGGATATAGG----A--ATTGTATATTT-AATCCGAT
* * * *
40534599 CCATTGCAACTTCAAGGGTATAGGAATTGTATCTTTAATCTGAT
1 CCACTGCAACTTCAAGGATATAGGAATTGTATATTTAATCCGAT
* * * ** * **
40534643 CTACTGCAACTTCAGGGATATAGGATTTGTA-GCTTCATCTTATT
1 CCACTGCAACTTCAAGGATATAGGAATTGTATATTTAATCCGA-T
* * * * *
40534687 CCACTGCAACTTCAAGGAAATAAGATTTGTCATTGTAATTTCATTCCGAC
1 CCACTGCAACTTCAAGGATATAGGAATTGT-A---T-ATTT-AATCCGAT
* * * * * *
40534737 CCACTGCAACTTCAGGGGTATAAGAATTGTATCTTCAATTCGAT
1 CCACTGCAACTTCAAGGATATAGGAATTGTATATTTAATCCGAT
* * * *
40534781 CCACTGCAACTTCAAGGATATA-GAATTTGTA-GTTTCATCTTGCT
1 CCACTGCAACTTCAAGGATATAGGAA-TTGTATATTTAATC-CGAT
40534825 CCACTGCAACTTCA
1 CCACTGCAACTTCA
40534839 GTAAGATAAG
Statistics
Matches: 246, Mismatches: 66, Indels: 44
0.69 0.19 0.12
Matches are distributed among these distances:
43 14 0.06
44 158 0.64
45 11 0.04
46 2 0.01
48 1 0.00
49 8 0.03
50 49 0.20
51 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (44 bp):
CCACTGCAACTTCAAGGATATAGGAATTGTATATTTAATCCGAT
Found at i:40534618 original size:138 final size:137
Alignment explanation
Indices: 40534389--40534852 Score: 633
Period size: 138 Copynumber: 3.4 Consensus size: 137
40534379 TATGGGTATT
* * * *
40534389 GGATTTGTATCTTTATCTTGTTCCACTGCAACTTCAGGAAGATAAGATTCACCATTATAATTTCA
1 GGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGG-AGATAAGATTCACCATTGTAATTTCA
* * *
40534454 TTCTGACCCACTGCAACTTCAGGGGTATAGGAATTGTATATTTAATCCGATCCACTGCAACTTTA
65 TTCCGACCCACTGCAACTTCAGGGGTATAGGAATTGTATCTTTAATCCGATCCACTGCAACTTCA
40534519 AGGATATA
130 AGGATATA
* *
40534527 GGATTTGTAGCTTCATATTGCTCCACTGCAACTTTC-GAGAGATAGGATTCACCATTGTAATTTC
1 GGATTTGTAGCTTCATCTTGCTCCACTGCAAC-TTCAG-GAGATAAGATTCACCATTGTAATTTC
* * * * *
40534591 ATTCCAACCCATTGCAACTTCAAGGGTATAGGAATTGTATCTTTAATCTGATCTACTGCAACTTC
64 ATTCCGACCCACTGCAACTTCAGGGGTATAGGAATTGTATCTTTAATCCGATCCACTGCAACTTC
*
40534656 AGGGATATA
129 AAGGATATA
** * ***
40534665 GGATTTGTAGCTTCATCTTATTCCACTGCAACTTCAAGGAAATAAGATTTGTCATTGTAATTTCA
1 GGATTTGTAGCTTCATCTTGCTCCACTGCAACTTC-AGGAGATAAGATTCACCATTGTAATTTCA
* * *
40534730 TTCCGACCCACTGCAACTTCAGGGGTATAAGAATTGTATCTTCAATTCGATCCACTGCAACTTCA
65 TTCCGACCCACTGCAACTTCAGGGGTATAGGAATTGTATCTTTAATCCGATCCACTGCAACTTCA
40534795 AGGATATA
130 AGGATATA
* * *
40534803 GAATTTGTAGTTTCATCTTGCTCCACTGCAACTTCAGTAAGATAAGATTC
1 GGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAG-GAGATAAGATTC
40534853 GTTATAGTAA
Statistics
Matches: 282, Mismatches: 39, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
137 5 0.02
138 272 0.96
139 5 0.02
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (137 bp):
GGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGAGATAAGATTCACCATTGTAATTTCAT
TCCGACCCACTGCAACTTCAGGGGTATAGGAATTGTATCTTTAATCCGATCCACTGCAACTTCAA
GGATATA
Found at i:40535676 original size:117 final size:117
Alignment explanation
Indices: 40535468--40535678 Score: 323
Period size: 117 Copynumber: 1.8 Consensus size: 117
40535458 TTTGATTTGT
* * * *
40535468 TGGTTATTTGTGATTTATTATTGCAATTTCAGTGCCACACTGTAGGGTTTGTTTTGTCGATTTTT
1 TGGTTAATTATGATTTATTATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGT
* *
40535533 GATGCGATAGTAATCCCGATGTTGTTGATAAAACTATTTTCAAAATTGTATA
66 GATGCGACAGTAATCCCGATGATGTTGATAAAACTATTTTCAAAATTGTATA
* *
40535585 TGGTTAATTATGATTTATTATTGCAATTTTAGTGCCACAATGTAGGGTTTGTTTTGTTGATTTGT
1 TGGTTAATTATGATTTATTATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGT
** *
40535650 GATGCGACAGTGGTCCCGGTGATGTTGAT
66 GATGCGACAGTAATCCCGATGATGTTGAT
40535679 TTCTGTTACC
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
117 83 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.44
Consensus pattern (117 bp):
TGGTTAATTATGATTTATTATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGT
GATGCGACAGTAATCCCGATGATGTTGATAAAACTATTTTCAAAATTGTATA
Found at i:40536604 original size:51 final size:51
Alignment explanation
Indices: 40536528--40536634 Score: 196
Period size: 51 Copynumber: 2.1 Consensus size: 51
40536518 ATAGTGAAGT
*
40536528 TGTTGCTGATGAATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAA
1 TGTTGCTGATGAATATGCTGGTGATTTTGCAACATCAGATGGACTGGATAA
*
40536579 TGTTGCTGATGAATATGTTGGTGATTTTGCAACATCAGATGGACTGGATAA
1 TGTTGCTGATGAATATGCTGGTGATTTTGCAACATCAGATGGACTGGATAA
40536630 TGTTG
1 TGTTG
40536635 TTGCTGCACG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.26, C:0.09, G:0.29, T:0.36
Consensus pattern (51 bp):
TGTTGCTGATGAATATGCTGGTGATTTTGCAACATCAGATGGACTGGATAA
Found at i:40536946 original size:9 final size:9
Alignment explanation
Indices: 40536932--40537000 Score: 88
Period size: 9 Copynumber: 7.7 Consensus size: 9
40536922 TTTGGTTAAA
40536932 AATTAACCG
1 AATTAACCG
*
40536941 AATTAACTG
1 AATTAACCG
40536950 AATTAACCG
1 AATTAACCG
40536959 AATT-ACTCG
1 AATTAAC-CG
40536968 AATT-ACCTG
1 AATTAACC-G
*
40536977 AATTACCCG
1 AATTAACCG
40536986 AATTAACCG
1 AATTAACCG
40536995 AATTAA
1 AATTAA
40537001 ATCACTACAT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
8 3 0.06
9 48 0.91
10 2 0.04
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:40536969 original size:27 final size:27
Alignment explanation
Indices: 40536932--40537000 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
40536922 TTTGGTTAAA
40536932 AATTAACCGAATTAACTGAATTAACCG
1 AATTAACCGAATTAACTGAATTAACCG
* *
40536959 AATT-ACTCGAATTACCTGAATTACCCG
1 AATTAAC-CGAATTAACTGAATTAACCG
40536986 AATTAACCGAATTAA
1 AATTAACCGAATTAA
40537001 ATCACTACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 2 0.05
27 33 0.89
28 2 0.05
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (27 bp):
AATTAACCGAATTAACTGAATTAACCG
Found at i:40537088 original size:5 final size:5
Alignment explanation
Indices: 40537078--40537103 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40537068 ATTTTTATGA
40537078 TTGGG TTGGG TTGGG TTGGG TTGGG T
1 TTGGG TTGGG TTGGG TTGGG TTGGG T
40537104 AATTGGGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.58, T:0.42
Consensus pattern (5 bp):
TTGGG
Found at i:40537111 original size:18 final size:18
Alignment explanation
Indices: 40537088--40537140 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
40537078 TTGGGTTGGG
40537088 TTGGGTTGGGTTGGGTAA
1 TTGGGTTGGGTTGGGTAA
* * * *
40537106 TTGGGTTAGGTTTGATAC
1 TTGGGTTGGGTTGGGTAA
*
40537124 TTGGGTTTGGATTGGGT
1 TTGGG-TTGGGTTGGGT
40537141 TTAGGTGAAT
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.11, C:0.02, G:0.43, T:0.43
Consensus pattern (18 bp):
TTGGGTTGGGTTGGGTAA
Found at i:40546675 original size:32 final size:33
Alignment explanation
Indices: 40546632--40546773 Score: 143
Period size: 32 Copynumber: 4.4 Consensus size: 33
40546622 TCACGATTTG
*
40546632 GTTTTAAGGGATTTC-ACGATTTTATTCTTAATA
1 GTTTT-AGGGATTTCAACGATTTGATTCTTAATA
* *
40546665 GTTTTAGGGA-TTCAATGATTTGATTCGTAA-A
1 GTTTTAGGGATTTCAACGATTTGATTCTTAATA
* * *
40546696 ATTGTTAGGGATTTC-ACGATTTCATTTTTAATA
1 GTT-TTAGGGATTTCAACGATTTGATTCTTAATA
*
40546729 GTTTTAGGGA-TTCAACGATTTGATT-TGTAAAA
1 GTTTTAGGGATTTCAACGATTTGATTCT-TAATA
*
40546761 TTTTTAGGGATTT
1 GTTTTAGGGATTT
40546774 TAAGAATATT
Statistics
Matches: 90, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
31 10 0.11
32 67 0.74
33 13 0.14
ACGTcount: A:0.27, C:0.07, G:0.19, T:0.46
Consensus pattern (33 bp):
GTTTTAGGGATTTCAACGATTTGATTCTTAATA
Found at i:40546739 original size:64 final size:64
Alignment explanation
Indices: 40546638--40546773 Score: 227
Period size: 64 Copynumber: 2.1 Consensus size: 64
40546628 TTTGGTTTTA
* *
40546638 AGGGATTTCACGATTTTATTCTTAATAGTTTTAGGGATTCAATGATTTGATTCGTAAAATTGTT
1 AGGGATTTCACGATTTCATTCTTAATAGTTTTAGGGATTCAACGATTTGATTCGTAAAATTGTT
* * *
40546702 AGGGATTTCACGATTTCATTTTTAATAGTTTTAGGGATTCAACGATTTGATTTGTAAAATTTTT
1 AGGGATTTCACGATTTCATTCTTAATAGTTTTAGGGATTCAACGATTTGATTCGTAAAATTGTT
40546766 AGGGATTT
1 AGGGATTT
40546774 TAAGAATATT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.46
Consensus pattern (64 bp):
AGGGATTTCACGATTTCATTCTTAATAGTTTTAGGGATTCAACGATTTGATTCGTAAAATTGTT
Found at i:40547207 original size:44 final size:44
Alignment explanation
Indices: 40547158--40547307 Score: 108
Period size: 44 Copynumber: 3.3 Consensus size: 44
40547148 TCAATCCGAC
* *
40547158 CCACTGCAACTTTAGGGGTATAGGATTTGTAACTTTATCTTGCT
1 CCACTGCAACTTCAGGGGTATAGGATTTGTAACTTAATCTTGCT
* * * *
40547202 CCACTGTAACTTCAGGAAG-ATAAGGCTCGCTATGGTAACTTCAATC-CGAC-
1 CCACTGCAACTTCAGG-GGTAT-AGGAT---T-T-GTAACTT-AATCTTG-CT
* * *
40547252 CCACTGCAACTTCAGGGATATAGGATTTGTAGCTTCATCTTGCT
1 CCACTGCAACTTCAGGGGTATAGGATTTGTAACTTAATCTTGCT
*
40547296 CCACTGCTACTT
1 CCACTGCAACTT
40547308 TAAGGAGATA
Statistics
Matches: 80, Mismatches: 14, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
43 4 0.05
44 34 0.43
45 6 0.08
46 1 0.01
48 1 0.01
49 5 0.06
50 25 0.31
51 4 0.05
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGGTATAGGATTTGTAACTTAATCTTGCT
Found at i:40547317 original size:94 final size:95
Alignment explanation
Indices: 40547143--40547413 Score: 354
Period size: 94 Copynumber: 2.9 Consensus size: 95
40547133 AAATTATGCC
* * *
40547143 TAACTTCAATCCGACCCACTGCAACTTTAGGGGTATAGGATTTGTAACTTTATCTTGCTCCACTG
1 TAACTTCAATCCGACCCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTG
* *
40547208 -TAAC-TTCAGGAAGATAAGGCTCGCTATGG
66 CT-ACTTTAAGGAAGATAAGACTCGCTATGG
*
40547237 TAACTTCAATCCGACCCACTGCAACTTCAGGGATATAGGATTTGTAGCTTCATCTTGCTCCACTG
1 TAACTTCAATCCGACCCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTG
**
40547302 CTACTTTAAGG-AGATAAGACTTTCTATGG
66 CTACTTTAAGGAAGATAAGACTCGCTATGG
* * ** * *
40547331 TAAATTCAATCTGACCCTTTGCAACTTCAGGGGTATAAGATTTGTAGCTTCATC-TACTCCACTG
1 TAACTTCAATCCGACCCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTG
* *
40547395 CAAC-TTCAGGAAGATAAGA
66 CTACTTTAAGGAAGATAAGA
40547414 TTTAAGGTTT
Statistics
Matches: 157, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
92 5 0.03
93 20 0.13
94 126 0.80
95 6 0.04
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (95 bp):
TAACTTCAATCCGACCCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTG
CTACTTTAAGGAAGATAAGACTCGCTATGG
Found at i:40550072 original size:18 final size:18
Alignment explanation
Indices: 40550049--40550115 Score: 80
Period size: 18 Copynumber: 3.7 Consensus size: 18
40550039 TTTGGTTAAA
40550049 AATTAACCGAATTACTCG
1 AATTAACCGAATTACTCG
* * *
40550067 AATTAACTGAATTACCCA
1 AATTAACCGAATTACTCG
* * *
40550085 AATTACCCTAATTAATCG
1 AATTAACCGAATTACTCG
40550103 AATTAACCGAATT
1 AATTAACCGAATT
40550116 GAATCACTAC
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (18 bp):
AATTAACCGAATTACTCG
Found at i:40550088 original size:27 final size:27
Alignment explanation
Indices: 40550049--40550115 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
40550039 TTTGGTTAAA
* *
40550049 AATTAACCGAATTACTCGAATTAA-CTG
1 AATTAACCAAATTACCCGAATTAATC-G
* *
40550076 AATTACCCAAATTACCCTAATTAATCG
1 AATTAACCAAATTACCCGAATTAATCG
*
40550103 AATTAACCGAATT
1 AATTAACCAAATT
40550116 GAATCACTAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (27 bp):
AATTAACCAAATTACCCGAATTAATCG
Found at i:40550108 original size:9 final size:9
Alignment explanation
Indices: 40550049--40550115 Score: 64
Period size: 9 Copynumber: 7.4 Consensus size: 9
40550039 TTTGGTTAAA
40550049 AATTAACCG
1 AATTAACCG
40550058 AATT-ACTCG
1 AATTAAC-CG
*
40550067 AATTAACTG
1 AATTAACCG
* *
40550076 AATTACCCA
1 AATTAACCG
* *
40550085 AATTACCCT
1 AATTAACCG
*
40550094 AATTAATCG
1 AATTAACCG
40550103 AATTAACCG
1 AATTAACCG
40550112 AATT
1 AATT
40550116 GAATCACTAC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
8 2 0.04
9 43 0.91
10 2 0.04
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (9 bp):
AATTAACCG
Found at i:40552706 original size:57 final size:56
Alignment explanation
Indices: 40552544--40552830 Score: 296
Period size: 56 Copynumber: 5.1 Consensus size: 56
40552534 ATTTTTCAAT
* * * * * * *
40552544 AGCAT-AATAATGCTTACTTTGAGACACTAAAGCAAC-ACTGTAATTTAATTTAGGGC
1 AGCATGAA-AATGCTCAATTTGAAACACTAAAACAACAACT-TAATTCAATTTAAGAC
* * * *
40552600 AGCAT-AATAATACTCAATTTGAAACA-TTAAACAACAGCTTAATTTAATTTAAGAC
1 AGCATGAA-AATGCTCAATTTGAAACACTAAAACAACAACTTAATTCAATTTAAGAC
* * * *
40552655 AACATGAAAATGCTCAATTTGATACACTAAAACACCAACTTTAATTCAATTTATGAC
1 AGCATGAAAATGCTCAATTTGAAACACTAAAACAACAAC-TTAATTCAATTTAAGAC
** * *
40552712 AGCATGAAAATGCTCAATTTGAAACACTAAAACAGTAGCTTGATTCAATTTAAGAC
1 AGCATGAAAATGCTCAATTTGAAACACTAAAACAACAACTTAATTCAATTTAAGAC
* *
40552768 AGTATGAAAATGCTCAATTTGAAACACTCAAACAACAACTTAAATTCAATTTATA-AC
1 AGCATGAAAATGCTCAATTTGAAACACTAAAACAACAACTT-AATTCAATTTA-AGAC
40552825 AGCATG
1 AGCATG
40552831 CAAACAGTAA
Statistics
Matches: 194, Mismatches: 31, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
55 41 0.21
56 86 0.44
57 66 0.34
58 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.29
Consensus pattern (56 bp):
AGCATGAAAATGCTCAATTTGAAACACTAAAACAACAACTTAATTCAATTTAAGAC
Found at i:40552780 original size:113 final size:113
Alignment explanation
Indices: 40552552--40552830 Score: 339
Period size: 113 Copynumber: 2.5 Consensus size: 113
40552542 ATAGCATAAT
* * * * * * * *
40552552 AATGCTTACTTTGAGACACTAAAGCAAC-ACTGTAATTTAATTTAGGGCAGCAT-AATAATACTC
1 AATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTATGACAGCATGAATAATACTC
* *
40552615 AATTTGAAACATTAAACAACAGCTTAATTTAATTTAAGACAACATGAA
66 AATTTGAAACATAAAACAACAGCTTAATTCAATTTAAGACAACATGAA
* * *
40552663 AATGCTCAATTTGATACACTAAAACACCAACTTTAATTCAATTTATGACAGCATGAA-AATGCTC
1 AATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTATGACAGCATGAATAATACTC
** * **
40552727 AATTTGAAACACTAAAACAGTAGCTTGATTCAATTTAAGACAGTATGAA
66 AATTTGAAACA-TAAAACAACAGCTTAATTCAATTTAAGACAACATGAA
* * *
40552776 AATGCTCAATTTGAAACACTCAAACAACAACTTAAATTCAATTTATAACAGCATG
1 AATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTATGACAGCATG
40552831 CAAACAGTAA
Statistics
Matches: 143, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
111 23 0.16
112 38 0.27
113 82 0.57
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (113 bp):
AATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTATGACAGCATGAATAATACTC
AATTTGAAACATAAAACAACAGCTTAATTCAATTTAAGACAACATGAA
Found at i:40553659 original size:23 final size:23
Alignment explanation
Indices: 40553629--40553682 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
40553619 AATTTTTATG
*
40553629 ATTGGGTTGGGTGGGGTTGGGTA
1 ATTGGGTTGGGTGGGGTTGGATA
*
40553652 ATTGGGTTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTGGGGTTGGATA
*
40553675 CTTGGGTT
1 ATTGGGTT
40553683 TGGATTGGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.09, C:0.02, G:0.50, T:0.39
Consensus pattern (23 bp):
ATTGGGTTGGGTGGGGTTGGATA
Found at i:40565016 original size:9 final size:9
Alignment explanation
Indices: 40565004--40565055 Score: 68
Period size: 9 Copynumber: 5.6 Consensus size: 9
40564994 ATTTTAATTT
40565004 TTTTTAAAA
1 TTTTTAAAA
40565013 TTTTTAAAA
1 TTTTTAAAA
*
40565022 TTTTTTAAA
1 TTTTTAAAA
*
40565031 TTTTTTAAA
1 TTTTTAAAA
40565040 TTTTTATAAA
1 TTTTTA-AAA
40565050 TATTTT
1 T-TTTT
40565056 GTATTTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
9 31 0.79
10 4 0.10
11 4 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:40565019 original size:19 final size:19
Alignment explanation
Indices: 40564995--40565055 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
40564985 GAAATTATTA
*
40564995 TTTTAATTTTTTTTAAAAT
1 TTTTAAATTTTTTTAAAAT
* *
40565014 TTTTAAAATTTTTTAAATT
1 TTTTAAATTTTTTTAAAAT
*
40565033 TTTTAAATTTTTATAAATAT
1 TTTTAAATTTTTTTAAA-AT
40565053 TTT
1 TTT
40565056 GTATTTTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
19 31 0.89
20 4 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTAAATTTTTTTAAAAT
Found at i:40565061 original size:19 final size:19
Alignment explanation
Indices: 40565020--40565079 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
40565010 AAATTTTTAA
* *
40565020 AATTTTT-TAAATTTTTTA
1 AATTTTTATAAATATTTTG
40565038 AATTTTTATAAATATTTTG
1 AATTTTTATAAATATTTTG
* *
40565057 TA-TTTTAAAAATTATTTTG
1 AATTTTTATAAA-TATTTTG
40565076 AATT
1 AATT
40565080 GTTTTATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
18 15 0.44
19 18 0.53
20 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (19 bp):
AATTTTTATAAATATTTTG
Found at i:40568587 original size:23 final size:23
Alignment explanation
Indices: 40568561--40568611 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
40568551 CAAGTTAGCT
40568561 TGTAATA-TCCCGAAAATTACTAC
1 TGTAATACT-CCGAAAATTACTAC
40568584 TGTAATACTCCGAAAATTACTAC
1 TGTAATACTCCGAAAATTACTAC
*
40568607 AGTAA
1 TGTAA
40568612 GAAAATATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATACTCCGAAAATTACTAC
Found at i:40571527 original size:17 final size:17
Alignment explanation
Indices: 40571505--40571543 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
40571495 TGAGCATTTT
40571505 GGGAACAAC-TCTATGTC
1 GGGAACAACATC-ATGTC
*
40571522 GGGAACAACATCATGTT
1 GGGAACAACATCATGTC
40571539 GGGAA
1 GGGAA
40571544 TGACTAGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (17 bp):
GGGAACAACATCATGTC
Found at i:40573480 original size:15 final size:16
Alignment explanation
Indices: 40573460--40573492 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
40573450 TAATAGCATG
40573460 ATTTAATTTT-TATTC
1 ATTTAATTTTATATTC
40573475 ATTTAATTTTATATTC
1 ATTTAATTTTATATTC
40573491 AT
1 AT
40573493 ATTTGGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTAATTTTATATTC
Found at i:40576478 original size:30 final size:31
Alignment explanation
Indices: 40576421--40576485 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
40576411 CTAGGTTTTT
*
40576421 TAAAATTTTAAATTAATCTTCTTAAAAATGA
1 TAAAAATTTAAATTAATCTTCTTAAAAATGA
* * *
40576452 TAAAAATTTAATTTAAT-TTTTTAAAAATTA
1 TAAAAATTTAAATTAATCTTCTTAAAAATGA
40576482 TAAA
1 TAAA
40576486 TATATAGGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (31 bp):
TAAAAATTTAAATTAATCTTCTTAAAAATGA
Found at i:40585863 original size:17 final size:17
Alignment explanation
Indices: 40585841--40585878 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
40585831 CTATTTTGCA
40585841 TTTGAATTATTTTATTT
1 TTTGAATTATTTTATTT
40585858 TTTGAATTATTTTATTT
1 TTTGAATTATTTTATTT
40585875 TTTG
1 TTTG
40585879 CACCGTCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (17 bp):
TTTGAATTATTTTATTT
Found at i:40599387 original size:29 final size:29
Alignment explanation
Indices: 40599346--40599447 Score: 70
Period size: 29 Copynumber: 3.5 Consensus size: 29
40599336 AAACATCGTA
40599346 AAAAAAATCTATAAAATATATAGAAATATAG
1 AAAAAAA--TATAAAATATATAGAAATATAG
*
40599377 AAAAAAATATAAAGTCATA-AGAAA-ATTA-
1 AAAAAAATATAAAAT-ATATAGAAATA-TAG
* * * *
40599405 TAAAAAATGTAAAGAAATATA-AAAT-TCG
1 AAAAAAATATAAA-ATATATAGAAATATAG
40599433 TAAAAAAATATAAAA
1 -AAAAAAATATAAAA
40599448 ATTATCGTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
27 1 0.02
28 19 0.34
29 26 0.46
30 3 0.05
31 7 0.12
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.24
Consensus pattern (29 bp):
AAAAAAATATAAAATATATAGAAATATAG
Found at i:40599425 original size:19 final size:20
Alignment explanation
Indices: 40599347--40599448 Score: 63
Period size: 19 Copynumber: 5.2 Consensus size: 20
40599337 AACATCGTAA
*
40599347 AAAAAATC-TATAAAATATAT
1 AAAAAATCGTA-AAAAAATAT
* *
40599367 AGAAATATAG-AAAAAAATAT
1 A-AAAAATCGTAAAAAAATAT
* * *
40599387 --AAAGTCATAAGAAAATTAT
1 AAAAAATCGTAA-AAAAATAT
*
40599406 AAAAAAT-GTAAAGAAATAT
1 AAAAAATCGTAAAAAAATAT
*
40599425 -AAAATTCGTAAAAAAATAT
1 AAAAAATCGTAAAAAAATAT
40599444 AAAAA
1 AAAAA
40599449 TTATCGTAAT
Statistics
Matches: 60, Mismatches: 14, Indels: 16
0.67 0.16 0.18
Matches are distributed among these distances:
17 3 0.05
18 7 0.12
19 24 0.40
20 16 0.27
21 10 0.17
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.24
Consensus pattern (20 bp):
AAAAAATCGTAAAAAAATAT
Done.