Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 129 of 185
Found at i:39683884 original size:21 final size:20
Alignment explanation
Indices: 39683834--39683904 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 20
39683824 AATATTAAAA
*
39683834 TATATATTTTTAATAATTTT
1 TATATATTTTAAATAATTTT
*
39683854 AATGAT-TTTTAAAATAATTTT
1 TAT-ATATTTT-AAATAATTTT
**
39683875 TATATATTTTTGA-AATTTT
1 TATATATTTTAAATAATTTT
39683894 TA-A-ATTTTAAA
1 TATATATTTTAAA
39683905 AAGTTAATTA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
17 6 0.15
18 1 0.02
19 8 0.20
20 9 0.22
21 17 0.41
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
TATATATTTTAAATAATTTT
Found at i:39685026 original size:21 final size:21
Alignment explanation
Indices: 39685002--39685051 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
39684992 AATTAGATTA
39685002 AATTATATATAAAAATTAAAT
1 AATTATATATAAAAATTAAAT
** *
39685023 AATTATAT-TCCATATTAAAT
1 AATTATATATAAAAATTAAAT
39685043 AA-TATATAT
1 AATTATATAT
39685052 TAATTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 5 0.20
20 12 0.48
21 8 0.32
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTATATATAAAAATTAAAT
Found at i:39691800 original size:42 final size:44
Alignment explanation
Indices: 39691741--39691838 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 44
39691731 CAAGTCAACA
* *
39691741 TAAAATGGCTTACAGGTCAACCGAAAATAAG-C-CATTTTTCAG
1 TAAAATGACTTACAGGTCAACAGAAAATAAGCCTCATTTTTCAG
* * *
39691783 TAAAATGACTTATAGGTCAACAGAAAATAAGCTCTCTTTTTTTAG
1 TAAAATGACTTACAGGTCAACAGAAAATAAGC-CTCATTTTTCAG
39691828 TAAAATGACTT
1 TAAAATGACTT
39691839 GTCATTTTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
42 28 0.58
44 1 0.02
45 19 0.40
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (44 bp):
TAAAATGACTTACAGGTCAACAGAAAATAAGCCTCATTTTTCAG
Found at i:39692003 original size:13 final size:14
Alignment explanation
Indices: 39691980--39692011 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
39691970 AATATTTAAA
39691980 AATATTAAAATATT
1 AATATTAAAATATT
39691994 AATA-TAAAATATT
1 AATATTAAAATATT
39692007 -ATATT
1 AATATT
39692012 TTTGAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 10 0.59
14 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATTAAAATATT
Found at i:39692094 original size:25 final size:22
Alignment explanation
Indices: 39692057--39692122 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 22
39692047 ATATTTAGTC
*
39692057 ATATAATAAATTATATTAATTA
1 ATATAATTAATTATATTAATTA
*
39692079 TATTCATAATTTATTATA-TAATTA
1 -A-T-ATAATTAATTATATTAATTA
*
39692103 ATATAATTAATTATTTTAAT
1 ATATAATTAATTATATTAAT
39692123 AAATTATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
21 11 0.31
22 5 0.14
23 2 0.06
24 7 0.19
25 11 0.31
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATAATTAATTATATTAATTA
Found at i:39692098 original size:37 final size:37
Alignment explanation
Indices: 39692057--39692130 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
39692047 ATATTTAGTC
* *
39692057 ATATAATAAAT-TATATTAATTATATTCATAATTTATT
1 ATATAATAAATATA-ATTAATTATATTAATAAATTATT
* *
39692094 ATATAATTAATATAATTAATTATTTTAATAAATTATT
1 ATATAATAAATATAATTAATTATATTAATAAATTATT
39692131 TAATATTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 30 0.94
38 2 0.06
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (37 bp):
ATATAATAAATATAATTAATTATATTAATAAATTATT
Found at i:39692172 original size:16 final size:16
Alignment explanation
Indices: 39692140--39692186 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
39692130 TTAATATTTC
*
39692140 AATTTTAATTTAATAAT
1 AATTTTAA-ATAATAAT
39692157 AAATTTTAAA-AATAAT
1 -AATTTTAAATAATAAT
39692173 AATTTTAAATAATA
1 AATTTTAAATAATA
39692187 TTCTTCACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 9 0.33
16 10 0.37
18 8 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTTAAATAATAAT
Found at i:39692237 original size:15 final size:15
Alignment explanation
Indices: 39692219--39692275 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
39692209 ATTCAATATT
39692219 AATATTTTAACAATA
1 AATATTTTAACAATA
*
39692234 AATATTTATTACAATTATA
1 AATATTT-TAAC-A--ATA
* *
39692253 AATATATTAATAATA
1 AATATTTTAACAATA
39692268 AATATTTT
1 AATATTTT
39692276 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 3 0.09
17 2 0.06
18 2 0.06
19 9 0.27
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAACAATA
Found at i:39696947 original size:44 final size:44
Alignment explanation
Indices: 39696886--39698195 Score: 228
Period size: 44 Copynumber: 29.6 Consensus size: 44
39696876 GATGCGATCT
* *
39696886 ACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCC
1 ACTCCACTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCC
* * * * * *
39696930 ACTCCACTGCAACTTCAGGGAGATAGAATTATCGGCTTCAATCTGATGTGATCT
1 ACTCCACTGTAACTTCAGAGAGAT--AA-GATCTG--T-AAT-T--T-TAATCC
* *
39696984 ACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTATTTTAATCC
1 ACTCCACTGTAACTTCAGAGAGATAAGAT-CTGTAATTTTAATCC
* * * ** * *
39697028 ACTCCACTGTAACTTCAGAGAGTTAGGAT-TACTAGCTTCAATCT
1 ACTCCACTGTAACTTCAGAGAGATAAGATCT-GTAATTTTAATCC
** * * * *** * *
39697072 ACTCCGTTATAATCTT-AGGGAGATAAGATCTCTGGCTTCAATCT
1 ACTCCACTGTAA-CTTCAGAGAGATAAGATCTGTAATTTTAATCC
* * * ** *
39697116 GCTCCACTGTAACCTCA-ATGAGATAAGATCTGAAATTCTTCGGTCT
1 ACTCCACTGTAACTTCAGA-GAGATAAGATCTGTAATT-TT-AATCC
* * *** *
39697162 ACTCCACTGTAACCTCAGGGAGATAAGATCTG--A-TGCGATCT
1 ACTCCACTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCC
* ** * * *
39697203 GCTCTGCTGTAACTTCAGAGAGATAAGATATTTTATTTTAATCC
1 ACTCCACTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCC
* * * ** * *
39697247 GCTCCACTGTAA-TCTCAGAGAGATAGGAT-TACTAGCTTCAATCT
1 ACTCCACTGTAACT-TCAGAGAGATAAGATCT-GTAATTTTAATCC
* * * * ***
39697291 GCTCCGCTGTAA-TCTCAGGGAGATAAGA-CT-TGATACGATAT--
1 ACTCCACTGTAACT-TCAGAGAGATAAGATCTGTAATTTTA-ATCC
** *
39697332 ACTTTACTGTAACTTCAGAGAGATAAGATCAT-TTATTTTAATCC
1 ACTCCACTGTAACTTCAGAGAGATAAGATC-TGTAATTTTAATCC
* * * * ** * *
39697376 GCTCCACTGCAA-TCTCAGGGAGATAAGAT-TACTAGCTTCAATCT
1 ACTCCACTGTAACT-TCAGAGAGATAAGATCT-GTAATTTTAATCC
* * * *** *
39697420 ACTCCGCTGTAA-TCTCAGGGAGATAAGA-CT-TGA-TACGATCT
1 ACTCCACTGTAACT-TCAGAGAGATAAGATCTGTAATTTTAATCC
* * *
39697461 ACTCTACTGTAACTTCAGAGAGATAAGATTCT-TTATTTTAATTC
1 ACTCCACTGTAACTTCAGAGAGATAAGA-TCTGTAATTTTAATCC
* * * * ** * *
39697505 GCTCCACTGTAA-TCTCAGGGAGATAGGAT-TACTAGCTTCAATCT
1 ACTCCACTGTAACT-TCAGAGAGATAAGATCT-GTAATTTTAATCC
* * * * *** *
39697549 GCTCCGCTGTAA-TCTCAGGGAGATAAGACCTG--A-TACGATCT
1 ACTCCACTGTAACT-TCAGAGAGATAAGATCTGTAATTTTAATCC
* * *
39697590 ACTCTACTGTAACTTCAGAGAGATAAGAT-TATTTATTTTAATCC
1 ACTCCACTGTAACTTCAGAGAGATAAGATCT-GTAATTTTAATCC
* * * ** * *
39697634 GCTCCACTGTAA-TCTCAG-GAAGATAGGAT-TACTAGCTTCAATCT
1 ACTCCACTGTAACT-TCAGAG-AGATAAGATCT-GTAATTTTAATCC
* * * *
39697678 GCTCCGCTGTAA-TCTCAGGGAGATAAGA-CTTGTGATTTTAATCC
1 ACTCCACTGTAACT-TCAGAGAGATAAGATC-TGTAATTTTAATCC
* * * * * *
39697722 ACTCCACTGCAACTTCAGGGAGATAGAATTATCGGCTTCAATCTGATGTGATCT
1 ACTCCACTGTAACTTCAGAGAGAT--AA-GATCTG--T-AAT-T--T-TAATCC
* *
39697776 ACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTATTTTAATCC
1 ACTCCACTGTAACTTCAGAGAGATAAGAT-CTGTAATTTTAATCC
* * * ** * *
39697820 ACTCCACTGTAACTTCAGAGAGTTAGGAT-TACTAGCTTCAATCT
1 ACTCCACTGTAACTTCAGAGAGATAAGATCT-GTAATTTTAATCC
* ** * * * * *
39697864 ACTTCGTTATAA-TCTCAGGGAGATAAGATCTGAAATTCTTCAGTCT
1 ACTCCACTGTAACT-TCAGAGAGATAAGATCTGTAATT-TT-AATCC
* * * *** *
39697910 ACTCCACTGTAACCTCAGGGAGATAAGA-CT-TGA-TGCGATCT
1 ACTCCACTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCC
* * * * *
39697951 ACTCTACCGTAACTTCAGAGAGATAAGATCATTTATTTTTAATAC
1 ACTCCACTGTAACTTCAGAGAGATAAGATC-TGTAATTTTAATCC
* * * * * ** *
39697996 GCTCCACTGTAACTTCAGGGAGATAGGATAGTGT--CTTCGATCT
1 ACTCCACTGTAACTTCAGAGAGATAAGAT-CTGTAATTTTAATCC
* * * ** * *
39698039 GCTCCGCTGTAA-TCTCAGGGAGATAAGATCTAAAATTTTTCAGTCT
1 ACTCCACTGTAACT-TCAGAGAGATAAGATCTGTAA-TTTT-AATCC
* * * * *** *
39698085 ATTCCACTGTAACCTCAGGGAGATAAGA-CT-TGA-TGCGATCT
1 ACTCCACTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCC
* * * * *
39698126 ACTCTACCGTAACTTCAGAGAGATAAGATCATTTATTTTTAATAC
1 ACTCCACTGTAACTTCAGAGAGATAAGATC-TGTAATTTTAATCC
* *
39698171 GCTCCACTGTAACTTCAGGGAGATA
1 ACTCCACTGTAACTTCAGAGAGATA
39698196 GGATAGTGTC
Statistics
Matches: 913, Mismatches: 264, Indels: 177
0.67 0.19 0.13
Matches are distributed among these distances:
40 1 0.00
41 160 0.18
42 18 0.02
43 56 0.06
44 433 0.47
45 72 0.08
46 88 0.10
47 8 0.01
48 5 0.01
49 4 0.00
50 4 0.00
51 6 0.01
52 6 0.01
53 2 0.00
54 50 0.05
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (44 bp):
ACTCCACTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCC
Found at i:39697043 original size:98 final size:98
Alignment explanation
Indices: 39696874--39697071 Score: 301
Period size: 98 Copynumber: 2.0 Consensus size: 98
39696864 AAGATAAGAC
39696874 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTG
* *
39696939 CAACTTCAGGGAGATAGAATTA-TCGGCTTCAAT
66 CAACTTCAGAGAGATAGAATTACT-AGCTTCAAT
* *
39696972 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTATTTTAATCCACTCCACT
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CTGTGATTTTAATCCACTCCACT
* * *
39697036 GTAACTTCAGAGAGTTAGGATTACTAGCTTCAAT
65 GCAACTTCAGAGAGATAGAATTACTAGCTTCAAT
39697070 CT
1 CT
39697072 ACTCCGTTAT
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
98 88 0.97
99 3 0.03
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (98 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTG
CAACTTCAGAGAGATAGAATTACTAGCTTCAAT
Found at i:39697341 original size:85 final size:85
Alignment explanation
Indices: 39697248--39697658 Score: 291
Period size: 85 Copynumber: 4.8 Consensus size: 85
39697238 TTTTAATCCG
* *
39697248 CTCCACTGTAATCTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG
1 CTCCACTGTAATCTCAGAGAGATAAGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
39697313 ATAAGACTTGATACGATATA
66 ATAAGACTTGATACGATATA
** * * * * * *
39697333 CTTTACTGTAA-CTTCAGAGAGATAAGATCATTTA-TTTTAATCCGCTCCACTGCAATCTCAGGG
1 CTCCACTGTAATC-TCAGAGAGATAAGATTA-CTAGCTTCAATCTGCTCCACTGTAATCTCAGGG
* * * * *
39697396 AGATAAGATTACTAGCTTCAATCTA
64 AGATAAG---ACTTGATACGATATA
* * * * * * * * *
39697421 CTCCGCTGTAATCTCAGGGAGATAAG---ACTTGATACGATCTACTCTACTGTAA-CTTCAGAGA
1 CTCCACTGTAATCTCAGAGAGATAAGATTACTAGCTTCAATCTGCTCCACTGTAATC-TCAGGGA
* *** *
39697482 GATAAGATTCTTTATTTTA-ATTCG
65 GATAAGA--CTTGATACGATA-T-A
* * *
39697506 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG
1 CTCCACTGTAATCTCAGAGAGATAAGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
* *
39697571 ATAAGACCTGATACGATCTA
66 ATAAGACTTGATACGATATA
* * * * * *
39697591 CTCTACTGTAA-CTTCAGAGAGATAAGATTATTTA-TTTTAATCCGCTCCACTGTAATCTCAGGA
1 CTCCACTGTAATC-TCAGAGAGATAAGATTA-CTAGCTTCAATCTGCTCCACTGTAATCTCAGGG
39697654 AGATA
64 AGATA
39697659 GGATTACTAG
Statistics
Matches: 244, Mismatches: 63, Indels: 38
0.71 0.18 0.11
Matches are distributed among these distances:
82 1 0.00
84 10 0.04
85 159 0.65
86 10 0.04
88 62 0.25
89 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (85 bp):
CTCCACTGTAATCTCAGAGAGATAAGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
ATAAGACTTGATACGATATA
Found at i:39697344 original size:129 final size:129
Alignment explanation
Indices: 39697163--39697709 Score: 918
Period size: 129 Copynumber: 4.2 Consensus size: 129
39697153 CTTCGGTCTA
* * * * *
39697163 CTCCACTGTAACCTCAGGGAGATAAGA-TCTGATGCGATCTGCTCTGCTGTAACTTCAGAGAGAT
1 CTCCGCTGTAATCTCAGGGAGATAAGACT-TGATACGATCTACTCTACTGTAACTTCAGAGAGAT
*
39697227 AAGA-TATTTTATTTTAATCCGCTCCACTGTAATCTCAGAGAGATAGGATTACTAGCTTCAATCT
65 AAGATTA-TTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCT
39697291 G
129 G
* *
39697292 CTCCGCTGTAATCTCAGGGAGATAAGACTTGATACGATATACTTTACTGTAACTTCAGAGAGATA
1 CTCCGCTGTAATCTCAGGGAGATAAGACTTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
* * * *
39697357 AGATCATTTATTTTAATCCGCTCCACTGCAATCTCAGGGAGATAAGATTACTAGCTTCAATCTA
66 AGATTATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
39697421 CTCCGCTGTAATCTCAGGGAGATAAGACTTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
1 CTCCGCTGTAATCTCAGGGAGATAAGACTTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
* *
39697486 AGATTCTTTATTTTAATTCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
66 AGATTATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
*
39697550 CTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
1 CTCCGCTGTAATCTCAGGGAGATAAGACTTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
*
39697615 AGATTATTTATTTTAATCCGCTCCACTGTAATCTCAGGAAGATAGGATTACTAGCTTCAATCTG
66 AGATTATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
39697679 CTCCGCTGTAATCTCAGGGAGATAAGACTTG
1 CTCCGCTGTAATCTCAGGGAGATAAGACTTG
39697710 TGATTTTAAT
Statistics
Matches: 391, Mismatches: 25, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
129 389 0.99
130 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (129 bp):
CTCCGCTGTAATCTCAGGGAGATAAGACTTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
AGATTATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
Found at i:39697927 original size:46 final size:44
Alignment explanation
Indices: 39697877--39698244 Score: 151
Period size: 41 Copynumber: 8.4 Consensus size: 44
39697867 TCGTTATAAT
39697877 CTCAGGGAGATAAGATCTGAAATTCTTCAGTCTACTCCACTGTAAC
1 CTCAGGGAGATAAGATCT--AATTCTTCAGTCTACTCCACTGTAAC
** * * *
39697923 CTCAGGGAGATAAGA-CT--TGATGC-GATCTACTCTACCGTAAC
1 CTCAGGGAGATAAGATCTAATTCTTCAG-TCTACTCCACTGTAAC
* * * * * *
39697964 TTCAGAGAGATAAGATCATTTATT-TTTAATAC-GCTCCACTGTAAC
1 CTCAGGGAGATAAGATC--TAATTCTTCAGT-CTACTCCACTGTAAC
* * * * * *
39698009 TTCAGGGAGATAGGA--TAGTGTCTTC-GATCTGCTCCGCTGTAAT
1 CTCAGGGAGATAAGATCTAAT-TCTTCAG-TCTACTCCACTGTAAC
* *
39698052 CTCAGGGAGATAAGATCTAAAATTTTTCAGTCTATTCCACTGTAAC
1 CTCAGGGAGATAAGATCT--AATTCTTCAGTCTACTCCACTGTAAC
** * * *
39698098 CTCAGGGAGATAAGA-CT--TGATGC-GATCTACTCTACCGTAAC
1 CTCAGGGAGATAAGATCTAATTCTTCAG-TCTACTCCACTGTAAC
* * * * * *
39698139 TTCAGAGAGATAAGATCATTTATT-TTTAATAC-GCTCCACTGTAAC
1 CTCAGGGAGATAAGATC--TAATTCTTCAGT-CTACTCCACTGTAAC
* * * * *
39698184 TTCAGGGAGATAGGA--TAGTGTCTTC-GATCTACTCCGCTGTAAT
1 CTCAGGGAGATAAGATCTAAT-TCTTCAG-TCTACTCCACTGTAAC
39698227 CTCAGGGAGATAAGATCT
1 CTCAGGGAGATAAGATCT
39698245 CTAATATTTA
Statistics
Matches: 235, Mismatches: 56, Indels: 63
0.66 0.16 0.18
Matches are distributed among these distances:
40 2 0.01
41 63 0.27
42 6 0.03
43 53 0.23
44 2 0.01
45 56 0.24
46 50 0.21
47 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.30
Consensus pattern (44 bp):
CTCAGGGAGATAAGATCTAATTCTTCAGTCTACTCCACTGTAAC
Found at i:39698012 original size:45 final size:45
Alignment explanation
Indices: 39697772--39698195 Score: 164
Period size: 45 Copynumber: 9.6 Consensus size: 45
39697762 ATCTGATGTG
* * * *
39697772 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTA-TTTTA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCATTTATTTTTA
** * * * * * ** *
39697816 ATCCACTCCACTGTAACTTCAGAGAGTTAGGATTA-CTAGCTTCA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCATTTATTTTTA
* * ** * ** *
39697860 ATCTACTTCGTTATAA-TCTCAGGGAGATAAGATC-TGAAATTCTTCA
1 ATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCAT-TTATT-TTTA
* * * * ***
39697906 GTCTACTCCACTGTAACCTCAGGGAGATAAGA-C-TTGA--TGCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCATTTATTTTTA
* * * *
39697947 ATCTACTCTACCGTAACTTCAGAGAGATAAGATCATTTATTTTTA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCATTTATTTTTA
* * * * **
39697992 ATAC-GCTCCACTGTAACTTCAGGGAGATAGGAT-A-GTGTCTTCG
1 AT-CTGCTCCACTGTAACTTCAGGGAGATAAGATCATTTATTTTTA
* **
39698035 ATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATC-TAAAATTTTTCA
1 ATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCAT-TTATTTTT-A
* ** * * ***
39698081 GTCTATTCCACTGTAACCTCAGGGAGATAAGA-C-TTGA--TGCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCATTTATTTTTA
* * * *
39698122 ATCTACTCTACCGTAACTTCAGAGAGATAAGATCATTTATTTTTA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCATTTATTTTTA
39698167 ATAC-GCTCCACTGTAACTTCAGGGAGATA
1 AT-CTGCTCCACTGTAACTTCAGGGAGATA
39698196 GGATAGTGTC
Statistics
Matches: 274, Mismatches: 83, Indels: 45
0.68 0.21 0.11
Matches are distributed among these distances:
41 55 0.20
42 5 0.02
43 40 0.15
44 58 0.21
45 59 0.22
46 57 0.21
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (45 bp):
ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCATTTATTTTTA
Found at i:39698015 original size:86 final size:83
Alignment explanation
Indices: 39697765--39698195 Score: 341
Period size: 87 Copynumber: 5.0 Consensus size: 83
39697755 GGCTTCAATC
* *
39697765 TGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTA-TTTTAATCCACTCCACTG
1 TGATGCGATCTACTCTACCGTAACTTCAGAGAGATAAGAT-CTTTATTTTTAAT-CACTCCACTG
* * *
39697829 TAACTTCAGAGAGTTAGGAT
64 TAACTTCAGGGAGATAAGAT
* * * * ** * *
39697849 T-ACTAGC-TTC-AATCTACTTCGTTATAATCTCAGGGAGATAAGATCTGAAATTCTTCAGTCTA
1 TGA-T-GCGATCTACTCTAC--CG-TA-ACT-TCAGAGAGATAAGATCT-TTATT-TTTAATC-A
*
39697911 CTCCACTGTAACCTCAGGGAGATAAGACT
56 CTCCACTGTAACTTCAGGGAGATAAGA-T
*
39697940 TGATGCGATCTACTCTACCGTAACTTCAGAGAGATAAGATCATTTATTTTTAATACGCTCCACTG
1 TGATGCGATCTACTCTACCGTAACTTCAGAGAGATAAGATC-TTTATTTTTAAT-CACTCCACTG
*
39698005 TAACTTCAGGGAGATAGGAT
64 TAACTTCAGGGAGATAAGAT
* * * ** * * ** * *
39698025 AGTGTCTTCGATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTAAAATTTTTCAGTCTATTC
1 --TG-ATGCGATCTACTCTACCGTAACT-TCAGAGAGATAAGATCT-TTATTTTT-AATC-ACTC
*
39698089 CACTGTAACCTCAGGGAGATAAGACT
59 CACTGTAACTTCAGGGAGATAAGA-T
*
39698115 TGATGCGATCTACTCTACCGTAACTTCAGAGAGATAAGATCATTTATTTTTAATACGCTCCACTG
1 TGATGCGATCTACTCTACCGTAACTTCAGAGAGATAAGATC-TTTATTTTTAAT-CACTCCACTG
39698180 TAACTTCAGGGAGATA
64 TAACTTCAGGGAGATA
39698196 GGATAGTGTC
Statistics
Matches: 267, Mismatches: 52, Indels: 54
0.72 0.14 0.14
Matches are distributed among these distances:
83 7 0.03
84 4 0.01
85 3 0.01
86 55 0.21
87 64 0.24
88 59 0.22
89 30 0.11
90 33 0.12
91 5 0.02
92 7 0.03
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (83 bp):
TGATGCGATCTACTCTACCGTAACTTCAGAGAGATAAGATCTTTATTTTTAATCACTCCACTGTA
ACTTCAGGGAGATAAGAT
Found at i:39698062 original size:175 final size:175
Alignment explanation
Indices: 39697765--39698244 Score: 784
Period size: 175 Copynumber: 2.7 Consensus size: 175
39697755 GGCTTCAATC
* * * * *
39697765 TGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTA-TTTTAATCCACTCCACTG
1 TGATGCGATCTACTCTACCGTAACTTCAGAGAGATAAGATCATTTATTTTTAATACGCTCCACTG
* * * * * * *
39697829 TAACTTCAGAGAGTTAGGATTACTAG-CTTCAATCTACTTCGTTATAATCTCAGGGAGATAAGAT
66 TAACTTCAGGGAGATAGGA-TAGT-GTCTTCGATCTACTCCGCTGTAATCTCAGGGAGATAAGAT
*
39697893 CTGAAATTCTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACT
129 CTAAAATTCTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACT
39697940 TGATGCGATCTACTCTACCGTAACTTCAGAGAGATAAGATCATTTATTTTTAATACGCTCCACTG
1 TGATGCGATCTACTCTACCGTAACTTCAGAGAGATAAGATCATTTATTTTTAATACGCTCCACTG
*
39698005 TAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
66 TAACTTCAGGGAGATAGGATAGTGTCTTCGATCTACTCCGCTGTAATCTCAGGGAGATAAGATCT
* *
39698070 AAAATTTTTCAGTCTATTCCACTGTAACCTCAGGGAGATAAGACT
131 AAAATTCTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACT
39698115 TGATGCGATCTACTCTACCGTAACTTCAGAGAGATAAGATCATTTATTTTTAATACGCTCCACTG
1 TGATGCGATCTACTCTACCGTAACTTCAGAGAGATAAGATCATTTATTTTTAATACGCTCCACTG
39698180 TAACTTCAGGGAGATAGGATAGTGTCTTCGATCTACTCCGCTGTAATCTCAGGGAGATAAGATCT
66 TAACTTCAGGGAGATAGGATAGTGTCTTCGATCTACTCCGCTGTAATCTCAGGGAGATAAGATCT
39698245 CTAATATTTA
Statistics
Matches: 286, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
174 1 0.00
175 252 0.88
176 33 0.12
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (175 bp):
TGATGCGATCTACTCTACCGTAACTTCAGAGAGATAAGATCATTTATTTTTAATACGCTCCACTG
TAACTTCAGGGAGATAGGATAGTGTCTTCGATCTACTCCGCTGTAATCTCAGGGAGATAAGATCT
AAAATTCTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACT
Found at i:39699485 original size:7 final size:7
Alignment explanation
Indices: 39699473--39699519 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
39699463 TTAGCCTCTC
39699473 CATTTTT
1 CATTTTT
39699480 CA-TTTT
1 CATTTTT
39699486 CATTTTT
1 CATTTTT
*
39699493 CATGTTT
1 CATTTTT
*
39699500 CA-TTCT
1 CATTTTT
39699506 CATTTTT
1 CATTTTT
39699513 CATTTTT
1 CATTTTT
39699520 TTGACTTAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
6 10 0.29
7 24 0.71
ACGTcount: A:0.15, C:0.17, G:0.02, T:0.66
Consensus pattern (7 bp):
CATTTTT
Found at i:39699491 original size:13 final size:13
Alignment explanation
Indices: 39699473--39699519 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
39699463 TTAGCCTCTC
39699473 CATTTTTCATTTT
1 CATTTTTCATTTT
39699486 CATTTTTCATGTTT
1 CATTTTTCAT-TTT
*
39699500 CA-TTCTCATTTTT
1 CATTTTTCA-TTTT
39699513 CATTTTT
1 CATTTTT
39699520 TTGACTTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 20 0.69
14 9 0.31
ACGTcount: A:0.15, C:0.17, G:0.02, T:0.66
Consensus pattern (13 bp):
CATTTTTCATTTT
Found at i:39699502 original size:20 final size:20
Alignment explanation
Indices: 39699477--39699515 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39699467 CCTCTCCATT
*
39699477 TTTCATTTTCATTTTTCATG
1 TTTCATTCTCATTTTTCATG
39699497 TTTCATTCTCATTTTTCAT
1 TTTCATTCTCATTTTTCAT
39699516 TTTTTTGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTCATTCTCATTTTTCATG
Found at i:39708776 original size:37 final size:35
Alignment explanation
Indices: 39708707--39708802 Score: 97
Period size: 35 Copynumber: 2.7 Consensus size: 35
39708697 AAAAAGGGAA
*
39708707 GAAAATGAAAAAAATCAAAATCAAAGTAAAAAAAC
1 GAAAATGAAAAAAATCAAAATCAAAGAAAAAAAAC
*
39708742 GAAAATGAAAAATCAATCAAAATCAAA-AACAAAAAGAA
1 GAAAATGAAAAA--AATCAAAATCAAAGAA-AAAAA-AC
* * *
39708780 GAAAAAG-TAAAAATTAAAATCAA
1 GAAAATGAAAAAAATCAAAATCAA
39708803 GGTCAAAGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
35 23 0.44
36 1 0.02
37 21 0.40
38 7 0.13
ACGTcount: A:0.71, C:0.08, G:0.08, T:0.12
Consensus pattern (35 bp):
GAAAATGAAAAAAATCAAAATCAAAGAAAAAAAAC
Found at i:39709680 original size:14 final size:15
Alignment explanation
Indices: 39709655--39709683 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39709645 ACCAATTCAA
39709655 AAAAAATGAAAAATG
1 AAAAAATGAAAAATG
39709670 AAAAAAT-AAAAATG
1 AAAAAATGAAAAATG
39709684 GAGAGCCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (15 bp):
AAAAAATGAAAAATG
Found at i:39711883 original size:128 final size:128
Alignment explanation
Indices: 39710876--39711864 Score: 1546
Period size: 128 Copynumber: 7.7 Consensus size: 128
39710866 ATTAGTGAAT
* * *
39710876 ATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCTC
1 ATTGTAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATC-T--TC
* * * * * *
39710941 AGGAGTAGGGAAACAGATTTAAGCCACAAGTTCTATGTCCCTGACCAGCAGTGGAATAGGTTGGA
63 AAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGAAATAGGTTGGA
39711006 A
128 A
* *
39711007 ATTGTAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCTC
1 ATTGTAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATC-T--TC
* * * * * *
39711072 AGGAGTAGGGAAACAGATTTAAGCCACAAGTTCTATGTCCCTGACCAGCAGTGGAATAGGTTGGA
63 AAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGAAATAGGTTGGA
39711137 A
128 A
*
39711138 ATTGTAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
1 ATTGTAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
* *
39711203 TGTAATGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAA
66 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGAAATAGGTTGGAA
** **
39711266 ATTACAGATCTTGTCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
1 ATTGTAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
*
39711331 TGTAATGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGAAATAGGTTGGAA
66 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGAAATAGGTTGGAA
* * **
39711394 ATTGTAGATCTTGTCTCCCTAAGAAGTAGCGGAGCAGATCAAAGACGAAGAATCTTATCTTCAAG
1 ATTGTAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
39711459 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGAAATAGGTTGGAA
66 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGAAATAGGTTGGAA
* * **
39711522 ATTGTAGATCTTGTCTCCCTAAGAAGTAGCGGAGCAGATCAAAGACGAAGAATCTTATCTTCAAG
1 ATTGTAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
39711587 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGAAATAGGTTGGAA
66 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGAAATAGGTTGGAA
** * * **
39711650 ATTGTAGATCTTGTCTCCCGGAGGAGTAGCGGAGCAGATCAAAGACGAAGAATCTTATCTTCAAG
1 ATTGTAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
39711715 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGAAATAGGTTGGAA
66 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGAAATAGGTTGGAA
*
39711778 ATTGTAGATCTTGTCTCCCTAAGCAGTAGCGAAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
1 ATTGTAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
* *
39711843 TGTAAGGAAGCAAATTGAAGCC
66 TGTAAGGAAGCAGATTTAAGCC
39711865 GATAATCCTG
Statistics
Matches: 825, Mismatches: 33, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
128 636 0.77
130 1 0.00
131 188 0.23
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25
Consensus pattern (128 bp):
ATTGTAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGAAATAGGTTGGAA
Found at i:39712094 original size:44 final size:44
Alignment explanation
Indices: 39711875--39712114 Score: 177
Period size: 44 Copynumber: 5.5 Consensus size: 44
39711865 GATAATCCTG
* *
39711875 TCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCGGATTGAAGTAATAGATCTTA
* * * * * * *
39711919 TCTCTCTGAAGTTGCAGTAGAGTGGATCGTA-TCA-AG-GCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCGGATTGAAGTAATAGATCTTA
* ** * * * * * *
39711960 TCCCCCTGAAGTCACAGTGGGGCAGACTGAAG-AAGCAAATCTTG
1 TCTCCCTGAAGTTGCAGTGGAGCGGATTGAAGTAA-TAGATCTTA
* * *
39712004 TCTCCCT-AAGGTTGCAGTGGAGCAGATTGAAGTCGATA-ATCCTA
1 TCTCCCTGAA-GTTGCAGTGGAGCGGATTGAAGT-AATAGATCTTA
* *
39712048 TCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCGGATTGAAGTAATAGATCTTA
* * *
39712092 TCTCTCTGAAGTAGCAGTAGAGC
1 TCTCCCTGAAGTTGCAGTGGAGC
39712115 AGAACGCATC
Statistics
Matches: 145, Mismatches: 42, Indels: 18
0.71 0.20 0.09
Matches are distributed among these distances:
41 25 0.17
42 2 0.01
43 8 0.06
44 106 0.73
45 3 0.02
46 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (44 bp):
TCTCCCTGAAGTTGCAGTGGAGCGGATTGAAGTAATAGATCTTA
Found at i:39723662 original size:20 final size:20
Alignment explanation
Indices: 39723613--39723670 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
39723603 CATTGATTTA
* *
39723613 TTTTTTTTTTATTTCTAGTTG
1 TTTTTATTTT-TTGCTAGTTG
39723634 TACTTTTATTTTTTGCTAGTTG
1 T--TTTTATTTTTTGCTAGTTG
*
39723656 TTTTTATTTTATGCT
1 TTTTTATTTTTTGCT
39723671 GAGACTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 13 0.41
21 1 0.03
22 10 0.31
23 8 0.25
ACGTcount: A:0.12, C:0.07, G:0.10, T:0.71
Consensus pattern (20 bp):
TTTTTATTTTTTGCTAGTTG
Found at i:39727263 original size:30 final size:30
Alignment explanation
Indices: 39727229--39727285 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
39727219 ACACTTATCA
*
39727229 TATTTCATATGT-TTTTAGAACTTTTTTTTT
1 TATTTCATAT-TCTTTTAGAACTCTTTTTTT
*
39727259 TATTTCATGTTCTTTTAGAACTCTTTT
1 TATTTCATATTCTTTTAGAACTCTTTT
39727286 ATAAAGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.19, C:0.11, G:0.07, T:0.63
Consensus pattern (30 bp):
TATTTCATATTCTTTTAGAACTCTTTTTTT
Found at i:39735110 original size:41 final size:41
Alignment explanation
Indices: 39735053--39735138 Score: 172
Period size: 41 Copynumber: 2.1 Consensus size: 41
39735043 TTATCCTAAA
39735053 AAGTGAAGAGAAAAATCATCAGTAGTTCAAACTTAATCAAG
1 AAGTGAAGAGAAAAATCATCAGTAGTTCAAACTTAATCAAG
39735094 AAGTGAAGAGAAAAATCATCAGTAGTTCAAACTTAATCAAG
1 AAGTGAAGAGAAAAATCATCAGTAGTTCAAACTTAATCAAG
39735135 AAGT
1 AAGT
39735139 CACATTCTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.49, C:0.12, G:0.17, T:0.22
Consensus pattern (41 bp):
AAGTGAAGAGAAAAATCATCAGTAGTTCAAACTTAATCAAG
Found at i:39737793 original size:23 final size:23
Alignment explanation
Indices: 39737765--39737827 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 23
39737755 TTTTCACAAA
39737765 CAAATTCTCTCTCAAATTTCC-TC
1 CAAATT-TCTCTCAAATTTCCTTC
39737788 TC-AATTTCCTCTC-AATTTCCTTC
1 -CAAATTT-CTCTCAAATTTCCTTC
39737811 CAAATTTCTCTCAAATT
1 CAAATTTCTCTCAAATT
39737828 CATATTTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
22 14 0.40
23 20 0.57
24 1 0.03
ACGTcount: A:0.25, C:0.32, G:0.00, T:0.43
Consensus pattern (23 bp):
CAAATTTCTCTCAAATTTCCTTC
Found at i:39737795 original size:11 final size:11
Alignment explanation
Indices: 39737773--39737808 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
39737763 AACAAATTCT
39737773 CTCTCAAATTTC
1 CTCTC-AATTTC
39737785 CTCTCAATTTC
1 CTCTCAATTTC
39737796 CTCTCAATTTC
1 CTCTCAATTTC
39737807 CT
1 CT
39737809 TCCAAATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 19 0.79
12 5 0.21
ACGTcount: A:0.19, C:0.36, G:0.00, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:39737807 original size:22 final size:22
Alignment explanation
Indices: 39737765--39737824 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 22
39737755 TTTTCACAAA
39737765 CAAATTCTCTCTCAAATTTCC-TC
1 CAAATT-TCTCTC-AATTTCCTTC
39737788 TC-AATTTCCTCTCAATTTCCTTC
1 -CAAATTT-CTCTCAATTTCCTTC
39737811 CAAATTTCTCTCAA
1 CAAATTTCTCTCAA
39737825 ATTCATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
22 16 0.48
23 16 0.48
24 1 0.03
ACGTcount: A:0.25, C:0.33, G:0.00, T:0.42
Consensus pattern (22 bp):
CAAATTTCTCTCAATTTCCTTC
Found at i:39737825 original size:11 final size:11
Alignment explanation
Indices: 39737765--39737827 Score: 60
Period size: 11 Copynumber: 5.5 Consensus size: 11
39737755 TTTTCACAAA
39737765 CAAATTCTCTCT
1 CAAATT-TCTCT
39737777 CAAATTTCCTCT
1 CAAATTT-CTCT
39737789 C-AATTTCCTCT
1 CAAATTT-CTCT
39737800 C-AATTTC-CTT
1 CAAATTTCTC-T
39737810 CCAAATTTCTCT
1 -CAAATTTCTCT
39737822 CAAATT
1 CAAATT
39737828 CATATTTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
9 1 0.02
10 2 0.04
11 24 0.52
12 18 0.39
13 1 0.02
ACGTcount: A:0.25, C:0.32, G:0.00, T:0.43
Consensus pattern (11 bp):
CAAATTTCTCT
Found at i:39737885 original size:51 final size:51
Alignment explanation
Indices: 39737786--39737885 Score: 137
Period size: 51 Copynumber: 2.0 Consensus size: 51
39737776 TCAAATTTCC
* *
39737786 TCTCAATTTCCTCTCAATTTCCTTCCAAATTTCTCTCAAATTCATATTTAA
1 TCTCAATTACCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAA
* ** * *
39737837 TCTCAATTAGCTCTCAATTTCCTTTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTACCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTT
39737886 TTAAATAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.26, C:0.26, G:0.01, T:0.47
Consensus pattern (51 bp):
TCTCAATTACCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAA
Found at i:39739066 original size:7 final size:7
Alignment explanation
Indices: 39739054--39739079 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39739044 TAGTCGATTG
39739054 GTATTTA
1 GTATTTA
39739061 GTATTTA
1 GTATTTA
39739068 GTATTTA
1 GTATTTA
39739075 GTATT
1 GTATT
39739080 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:39740373 original size:21 final size:21
Alignment explanation
Indices: 39740349--39740881 Score: 175
Period size: 22 Copynumber: 24.6 Consensus size: 21
39740339 TAACCCTAAT
*
39740349 CCTAACACTTAACTTAAAAAC
1 CCTAACCCTTAACTTAAAAAC
*
39740370 CCTAACCCTTCAA-TTAAAAAT
1 CCTAACCCTT-AACTTAAAAAC
*
39740391 ACTAACCCTTAACTTAAAAATC
1 CCTAACCCTTAACTTAAAAA-C
* *
39740413 CCAAACCCTAAACTTAAAAACCATAAAC
1 CCTAACCCTTAACTT----A--A-AAAC
* *
39740441 CCTAAACCTTAAACCTAAAAAC
1 CCTAACCCTT-AACTTAAAAAC
* *
39740463 CATAACCTTTAACTTAAAAAC
1 CCTAACCCTTAACTTAAAAAC
* * *
39740484 CTCAAACCCTAAACCTAAAAA-
1 C-CTAACCCTTAACTTAAAAAC
* * *
39740505 CATAACCCTTAACCTAAAACC
1 CCTAACCCTTAACTTAAAAAC
*
39740526 CCTAAACCCTAAACTTAAAAAC
1 CCT-AACCCTTAACTTAAAAAC
* *
39740548 CTTAAACCCTAAAACTTTAGCTTTCAAAAC
1 CCT-AACCCT-TAAC-TTA------AAAAC
*
39740578 CCTAA-CCTTAATCCT---AAC
1 CCTAACCCTTAA-CTTAAAAAC
39740596 CCTTAA--C-T----TAAAAAC
1 CC-TAACCCTTAACTTAAAAAC
39740611 CCTAACCCTTAAAC-TAAAAAC
1 CCTAACCCTT-AACTTAAAAAC
**
39740632 GTTAACCCTTAAC-TAAAAACC
1 CCTAACCCTTAACTTAAAAA-C
* *
39740653 CCAAACCCTAAAC-TAAAAAC
1 CCTAACCCTTAACTTAAAAAC
* * *
39740673 CATAAACCATAAACTTAAAAATC
1 CCT-AACCCTTAACTTAAAAA-C
* * * *
39740696 CCAAACTCTAAACTAAAAAAC
1 CCTAACCCTTAACTTAAAAAC
* * *
39740717 CTTAAACTCTAAACTTAAAAACC
1 CCT-AACCCTTAACTTAAAAA-C
* * * *
39740740 CCAAACACTAAACCTAAAAAC
1 CCTAACCCTTAACTTAAAAAC
*
39740761 ACTAA-CCTTAAACTTAAAAAC
1 CCTAACCCTT-AACTTAAAAAC
* * *
39740782 CCTAAACCCTAAAC-CATAAAAT
1 CCT-AACCCTTAACTTA-AAAAC
*
39740804 CCTAAACCTTAAACTTAAAAAC
1 CCTAACCCTT-AACTTAAAAAC
* * *
39740826 CATGAACCCTAAACCTAAAAAC
1 CCT-AACCCTTAACTTAAAAAC
* * * *
39740848 CTTAAACCTTAAACTTTAAAAT
1 CCTAACCCTT-AACTTAAAAAC
*
39740870 CCTAAACCTTAA
1 CCTAACCCTTAA
39740882 AACCTTAACT
Statistics
Matches: 387, Mismatches: 77, Indels: 96
0.69 0.14 0.17
Matches are distributed among these distances:
12 1 0.00
14 3 0.01
15 5 0.01
16 1 0.00
17 2 0.01
18 6 0.02
19 3 0.01
20 30 0.08
21 117 0.30
22 164 0.42
23 18 0.05
24 3 0.01
25 1 0.00
26 1 0.00
27 3 0.01
28 13 0.03
29 9 0.02
30 7 0.02
ACGTcount: A:0.48, C:0.29, G:0.01, T:0.22
Consensus pattern (21 bp):
CCTAACCCTTAACTTAAAAAC
Found at i:39740553 original size:22 final size:22
Alignment explanation
Indices: 39740437--39740882 Score: 312
Period size: 22 Copynumber: 20.8 Consensus size: 22
39740427 TAAAAACCAT
* *
39740437 AAACCCTAAACCTTAAACCTAA
1 AAACCCTAAACCCTAAACTTAA
* * *
39740459 AAACCAT-AACCTTTAACTTAA
1 AAACCCTAAACCCTAAACTTAA
*
39740480 AAA-CCTCAAACCCTAAACCTAA
1 AAACCCT-AAACCCTAAACTTAA
* * *
39740502 AAA-CAT-AACCCTTAACCTAA
1 AAACCCTAAACCCTAAACTTAA
*
39740522 AACCCCTAAACCCTAAACTTAA
1 AAACCCTAAACCCTAAACTTAA
* *
39740544 AAACCTTAAACCCTAAAACTTTA
1 AAACCCTAAACCCT-AAACTTAA
***** * *
39740567 GCTTTCAAAACCCTAACCTTAA
1 AAACCCTAAACCCTAAACTTAA
* *
39740589 T---CCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTAAACTTAA
39740607 AAACCCT-AACCCTTAAAC-TAA
1 AAACCCTAAACCC-TAAACTTAA
* * *
39740628 AAA-CGTTAACCCTTAAC-TAA
1 AAACCCTAAACCCTAAACTTAA
*
39740648 AAACCCCAAACCCTAAAC-TAA
1 AAACCCTAAACCCTAAACTTAA
* *
39740669 AAACCATAAACCATAAACTTAA
1 AAACCCTAAACCCTAAACTTAA
* *
39740691 AAATCCC-AAACTCTAAACTAAA
1 AAA-CCCTAAACCCTAAACTTAA
* *
39740713 AAACCTTAAACTCTAAACTTAA
1 AAACCCTAAACCCTAAACTTAA
* * *
39740735 AAACCCCAAACACTAAACCTAA
1 AAACCCTAAACCCTAAACTTAA
* *
39740757 AAACACT-AACCTTAAACTTAA
1 AAACCCTAAACCCTAAACTTAA
*
39740778 AAACCCTAAACCCTAAAC-CATA
1 AAACCCTAAACCCTAAACTTA-A
* *
39740800 AAATCCTAAACCTTAAACTTAA
1 AAACCCTAAACCCTAAACTTAA
* * *
39740822 AAACCATGAACCCTAAACCTAA
1 AAACCCTAAACCCTAAACTTAA
* * *
39740844 AAACCTTAAACCTTAAACTTTA
1 AAACCCTAAACCCTAAACTTAA
* *
39740866 AAATCCTAAACCTTAAA
1 AAACCCTAAACCCTAAA
39740883 ACCTTAACTT
Statistics
Matches: 333, Mismatches: 74, Indels: 34
0.76 0.17 0.08
Matches are distributed among these distances:
18 12 0.04
19 1 0.00
20 29 0.09
21 84 0.25
22 190 0.57
23 17 0.05
ACGTcount: A:0.49, C:0.29, G:0.01, T:0.21
Consensus pattern (22 bp):
AAACCCTAAACCCTAAACTTAA
Found at i:39740822 original size:6 final size:7
Alignment explanation
Indices: 39740764--39740889 Score: 62
Period size: 7 Copynumber: 17.1 Consensus size: 7
39740754 TAAAAACACT
39740764 AACCTTA
1 AACCTTA
39740771 AA-CTTAAA
1 AACCTT--A
*
39740779 AACCCTA
1 AACCTTA
*
39740786 AACCCTA
1 AACCTTA
*
39740793 AACCATAA
1 AACC-TTA
39740801 AATCC-TA
1 AA-CCTTA
39740808 AACCTTA
1 AACCTTA
39740815 AA-CTTAAA
1 AACCTT--A
* *
39740823 AACCATG
1 AACCTTA
*
39740830 AACCCTA
1 AACCTTA
*
39740837 AACCTAAA
1 AACCT-TA
39740845 AACCTTA
1 AACCTTA
39740852 AACCTTA
1 AACCTTA
*
39740859 AACTTTAA
1 AACCTT-A
39740867 AATCC-TA
1 AA-CCTTA
39740874 AACCTTAA
1 AACCTT-A
39740882 AACCTTA
1 AACCTTA
39740889 A
1 A
39740890 CTTAAAAACC
Statistics
Matches: 92, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
6 10 0.11
7 49 0.53
8 26 0.28
9 7 0.08
ACGTcount: A:0.49, C:0.27, G:0.01, T:0.23
Consensus pattern (7 bp):
AACCTTA
Found at i:39740884 original size:8 final size:8
Alignment explanation
Indices: 39740836--39740889 Score: 53
Period size: 8 Copynumber: 7.1 Consensus size: 8
39740826 CATGAACCCT
*
39740836 AAACCTAA
1 AAACCTTA
39740844 AAACCTT-
1 AAACCTTA
39740851 AAACCTT-
1 AAACCTTA
*
39740858 AAACTTTA
1 AAACCTTA
39740866 AAATCC-T-
1 AAA-CCTTA
39740873 AAACCTTA
1 AAACCTTA
39740881 AAACCTTA
1 AAACCTTA
39740889 A
1 A
39740890 CTTAAAAACC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 2 0.05
7 17 0.44
8 19 0.49
9 1 0.03
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (8 bp):
AAACCTTA
Found at i:39744731 original size:125 final size:124
Alignment explanation
Indices: 39744400--39744736 Score: 424
Period size: 125 Copynumber: 2.7 Consensus size: 124
39744390 CTCTAAGCTA
* * *
39744400 CGAAATAATTTTTTCAGAACCTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATT
1 CGAAATTATTTTTCCAGGACCTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATT
* *
39744465 ATTCTCATAAAGCATCCTAG-TAGAAGCAATTTTATACTATTTGCTCAGAAACGTCAACT
66 CTTCTCATAAAGCATCCT-GCTTGAAGCAATTTTATACTATTTGCTCAGAAACGTCAACT
* * ** * * *
39744524 CGAAATTATTTCTTCCAGGACCAATTGTAGCAAAAGTACGTCCAGGAGAGCGCGATTTCACAAAT
1 CGAAATTATTT-TTCCAGGACCTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAAT
* * * * *
39744589 TCTTCGCATATAGCATCCTGCTTGAAGTATTTTTTATACTATTTGCTCGGAAACGTCAACT
65 TCTTCTCATAAAGCATCCTGCTTGAAGCA-ATTTTATACTATTTGCTCAGAAACGTCAACT
* * * * *
39744650 CGAAATTATTTTTCCAGGACCTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTGCAAAAATC
1 CGAAATTATTTTTCCAGGACCTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATT
* *
39744715 CTTCTAATAAATCATCCTGCTT
66 CTTCTCATAAAGCATCCTGCTT
39744737 TGATTTTATC
Statistics
Matches: 177, Mismatches: 33, Indels: 5
0.82 0.15 0.02
Matches are distributed among these distances:
124 11 0.06
125 126 0.71
126 40 0.23
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (124 bp):
CGAAATTATTTTTCCAGGACCTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATT
CTTCTCATAAAGCATCCTGCTTGAAGCAATTTTATACTATTTGCTCAGAAACGTCAACT
Found at i:39748248 original size:25 final size:24
Alignment explanation
Indices: 39748208--39748254 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
39748198 AAAATCTGAC
*
39748208 ATTTTTTCTATTCTCTTTCTCTCT
1 ATTTTTTCTATTCTCTCTCTCTCT
**
39748232 ATTTTTTCT-TTAGCTCTCTCTCT
1 ATTTTTTCTATTCTCTCTCTCTCT
39748255 GCCGAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.09, C:0.26, G:0.02, T:0.64
Consensus pattern (24 bp):
ATTTTTTCTATTCTCTCTCTCTCT
Found at i:39753616 original size:17 final size:19
Alignment explanation
Indices: 39753582--39753622 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
39753572 ATATACACAT
39753582 TAAAAAATATAAATATATA
1 TAAAAAATATAAATATATA
39753601 -AAAAAAT-TCAAA-ATATA
1 TAAAAAATAT-AAATATATA
39753618 TAAAA
1 TAAAA
39753623 TCTAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAAAAATATAAATATATA
Found at i:39753879 original size:21 final size:20
Alignment explanation
Indices: 39753848--39753900 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
39753838 TATAAATACT
* *
39753848 TTTTTTATTTTT-TTTATAA
1 TTTTTAATTTTTATATATAA
*
39753867 TTTTTCAATTTTTATATATTA
1 TTTTT-AATTTTTATATATAA
39753888 TTTTTAATTTTTA
1 TTTTTAATTTTTA
39753901 AAATTTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.17
20 14 0.48
21 10 0.34
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTAATTTTTATATATAA
Found at i:39764396 original size:18 final size:15
Alignment explanation
Indices: 39764365--39764405 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 15
39764355 TTGAGTAAAT
39764365 AAATATATTTTATACTA
1 AAATATATTTTATA--A
39764382 AAATATATATTTATAA
1 AAATATAT-TTTATAA
39764398 AAATATAT
1 AAATATAT
39764406 CAAAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.39
17 8 0.35
18 6 0.26
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATATATTTTATAA
Found at i:39764752 original size:214 final size:213
Alignment explanation
Indices: 39764391--39764833 Score: 698
Period size: 215 Copynumber: 2.1 Consensus size: 213
39764381 AAAATATATA
* * * *
39764391 TTTATAAAAATATATCAAAAATTATTATTAGTGGAATTAAGGGTAAAGCCAAAAAATTTTTTTTG
1 TTTAT-AAATTATATCAAAAATTATTATTAGTGAAATCAAGGGTAAAGCAAAAAAATTTTTTTTG
* * * *
39764456 GGTAAAATTAATTTATGTATTTTTTACTATGTTAAAAATACAATTTCATCATTTTAATAGCCTAA
65 AGTAAAATTAATTTATGTATTTTTTACGATATTAAAAATACAAATTCATCATTTTAATAGCCTAA
39764521 ATTTTTATAATTTTTAAATAA-TTAAATTAAAATTTTATCAT-TCTTAAGGGTTAAAGTGTAATT
130 ATTTTTATAATTTTTAAA-AATTTAAATTAAAATTTTATCATCT-TTAAGGGTTAAAGTGTAATT
39764584 TTACCAATACAAATTTAAAAT
193 TTACCAATACAAATTTAAAAT
*
39764605 TTTATAAATTATATCAACAAATTATTCTTAGTGAAATCAAGGGTAAAGACAAAAAAATTATTTTT
1 TTTATAAATTATATCAA-AAATTATTATTAGTGAAATCAAGGGTAAAG-CAAAAAAA-T-TTTTT
39764670 TTGAGTAAAATTAATTTATGTA-TTTTTACGATATTAAAAATACAAATT-ATCATTTTAATAGCC
62 TTGAGTAAAATTAATTTATGTATTTTTTACGATATTAAAAATACAAATTCATCATTTTAATAGCC
39764733 TAAATTTTTATAA-TTTTAAAAATTTTAAATTAAAATTTTATCATCTTTAAGGGTTAAAGTGTAA
127 TAAATTTTTATAATTTTTAAAAA-TTTAAATTAAAATTTTATCATCTTTAAGGGTTAAAGTGTAA
39764797 TTTTACCAATACAAATTTAAAAT
191 TTTTACCAATACAAATTTAAAAT
39764820 TTTATAAATTATAT
1 TTTATAAATTATAT
39764834 AGGGACTTAA
Statistics
Matches: 213, Mismatches: 9, Indels: 13
0.91 0.04 0.06
Matches are distributed among these distances:
213 13 0.06
214 39 0.18
215 110 0.52
216 25 0.12
217 26 0.12
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.43
Consensus pattern (213 bp):
TTTATAAATTATATCAAAAATTATTATTAGTGAAATCAAGGGTAAAGCAAAAAAATTTTTTTTGA
GTAAAATTAATTTATGTATTTTTTACGATATTAAAAATACAAATTCATCATTTTAATAGCCTAAA
TTTTTATAATTTTTAAAAATTTAAATTAAAATTTTATCATCTTTAAGGGTTAAAGTGTAATTTTA
CCAATACAAATTTAAAAT
Found at i:39770553 original size:17 final size:17
Alignment explanation
Indices: 39770531--39770566 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
39770521 CTAAACCATG
39770531 CTTCAAAGTTGACTCTT
1 CTTCAAAGTTGACTCTT
*
39770548 CTTCAAAGTTTACTCTT
1 CTTCAAAGTTGACTCTT
39770565 CT
1 CT
39770567 AAACCCATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.25, G:0.08, T:0.44
Consensus pattern (17 bp):
CTTCAAAGTTGACTCTT
Found at i:39770849 original size:41 final size:41
Alignment explanation
Indices: 39770787--39771063 Score: 337
Period size: 41 Copynumber: 6.8 Consensus size: 41
39770777 TTTTGAGGCA
* **
39770787 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTTGGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAGGGC
*
39770828 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATTCTCAGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAGGGC
* * *
39770869 TTTAACGAG-TTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
1 TTTAGCG-GCGTTTTTGGGAAAGCGCCGCTAATGCTCAGGGC
*
39770910 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAGGGA
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAGGGC
* * * *
39770951 TTTAGCGACGTTTTTGAGAAAGTGCCGCTAATGCTCAGGGA
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAGGGC
* * * * *
39770992 TTCAGTGGCG-TTTTGAGAATGCGCCGCTAATGCTC-GTGCC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAG-GGC
*
39771032 TTTAGCGGCGTTTTT-GAAAATGCGCCGCTAAT
1 TTTAGCGGCGTTTTTGGGAAA-GCGCCGCTAAT
39771064 AATAAAATCT
Statistics
Matches: 204, Mismatches: 27, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
39 1 0.00
40 35 0.17
41 167 0.82
42 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAGGGC
Found at i:39776419 original size:43 final size:43
Alignment explanation
Indices: 39776390--39776674 Score: 284
Period size: 43 Copynumber: 6.7 Consensus size: 43
39776380 TTTTTGCTAG
* * ***
39776390 AAGCGCCGCTAAAGGTCATGATCTTTAGTGGCGTTTGTAATAA
1 AAGCGCCGCTAAAGGTCGTGATCTTTAGCGGCGTTTGTGGGAA
* * * * * *
39776433 TAGCGCCGCTAAAGGTCATGATCTTTAGCAGCGATTATGGGAG
1 AAGCGCCGCTAAAGGTCGTGATCTTTAGCGGCGTTTGTGGGAA
* * *
39776476 AAGCGCTGCTAAAGGTCGTGGTCTATAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCGTGATCTTTAGCGGCGTTTGTGGGAA
* * * *
39776519 AAGTGCTGCTAAAGGTCGTGATCTATAGCGGTGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCGTGATCTTTAGCGGCGTTTGTGGGAA
* * *
39776562 AAGCGTCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGCG-A
1 AAGCGCCGCTAAAGGTCGTGATCTTTAGCGGCGTTTGTGGGAA
* * * * **
39776604 AAGTGTCGCTAAAGGTTGTGATCTATAGTAGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCGTGATCTTTAGCGGCGTTTGTGGGAA
* * * *
39776647 AAGTGTCGCTAAAGGTCTTGGTCTTTAG
1 AAGCGCCGCTAAAGGTCGTGATCTTTAG
39776675 TGACGTTTTT
Statistics
Matches: 202, Mismatches: 39, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
42 35 0.17
43 167 0.83
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.29
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCGTGATCTTTAGCGGCGTTTGTGGGAA
Found at i:39776530 original size:86 final size:86
Alignment explanation
Indices: 39776390--39776674 Score: 324
Period size: 86 Copynumber: 3.3 Consensus size: 86
39776380 TTTTTGCTAG
* * * * * * * * * *
39776390 AAGCGCCGCTAAAGGTCATGATCTTTAGTGGCGTTTGTAATAATAGCGCCGCTAAAGGTCATGAT
1 AAGCGTCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGAGAAAAGTGCTGCTAAAGGTCGTGAT
* * * *
39776455 CTTTAGCAGCGATTATGGGAG
66 CTATAGCAGCGTTTGTGGGAA
* *
39776476 AAGCG-CTGCTAAAGGTCGTGGTCTATAGCGGCGTTTGTGGGAAAAGTGCTGCTAAAGGTCGTGA
1 AAGCGTC-GCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGAGAAAAGTGCTGCTAAAGGTCGTGA
* *
39776540 TCTATAGCGGTGTTTGTGGGAA
65 TCTATAGCAGCGTTTGTGGGAA
* *
39776562 AAGCGTCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGCG-AAAGTG-TCGCTAAAGGTTGTGA
1 AAGCGTCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGAGAAAAGTGCT-GCTAAAGGTCGTGA
*
39776625 TCTATAGTAGCGTTTGTGGGAA
65 TCTATAGCAGCGTTTGTGGGAA
* *
39776647 AAGTGTCGCTAAAGGTCTTGGTCTTTAG
1 AAGCGTCGCTAAAGGTCGTGGTCTTTAG
39776675 TGACGTTTTT
Statistics
Matches: 171, Mismatches: 25, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
84 1 0.01
85 65 0.38
86 104 0.61
87 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.29
Consensus pattern (86 bp):
AAGCGTCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGAGAAAAGTGCTGCTAAAGGTCGTGAT
CTATAGCAGCGTTTGTGGGAA
Found at i:39776555 original size:129 final size:128
Alignment explanation
Indices: 39776396--39776663 Score: 315
Period size: 129 Copynumber: 2.1 Consensus size: 128
39776386 CTAGAAGCGC
* * * *
39776396 CGCTAAAGGTCATGATCTTTAGTGGCGTTTGTAATAATAGCGCCGCTAAAGGTCATGATCTTTAG
1 CGCTAAAGGTCATGATCTATAGCGGCGTTTGTAAGAAAAGCGCCGCTAAAGGTCATGATCTTTAG
* * *
39776461 CAGCGATTATGGGAGAAGCG-CTGCTAAAGGTCGTGGTCTATAGCGGCGTTTGTGGGAAAAGTG-
66 CAGCGATTATGCGA-AAGCGTC-GCTAAAGGTCGTGATCTATAGCAGCGTTTGTGGGAAAAGTGT
* * ** * * *
39776524 CTGCTAAAGGTCGTGATCTATAGCGGTGTTTGTGGGAAAAGCGTCGCTAAAGGTCGTGGTCTTTA
1 C-GCTAAAGGTCATGATCTATAGCGGCGTTTGTAAGAAAAGCGCCGCTAAAGGTCATGATCTTTA
* * * * * *
39776589 GCGGCGTTTGTGCGAAAGTGTCGCTAAAGGTTGTGATCTATAGTAGCGTTTGTGGGAAAAGTGT
65 GCAGCGATTATGCGAAAGCGTCGCTAAAGGTCGTGATCTATAGCAGCGTTTGTGGGAAAAGTGT
39776653 CGCTAAAGGTC
1 CGCTAAAGGTC
39776664 TTGGTCTTTA
Statistics
Matches: 117, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
128 52 0.44
129 65 0.56
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (128 bp):
CGCTAAAGGTCATGATCTATAGCGGCGTTTGTAAGAAAAGCGCCGCTAAAGGTCATGATCTTTAG
CAGCGATTATGCGAAAGCGTCGCTAAAGGTCGTGATCTATAGCAGCGTTTGTGGGAAAAGTGT
Found at i:39778936 original size:28 final size:29
Alignment explanation
Indices: 39778885--39778942 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
39778875 GTAGCGACAT
*
39778885 AATAATGAAATGGTAACAAAATAGTGAAAA
1 AATAATGAAATGGTAAAAAAATAGT-AAAA
39778915 AATAA-GAAATGG-AAAAAAATAGTAAAA
1 AATAATGAAATGGTAAAAAAATAGTAAAA
39778942 A
1 A
39778943 CAACAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 5 0.19
28 10 0.37
29 7 0.26
30 5 0.19
ACGTcount: A:0.66, C:0.02, G:0.16, T:0.17
Consensus pattern (29 bp):
AATAATGAAATGGTAAAAAAATAGTAAAA
Found at i:39779710 original size:25 final size:25
Alignment explanation
Indices: 39779666--39779725 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
39779656 TATTCTCTCA
39779666 AATTATTTTCCCCAAATCCCTAACTT
1 AATT-TTTTCCCCAAATCCCTAACTT
* * *
39779692 AGTTTTTTCCTCAATTCCCTAACTT
1 AATTTTTTCCCCAAATCCCTAACTT
39779717 AATTTTTTC
1 AATTTTTTC
39779726 TTTCCCATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 27 0.90
26 3 0.10
ACGTcount: A:0.25, C:0.27, G:0.02, T:0.47
Consensus pattern (25 bp):
AATTTTTTCCCCAAATCCCTAACTT
Found at i:39782334 original size:64 final size:64
Alignment explanation
Indices: 39782229--39782354 Score: 216
Period size: 64 Copynumber: 2.0 Consensus size: 64
39782219 AGGTAAGATG
*
39782229 GTCGATAGTTTTGGAAATTGACTGTTGTAAGTAATTCAGATTAAGTGACTGAGATTGAGTTTTT
1 GTCGATAGTTTTGGAAATTGACTGTTGTAAGTAATTCAGATTAAGTGACTAAGATTGAGTTTTT
* * *
39782293 GTCGATAGTTTTGGGAATTGATTGTTGTAAGTAATTTAGATTAAGTGACTAAGATTGAGTTT
1 GTCGATAGTTTTGGAAATTGACTGTTGTAAGTAATTCAGATTAAGTGACTAAGATTGAGTTT
39782355 CCAATTGTCG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.29, C:0.05, G:0.25, T:0.41
Consensus pattern (64 bp):
GTCGATAGTTTTGGAAATTGACTGTTGTAAGTAATTCAGATTAAGTGACTAAGATTGAGTTTTT
Found at i:39782701 original size:17 final size:19
Alignment explanation
Indices: 39782670--39782710 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
39782660 AAGGCCATTT
*
39782670 TGGGCTGTGT-GGGCCACA
1 TGGGCTGTGTAGGCCCACA
39782688 TGGGC-GTGTAGGCCCACA
1 TGGGCTGTGTAGGCCCACA
39782706 TGGGC
1 TGGGC
39782711 ATGCAATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.12, C:0.24, G:0.44, T:0.20
Consensus pattern (19 bp):
TGGGCTGTGTAGGCCCACA
Found at i:39786529 original size:30 final size:30
Alignment explanation
Indices: 39786495--39786551 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
39786485 TGCGGCATAA
39786495 TCTTGATGTCATGCATATTGAAAAGAATGT
1 TCTTGATGTCATGCATATTGAAAAGAATGT
39786525 TCTTGATGTCATGCATATTGAAAAGAA
1 TCTTGATGTCATGCATATTGAAAAGAA
39786552 ATTTTGCGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (30 bp):
TCTTGATGTCATGCATATTGAAAAGAATGT
Found at i:39788797 original size:7 final size:7
Alignment explanation
Indices: 39788785--39788816 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
39788775 AAACCACCAC
39788785 TATCTCA
1 TATCTCA
39788792 TATCTCA
1 TATCTCA
39788799 TATCTCA
1 TATCTCA
39788806 TATCTCA
1 TATCTCA
39788813 TATC
1 TATC
39788817 AATGCTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (7 bp):
TATCTCA
Found at i:39792749 original size:43 final size:44
Alignment explanation
Indices: 39792687--39792782 Score: 104
Period size: 43 Copynumber: 2.2 Consensus size: 44
39792677 GCGTTTTCCC
* * * * *
39792687 ACAAATGCCGTTATAGAACATAATCCTTAGCAGTGCTTTTA-CT
1 ACAAACGCCGCTAAAGAACATAATCCTTAGCAGCGCTTCTAGCT
* * * *
39792730 ACAAACGCCGCTAAAGAACATGATCTTTTGCGGCGCTTCTAGCT
1 ACAAACGCCGCTAAAGAACATAATCCTTAGCAGCGCTTCTAGCT
39792774 ACAAACGCC
1 ACAAACGCC
39792783 ACAACATGCT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
43 32 0.74
44 11 0.26
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (44 bp):
ACAAACGCCGCTAAAGAACATAATCCTTAGCAGCGCTTCTAGCT
Found at i:39795153 original size:26 final size:26
Alignment explanation
Indices: 39795101--39795175 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
39795091 GTCTCGATAT
*
39795101 AAGGCTCTTCGTAAGCTTCCCGCTTA
1 AAGGCTCTTCGTAAGCTTCCCGATTA
* *
39795127 AAGGCTCTTTGTAAGCTTCCTGATTA
1 AAGGCTCTTCGTAAGCTTCCCGATTA
* * * *
39795153 ATGGATC-TCCTAAGCTTTCCGAT
1 AAGGCTCTTCGTAAGCTTCCCGAT
39795176 ATGGCTTGCT
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
25 12 0.30
26 28 0.70
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (26 bp):
AAGGCTCTTCGTAAGCTTCCCGATTA
Found at i:39813698 original size:23 final size:21
Alignment explanation
Indices: 39813672--39813717 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
39813662 CATACTTCGT
*
39813672 TTATAGCATTTTATTATATATTA
1 TTATA-CATATTATT-TATATTA
39813695 TTATACATATTATTTATATTA
1 TTATACATATTATTTATATTA
39813716 TT
1 TT
39813718 GTTAGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
22 8 0.36
23 5 0.23
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (21 bp):
TTATACATATTATTTATATTA
Found at i:39822921 original size:23 final size:21
Alignment explanation
Indices: 39822895--39822935 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
39822885 AATTAAATTA
39822895 TATATATTATGATTTTAGTAT
1 TATATATTATGATTTTAGTAT
39822916 TATATATTATGATTTTAGTA
1 TATATATTATGATTTTAGTA
39822936 AATTCATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (21 bp):
TATATATTATGATTTTAGTAT
Found at i:39823096 original size:61 final size:60
Alignment explanation
Indices: 39822914--39823101 Score: 215
Period size: 61 Copynumber: 3.2 Consensus size: 60
39822904 TGATTTTAGT
39822914 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAAAATTTTATTAA
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT-AAAATTTTATTAA
* * * * * * * * * * *
39822975 ATTATATATTTTTATCTAATTATATTTA-ATAATAAT-TTTAA-ATT-ATATTTT-GTAGT
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAAATTTTATTA-A
39823031 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAA-AATTTTATTAA
39823092 ATTATATATT
1 ATTATATATT
39823102 TTTATCTTGC
Statistics
Matches: 98, Mismatches: 22, Indels: 14
0.73 0.16 0.10
Matches are distributed among these distances:
55 2 0.02
56 27 0.28
57 7 0.07
58 8 0.08
59 8 0.08
60 8 0.08
61 36 0.37
62 2 0.02
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (60 bp):
ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAAATTTTATTAA
Found at i:39825008 original size:23 final size:21
Alignment explanation
Indices: 39824982--39825022 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
39824972 AATTAAATTA
39824982 TATATATTATGATTTTAGTAT
1 TATATATTATGATTTTAGTAT
39825003 TATATATTATGATTTTAGTA
1 TATATATTATGATTTTAGTA
39825023 AATTCATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (21 bp):
TATATATTATGATTTTAGTAT
Found at i:39825069 original size:37 final size:37
Alignment explanation
Indices: 39825006--39825189 Score: 97
Period size: 38 Copynumber: 4.7 Consensus size: 37
39824996 TTAGTATTAT
* *
39825006 ATATTATG-ATTTTAGTAAATTCATATAAGAATATTTA
1 ATATTAAGAATTTTATTAAATT-ATATAAGAATATTTA
**** *
39825043 ATATTAAGAATTTTATTAAATTATATATTTTTATCTAATT
1 ATATTAAGAATTTTATTAAATTATATAAGAATAT-T--TA
* ** *
39825083 ATATTTAATAATAATAATT-TTAAATTATATTTTGTAGTA-TTA
1 ATA-TTAAGAAT--T--TTATTAAATTATA-TAAG-AATATTTA
* * *
39825125 TATCTTATG-ATTTTAGTAAATTCATATAAGAATATTTA
1 -ATATTAAGAATTTTATTAAATT-ATATAAGAATATTTA
39825163 ATATTAAGAATTTTATTAAATTATATA
1 ATATTAAGAATTTTATTAAATTATATA
39825190 TTTTTATTAA
Statistics
Matches: 108, Mismatches: 23, Indels: 32
0.66 0.14 0.20
Matches are distributed among these distances:
37 31 0.29
38 36 0.33
39 4 0.04
40 4 0.04
41 9 0.08
42 4 0.04
43 3 0.03
44 11 0.10
45 4 0.04
46 2 0.02
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.50
Consensus pattern (37 bp):
ATATTAAGAATTTTATTAAATTATATAAGAATATTTA
Found at i:39825301 original size:120 final size:120
Alignment explanation
Indices: 39824997--39825293 Score: 533
Period size: 120 Copynumber: 2.5 Consensus size: 120
39824987 ATTATGATTT
39824997 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
*
39825062 ATTATATATTTTTATCTAATTATATTTAATAATAATAATTTTAAATTATATTTTG
66 ATTATATATTTTTATCTAATTATATTTAATAATAATAATTTTAAATTATATTTTA
*
39825117 TAGTATTATATCTTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
*
39825182 ATTATATATTTTTAT-TAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
66 ATTATATATTTTTATCT-AATTATATTTAATAATAATAATTTTAAATTATATTTTA
* *
39825237 TATTATTATATATTATGATTTTAGTAAATTCATATAAGAAGATTTAATATTAAGAAT
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAAT
39825294 CGAATTAACA
Statistics
Matches: 170, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
119 1 0.01
120 169 0.99
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (120 bp):
TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
ATTATATATTTTTATCTAATTATATTTAATAATAATAATTTTAAATTATATTTTA
Found at i:39825473 original size:23 final size:21
Alignment explanation
Indices: 39825447--39825487 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
39825437 AATTAAATTA
39825447 TATATATTATGATTTTAGTAT
1 TATATATTATGATTTTAGTAT
39825468 TATATATTATGATTTTAGTA
1 TATATATTATGATTTTAGTA
39825488 AATTCATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (21 bp):
TATATATTATGATTTTAGTAT
Found at i:39825517 original size:16 final size:16
Alignment explanation
Indices: 39825496--39825538 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
39825486 TAAATTCATA
39825496 TAAGAATATTTAATAT
1 TAAGAATATTTAATAT
39825512 TAAGAATATTTAATAT
1 TAAGAATATTTAATAT
39825528 TAAGAAT-TTTA
1 TAAGAATATTTA
39825539 TTAAATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.15
16 23 0.85
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (16 bp):
TAAGAATATTTAATAT
Found at i:39825704 original size:120 final size:120
Alignment explanation
Indices: 39825462--39825929 Score: 782
Period size: 120 Copynumber: 3.9 Consensus size: 120
39825452 ATTATGATTT
39825462 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATATTTA--A
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAAT-TTTATTA
* * *
39825525 TATTA-AGAATTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
65 AATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
39825580 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
* *
39825645 ATTATATATTTTTATCT-AATTATATTTAATAATAATAATTTTAAATTATATTTTG
66 ATTATATATTTTTAT-TAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
*
39825700 TAGTATTATATCTTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
*
39825765 ATTATATATTTTTATTAAATTATATTTAATAATAATTACTTTAAATTATATTTTA
66 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
* *
39825820 TATTATTATATATTATGATTTTAGTAAATTCATATAAAAATATTTAATATTAAGAATTTTATTAA
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
* * *
39825885 ATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
66 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
39825930 ATATGATTAA
Statistics
Matches: 329, Mismatches: 16, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
117 4 0.01
118 57 0.17
119 6 0.02
120 261 0.79
121 1 0.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (120 bp):
TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
Found at i:39825901 original size:18 final size:17
Alignment explanation
Indices: 39825875--39825909 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39825865 AATATTAAGA
*
39825875 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39825892 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39825910 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39826119 original size:44 final size:45
Alignment explanation
Indices: 39826064--39826158 Score: 131
Period size: 44 Copynumber: 2.1 Consensus size: 45
39826054 CTATTACACA
*
39826064 TCCATTCCATTCAACCAAACACA-AGAA-TACTATTATGCCTCTAT
1 TCCATTCCATTCAACCAAACA-ATAGAATTACTATTACGCCTCTAT
* * *
39826108 TCCATTGCATTCAACCAAACAATTGAATTGCTATTACGCCTCTAT
1 TCCATTCCATTCAACCAAACAATAGAATTACTATTACGCCTCTAT
39826153 TCCATT
1 TCCATT
39826159 ACGCCTCTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 21 0.47
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (45 bp):
TCCATTCCATTCAACCAAACAATAGAATTACTATTACGCCTCTAT
Found at i:39829325 original size:12 final size:11
Alignment explanation
Indices: 39829310--39829340 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
39829300 TTTTTATTGT
39829310 TTATTATTATAA
1 TTATTATTAT-A
39829322 TTATTATTATA
1 TTATTATTATA
39829333 TTATTATT
1 TTATTATT
39829341 GTATGTACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATTATTATA
Found at i:39840953 original size:18 final size:18
Alignment explanation
Indices: 39840930--39840965 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
39840920 GACAACGCAC
39840930 TGAATTTGAATAACAGCA
1 TGAATTTGAATAACAGCA
39840948 TGAATTTGAATAACAGCA
1 TGAATTTGAATAACAGCA
39840966 CCATAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (18 bp):
TGAATTTGAATAACAGCA
Found at i:39843415 original size:37 final size:38
Alignment explanation
Indices: 39843365--39843442 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 38
39843355 TGAAGATAGC
* * *
39843365 AGATCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGA
1 AGATCCTGTCTTCCCATATTGGTAGCGAAGTAGATCAA
* *
39843402 AGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAA
1 AGATCCTGTCTTCCCATATTGGTAGCGAAGTAGATCAA
39843440 AGA
1 AGA
39843443 AAGTAGATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
37 22 0.63
38 13 0.37
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (38 bp):
AGATCCTGTCTTCCCATATTGGTAGCGAAGTAGATCAA
Found at i:39843433 original size:126 final size:126
Alignment explanation
Indices: 39843192--39844176 Score: 1529
Period size: 126 Copynumber: 7.7 Consensus size: 126
39843182 TTTAAGTTGC
* *
39843192 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCGGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
39843257 TTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAA
66 TTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAA
* * * * *
39843318 AGTAGATATTTTCTTTATGTATTGGCGTGAAGTAGATTGAAGATAGCAGATCCTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
39843383 TTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAA
66 TTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAA
* * * * *
39843444 AGTAGATATTTTCTTTATGTATTGGCGTGAAGTAGATTGAAGATAGCAGATCCTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* *
39843509 TTGGTAGCGAAGTGGATCGAAGATGCAGGTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAA
66 TTGGTAG-GAAGTGGATCG-A-A-G-A--TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAA
39843574 GAA
124 GAA
* *
39843577 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCGGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
39843642 TTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAA
66 TTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAA
* * * *
39843703 AGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAAATAGCAGATCTTGTATTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* *
39843768 TTGGTAGCGAAGTGGATCGAAGATGCAGGTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAA
66 TTGGTAG-GAAGTGGATCG-A-A-G-A--TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAA
39843833 GAA
124 GAA
* * *
39843836 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAGCAAATCCTATCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* * * *
39843901 TTAGTAGGAAGTAGATCGAAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA
66 TTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAA
*
39843962 AACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* *
39844027 TTGGTAGGAAGTGGATCTAAGATCTTGTCTTTCCATATTGGTGGCGAAGTAGATCAAAGAA
66 TTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAA
* *
39844088 AGCAGATCTTGTTTTCATGTATTGGCGTGAAGTAGATCGAAGATAGTAGATCCTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
39844153 TTGGTAGCGAAGTGGATCGAAGAT
66 TTGGTAG-GAAGTGGATCGAAGAT
39844177 GCAAATCTTG
Statistics
Matches: 795, Mismatches: 49, Indels: 29
0.91 0.06 0.03
Matches are distributed among these distances:
126 518 0.65
127 37 0.05
128 4 0.01
129 4 0.01
130 4 0.01
131 4 0.01
132 21 0.03
133 203 0.26
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (126 bp):
AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
TTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAA
Found at i:39843929 original size:385 final size:389
Alignment explanation
Indices: 39843192--39844191 Score: 1635
Period size: 385 Copynumber: 2.6 Consensus size: 389
39843182 TTTAAGTTGC
39843192 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCGGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCGGTCTTCCTATA
39843257 TTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAGTA
66 TTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAGTA
* * * *
39843322 GATATTTTCTTTATGTATTGGCGTGAAGTAGATTGAAGATAGCAGATCCTGTCTTCCTATATTGG
131 GATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGG
* *
39843387 TAG-GAAGTGGATCG-A-A-G-ATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAGT
196 TAGCGAAGTGGATCGAAGATGCATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAGC
* * * * * * *
39843447 AGATATTTTCTTTATGTATTGGCGTGAAGTAGATTGAAGATAGCAGATCCTGTCTTCCTATATTG
261 AGATATTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAGCAAATCCTATCTTCCTATATTA
*
39843512 GTAGCGAAGTGGATCGAAGATGCAGGTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA
326 GTAGCGAAGTAGATCGAAGATGCA-GTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA
39843577 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCGGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCGGTCTTCCTATA
39843642 TTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAGTA
66 TTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAGTA
* * *
39843707 GATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAAATAGCAGATCTTGTATTCCTATATTGG
131 GATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGG
*
39843772 TAGCGAAGTGGATCGAAGATGCAGGTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAA
196 TAGCGAAGTGGATCGAAGATGCA--TCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAA
*
39843837 GCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAGCAAATCCTATCTTCCTATAT
259 GCAGATATTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAGCAAATCCTATCTTCCTATAT
39843902 TAGTAG-GAAGTAGATCG-A-A-G-A-TCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA
324 TAGTAGCGAAGTAGATCGAAGATGCAGTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA
39843961 A
389 A
* * *
39843962 AACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCGGTCTTCCTATA
* * *
39844027 TTGGTAGGAAGTGGATCTAAGATCTTGTCTTTCCATATTGGTGGCGAAGTAGATCAAAGAAAGCA
66 TTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAGTA
* *
39844092 GATCTTGTTTTCATGTATTGGCGTGAAGTAGATCGAAGATAGTAGATCCTGTCTTCCTATATTGG
131 GATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGG
39844157 TAGCGAAGTGGATCGAAGATGCAAATCTTGTCTTC
196 TAGCGAAGTGGATCGAAGATGC--ATCTTGTCTTC
39844192 ATGTATTGGC
Statistics
Matches: 576, Mismatches: 30, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
385 446 0.77
386 11 0.02
387 3 0.01
388 2 0.00
389 2 0.00
390 2 0.00
391 10 0.02
392 100 0.17
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (389 bp):
AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCGGTCTTCCTATA
TTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAGTA
GATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGG
TAGCGAAGTGGATCGAAGATGCATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAGC
AGATATTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAGCAAATCCTATCTTCCTATATTA
GTAGCGAAGTAGATCGAAGATGCAGTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA
Found at i:39844065 original size:37 final size:38
Alignment explanation
Indices: 39844009--39844086 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
39843999 CGAAGATAGC
* *
39844009 AGATCCTGTCTTCCTATATTGGTAG-GAAGTGGATCTA
1 AGATCCTGTCTTCCTATATTGGTAGCGAAGTAGATCAA
* *
39844046 AGATCTTGTCTTTCC-ATATTGGTGGCGAAGTAGATCAA
1 AGATCCTGTC-TTCCTATATTGGTAGCGAAGTAGATCAA
39844084 AGA
1 AGA
39844087 AAGCAGATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 18 0.51
38 17 0.49
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.33
Consensus pattern (38 bp):
AGATCCTGTCTTCCTATATTGGTAGCGAAGTAGATCAA
Found at i:39844191 original size:259 final size:258
Alignment explanation
Indices: 39843192--39844176 Score: 1553
Period size: 259 Copynumber: 3.9 Consensus size: 258
39843182 TTTAAGTTGC
* *
39843192 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCGGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
*
39843257 TTGGTAG-GAAGTGGATCG-A-A-G-A-TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAG
66 TTGGTAGCGAAGTGGATCGAAGATGCAGTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAG
* * * * *
39843316 AAAGTAGATATTTTCTTTATGTATTGGCGTGAAGTAGATTGAAGATAGCAGATCCTGTCTTCCTA
131 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTA
39843381 TATTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAA
196 TATTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAA
* * * * *
39843444 AGTAGATATTTTCTTTATGTATTGGCGTGAAGTAGATTGAAGATAGCAGATCCTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
*
39843509 TTGGTAGCGAAGTGGATCGAAGATGCAGGTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAA
66 TTGGTAGCGAAGTGGATCGAAGATGCA-GTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAA
* *
39843574 GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCGGTCTTCCT
130 GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCT
39843639 ATATTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAA
195 ATATTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAA
* * * *
39843703 AGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAAATAGCAGATCTTGTATTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
*
39843768 TTGGTAGCGAAGTGGATCGAAGATGCAGGTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAA
66 TTGGTAGCGAAGTGGATCGAAGATGCA-GTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAA
* * *
39843833 GAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAGCAAATCCTATCTTCCT
130 GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCT
* * * *
39843898 ATATTAGTAGGAAGTAGATCGAAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA
195 ATATTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAA
*
39843962 AACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* * *
39844027 TTGGTAG-GAAGTGGATC-TA-A-G-A-TCTTGTCTTTCCATATTGGTGGCGAAGTAGATCAAAG
66 TTGGTAGCGAAGTGGATCGAAGATGCAGTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAG
* *
39844086 AAAGCAGATCTTGTTTTCATGTATTGGCGTGAAGTAGATCGAAGATAGTAGATCCTGTCTTCCTA
131 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTA
39844151 TATTGGTAGCGAAGTGGATCGAAGAT
196 TATTGGTAG-GAAGTGGATCGAAGAT
39844177 GCAAATCTTG
Statistics
Matches: 677, Mismatches: 48, Indels: 15
0.91 0.06 0.02
Matches are distributed among these distances:
252 167 0.25
253 26 0.04
254 2 0.00
255 2 0.00
256 2 0.00
257 2 0.00
258 10 0.01
259 466 0.69
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (258 bp):
AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
TTGGTAGCGAAGTGGATCGAAGATGCAGTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAG
AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTA
TATTGGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAA
Found at i:39844299 original size:385 final size:385
Alignment explanation
Indices: 39843194--39844307 Score: 1561
Period size: 385 Copynumber: 2.9 Consensus size: 385
39843184 TAAGTTGCAG
39843194 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCGGTCTTCCTATATT
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCGGTCTTCCTATATT
39843259 GGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAGTAGA
66 GGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAGTAGA
* * *
39843324 TATT-TTCTTTATGTATTGGCGTGAAGTAGATTGAAGATAGCAGATCCTGTCTTCCTATATTGGT
131 TCTTGTT-TTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGT
*
39843388 AG-GAAGTGGATCG-A-A-G--ATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAGT
195 AGCGAAGTGGATCGAAGATGCAATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAA-T
* ** * * * **
39843447 -AGAT-ATTTTCTTTATGTATTGGCGTGAAGTAGATTGAAGATAGCAGATCCTGTCTTCCTATAT
259 CAGATCATGTT-TTCCTATATTAGTGCAAAGTAGATTGAAGATAGCAGATCCTGTCTTCCTATAT
*
39843510 TGGTAGCGAAGTGGATCGAAGATGCAGGTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
323 TGGTA-CGAAGTAGATCG-A-A-G-A-GTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
*
39843575 AAAG
382 AAAA
39843579 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCGGTCTTCCTATATT
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCGGTCTTCCTATATT
39843644 GGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAGTAGA
66 GGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAGTAGA
* * * *
39843709 TCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAAATAGCAGATCTTGTATTCCTATATTGGTA
131 TCTTGTTTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTA
* * *
39843774 GCGAAGTGGATCGAAGATGCAGGTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGC
196 GCGAAGTGGATCGAAGATGCA-ATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAATC
* * * * * * *
39843839 AGATCTTGTCTTCATGTATT-G-GCATGAAGTAGATCGAAGATAGCAAATCCTATCTTCCTATAT
260 AGATCATGTTTTCCTATATTAGTGCA--AAGTAGATTGAAGATAGCAGATCCTGTCTTCCTATAT
* *
39843902 TAGTAGGAAGTAGATCGAAGA-TCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAA
323 TGGTACGAAGTAGATCGAAGAGTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAA
* *
39843964 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATT
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCGGTCTTCCTATATT
* * *
39844029 GGTAGGAAGTGGATCTAAGATCTTGTCTTTCCATATTGGTGGCGAAGTAGATCAAAGAAAGCAGA
66 GGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAGTAGA
*
39844094 TCTTGTTTTCATGTATTGGCGTGAAGTAGATCGAAGATAGTAGATCCTGTCTTCCTATATTGGTA
131 TCTTGTTTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTA
*** * * *
39844159 GCGAAGTGGATCGAAGATGCAAATCTTGTCTTCATGTATTGG-CGTGAAATAGATCGAAGAAATC
196 GCGAAGTGGATCGAAGATGC-AATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAATC
* * * * * *
39844223 AAATCATGTTTTCCTATATTAGTAGCAAAGTGGATTGAAGATAGCAGATCTTGTTTTCATGTATT
260 AGATCATGTTTTCCTATATTAGT-GCAAAGTAGATTGAAGATAGCAGATCCTGTCTTCCTATATT
* *
39844288 GGCATGAAGTAGATCGAAGA
324 GGTACGAAGTAGATCGAAGA
39844308 AAGCAAATCC
Statistics
Matches: 654, Mismatches: 59, Indels: 32
0.88 0.08 0.04
Matches are distributed among these distances:
384 33 0.05
385 495 0.76
386 13 0.02
387 5 0.01
388 2 0.00
389 2 0.00
390 2 0.00
391 11 0.02
392 89 0.14
393 2 0.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.31
Consensus pattern (385 bp):
CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCGGTCTTCCTATATT
GGTAGGAAGTGGATCGAAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAGTAGA
TCTTGTTTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTA
GCGAAGTGGATCGAAGATGCAATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAATCA
GATCATGTTTTCCTATATTAGTGCAAAGTAGATTGAAGATAGCAGATCCTGTCTTCCTATATTGG
TACGAAGTAGATCGAAGAGTCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAA
Found at i:39844337 original size:89 final size:89
Alignment explanation
Indices: 39844052--39844363 Score: 421
Period size: 89 Copynumber: 3.5 Consensus size: 89
39844042 TCTAAGATCT
* * *
39844052 TGTCTTTCC-ATATTGGTGGCGAAGTAGATCAAAGAAAGCAGATCTTGTTTTCATGTATTGGCGT
1 TGTC-TTCCTATATTGGTAGCGAAGTAGATCGAAGATAGCAGATCTTGTTTTCATGTATTGGCGT
* * *
39844116 GAAGTAGATCGAAGATAGTAGATCC
65 GAAGTAGATCGAAGAAAGCAAATCC
* * *
39844141 TGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGAT-GCAAATCTTGTCTTCATGTATTGGCGTG
1 TGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGCAGATCTTGTTTTCATGTATTGGCGTG
* * *
39844205 AAATAGATCGAAGAAATCAAATCA
66 AAGTAGATCGAAGAAAGCAAATCC
* * * * * *
39844229 TGTTTTCCTATATTAGTAGCAAAGTGGATTGAAGATAGCAGATCTTGTTTTCATGTATTGGCATG
1 TGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGCAGATCTTGTTTTCATGTATTGGCGTG
39844294 AAGTAGATCGAAGAAAGCAAATCC
66 AAGTAGATCGAAGAAAGCAAATCC
* *
39844318 TATCTTCCTATATTGGTAGCGAAGTAGATTGAAGATAGCAGATCTT
1 TGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGCAGATCTT
39844364 ATCTTCCCAT
Statistics
Matches: 194, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
88 80 0.41
89 114 0.59
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.32
Consensus pattern (89 bp):
TGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGCAGATCTTGTTTTCATGTATTGGCGTG
AAGTAGATCGAAGAAAGCAAATCC
Found at i:39846357 original size:100 final size:102
Alignment explanation
Indices: 39846216--39846423 Score: 375
Period size: 100 Copynumber: 2.1 Consensus size: 102
39846206 TTTTGTACCC
*
39846216 TTTTTTCTCTTTATATTTTTTGTTGTTGTTTATTTTGTTCATTTGCTTATTGATATATGTTTTCA
1 TTTTTTCTCTTTATATTTTTTGTTGTTGTTTATTTTCTTCATTTGCTTATTGATATATGTTTTCA
39846281 TTTATAATTTGTTCATTTGATACGTTACATGTCGTTG
66 TTTATAATTTGTTCATTTGATACGTTACATGTCGTTG
*
39846318 TTTTTT-TCTTTATATTTTTT-TTGTTGTTTATTTTCTTCATTTGCTTATTGATGTATGTTTTCA
1 TTTTTTCTCTTTATATTTTTTGTTGTTGTTTATTTTCTTCATTTGCTTATTGATATATGTTTTCA
*
39846381 TTTATAATTTGTTCATTTGATACTTTACATGTCGTTG
66 TTTATAATTTGTTCATTTGATACGTTACATGTCGTTG
39846418 TTTTTT
1 TTTTTT
39846424 ATGTACATTA
Statistics
Matches: 103, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
100 83 0.81
101 14 0.14
102 6 0.06
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.64
Consensus pattern (102 bp):
TTTTTTCTCTTTATATTTTTTGTTGTTGTTTATTTTCTTCATTTGCTTATTGATATATGTTTTCA
TTTATAATTTGTTCATTTGATACGTTACATGTCGTTG
Found at i:39852745 original size:14 final size:14
Alignment explanation
Indices: 39852726--39852753 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39852716 TCATTTACTC
39852726 ATTTACTCTCTTTT
1 ATTTACTCTCTTTT
39852740 ATTTACTCTCTTTT
1 ATTTACTCTCTTTT
39852754 CTTTTCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTACTCTCTTTT
Found at i:39853869 original size:3 final size:3
Alignment explanation
Indices: 39853861--39853950 Score: 92
Period size: 3 Copynumber: 30.3 Consensus size: 3
39853851 CGAATTTTTC
* * * * * *
39853861 TCT TCT TCT CCT CCT CCT -CT TCC TCT TCC TCT TCT TCT TCT TCC TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * *
39853908 TCT TCT TTT TCT TCT TCT TTT TCT TCT TCT TCT TCT TTT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
39853951 TTATTGCCCA
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
2 2 0.03
3 71 0.97
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:39855489 original size:13 final size:13
Alignment explanation
Indices: 39855459--39855507 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
39855449 ATGTGAATTA
*
39855459 TAAAATATATATA
1 TAAAATATATATT
* *
39855472 AAAAATATACATT
1 TAAAATATATATT
*
39855485 TAAAATGTATATTT
1 TAAAATATATA-TT
39855499 TAAAATATA
1 TAAAATATA
39855508 AAGAATATAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
13 18 0.64
14 10 0.36
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (13 bp):
TAAAATATATATT
Found at i:39858672 original size:40 final size:40
Alignment explanation
Indices: 39858545--39858684 Score: 131
Period size: 40 Copynumber: 3.4 Consensus size: 40
39858535 ATATTTTGGG
* * * * * *
39858545 GCCTTTAGTGGCGTTTTTGACAAATCGCCGCTAATTCTC-C
1 GCCTTTAGCGGCGTTTTCG-TAAAGCGCCGCTAATGCTCTA
39858585 GACCTTTTAGCGGCGATTTTCGTAAAGCGCCGCTAATGCTCTA
1 G-CC-TTTAGCGGCG-TTTTCGTAAAGCGCCGCTAATGCTCTA
* * * *
39858628 GCCTTTAGCGGC-TTTTCTTATAAGCGCTGCTAATGTTCTG
1 GCCTTTAGCGGCGTTTTCGTA-AAGCGCCGCTAATGCTCTA
39858668 GCCTTTAGCGGCGTTTT
1 GCCTTTAGCGGCGTTTT
39858685 TTGGAAAAGC
Statistics
Matches: 84, Mismatches: 10, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
39 7 0.08
40 29 0.35
41 15 0.18
42 27 0.32
43 6 0.07
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (40 bp):
GCCTTTAGCGGCGTTTTCGTAAAGCGCCGCTAATGCTCTA
Found at i:39859762 original size:27 final size:28
Alignment explanation
Indices: 39859718--39859777 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
39859708 ATAGAAAAAG
* * *
39859718 ATATA-TATGCAACGATATATATATGTT
1 ATATATTATGAAACGATATAAATATATT
39859745 ATATATTATGAAAC-ATATAAATATATT
1 ATATATTATGAAACGATATAAATATATT
39859772 A-ATATT
1 ATATATT
39859778 GTGTTAGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 5 0.17
27 17 0.59
28 7 0.24
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (28 bp):
ATATATTATGAAACGATATAAATATATT
Found at i:39860457 original size:115 final size:116
Alignment explanation
Indices: 39860205--39860468 Score: 282
Period size: 116 Copynumber: 2.3 Consensus size: 116
39860195 GCTTGGGGCT
* * * *
39860205 TTAGCGGCGGTTTTTCCTA-AAACGCCGCAAATATTTCTTTAATACGACATCGTTTAGTGTTATG
1 TTAGCGGC-GTTTTT-ATATAAACGCCGCAAAAATTTCTGTAATACGACATCGTTTACTGTTATG
* * * *
39860269 CTCTGGTCGAAAAGTTCGACAAAATGACGTCGCTTTGATGATGTTTACCGGTA
64 ATCTGGTCGAAAAGTTAGACAAAAAGACATCGCTTTGATGATGTTTACCGGTA
* * * * *
39860322 TTAGCGGCGGTTTTACATAAACGCCGCAAAAATTTCTGTAATACGACGTCGTTTACTTTTATTAT
1 TTAGCGGCGTTTTTATATAAACGCCGCAAAAATTTCTGTAATACGACATCGTTTACTGTTATGAT
* * * * **
39860387 TTGGTTG-AAAGTTAGACAAAAAGACATCGTTTTTAT-ACTGTTTATTGGTA
66 CTGGTCGAAAAGTTAGACAAAAAGACATCGCTTTGATGA-TGTTTACCGGTA
*
39860437 TTAGCGGCGTTTTTTTATAAAAACGCCGCAAA
1 TTAGCGGCG--TTTTTATATAAACGCCGCAAA
39860469 GGAAATAAAT
Statistics
Matches: 121, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
114 1 0.01
115 44 0.36
116 50 0.41
117 26 0.21
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (116 bp):
TTAGCGGCGTTTTTATATAAACGCCGCAAAAATTTCTGTAATACGACATCGTTTACTGTTATGAT
CTGGTCGAAAAGTTAGACAAAAAGACATCGCTTTGATGATGTTTACCGGTA
Found at i:39861941 original size:21 final size:20
Alignment explanation
Indices: 39861917--39861955 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
39861907 CAATTTCTCT
39861917 CTGAAATCCCTAAGTGTTTCA
1 CTGAAATCCCTAAG-GTTTCA
39861938 CTGAAATCCCTAAGGTTT
1 CTGAAATCCCTAAGGTTT
39861956 TTTCCTATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33
Consensus pattern (20 bp):
CTGAAATCCCTAAGGTTTCA
Found at i:39862485 original size:29 final size:28
Alignment explanation
Indices: 39862443--39862498 Score: 103
Period size: 29 Copynumber: 2.0 Consensus size: 28
39862433 TCTGAAGGTA
39862443 CAAATATATATGTAGGAAAATTTGATGTG
1 CAAATATATATGTAGGAAAATTT-ATGTG
39862472 CAAATATATATGTAGGAAAATTTATGT
1 CAAATATATATGTAGGAAAATTTATGT
39862499 TTTCTGCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.36
Consensus pattern (28 bp):
CAAATATATATGTAGGAAAATTTATGTG
Found at i:39862497 original size:14 final size:14
Alignment explanation
Indices: 39862451--39862498 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
39862441 TACAAATATA
39862451 TATGTAGGAAAATT
1 TATGTAGGAAAATT
* *
39862465 TGATGT-GCAAATATA
1 T-ATGTAGGAAA-ATT
39862480 TATGTAGGAAAATT
1 TATGTAGGAAAATT
39862494 TATGT
1 TATGT
39862499 TTTCTGCATC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.38
Consensus pattern (14 bp):
TATGTAGGAAAATT
Found at i:39864897 original size:21 final size:21
Alignment explanation
Indices: 39864872--39864936 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
39864862 CAACAACTTA
*
39864872 AAGCAGAGGCAGCAGCGAGGG
1 AAGCAGAGGCAGCAGCGAGAG
39864893 AAGCAGAGGCTA-CAGCGAGAG
1 AAGCAGAGGC-AGCAGCGAGAG
* *
39864914 AAGCAGAGGCTGCAGCAAGAG
1 AAGCAGAGGCAGCAGCGAGAG
39864935 AA
1 AA
39864937 ATAGCGAGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
21 38 0.97
22 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.40, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGAG
Found at i:39865471 original size:43 final size:42
Alignment explanation
Indices: 39865358--39865627 Score: 323
Period size: 43 Copynumber: 6.3 Consensus size: 42
39865348 TTTTTTAAAA
*
39865358 AAGCGCCGCTAAAGAACACT-A-CTGTTAGCGGCGTTTTTGACC-
1 AAGCGCCGCTAAAGAACA-TGATCT-TTAGCGGCGTTTTT-TCCT
* * * *
39865400 AAACGCTGCTATAGAACATTA-CTTTTAGCGGCGTTTTCTTCCT
1 AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTT-TTCCT
*
39865443 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCCC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT-CCT
* *
39865486 AAGCACCGCTAGAGAACATGATCTTTAGCGGCGTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCT
* *
39865528 AAGCGCCGCTAAAGAACATGATCTTTAGCAGCGTTTTTTCAT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCT
* *
39865570 AAAGTGCCGCTAAAGAACATAATCTTTAGCGGCGTTTATTTCCT
1 -AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTCCT
*
39865614 TAGCGCCGCTAAAG
1 AAGCGCCGCTAAAG
39865628 GCCTAAAAAA
Statistics
Matches: 198, Mismatches: 22, Indels: 15
0.84 0.09 0.06
Matches are distributed among these distances:
41 1 0.01
42 74 0.37
43 117 0.59
44 6 0.03
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCT
Found at i:39865527 original size:85 final size:85
Alignment explanation
Indices: 39865358--39865627 Score: 341
Period size: 85 Copynumber: 3.2 Consensus size: 85
39865348 TTTTTTAAAA
* * * * *
39865358 AAGCGCCGCTAAAGAACACT-A-CTGTTAGCGGCG-TTTTTGACCAAACGCTGCTATAGAACATT
1 AAGCGCCGCTAAAGAACA-TGATCT-TTAGCGGCGTTTTTTCACCAAGCGCCGCTAAAGAACATA
39865420 A-CTTTTAGCGGCGTTTTCTTCCT
64 ATC-TTTAGCGGCGTTTT-TTCCT
* * * *
39865443 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCCCAAGCACCGCTAGAGAACATGAT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCACCAAGCGCCGCTAAAGAACATAAT
39865508 CTTTAGCGGCGTTTTTTCCT
66 CTTTAGCGGCGTTTTTTCCT
* ** *
39865528 AAGCGCCGCTAAAGAACATGATCTTTAGCAGCGTTTTTTCATAAAGTGCCGCTAAAGAACATAAT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCACCAAGCGCCGCTAAAGAACATAAT
39865593 CTTTAGCGGCGTTTATTTCCT
66 CTTTAGCGGCGTTT-TTTCCT
*
39865614 TAGCGCCGCTAAAG
1 AAGCGCCGCTAAAG
39865628 GCCTAAAAAA
Statistics
Matches: 164, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
84 1 0.01
85 104 0.63
86 58 0.35
87 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (85 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCACCAAGCGCCGCTAAAGAACATAAT
CTTTAGCGGCGTTTTTTCCT
Found at i:39865623 original size:128 final size:128
Alignment explanation
Indices: 39865358--39865627 Score: 327
Period size: 128 Copynumber: 2.1 Consensus size: 128
39865348 TTTTTTAAAA
* * *
39865358 AAGCGCCGCTAAAGAACACTACTGTTAGCGGCGTTTTTGACCAAACGCTGCTATAGAACATTACT
1 AAGCGCCGCTAAAGAACACTACTGTTAGCGGCGTTTTTGACCAAACGCCGCTAAAGAACATGACT
* * *
39865423 TTTAGCGGCGTTTTCTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCCC
66 TTTAGCAGCGTTTTCTTCATAAGCGCCGCTAAAGAACATAATCTTTAGCGGCGTTTTTTCCCC
* * * *
39865486 AAGCACCGCTAGAGAACA-TGATCT-TTAGCGGCGTTTTT-TCCTAAGCGCCGCTAAAGAACATG
1 AAGCGCCGCTAAAGAACACT-A-CTGTTAGCGGCGTTTTTGACC-AAACGCCGCTAAAGAACATG
*
39865548 A-TCTTTAGCAGCGTTTT-TTCATAAAGTGCCGCTAAAGAACATAATCTTTAGCGGCGTTTATTT
63 ACT-TTTAGCAGCGTTTTCTTCAT-AAGCGCCGCTAAAGAACATAATCTTTAGCGGCGTTT-TTT
*
39865611 -CCT
125 CCCC
*
39865614 TAGCGCCGCTAAAG
1 AAGCGCCGCTAAAG
39865628 GCCTAAAAAA
Statistics
Matches: 121, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
127 8 0.07
128 108 0.89
129 5 0.04
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (128 bp):
AAGCGCCGCTAAAGAACACTACTGTTAGCGGCGTTTTTGACCAAACGCCGCTAAAGAACATGACT
TTTAGCAGCGTTTTCTTCATAAGCGCCGCTAAAGAACATAATCTTTAGCGGCGTTTTTTCCCC
Found at i:39866350 original size:25 final size:26
Alignment explanation
Indices: 39866308--39866362 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
39866298 TGCATCACAA
*
39866308 TATTTTTATAAAGATTTT-AATTAAT
1 TATTTTTATAAACATTTTAAATTAAT
* * *
39866333 TATTTTTATAATCCTTTTAAATTATT
1 TATTTTTATAAACATTTTAAATTAAT
39866359 TATT
1 TATT
39866363 ATATCAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (26 bp):
TATTTTTATAAACATTTTAAATTAAT
Found at i:39871102 original size:13 final size:13
Alignment explanation
Indices: 39871084--39871112 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
39871074 AGCCAAGTGT
39871084 ATCTGCTATAGTC
1 ATCTGCTATAGTC
39871097 ATCTGCTATAGTC
1 ATCTGCTATAGTC
39871110 ATC
1 ATC
39871113 AACAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (13 bp):
ATCTGCTATAGTC
Found at i:39879829 original size:16 final size:15
Alignment explanation
Indices: 39879786--39879832 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
39879776 ATTTAAGAAT
* *
39879786 AATAGAAATGTAT-A
1 AATATAAATATATAA
*
39879800 AATATATATATATAA
1 AATATAAATATATAA
39879815 AATATAAAGTATATAA
1 AATATAAA-TATATAA
39879831 AA
1 AA
39879833 GTTTAAAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 10 0.37
15 8 0.30
16 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (15 bp):
AATATAAATATATAA
Found at i:39880026 original size:3 final size:3
Alignment explanation
Indices: 39880005--39880056 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
39879995 TGTACATGAA
* * *
39880005 AAT AAT GAAT AAT ATT AAT AAT AAT AAT AAT AGAC AAT AAT AGT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
39880052 AAT AA
1 AAT AA
39880057 CAAGTAATAG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 36 0.88
4 5 0.12
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39880035 original size:25 final size:27
Alignment explanation
Indices: 39880005--39880066 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
39879995 TGTACATGAA
*
39880005 AATAAT-G-AATAATATTAATAATAAT
1 AATAATAGAAATAATAGTAATAATAAT
*
39880030 AATAATAGACAATAATAGTAATAATAAC
1 AATAATAGA-AATAATAGTAATAATAAT
39880058 AAGTAATAG
1 AA-TAATAG
39880067 TACCATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 6 0.19
26 1 0.03
28 18 0.58
29 6 0.19
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.29
Consensus pattern (27 bp):
AATAATAGAAATAATAGTAATAATAAT
Found at i:39880043 original size:19 final size:18
Alignment explanation
Indices: 39880005--39880065 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 18
39879995 TGTACATGAA
**
39880005 AATAATGAATAATATTAAT
1 AATAAT-AATAATAACAAT
39880024 AATAATAATAATAGACAAT
1 AATAATAATAATA-ACAAT
*
39880043 AATAGTAATAATAACAAGT
1 AATAATAATAATAACAA-T
39880062 AATA
1 AATA
39880066 GTACCATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 11 0.30
19 26 0.70
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.30
Consensus pattern (18 bp):
AATAATAATAATAACAAT
Found at i:39880066 original size:19 final size:19
Alignment explanation
Indices: 39880021--39880068 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
39880011 GAATAATATT
*
39880021 AATAATAATAATAATAGAC
1 AATAATAGTAATAATAGAC
39880040 AATAATAGTAATAATA-AC
1 AATAATAGTAATAATAGAC
39880058 AAGTAATAGTA
1 AA-TAATAGTA
39880069 CCATAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.27
Consensus pattern (19 bp):
AATAATAGTAATAATAGAC
Found at i:39881931 original size:50 final size:50
Alignment explanation
Indices: 39881877--39882014 Score: 122
Period size: 51 Copynumber: 2.7 Consensus size: 50
39881867 TGCAATGTTG
* *
39881877 GGGAAACTAGATCCGCCGTCGTAGCTTCAATCTGTTCGACCGC-ATCGTCA
1 GGGAAACTAGATCCGCCGTCGTAGCTTCAATCTGTTCAACCGCAAT-ATCA
* * ** *
39881927 GGG-AAGTAAGATCCGCCG-CTGTGGCTTCAATCTTTGTT-AATTGCAATATTA
1 GGGAAACT-AGATCCGCCGTC-GTAGCTTCAATC--TGTTCAACCGCAATATCA
* *
39881978 GGGAAACCAGATCCGCCGTCGTAGCTTTAATCTGTTC
1 GGGAAACTAGATCCGCCGTCGTAGCTTCAATCTGTTC
39882015 TACTGCACTG
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
49 8 0.12
50 24 0.35
51 28 0.41
52 9 0.13
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (50 bp):
GGGAAACTAGATCCGCCGTCGTAGCTTCAATCTGTTCAACCGCAATATCA
Found at i:39881984 original size:101 final size:102
Alignment explanation
Indices: 39881857--39882058 Score: 284
Period size: 101 Copynumber: 2.0 Consensus size: 102
39881847 TAATCTTTAA
* * *
39881857 TTTGTTCAATTGCAATGTTGGGGAAACTAGATCCGCCGTCGTAGCTTCAATCTGTTCGACCGCA-
1 TTTGTTCAATTGCAATATTAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCGACCGCAC
* *
39881921 T-CGTCAGGGAAGTAAGATCCGCCGCTGTGGCTTCAATC
66 TGC-T-AAGGAAGTAAGACCCGCCGCTGTGGCTTCAATC
* * *
39881959 TTTGTT-AATTGCAATATTAGGGAAACCAGATCCGCCGTCGTAGCTTTAATCTGTTCTACTGCAC
1 TTTGTTCAATTGCAATATTAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCGACCGCAC
*
39882023 TGCTAAGGAAGTAAGACCCGCCGTTGTGGCTTCAAT
66 TGCTAAGGAAGTAAGACCCGCCGCTGTGGCTTCAAT
39882059 GGGAAACCAG
Statistics
Matches: 89, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
101 80 0.90
102 8 0.09
103 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (102 bp):
TTTGTTCAATTGCAATATTAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCGACCGCAC
TGCTAAGGAAGTAAGACCCGCCGCTGTGGCTTCAATC
Found at i:39882010 original size:51 final size:52
Alignment explanation
Indices: 39881857--39882010 Score: 147
Period size: 50 Copynumber: 3.0 Consensus size: 52
39881847 TAATCTTTAA
* *
39881857 TTTGTTCAATTGCAATGTTGGGGAAACTAGATCCGCCGTCGTAGCTTCAATC
1 TTTGTTCAATTGCAATGTTAGGGAAACAAGATCCGCCGTCGTAGCTTCAATC
* ** * ** *
39881909 --TGTTCGACCGC-ATCGTCAGGGAAGTAAGATCCGCCG-CTGTGGCTTCAATC
1 TTTGTTCAATTGCAAT-GTTAGGGAAACAAGATCCGCCGTC-GTAGCTTCAATC
* * *
39881959 TTTGTT-AATTGCAATATTAGGGAAACCAGATCCGCCGTCGTAGCTTTAATC
1 TTTGTTCAATTGCAATGTTAGGGAAACAAGATCCGCCGTCGTAGCTTCAATC
39882010 T
1 T
39882011 GTTCTACTGC
Statistics
Matches: 77, Mismatches: 19, Indels: 13
0.71 0.17 0.12
Matches are distributed among these distances:
49 3 0.04
50 36 0.47
51 31 0.40
52 7 0.09
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (52 bp):
TTTGTTCAATTGCAATGTTAGGGAAACAAGATCCGCCGTCGTAGCTTCAATC
Found at i:39882113 original size:81 final size:81
Alignment explanation
Indices: 39881978--39882135 Score: 280
Period size: 81 Copynumber: 2.0 Consensus size: 81
39881968 TGCAATATTA
*
39881978 GGGAAACCAGATCCGCCGTCGTAGCTTTAATCTGTTCTACTGCACTGCTAAGGAAGTAAGACCCG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCTACTGCACTGCTAAGGAAGTAAGACCCG
39882043 CCGTTGTGGCTTCAAT
66 CCGTTGTGGCTTCAAT
* * *
39882059 GGGAAACCAGATTCGCCGTCGTAGCTTCAATCTGTTCTACTGCACTGCTAAGGAAGTAAGATCTG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCTACTGCACTGCTAAGGAAGTAAGACCCG
39882124 CCGTTGTGGCTT
66 CCGTTGTGGCTT
39882136 AAATCCTTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 73 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (81 bp):
GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCTACTGCACTGCTAAGGAAGTAAGACCCG
CCGTTGTGGCTTCAAT
Found at i:39882203 original size:181 final size:182
Alignment explanation
Indices: 39881877--39882219 Score: 530
Period size: 181 Copynumber: 1.9 Consensus size: 182
39881867 TGCAATGTTG
* *
39881877 GGGAAACTAGATCCGCCGTCGTAGCTTCAATCTGTTCGACCGCATCGTCAGGGAAGTAAGATCCG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCGACCGCATCGTCAAGGAAGTAAGATCCG
* * * *
39881942 CCGCTGTGGCTTCAATCTTTGTTAATTGCAATATTAGGGAAACCAGATCCGCCGTCGTAGCTTTA
66 CCGCTGTGGCTTAAATCCTTGTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCA
*
39882007 ATCTGTTCTACTGCACTGCTAAGGAAGTAAGACCCGCCGTTGTGGCTTCAAT
131 ATCTGTTCCACTGCACTGCTAAGGAAGTAAGACCCGCCGTTGTGGCTTCAAT
* * *
39882059 GGGAAACCAGATTCGCCGTCGTAGCTTCAATCTGTTCTACTGCA-C-TGCTAAGGAAGTAAGATC
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCGACCGCATCGT-C-AAGGAAGTAAGATC
* * *
39882122 TGCCGTTGTGGCTTAAATCCTT-TTAATTGCAATATCAGGGAAACCAGATCCGCCGTTGTAGCTT
64 CGCCGCTGTGGCTTAAATCCTTGTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTT
39882186 CAATCTGTTCCACTGCACTGCTAAGGAAGTAAGA
129 CAATCTGTTCCACTGCACTGCTAAGGAAGTAAGA
39882220 TCCGTTCAAT
Statistics
Matches: 146, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
180 1 0.01
181 74 0.51
182 71 0.49
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (182 bp):
GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCGACCGCATCGTCAAGGAAGTAAGATCCG
CCGCTGTGGCTTAAATCCTTGTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCA
ATCTGTTCCACTGCACTGCTAAGGAAGTAAGACCCGCCGTTGTGGCTTCAAT
Found at i:39882223 original size:50 final size:50
Alignment explanation
Indices: 39882067--39882281 Score: 148
Period size: 50 Copynumber: 4.5 Consensus size: 50
39882057 ATGGGAAACC
* * *
39882067 AGATTCGCCGTCGTAGCTTCAATCTGTTCTACTGCACTGCTAAGGAAGTA
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTA
* * * ** * * * * ***
39882117 AGATCTGCCGTTGTGGCTTAAATCCT-TTTAATTGCAAT-ATCAGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAAT-CTGTTCCACTGCACTGCT-AAGGAAGTA
39882167 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTA
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTA
* *
39882217 AGAT---CC------G-TTCAATCTGTTCCGCTGCACTACTAAGGAAGTA
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTA
* * *
39882257 AGATCTGCCATTGTGGCTTCAATCT
1 AGATCCGCCGTTGTAGCTTCAATCT
39882282 TTTTACTTTT
Statistics
Matches: 123, Mismatches: 28, Indels: 28
0.69 0.16 0.16
Matches are distributed among these distances:
40 35 0.28
41 1 0.01
43 2 0.02
47 2 0.02
49 4 0.03
50 76 0.62
51 3 0.02
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (50 bp):
AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTA
Found at i:39882242 original size:40 final size:40
Alignment explanation
Indices: 39882184--39882261 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
39882174 CCGTTGTAGC
*
39882184 TTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCG
1 TTCAATCTGTTCCACTGCACTACTAAGGAAGTAAGATCCG
*
39882224 TTCAATCTGTTCCGCTGCACTACTAAGGAAGTAAGATC
1 TTCAATCTGTTCCACTGCACTACTAAGGAAGTAAGATC
39882262 TGCCATTGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (40 bp):
TTCAATCTGTTCCACTGCACTACTAAGGAAGTAAGATCCG
Found at i:39890245 original size:20 final size:20
Alignment explanation
Indices: 39890220--39890259 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
39890210 TAAAGGTCTT
39890220 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
39890240 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
39890260 ATGAGGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (20 bp):
TAATGCATATGATGCGATGC
Found at i:39893556 original size:28 final size:28
Alignment explanation
Indices: 39893525--39893580 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
39893515 AGAACATATA
*
39893525 TATATACTAGTAAAA-TAATAAAAAAATT
1 TATACACTAGTAAAAGTAA-AAAAAAATT
* *
39893553 TATACATTTGTAAAAGTAAAAAAAAATT
1 TATACACTAGTAAAAGTAAAAAAAAATT
39893581 AAACCGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 21 0.88
29 3 0.12
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.32
Consensus pattern (28 bp):
TATACACTAGTAAAAGTAAAAAAAAATT
Found at i:39893636 original size:3 final size:3
Alignment explanation
Indices: 39893621--39893698 Score: 77
Period size: 3 Copynumber: 24.7 Consensus size: 3
39893611 TGTACATGAA
* *
39893621 AAT AAT GAAT AAT AAT AAT AAT AAT AAT AAT AGAC AAT AAT AGT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
*
39893668 AAT AAC AAGT AAT AAT ACCAT AA- AAT AAT AA
1 AAT AAT AA-T AAT AAT A--AT AAT AAT AAT AA
39893699 CGTAAAAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
2 2 0.03
3 51 0.81
4 7 0.11
5 3 0.05
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:39893648 original size:22 final size:21
Alignment explanation
Indices: 39893621--39893698 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 21
39893611 TGTACATGAA
39893621 AATAATGAATAATAATAATAAT
1 AATAAT-AATAATAATAATAAT
* *
39893643 AATAATAATAGACAATAATAGT
1 AATAATAATA-ATAATAATAAT
*
39893665 AATAATAACAAGTAATAATACCAT
1 AATAATAATAA-TAATAATA--AT
39893689 AA-AATAATAA
1 AATAATAATAA
39893699 CGTAAAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
21 5 0.11
22 31 0.67
23 7 0.15
24 3 0.07
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (21 bp):
AATAATAATAATAATAATAAT
Found at i:39899953 original size:16 final size:15
Alignment explanation
Indices: 39899932--39899961 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
39899922 AAAGAATAGC
39899932 AAATAAATAAACAACG
1 AAATAAAT-AACAACG
39899948 AAATAAATAACAAC
1 AAATAAATAACAAC
39899962 AAGGATGACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.70, C:0.13, G:0.03, T:0.13
Consensus pattern (15 bp):
AAATAAATAACAACG
Found at i:39900016 original size:15 final size:15
Alignment explanation
Indices: 39899993--39900022 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39899983 AACAAGCCAA
*
39899993 TAAATAAATAAATAC
1 TAAACAAATAAATAC
39900008 TAAACAAATAAATAC
1 TAAACAAATAAATAC
39900023 ATACTAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAACAAATAAATAC
Found at i:39901731 original size:44 final size:43
Alignment explanation
Indices: 39901683--39902170 Score: 194
Period size: 44 Copynumber: 11.2 Consensus size: 43
39901673 TACCTCGGGA
* *
39901683 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTCAGGG
1 AGATAAGA-TCACCATCTTCAATCTGCTCCACTACTGCTCAGGG
* * * * *
39901727 AGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAAGG
1 AGATAAGATC-ACCATCTTCAATCTGCTCCACTACTGCTCAGGG
*** *
39901771 AGATAAGACTGGTCA-CTTAAATCTGCTTCCTACTAC--CTC-GGG
1 AGATAAGA-TCACCATCTTCAATCTGC-TCC-ACTACTGCTCAGGG
* * * *
39901813 AAGATAAGATTCACCATTTTCGATCTGCTCCACTACTGCTTAAGG
1 -AGATAAGA-TCACCATCTTCAATCTGCTCCACTACTGCTCAGGG
* * * *
39901858 AGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGG
1 AGATAAGATC-ACCATCTTCAATCTGCTCCACTACTGCTCAGGG
** * * * **
39901902 AGAT-AGA--ACTGGTGGCTTAAATCTGTTTCTTACTA-T-CTC-GAAA
1 AGATAAGATCAC-CAT--CTTCAATCTG-CTC-CACTACTGCTCAG-GG
* * * * * *
39901945 AGATAAAACTCACCGTCTTCGATCTACTTCACTACTGCTTAGGG
1 AGATAAGA-TCACCATCTTCAATCTGCTCCACTACTGCTCAGGG
* * *
39901989 AGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAGGG
1 AGATAAGATC-ACCATCTTCAATCTGCTCCACTACTGCTCAGGG
* **** *
39902033 AGATAGGA-CTAGTGGCTTAAATCTGCTTCCTACTAC--CTC-GGG
1 AGATAAGATC-ACCATCTTCAATCTGC-TCC-ACTACTGCTCAGGG
** * * * * *
39902075 AAGATAAGATTCGTCATTTTCGATCTGCTCTACTACTTCTTAGGG
1 -AGATAAGA-TCACCATCTTCAATCTGCTCCACTACTGCTCAGGG
*** * * *
39902120 AGATAAGATCTGTAATCTTCAACCTACTCCACTGCTGCTCAGGG
1 AGATAAGATC-ACCATCTTCAATCTGCTCCACTACTGCTCAGGG
39902164 AGATAAG
1 AGATAAG
39902171 GCTTGATATG
Statistics
Matches: 322, Mismatches: 89, Indels: 66
0.68 0.19 0.14
Matches are distributed among these distances:
40 2 0.01
41 1 0.00
42 20 0.06
43 75 0.23
44 200 0.62
45 20 0.06
46 2 0.01
47 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (43 bp):
AGATAAGATCACCATCTTCAATCTGCTCCACTACTGCTCAGGG
Found at i:39901808 original size:131 final size:131
Alignment explanation
Indices: 39901573--39902170 Score: 883
Period size: 131 Copynumber: 4.6 Consensus size: 131
39901563 CATGGTTTTA
* * *
39901573 ATCTGCTCCGCTACTGCTTTGGAAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAG
* * * *
39901638 GGAGGTAGGACTGGTGGCTTAAATCTGCTTCCTATTACCTCGGGAAGATAAGATTCACCGTCTTC
66 GGAGATAAGACTGGTGGCTTAAATCTGCTTCCTACTACCTCGGGAAGATAAGATTCACCATCTTC
39901703 G
131 G
* *
39901704 ATCTGCTCCACTACTGCTCAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAG
** *
39901769 GGAGATAAGACTGGTCACTTAAATCTGCTTCCTACTACCTCGGGAAGATAAGATTCACCATTTTC
66 GGAGATAAGACTGGTGGCTTAAATCTGCTTCCTACTACCTCGGGAAGATAAGATTCACCATCTTC
39901834 G
131 G
*
39901835 ATCTGCTCCACTACTGCTTAAGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAG
* * * ** * * *
39901900 GGAGAT-AGAACTGGTGGCTTAAATCTGTTTCTTACTATCTCGAAAAGATAAAACTCACCGTCTT
66 GGAGATAAG-ACTGGTGGCTTAAATCTGCTTCCTACTACCTCGGGAAGATAAGATTCACCATCTT
39901964 CG
130 CG
* * *
39901966 ATCTACTTCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAG
* * ** *
39902031 GGAGATAGGACTAGTGGCTTAAATCTGCTTCCTACTACCTCGGGAAGATAAGATTCGTCATTTTC
66 GGAGATAAGACTGGTGGCTTAAATCTGCTTCCTACTACCTCGGGAAGATAAGATTCACCATCTTC
39902096 G
131 G
* * **
39902097 ATCTGCTCTACTACTTCTTAGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAG
39902162 GGAGATAAG
66 GGAGATAAG
39902171 GCTTGATATG
Statistics
Matches: 414, Mismatches: 51, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
130 2 0.00
131 411 0.99
132 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (131 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAG
GGAGATAAGACTGGTGGCTTAAATCTGCTTCCTACTACCTCGGGAAGATAAGATTCACCATCTTC
G
Found at i:39914317 original size:4 final size:4
Alignment explanation
Indices: 39914308--39914354 Score: 69
Period size: 4 Copynumber: 12.0 Consensus size: 4
39914298 TGAACAAGCC
* *
39914308 AATA AATA AATA AATA AATA AATA AATA AAT- ACTA AACA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
39914355 CATACTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 2 0.05
4 36 0.95
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:39915208 original size:12 final size:12
Alignment explanation
Indices: 39915191--39915228 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
39915181 ATAAAAAGAT
39915191 AAAAAGAATCAA
1 AAAAAGAATCAA
39915203 AAAAAGAA--AA
1 AAAAAGAATCAA
39915213 AAAAAGAATCAA
1 AAAAAGAATCAA
39915225 AAAA
1 AAAA
39915229 GAAAAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.42
12 14 0.58
ACGTcount: A:0.82, C:0.05, G:0.08, T:0.05
Consensus pattern (12 bp):
AAAAAGAATCAA
Found at i:39915215 original size:21 final size:20
Alignment explanation
Indices: 39915191--39915236 Score: 74
Period size: 22 Copynumber: 2.2 Consensus size: 20
39915181 ATAAAAAGAT
39915191 AAAAAGAATCAAAAAAAGAAAA
1 AAAAAGAATC-AAAAAAG-AAA
39915213 AAAAAGAATCAAAAAAGAAA
1 AAAAAGAATCAAAAAAGAAA
39915233 AAAA
1 AAAA
39915237 TCACCTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.29
21 7 0.29
22 10 0.42
ACGTcount: A:0.83, C:0.04, G:0.09, T:0.04
Consensus pattern (20 bp):
AAAAAGAATCAAAAAAGAAA
Found at i:39915219 original size:22 final size:21
Alignment explanation
Indices: 39915191--39915236 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 21
39915181 ATAAAAAGAT
39915191 AAAAAGAATCAAAAAAAGAAAA
1 AAAAAGAATC-AAAAAAGAAAA
39915213 AAAAAGAATCAAAAAAGAAAA
1 AAAAAGAATCAAAAAAGAAAA
39915234 AAA
1 AAA
39915237 TCACCTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.83, C:0.04, G:0.09, T:0.04
Consensus pattern (21 bp):
AAAAAGAATCAAAAAAGAAAA
Found at i:39918052 original size:18 final size:18
Alignment explanation
Indices: 39918014--39918049 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39918004 TTATTATTTT
*
39918014 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
39918032 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
39918050 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:39919079 original size:17 final size:17
Alignment explanation
Indices: 39919028--39919079 Score: 86
Period size: 17 Copynumber: 3.0 Consensus size: 17
39919018 GGATCCAATG
*
39919028 GAAACACGAGAATTTTT
1 GAAACACGAAAATTTTT
39919045 GAAAACACGAAAATTTTT
1 G-AAACACGAAAATTTTT
39919063 GAAACACGAAAATTTTT
1 GAAACACGAAAATTTTT
39919080 ATAAATTACA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 17 0.52
18 16 0.48
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (17 bp):
GAAACACGAAAATTTTT
Found at i:39919847 original size:7 final size:7
Alignment explanation
Indices: 39919833--39919902 Score: 65
Period size: 7 Copynumber: 10.0 Consensus size: 7
39919823 ATTTTTTTCC
39919833 TTTC-TT
1 TTTCTTT
39919839 TTTCTTT
1 TTTCTTT
39919846 TTTC-TT
1 TTTCTTT
39919852 TTTCTTT
1 TTTCTTT
*
39919859 CCTTTTTTT
1 --TTTCTTT
39919868 TTTCTTT
1 TTTCTTT
*
39919875 TTT-TTCC
1 TTTCTT-T
*
39919882 TTTCTTC
1 TTTCTTT
39919889 TTTCTTT
1 TTTCTTT
39919896 TTTCTTT
1 TTTCTTT
39919903 CCTTTTCCGT
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
6 12 0.22
7 34 0.63
8 2 0.04
9 6 0.11
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTCTTT
Found at i:39919859 original size:28 final size:27
Alignment explanation
Indices: 39919824--39919902 Score: 105
Period size: 28 Copynumber: 3.1 Consensus size: 27
39919814 CTCCTTTTTA
39919824 TTTTTTTCCTTTCTTTTTCTTTTTTC-
1 TTTTTTTCCTTTCTTTTTCTTTTTTCT
*
39919850 --TTTTT-CTTTCCTTTT-TTTTTTCT
1 TTTTTTTCCTTTCTTTTTCTTTTTTCT
39919873 TTTTTTTCCTTTCTTCTTTCTTTTTTCT
1 TTTTTTTCCTTTCTT-TTTCTTTTTTCT
39919901 TT
1 TT
39919903 CCTTTTCCGT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
22 7 0.16
23 9 0.20
24 5 0.11
25 5 0.11
26 6 0.13
27 3 0.07
28 10 0.22
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (27 bp):
TTTTTTTCCTTTCTTTTTCTTTTTTCT
Found at i:39919917 original size:24 final size:23
Alignment explanation
Indices: 39919825--39919909 Score: 97
Period size: 23 Copynumber: 3.7 Consensus size: 23
39919815 TCCTTTTTAT
*
39919825 TTTTTTCCTTTCTTTTTCTTTTT-
1 TTTTTT-CTTTCCTTTTCTTTTTC
*
39919848 TCTTTTTCTTTCCTTTTTTTTTTC
1 T-TTTTTCTTTCCTTTTCTTTTTC
39919872 -TTTTT-TTTCC-TTTCTTCTTTC
1 TTTTTTCTTTCCTTTTCTT-TTTC
39919893 TTTTTTCTTTCCTTTTC
1 TTTTTTCTTTCCTTTTC
39919910 CGTTTTCTCC
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
20 5 0.09
21 9 0.17
22 10 0.19
23 20 0.38
24 9 0.17
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTTTCTTTCCTTTTCTTTTTC
Done.