Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 22 of 214
Found at i:6188244 original size:23 final size:24
Alignment explanation
Indices: 6188199--6188245 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
6188189 ATTTCTCACA
**
6188199 TTTTCAATTCAATAATTTTTCCAC
1 TTTTCAATTCAATAATTAATCCAC
6188223 TTTTCAA-TCAATAATTAATCCAC
1 TTTTCAATTCAATAATTAATCCAC
6188246 AAATTTACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTTCAATTCAATAATTAATCCAC
Found at i:6188399 original size:3 final size:3
Alignment explanation
Indices: 6188391--6188419 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6188381 CCACTCATCT
6188391 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
6188420 CTTACCTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:6190047 original size:10 final size:10
Alignment explanation
Indices: 6190034--6190058 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6190024 TTATTGAAAA
6190034 TTTTAATTAT
1 TTTTAATTAT
6190044 TTTTAATTAT
1 TTTTAATTAT
6190054 TTTTA
1 TTTTA
6190059 TAGGTTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTAATTAT
Found at i:6191223 original size:22 final size:22
Alignment explanation
Indices: 6191181--6191232 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
6191171 TCCATTTCCT
* *
6191181 ATTTAGTTTTTTTCTATTTGTA
1 ATTTAGTTTTATTCTAGTTGTA
6191203 ATTTAGTTTCTATTC-AGTTGTA
1 ATTTAGTTT-TATTCTAGTTGTA
6191225 ATTCTAGT
1 ATT-TAGT
6191233 AGTTTATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.21, C:0.08, G:0.12, T:0.60
Consensus pattern (22 bp):
ATTTAGTTTTATTCTAGTTGTA
Found at i:6207539 original size:22 final size:22
Alignment explanation
Indices: 6207514--6207555 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6207504 ACTATCAAGT
*
6207514 AAATGT-ATATATATTAATTTCA
1 AAATGTCAT-TATAGTAATTTCA
6207536 AAATGTCATTATAGTAATTT
1 AAATGTCATTATAGTAATTT
6207556 TTATAGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (22 bp):
AAATGTCATTATAGTAATTTCA
Found at i:6209419 original size:40 final size:40
Alignment explanation
Indices: 6209337--6209593 Score: 326
Period size: 40 Copynumber: 6.5 Consensus size: 40
6209327 AAGCCAAGTA
* * * *
6209337 CCTTCGGGATTTA-ACCGGATATAGCT-ACCCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
6209375 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
6209415 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
6209455 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
6209495 CCTTCGGGACTTAGCTCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
6209535 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAG-AGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA-CAAATG
6209575 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
6209594 TTATCATCCG
Statistics
Matches: 197, Mismatches: 17, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
38 12 0.06
39 17 0.09
40 168 0.85
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:6211665 original size:27 final size:27
Alignment explanation
Indices: 6211615--6211666 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
6211605 ATGAAGGGTT
6211615 TTTTTTTATAGAATCAAATCGATTTGG
1 TTTTTTTATAGAATCAAATCGATTTGG
6211642 TTTTTTTATAGAATCAAATCGATTT
1 TTTTTTTATAGAATCAAATCGATTT
6211667 TGACAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.50
Consensus pattern (27 bp):
TTTTTTTATAGAATCAAATCGATTTGG
Found at i:6240792 original size:21 final size:24
Alignment explanation
Indices: 6240736--6240794 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 24
6240726 CATATAACCC
*
6240736 CAATTCAATCACAATTTCTCACATTT
1 CAATTCAAT-A-ATTTTCTCACATTT
6240762 CAATTCAATAATTTTC-CAC-TTT
1 CAATTCAATAATTTTCTCACATTT
6240784 CAA-TCAATAAT
1 CAATTCAATAAT
6240795 AATCCACAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 8 0.25
22 6 0.19
23 3 0.09
24 5 0.16
25 1 0.03
26 9 0.28
ACGTcount: A:0.37, C:0.24, G:0.00, T:0.39
Consensus pattern (24 bp):
CAATTCAATAATTTTCTCACATTT
Found at i:6240800 original size:21 final size:22
Alignment explanation
Indices: 6240759--6240801 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
6240749 ATTTCTCACA
**
6240759 TTTCAATTCAATAATTTTCCAC
1 TTTCAATTCAATAATAATCCAC
6240781 TTTCAA-TCAATAATAATCCAC
1 TTTCAATTCAATAATAATCCAC
6240802 AATTACACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTCAATTCAATAATAATCCAC
Found at i:6240938 original size:3 final size:3
Alignment explanation
Indices: 6240930--6240958 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6240920 CCACTCATCT
6240930 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
6240959 CTTACCTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:6242585 original size:10 final size:10
Alignment explanation
Indices: 6242572--6242596 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6242562 TTATTGAAAA
6242572 TTTTAATTAT
1 TTTTAATTAT
6242582 TTTTAATTAT
1 TTTTAATTAT
6242592 TTTTA
1 TTTTA
6242597 TAGGTTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTAATTAT
Found at i:6247332 original size:13 final size:13
Alignment explanation
Indices: 6247314--6247338 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6247304 TTTTTTCTAA
6247314 TTTTAATTTTAAT
1 TTTTAATTTTAAT
6247327 TTTTAATTTTAA
1 TTTTAATTTTAA
6247339 ACCCCCTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTAATTTTAAT
Found at i:6251119 original size:6 final size:6
Alignment explanation
Indices: 6251110--6251135 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
6251100 GTAAAATAAA
6251110 AATTTT AATTTT AATTTT AATTTT AA
1 AATTTT AATTTT AATTTT AATTTT AA
6251136 AAATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
AATTTT
Found at i:6256438 original size:14 final size:15
Alignment explanation
Indices: 6256419--6256454 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
6256409 AATATTTATT
6256419 ATATAAA-TACTTAA
1 ATATAAAGTACTTAA
6256433 ATATAAAGTACTTAA
1 ATATAAAGTACTTAA
6256448 ATATAAA
1 ATATAAA
6256455 AATGGATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (15 bp):
ATATAAAGTACTTAA
Found at i:6257960 original size:128 final size:129
Alignment explanation
Indices: 6257780--6258031 Score: 287
Period size: 128 Copynumber: 2.0 Consensus size: 129
6257770 AGATGAATTT
* * * *
6257780 GATGCGATCTGCTCTACTGTAATTTCAGAGAGATAAGATCCATCATTCTAATCCACTCCGCTACA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
* * *
6257845 ACCTT-AAGGAGATAGGATT-T-GTTTATTTAGTCTGCTCCACTACAACTTCAGGGAGATAAGAC
66 A-CTTCAAGGAGATAGGATTATCG--GATTTAATCTGCTCCACTACAACTTCAAGGAGATAAGAC
6257907 TA
128 TA
* * ** * * * *
6257909 GATGCGTTCTGCTCT-CTGCAACTTCAGAGAGATAAGATTCAAGGTTTTAATCCGCTTCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
* * *
6257973 ACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAA
66 ACTTCAAGGAGATAGGATTATCGGATTTAATCTGCTCCACTACAACTTCAAGGAGATAA
6258032 AATTTGCCAT
Statistics
Matches: 102, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
127 3 0.03
128 83 0.81
129 15 0.15
130 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (129 bp):
GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
ACTTCAAGGAGATAGGATTATCGGATTTAATCTGCTCCACTACAACTTCAAGGAGATAAGACTA
Found at i:6257976 original size:44 final size:44
Alignment explanation
Indices: 6257924--6258031 Score: 130
Period size: 44 Copynumber: 2.5 Consensus size: 44
6257914 GTTCTGCTCT
* *
6257924 CTGCAACTTCAGAGAGATAAGATTCA-AGGTTTTAATCCGCTTCA
1 CTGCAACTTCAGAGAGATAAGATT-ATAGGCTTTAATCCGCTCCA
* * * *
6257968 CTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCA
1 CTGCAACTTCAGAGAGATAAGATTATAGGCTTTAATCCGCTCCA
6258012 CTGCAACTTCA-AGGAGATAA
1 CTGCAACTTCAGA-GAGATAA
6258032 AATTTGCCAT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
43 1 0.02
44 53 0.98
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (44 bp):
CTGCAACTTCAGAGAGATAAGATTATAGGCTTTAATCCGCTCCA
Found at i:6258392 original size:44 final size:44
Alignment explanation
Indices: 6258338--6258757 Score: 500
Period size: 44 Copynumber: 9.7 Consensus size: 44
6258328 GCTATTTTCC
* *
6258338 ACCTACTCCACTGCTG-CTCAGGGAGATAGGGTTCACAATCTTCA
1 ACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATCTTCA
* *
6258382 ACCTATTCCACTGTTGACCAGGGAGATAGGA-CCTACAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC-ACAATCTTCA
* * * * *
6258426 ATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATTTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
*
6258470 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* *
6258514 ACCTATTCCACTGCTGTCCAGGGAGATAGGGTT--C--T-TT-A
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* * *
6258552 ATCTATTCCACTGCTG-CCTAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGACC-AGGGAGATAGGATTCACAATCTTCA
*
6258596 ACCTATTCCACTGCTGACCAGGGAGATAGGA-TCTACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC-ACAATCTTCA
* * * ** *
6258640 ATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTTAATTTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* * *
6258684 ACCTATTCCACTGCTGACGAGGGAGATAGGATTCACAATATTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
*
6258728 ACCTATTCCACTGCTGACTAGGGAGATAGG
1 ACCTATTCCACTGCTGACCAGGGAGATAGG
6258758 GCTGGGATCA
Statistics
Matches: 321, Mismatches: 42, Indels: 26
0.83 0.11 0.07
Matches are distributed among these distances:
37 2 0.01
38 28 0.09
39 2 0.01
40 2 0.01
42 2 0.01
43 5 0.02
44 274 0.85
45 6 0.02
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (44 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
Found at i:6258713 original size:214 final size:214
Alignment explanation
Indices: 6258344--6258758 Score: 715
Period size: 214 Copynumber: 1.9 Consensus size: 214
6258334 TTCCACCTAC
** *
6258344 TCCACTGCTGCTCAGGGAGATAGGGTTCACAATCTTCAACCTATTCCACTGTTGACCAGGGAGAT
1 TCCACTGCTGCTCAGGGAGATAGAATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGAT
6258409 AGGACCTACAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATTTTCAACCT
66 AGGACCTACAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATTTTCAACCT
* *
6258474 ATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAGGGAG
131 ATTCCACTGCTGACCAGGGAGATAGGATTCACAATATTTAACCTATTCCACTGCTGACCAGGGAG
6258539 ATAGGGTTCTTTAATCTAT
196 ATAGGGTTCTTTAATCTAT
*
6258558 TCCACTGCTGC-CTAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACCAGGGAGA
1 TCCACTGCTGCTC-AGGGAGATAGAATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGA
* * *
6258622 TAGGATCTACAATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTTAATTTTCAACC
65 TAGGACCTACAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATTTTCAACC
* *
6258687 TATTCCACTGCTGACGAGGGAGATAGGATTCACAATATTTAACCTATTCCACTGCTGACTAGGGA
130 TATTCCACTGCTGACCAGGGAGATAGGATTCACAATATTTAACCTATTCCACTGCTGACCAGGGA
6258752 GATAGGG
195 GATAGGG
6258759 CTGGGATCAT
Statistics
Matches: 189, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
213 1 0.01
214 188 0.99
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (214 bp):
TCCACTGCTGCTCAGGGAGATAGAATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGAT
AGGACCTACAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATTTTCAACCT
ATTCCACTGCTGACCAGGGAGATAGGATTCACAATATTTAACCTATTCCACTGCTGACCAGGGAG
ATAGGGTTCTTTAATCTAT
Found at i:6258816 original size:88 final size:87
Alignment explanation
Indices: 6258757--6259256 Score: 694
Period size: 88 Copynumber: 5.7 Consensus size: 87
6258747 AGGGAGATAG
* * *
6258757 GGCTGGGATCATCAATCTGCTTCGCTGCCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGG-TCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
6258822 TCCGCTGCAACCTAGGGATGCAA
65 TCCGCTGCAACCCAGGGAGGCAA
* * * *
6258845 GACTGGTGTCTTCAATCTGCTTCGCTGCCGGTGCAGGAATGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGG-GTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
6258910 TCCGCTGCAACCCAGGGAGGCAA
65 TCCGCTGCAACCCAGGGAGGCAA
*
6258933 GGCTGGGTATCTTCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTG
1 GGCTGGG--TCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTG
6258998 CTCCGCTGCAACCCAGGGAGGCAA
64 CTCCGCTGCAACCCAGGGAGGCAA
* * * * *
6259022 GGCTGGTATCTTCGATCTGATTCACTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTAC
1 GGCTGG-GTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
6259087 TCCACTGCAACCCAGGGAGGCAA
65 TCCGCTGCAACCCAGGGAGGCAA
* * * * * *
6259110 GGCTAGTGTCTTTGATCTACTTCGCTGTCAGTGCAGAAAGGCAAGATTTGCTATTTTTAACCTGC
1 GGCT-GGGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
6259175 TTCGCTGCAACCTAGGGAGGCAA
65 TCCGCTGCAACCCAGGGAGGCAA
* * *
6259198 GGCTGGTGTCTTTGATCTGCTTCGCTGTCGGTGTAGGAATGCAAGATCTGCTATTTTTA
1 GGCTGG-GTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
6259257 CTAATCTGCT
Statistics
Matches: 370, Mismatches: 36, Indels: 12
0.89 0.09 0.03
Matches are distributed among these distances:
87 2 0.01
88 284 0.77
89 84 0.23
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (87 bp):
GGCTGGGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCT
CCGCTGCAACCCAGGGAGGCAA
Found at i:6258887 original size:44 final size:45
Alignment explanation
Indices: 6258768--6259006 Score: 148
Period size: 45 Copynumber: 5.4 Consensus size: 45
6258758 GCTGGGATCA
* *
6258768 TCAATCTGCTTCGCTGCCGGTGCAGGAAGGCAAGATCTGCTATTT
1 TCAATCTGCTTCGCTGCCGGTGCAGGAATGCAAGATCTGCTATCT
* * * * * * *
6258813 TTAACCTGCTCCGCTGCAAC-CT--AGGGATGCAAGA-CTGGTGTCT
1 TCAATCTGCTTCGCTGC--CGGTGCAGGAATGCAAGATCTGCTATCT
*
6258856 TCAATCTGCTTCGCTGCCGGTGCAGGAATGCAAGATCTGCTATTT
1 TCAATCTGCTTCGCTGCCGGTGCAGGAATGCAAGATCTGCTATCT
* * * **** * * * *
6258901 TTAACCTGCTCCGCTG-CAACCCAGGGAGGCAAG-GCTGGGTATCT
1 TCAATCTGCTTCGCTGCCGGTGCAGGAATGCAAGATCT-GCTATCT
* * * * *
6258945 TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTT
1 TCAATCTGCTTCGCTGCCGGTGCAGGAATGCAAGATCTGCTATCT
* * *
6258990 TTAACCTGCTCCGCTGC
1 TCAATCTGCTTCGCTGC
6259007 AACCCAGGGA
Statistics
Matches: 137, Mismatches: 48, Indels: 18
0.67 0.24 0.09
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 22 0.16
44 48 0.35
45 61 0.45
46 3 0.02
47 1 0.01
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.28
Consensus pattern (45 bp):
TCAATCTGCTTCGCTGCCGGTGCAGGAATGCAAGATCTGCTATCT
Found at i:6259064 original size:44 final size:44
Alignment explanation
Indices: 6258922--6259066 Score: 121
Period size: 45 Copynumber: 3.3 Consensus size: 44
6258912 CGCTGCAACC
*
6258922 CAGGGAGGCAAGGCTGGGTATCTTCGATCTGCTTCACTGTCGGTG
1 CAGGAAGGCAAGGCT-GGTATCTTCGATCTGCTTCACTGTCGGTG
* * * ** * * * ****
6258967 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACC
1 CAGGAAGGCAAG-GCTGGTATCTTCGATCTGCTTCACTGTCGGTG
* *
6259011 CAGGGAGGCAAGGCTGGTATCTTCGATCTGATTCACTGTCGGTG
1 CAGGAAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTG
*
6259055 TAGGAAGGCAAG
1 CAGGAAGGCAAG
6259067 ATCTGCTATT
Statistics
Matches: 69, Mismatches: 29, Indels: 5
0.67 0.28 0.05
Matches are distributed among these distances:
43 17 0.25
44 23 0.33
45 27 0.39
46 2 0.03
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25
Consensus pattern (44 bp):
CAGGAAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTG
Found at i:6259068 original size:177 final size:177
Alignment explanation
Indices: 6258757--6259256 Score: 761
Period size: 177 Copynumber: 2.8 Consensus size: 177
6258747 AGGGAGATAG
* * *
6258757 GGCTGGG-ATCATCAATCTGCTTCGCTGCCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTG
1 GGCTGGGTATCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTG
* * * * *
6258821 CTCCGCTGCAACCTAGGGATGCAAGACTGGTGTCTTCAATCTGCTTCGCTGCCGGTGCAGGAATG
66 CTCCGCTGCAACCTAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGTAGGAATG
* *
6258886 CAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAA
131 CAAGATCTGCTATTTTTAACCTACTCCACTGCAACCCAGGGAGGCAA
*
6258933 GGCTGGGTATCTTCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTG
1 GGCTGGGTATCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTG
* * * * *
6258998 CTCCGCTGCAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGATTCACTGTCGGTGTAGGAAGG
66 CTCCGCTGCAACCTAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGTAGGAATG
6259063 CAAGATCTGCTATTTTTAACCTACTCCACTGCAACCCAGGGAGGCAA
131 CAAGATCTGCTATTTTTAACCTACTCCACTGCAACCCAGGGAGGCAA
* * * * * * *
6259110 GGCT-AGTGTCTTTGATCTACTTCGCTGTCAGTGCAGAAAGGCAAGATTTGCTATTTTTAACCTG
1 GGCTGGGTATCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTG
* *
6259174 CTTCGCTGCAACCTAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTCGGTGTAGGAATG
66 CTCCGCTGCAACCTAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGTAGGAATG
6259239 CAAGATCTGCTATTTTTA
131 CAAGATCTGCTATTTTTA
6259257 CTAATCTGCT
Statistics
Matches: 292, Mismatches: 31, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
176 135 0.46
177 157 0.54
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (177 bp):
GGCTGGGTATCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTG
CTCCGCTGCAACCTAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGTAGGAATG
CAAGATCTGCTATTTTTAACCTACTCCACTGCAACCCAGGGAGGCAA
Found at i:6259197 original size:265 final size:264
Alignment explanation
Indices: 6258757--6259256 Score: 739
Period size: 265 Copynumber: 1.9 Consensus size: 264
6258747 AGGGAGATAG
* * *
6258757 GGCTGGGATCATCAATCTGCTTCGCTGCCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGGATCATCAATCTGATTCACTGCCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTAC
* * * * * * * *
6258822 TCCGCTGCAACCTAGGGATGCAAGACTGGTGTCTTCAATCTGCTTCGCTGCCGGTGCAGGAATGC
66 TCCACTGCAACCCAGGGAGGCAAGACTAGTGTCTTCAATCTACTTCGCTGCCAGTGCAGAAAGGC
6258887 AAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGGTATCTTCGATCT
131 AAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCT-GGTATCTTCGATCT
6258952 GCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGGA
195 GCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGGA
6259017 GGCAA
260 GGCAA
* * * * *
6259022 GGCTGGTATCTTCGATCTGATTCACTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTAC
1 GGCTGGGATCATCAATCTGATTCACTGCCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTAC
* ** *
6259087 TCCACTGCAACCCAGGGAGGCAAGGCTAGTGTCTTTGATCTACTTCGCTGTCAGTGCAGAAAGGC
66 TCCACTGCAACCCAGGGAGGCAAGACTAGTGTCTTCAATCTACTTCGCTGCCAGTGCAGAAAGGC
* * * * *
6259152 AAGATTTGCTATTTTTAACCTGCTTCGCTGCAACCTAGGGAGGCAAGGCTGGTGTCTTTGATCTG
131 AAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTG
* * *
6259217 CTTCGCTGTCGGTGTAGGAATGCAAGATCTGCTATTTTTA
196 CTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
6259257 CTAATCTGCT
Statistics
Matches: 207, Mismatches: 28, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
264 50 0.24
265 157 0.76
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (264 bp):
GGCTGGGATCATCAATCTGATTCACTGCCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTAC
TCCACTGCAACCCAGGGAGGCAAGACTAGTGTCTTCAATCTACTTCGCTGCCAGTGCAGAAAGGC
AAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTG
CTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAG
GCAA
Found at i:6259221 original size:43 final size:42
Alignment explanation
Indices: 6259091--6259224 Score: 106
Period size: 43 Copynumber: 3.1 Consensus size: 42
6259081 ACCTACTCCA
* *
6259091 CTGCAACCCAGGGAGGCAAGGCTAGTGTCTTTGATCTACTTCG
1 CTGCAA-CCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCG
** ** ** * * * * *
6259134 CTGTCAGTGCAGAAAGGCAAGATTTGCTATTTTTAACCTGCTTCG
1 CTG-CA-ACCAGGGAGGCAAG-GCTGGTGTCTTTGATCTGCTTCG
6259179 CTGCAACCTAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCG
1 CTGCAACC-AGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCG
6259222 CTG
1 CTG
6259225 TCGGTGTAGG
Statistics
Matches: 63, Mismatches: 24, Indels: 8
0.66 0.25 0.08
Matches are distributed among these distances:
43 23 0.37
44 23 0.37
45 17 0.27
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.29
Consensus pattern (42 bp):
CTGCAACCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCG
Found at i:6266177 original size:14 final size:15
Alignment explanation
Indices: 6266160--6266194 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
6266150 ATATTTATTG
6266160 TATAAA-TACTTAAA
1 TATAAAGTACTTAAA
6266174 TATAAAGTACTTAAA
1 TATAAAGTACTTAAA
6266189 TATAAA
1 TATAAA
6266195 AATGGATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (15 bp):
TATAAAGTACTTAAA
Found at i:6266893 original size:13 final size:13
Alignment explanation
Indices: 6266868--6266900 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
6266858 AGAACAGATC
6266868 AATAAATAAATAAA
1 AATAAA-AAATAAA
6266882 AATAAAAAATAAA
1 AATAAAAAATAAA
6266895 AA-AAAA
1 AATAAAA
6266901 CTTTGAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.21
13 9 0.47
14 6 0.32
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AATAAAAAATAAA
Found at i:6266897 original size:14 final size:14
Alignment explanation
Indices: 6266868--6266896 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6266858 AGAACAGATC
6266868 AATAAATAAATAAA
1 AATAAATAAATAAA
6266882 AATAAA-AAATAAA
1 AATAAATAAATAAA
6266895 AA
1 AA
6266897 AAAACTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AATAAATAAATAAA
Found at i:6269742 original size:19 final size:19
Alignment explanation
Indices: 6269707--6269746 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
6269697 TTACAGTAAC
*
6269707 AATTAAATAAATTTTTTGAA
1 AATTAAATAAATATTTT-AA
6269727 AATTAAA-AAATATTTTAA
1 AATTAAATAAATATTTTAA
6269745 AA
1 AA
6269747 GATTTATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 8 0.42
20 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
AATTAAATAAATATTTTAA
Found at i:6271797 original size:29 final size:31
Alignment explanation
Indices: 6271745--6271805 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
6271735 AGTTATTATG
**
6271745 ATATAATAATATTAAAATTCTAATTAAAACA
1 ATATAATAATATTAAAATAATAATTAAAACA
*
6271776 ATATAA-AATA-TAAAATAATAATTATAACA
1 ATATAATAATATTAAAATAATAATTAAAACA
6271805 A
1 A
6271806 AACAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 17 0.63
30 4 0.15
31 6 0.22
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (31 bp):
ATATAATAATATTAAAATAATAATTAAAACA
Found at i:6275819 original size:20 final size:20
Alignment explanation
Indices: 6275794--6275831 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6275784 CTTGTAGCAA
* *
6275794 AAAATTTGCAAATTTTTCTT
1 AAAATTTCCAAATGTTTCTT
6275814 AAAATTTCCAAATGTTTC
1 AAAATTTCCAAATGTTTC
6275832 CAAATTGGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (20 bp):
AAAATTTCCAAATGTTTCTT
Found at i:6280740 original size:13 final size:13
Alignment explanation
Indices: 6280722--6280748 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6280712 GCCAAAATAC
6280722 ACCATGTGATCAA
1 ACCATGTGATCAA
6280735 ACCATGTGATCAA
1 ACCATGTGATCAA
6280748 A
1 A
6280749 AAACATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (13 bp):
ACCATGTGATCAA
Found at i:6281258 original size:67 final size:67
Alignment explanation
Indices: 6281112--6281243 Score: 192
Period size: 67 Copynumber: 2.0 Consensus size: 67
6281102 ATTTGAACCA
* ** * * *
6281112 TTCAAACATGAATTCGTTTATATGCCAATTTCACATATTTCATTTCTATACATACATGTTTCAAA
1 TTCAAACATGAATTCATTTATATGCCAATAGCACAGATTTCATTTCTATACACACACGTTTCAAA
6281177 GG
66 GG
* *
6281179 TTCAAACATGAATTCATTTATATGCCAATAGCACAGCTTTCGTTTCTATACACACACGTTTCAAA
1 TTCAAACATGAATTCATTTATATGCCAATAGCACAGATTTCATTTCTATACACACACGTTTCAAA
6281244 TGTTAGCAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.37
Consensus pattern (67 bp):
TTCAAACATGAATTCATTTATATGCCAATAGCACAGATTTCATTTCTATACACACACGTTTCAAA
GG
Found at i:6284663 original size:41 final size:42
Alignment explanation
Indices: 6284518--6284664 Score: 194
Period size: 41 Copynumber: 3.6 Consensus size: 42
6284508 TTTAACATAT
*
6284518 TCACCGGCACTTAACCTGCTA-AGCTTATAGCCTGA-TTCAGA
1 TCACCGGCACTTAGCCTGCTAGA-CTTATAGCCTGATTTCAGA
* * ** *
6284559 TCACCGGCACTTAGCTTACTAGGTTTATAACCTGATTT-AGA
1 TCACCGGCACTTAGCCTGCTAGACTTATAGCCTGATTTCAGA
6284600 TCACCGGCACTTAGCCTGCTAGACTTATAGCCT-ATTTCAGA
1 TCACCGGCACTTAGCCTGCTAGACTTATAGCCTGATTTCAGA
*
6284641 TCACCGACACTTAGCCTGCTAGAC
1 TCACCGGCACTTAGCCTGCTAGAC
6284665 GTAAATTCCA
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
40 4 0.04
41 85 0.93
42 2 0.02
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (42 bp):
TCACCGGCACTTAGCCTGCTAGACTTATAGCCTGATTTCAGA
Found at i:6285249 original size:114 final size:115
Alignment explanation
Indices: 6285130--6285372 Score: 404
Period size: 114 Copynumber: 2.1 Consensus size: 115
6285120 CTCAAGATCT
*
6285130 TATACATTTTCATATATAC-T-TATTCGAACTTCATTTATGCATATATATAACATTCATACTTAA
1 TATACATTAT-ATATATACATATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAA
*
6285193 CTAATTTCAATTTATATACTTTCAATTATAGCTCATCAAATATACAATAGA
65 CTAATTTCAATTCATATACTTTCAATTATAGCTCATCAAATATACAATAGA
*
6285244 TATACA-TATATATTTACATATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAAC
1 TATACATTATATATATACATATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAAC
* *
6285308 TAATTTCAATTCATATATTTTTAATTATAGCTCATCAAATATACAATAGA
66 TAATTTCAATTCATATACTTTCAATTATAGCTCATCAAATATACAATAGA
6285358 TATACA-TATATATAT
1 TATACATTATATATAT
6285373 TCTGATTTAA
Statistics
Matches: 121, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
112 7 0.06
113 3 0.02
114 111 0.92
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.42
Consensus pattern (115 bp):
TATACATTATATATATACATATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAAC
TAATTTCAATTCATATACTTTCAATTATAGCTCATCAAATATACAATAGA
Found at i:6286800 original size:11 final size:11
Alignment explanation
Indices: 6286784--6286810 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
6286774 CTATATAATG
6286784 CCATAGCTTTT
1 CCATAGCTTTT
6286795 CCATAGCTTTT
1 CCATAGCTTTT
6286806 CCATA
1 CCATA
6286811 CCATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.30, G:0.07, T:0.41
Consensus pattern (11 bp):
CCATAGCTTTT
Found at i:6288305 original size:26 final size:26
Alignment explanation
Indices: 6288276--6288325 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
6288266 AATTTTAAAC
6288276 CTATGAATTTTAA-ATTGTATTAATTA
1 CTAT-AATTTTAATATTGTATTAATTA
* *
6288302 CTATACTTTTAATTTTGTATTAAT
1 CTATAATTTTAATATTGTATTAAT
6288326 CATGAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (26 bp):
CTATAATTTTAATATTGTATTAATTA
Found at i:6288883 original size:19 final size:20
Alignment explanation
Indices: 6288854--6288898 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
6288844 TGTGTTTAAT
*
6288854 TATTCTTTTAAAATTAT-TTA
1 TATT-TTTTAAAAATATATTA
6288874 TATTTTTTAAAAATATATTA
1 TATTTTTTAAAAATATATTA
6288894 TATTT
1 TATTT
6288899 AAAATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTTTTAAAAATATATTA
Found at i:6289517 original size:6 final size:6
Alignment explanation
Indices: 6289472--6289574 Score: 50
Period size: 6 Copynumber: 16.5 Consensus size: 6
6289462 TGTTAGTTAA
* * * *
6289472 TTTTTC TTTCTT- TCTTTC CTTTTC CTTTTC CTTTTC -TTTTC TTTTTAC
1 TTTTTC TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT-C
* * * *
6289520 GTTTTC -TATCC TTCTTTC TTTTTC TCTGTTTC TTTTTAT TATTTTC TTTTTC
1 TTTTTC TTTTTC TT-TTTC TTTTTC T-T-TTTC TTTTT-C T-TTTTC TTTTTC
6289572 TTT
1 TTT
6289575 GCATTTTCTT
Statistics
Matches: 77, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
5 10 0.13
6 43 0.56
7 15 0.19
8 9 0.12
ACGTcount: A:0.04, C:0.21, G:0.02, T:0.73
Consensus pattern (6 bp):
TTTTTC
Found at i:6290195 original size:63 final size:63
Alignment explanation
Indices: 6290114--6290261 Score: 188
Period size: 63 Copynumber: 2.3 Consensus size: 63
6290104 TGTTATTGGT
* * ** * * *
6290114 CGTGTAACCCACTATTTGTGAATTAAGGTCACATGGGCTAGGGACACGAGTGTGTATCTAGGC
1 CGTGTAACTCACTGTTTGTGAATTAAGGTCACACAGGCCAAGGACACGAGTGTGTATCCAGGC
* * *
6290177 CGTGTAACTCACTGTTTGTGAATTAGGGTCACACAGGCCAAGGACACGGGTGTGTGTCCAGGC
1 CGTGTAACTCACTGTTTGTGAATTAAGGTCACACAGGCCAAGGACACGAGTGTGTATCCAGGC
* *
6290240 CATGTAACTCATTGTTTGTGAA
1 CGTGTAACTCACTGTTTGTGAA
6290262 CTAGTGTCAC
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 73 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (63 bp):
CGTGTAACTCACTGTTTGTGAATTAAGGTCACACAGGCCAAGGACACGAGTGTGTATCCAGGC
Found at i:6290296 original size:63 final size:63
Alignment explanation
Indices: 6290173--6290296 Score: 142
Period size: 63 Copynumber: 2.0 Consensus size: 63
6290163 GTGTGTATCT
* * * * **
6290173 AGGCCGTGTAACTCACTGTTTGTGAATTAGGGTCACACAGGCCAAGGACACGGGTGTGTGTCC
1 AGGCCATGTAACTCACTGTTTGTGAACTAGGGTCACACAGGCCAAGGACAAGAGCATGTGTCC
* * * *
6290236 AGGCCATGTAACTCATTGTTTGTGAACTAGTGTCACACTGG-CTAGAGACAAGAGCATGTGT
1 AGGCCATGTAACTCACTGTTTGTGAACTAGGGTCACACAGGCCAAG-GACAAGAGCATGTGT
6290297 TAAGACCATG
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 3 0.06
63 47 0.94
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (63 bp):
AGGCCATGTAACTCACTGTTTGTGAACTAGGGTCACACAGGCCAAGGACAAGAGCATGTGTCC
Found at i:6291517 original size:4 final size:4
Alignment explanation
Indices: 6291508--6291534 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
6291498 TATTTTAAAT
6291508 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
6291535 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:6292582 original size:11 final size:11
Alignment explanation
Indices: 6292568--6292634 Score: 56
Period size: 11 Copynumber: 6.6 Consensus size: 11
6292558 CGGCCCGAAT
6292568 TATATATTAAA
1 TATATATTAAA
6292579 TATATATT---
1 TATATATTAAA
**
6292587 TATATATTATT
1 TATATATTAAA
* *
6292598 TTTA-ATCAAA
1 TATATATTAAA
6292608 TATATATT--A
1 TATATATTAAA
6292617 TATATATTAAA
1 TATATATTAAA
6292628 TATATAT
1 TATATAT
6292635 AATATGGGCC
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
8 8 0.18
9 9 0.20
10 6 0.14
11 21 0.48
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (11 bp):
TATATATTAAA
Found at i:6300664 original size:17 final size:18
Alignment explanation
Indices: 6300629--6300666 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
6300619 CCCGGCGCAG
6300629 AGGAACAAAACACGAACA
1 AGGAACAAAACACGAACA
6300647 AGGAAGCAAAA-A-GAACA
1 AGGAA-CAAAACACGAACA
6300664 AGG
1 AGG
6300667 CTAACAGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.61, C:0.16, G:0.24, T:0.00
Consensus pattern (18 bp):
AGGAACAAAACACGAACA
Found at i:6301183 original size:26 final size:26
Alignment explanation
Indices: 6301147--6301197 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
6301137 AGATTAAACA
*
6301147 CTTAATTTGTTCTTTCCATCAAAGAT
1 CTTAACTTGTTCTTTCCATCAAAGAT
*
6301173 CTTAACTTGTTCTTTCCATTAAAGA
1 CTTAACTTGTTCTTTCCATCAAAGA
6301198 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.45
Consensus pattern (26 bp):
CTTAACTTGTTCTTTCCATCAAAGAT
Found at i:6303177 original size:20 final size:21
Alignment explanation
Indices: 6303149--6303191 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6303139 TAATTAAGTA
*
6303149 TTTACTTTA-GTGGTTAAGTGT
1 TTTACTTTATGTGCTTAAG-GT
6303170 TTTA-TTTATGTGCTTAAGGT
1 TTTACTTTATGTGCTTAAGGT
6303190 TT
1 TT
6303192 GGGGTTCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.56
Consensus pattern (21 bp):
TTTACTTTATGTGCTTAAGGT
Found at i:6303683 original size:273 final size:273
Alignment explanation
Indices: 6303196--6303736 Score: 920
Period size: 273 Copynumber: 2.0 Consensus size: 273
6303186 AGGTTTGGGG
* *
6303196 TTCAAGTCCCATTTTTGGAAATTTTGCTTTTTGTTTTGAATCAACCCTCACTTTCAAACTTTTGA
1 TTCAAGTCCCATTTTTGGAAATTTTGCTATTTGTTTTGAATCAACCCTCACTTTCAAACTTTCGA
** **
6303261 CTTAAGATTAATTTTGTGTAAACTTATATTAAGAATGAGCTTGTTGGTTTAATAGTTAAACTTTT
66 CTTAAGATTAATTTTGCATAAACTTATATTAAGAATGAGCTTACTGGTTTAATAGTTAAACTTTT
* * * *
6303326 GTATAACCTTTGGTCTTATGTTCGAGTTTCTGCAAAAGCTATGAGAAAATATCTTATGCTAGTTT
131 GTATAACCTTTGCTCTTATGTTCAAGTTTCTGCAAAAGCTATGAGAAAACATCTTATACTAGTTT
* *
6303391 ATAAAAATTAGTTTATTTTAAGGTAATTAAATTCCTTTATTTTTGTTAAAATTTTTTTCACGTTT
196 ATAAAAATTAGTCTATTTTAAGGTAATTAAATTCCTTTATTTTTGTTAAAATTTCTTTCACGTTT
6303456 TATTTCTTTCACA
261 TATTTCTTTCACA
*
6303469 TTCAAGTCCCATTTTTGGAAATTTTGCTATTTGTTTTGAATCAACCCTCACTTTTAAACTTTCGA
1 TTCAAGTCCCATTTTTGGAAATTTTGCTATTTGTTTTGAATCAACCCTCACTTTCAAACTTTCGA
* * *
6303534 CTTAAGATTAATTTTGCATAAACTTGTGTTAAGAATGAGCTTACTGGTTTAATGGTTAAACTTTT
66 CTTAAGATTAATTTTGCATAAACTTATATTAAGAATGAGCTTACTGGTTTAATAGTTAAACTTTT
* *
6303599 GTATACCCTTTGCTCTTGTGTTCAAGTTTCTGCAAAAGCTATGAGAAAACATCTTATACTAGTTT
131 GTATAACCTTTGCTCTTATGTTCAAGTTTCTGCAAAAGCTATGAGAAAACATCTTATACTAGTTT
6303664 ATAAAAATTAGTCTATTTTAAGGTAATTAAATTCCTTTATTTTTGTTAAAATTTCTTTCACGTTT
196 ATAAAAATTAGTCTATTTTAAGGTAATTAAATTCCTTTATTTTTGTTAAAATTTCTTTCACGTTT
6303729 TATTTCTT
261 TATTTCTT
6303737 CCTTTATCCT
Statistics
Matches: 250, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
273 250 1.00
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.46
Consensus pattern (273 bp):
TTCAAGTCCCATTTTTGGAAATTTTGCTATTTGTTTTGAATCAACCCTCACTTTCAAACTTTCGA
CTTAAGATTAATTTTGCATAAACTTATATTAAGAATGAGCTTACTGGTTTAATAGTTAAACTTTT
GTATAACCTTTGCTCTTATGTTCAAGTTTCTGCAAAAGCTATGAGAAAACATCTTATACTAGTTT
ATAAAAATTAGTCTATTTTAAGGTAATTAAATTCCTTTATTTTTGTTAAAATTTCTTTCACGTTT
TATTTCTTTCACA
Found at i:6304473 original size:42 final size:43
Alignment explanation
Indices: 6304384--6304474 Score: 105
Period size: 42 Copynumber: 2.1 Consensus size: 43
6304374 ATGACATGGG
* * * * *
6304384 TGTGTATCTAGACCGTGTGACTCTCTAACTTGAGTAACATGGT
1 TGTGTGTCTAGACCGTATAACTCTCTAACTTGAGTAACACGGC
*
6304427 TGTGTGTC-AGACCGTATAACTCTCTAACTT-AGGTCACACGGC
1 TGTGTGTCTAGACCGTATAACTCTCTAACTTGA-GTAACACGGC
6304469 TGTGTG
1 TGTGTG
6304475 CCAGGTCGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 1 0.02
42 33 0.80
43 7 0.17
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (43 bp):
TGTGTGTCTAGACCGTATAACTCTCTAACTTGAGTAACACGGC
Found at i:6313114 original size:12 final size:12
Alignment explanation
Indices: 6313097--6313121 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6313087 ACATCAATTC
6313097 AATAATATACCA
1 AATAATATACCA
6313109 AATAATATACCA
1 AATAATATACCA
6313121 A
1 A
6313122 TTGCATTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAATATACCA
Found at i:6314052 original size:19 final size:19
Alignment explanation
Indices: 6314024--6314081 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
6314014 TACTAGCGTG
*
6314024 CAAAACGCATCCTGGCGCA
1 CAAAATGCATCCTGGCGCA
* *
6314043 -AAAAGTGCATACTGGCACA
1 CAAAA-TGCATCCTGGCGCA
*
6314062 CAAAATACATCCTGGCGCA
1 CAAAATGCATCCTGGCGCA
6314081 C
1 C
6314082 GAAGCGCATA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
18 4 0.13
19 23 0.74
20 4 0.13
ACGTcount: A:0.36, C:0.31, G:0.19, T:0.14
Consensus pattern (19 bp):
CAAAATGCATCCTGGCGCA
Found at i:6314066 original size:38 final size:38
Alignment explanation
Indices: 6314024--6314206 Score: 150
Period size: 39 Copynumber: 4.8 Consensus size: 38
6314014 TACTAGCGTG
* **
6314024 CAAAACGCATCCTGGCGCAAAAAGTGCATACTGGCACA
1 CAAAATGCATCCTGGCGCACGAAGTGCATACTGGCACA
* * *
6314062 CAAAATACATCCTGGCGCACGAAGCGCATATCTGGAACA
1 CAAAATGCATCCTGGCGCACGAAGTGCATA-CTGGCACA
* * * * *
6314101 CGATATGCATCTTGGCACACGAAGTGCATACTGGCATA
1 CAAAATGCATCCTGGCGCACGAAGTGCATACTGGCACA
* * * * *
6314139 CAAAGTGCATCCTAGTGCACGAAGCGTATATCTGGCACA
1 CAAAATGCATCCTGGCGCACGAAGTGCATA-CTGGCACA
* ** * * *
6314178 CGATGTGTATCTTGGCACACGAAGTGCAT
1 CAAAATGCATCCTGGCGCACGAAGTGCAT
6314207 TATGAAGAAT
Statistics
Matches: 110, Mismatches: 33, Indels: 3
0.75 0.23 0.02
Matches are distributed among these distances:
38 52 0.47
39 58 0.53
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.20
Consensus pattern (38 bp):
CAAAATGCATCCTGGCGCACGAAGTGCATACTGGCACA
Found at i:6314126 original size:77 final size:77
Alignment explanation
Indices: 6314045--6314206 Score: 243
Period size: 77 Copynumber: 2.1 Consensus size: 77
6314035 CTGGCGCAAA
*
6314045 AAGTGCATACTGGCACACAAAATACATCCTGGCGCACGAAGCGCATATCTGGAACACGATATGCA
1 AAGTGCATACTGGCACACAAAATACATCCTAGCGCACGAAGCGCATATCTGGAACACGATATGCA
6314110 TCTTGGCACACG
66 TCTTGGCACACG
* * * * * * * *
6314122 AAGTGCATACTGGCATACAAAGTGCATCCTAGTGCACGAAGCGTATATCTGGCACACGATGTGTA
1 AAGTGCATACTGGCACACAAAATACATCCTAGCGCACGAAGCGCATATCTGGAACACGATATGCA
6314187 TCTTGGCACACG
66 TCTTGGCACACG
6314199 AAGTGCAT
1 AAGTGCAT
6314207 TATGAAGAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (77 bp):
AAGTGCATACTGGCACACAAAATACATCCTAGCGCACGAAGCGCATATCTGGAACACGATATGCA
TCTTGGCACACG
Found at i:6314128 original size:19 final size:19
Alignment explanation
Indices: 6314045--6314206 Score: 87
Period size: 19 Copynumber: 8.4 Consensus size: 19
6314035 CTGGCGCAAA
*
6314045 AAGTGCATAC-TGGCACACA
1 AAGTGCAT-CTTGGCACACG
* * * *
6314064 AAATACATCCTGGCGCACG
1 AAGTGCATCTTGGCACACG
* * *
6314083 AAGCGCATATCTGGAACACG
1 AAGTGCATCT-TGGCACACG
6314103 ATA-TGCATCTTGGCACACG
1 A-AGTGCATCTTGGCACACG
* *
6314122 AAGTGCATAC-TGGCATACA
1 AAGTGCAT-CTTGGCACACG
* * **
6314141 AAGTGCATCCTAGTGCACG
1 AAGTGCATCTTGGCACACG
* * *
6314160 AAGCGTATATCTGGCACACG
1 AAGTGCATCT-TGGCACACG
* *
6314180 ATGTGTATCTTGGCACACG
1 AAGTGCATCTTGGCACACG
6314199 AAGTGCAT
1 AAGTGCAT
6314207 TATGAAGAAT
Statistics
Matches: 103, Mismatches: 33, Indels: 14
0.69 0.22 0.09
Matches are distributed among these distances:
18 3 0.03
19 72 0.70
20 27 0.26
21 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (19 bp):
AAGTGCATCTTGGCACACG
Found at i:6317964 original size:11 final size:11
Alignment explanation
Indices: 6317944--6317985 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
6317934 AAATTGCAAC
6317944 AGAAAGAAAAA
1 AGAAAGAAAAA
6317955 AGAAA-AAAAA
1 AGAAAGAAAAA
*
6317965 TGAAAGAAAAA
1 AGAAAGAAAAA
*
6317976 AGATAGAAAA
1 AGAAAGAAAA
6317986 CTCTCTGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (11 bp):
AGAAAGAAAAA
Found at i:6319204 original size:45 final size:44
Alignment explanation
Indices: 6319138--6319606 Score: 302
Period size: 45 Copynumber: 10.5 Consensus size: 44
6319128 TCACGCCAAT
* * * *
6319138 GAAGACAAGGTCTGTTCTCTTCGATCTACTCCACCACCAGTATGG
1 GAAGACAAGATCTATT-TCTTTGATCTACTTCACCACCAGTATGG
* * * * **
6319183 GGAGACAAGATCTATTGTCTTCGATCTACTTCA-CGCTAGTATAT
1 GAAGACAAGATCTATT-TCTTTGATCTACTTCACCACCAGTATGG
* *
6319227 GAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTA-TTTCTTTGATCTACTTCACCACCAGTATGG
* * * * * ***
6319272 GAAGGCAAGATCTGGTATCTCTGATCTACTTCA-CGCCAGTACAT
1 GAAGACAAGATCT-ATTTCTTTGATCTACTTCACCACCAGTATGG
* * **
6319316 GAAGACAAGATCTGCTTTCTTTGATCTGCTTTGCCACCAGTATGG
1 GAAGACAAGATCT-ATTTCTTTGATCTACTTCACCACCAGTATGG
* * * ***
6319361 GAAGGCAAGATCTGTTATCTTTGATCTACTTCA-CGCCAGTACAT
1 GAAGACAAGATCTATT-TCTTTGATCTACTTCACCACCAGTATGG
* * *
6319405 GAAGACAATATCTATTTTCTTTGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTA-TTTCTTTGATCTACTTCACCACCAGTATGG
* * * ** ** ***
6319450 GAAGGCAAGATCTGGTATCTCCGATCTACTTCA-TGCCAGTACAT
1 GAAGACAAGATCT-ATTTCTTTGATCTACTTCACCACCAGTATGG
* * *
6319494 GAAGACAAGATCTTCTTTCTTTGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATC-TATTTCTTTGATCTACTTCACCACCAGTATGG
* * * * ***
6319539 GAA-AGCAAGATTTGTTATCTCTGATCTACTTCA-CGCCAGTACAT
1 GAAGA-CAAGATCTATT-TCTTTGATCTACTTCACCACCAGTATGG
*
6319583 GAAGACAAGATCTGCTTTCTTTGA
1 GAAGACAAGATCT-ATTTCTTTGA
6319607 ACCTGCTCCA
Statistics
Matches: 317, Mismatches: 93, Indels: 29
0.72 0.21 0.07
Matches are distributed among these distances:
44 157 0.50
45 160 0.50
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (44 bp):
GAAGACAAGATCTATTTCTTTGATCTACTTCACCACCAGTATGG
Found at i:6319264 original size:89 final size:89
Alignment explanation
Indices: 6319136--6319606 Score: 669
Period size: 89 Copynumber: 5.3 Consensus size: 89
6319126 CCTCACGCCA
* * * * * * * * * *
6319136 ATGAAGACAAGGTCT-GTTCTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTATTG
1 ATGAAGACAAGATCTACTT-TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTA
* *
6319200 TCTTCGATCTACTTCACGCTAGTAT
65 TCTTCGATCTACTTCACGCCAGTAC
*
6319225 ATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTAT
1 ATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTAT
6319290 C-TCTGATCTACTTCACGCCAGTAC
66 CTTC-GATCTACTTCACGCCAGTAC
* *
6319314 ATGAAGACAAGATCTGCTTTCTTTGATCTGCTTTGCCACCAGTATGGGAAGGCAAGATCTGTTAT
1 ATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTAT
*
6319379 CTTTGATCTACTTCACGCCAGTAC
66 CTTCGATCTACTTCACGCCAGTAC
* * *
6319403 ATGAAGACAATATCTATTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTAT
1 ATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTAT
* *
6319468 CTCCGATCTACTTCATGCCAGTAC
66 CTTCGATCTACTTCACGCCAGTAC
* * *
6319492 ATGAAGACAAGATCTTCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAAGCAAGATTTGTTAT
1 ATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTAT
6319557 C-TCTGATCTACTTCACGCCAGTAC
66 CTTC-GATCTACTTCACGCCAGTAC
*
6319581 ATGAAGACAAGATCTGCTTTCTTTGA
1 ATGAAGACAAGATCTACTTTCTTTGA
6319607 ACCTGCTCCA
Statistics
Matches: 344, Mismatches: 34, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
88 3 0.01
89 338 0.98
90 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (89 bp):
ATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTAT
CTTCGATCTACTTCACGCCAGTAC
Found at i:6327341 original size:43 final size:43
Alignment explanation
Indices: 6327271--6327418 Score: 215
Period size: 43 Copynumber: 3.4 Consensus size: 43
6327261 TGTCCCAAAC
* ***
6327271 ATGGTCTTACATGGAAATCTTGTATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACA-CGAAATCTCAAATCGATGCCAATAGCCCAGCT
* * *
6327315 ATAGTCTTACATGAAATCTCAAATCGATGCCAATAGCCCAGTT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
*
6327358 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCGCAGCT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
6327401 ATGGTCTTACACGAAATC
1 ATGGTCTTACACGAAATC
6327419 ACACCTCAGA
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
43 84 0.89
44 10 0.11
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
Found at i:6327633 original size:31 final size:31
Alignment explanation
Indices: 6327528--6327636 Score: 166
Period size: 31 Copynumber: 3.5 Consensus size: 31
6327518 AACTAGTCTC
* * *
6327528 AATTCGGCAATATATATCCATATACAAATCA
1 AATTCGACAATGTATATCTATATACAAATCA
*
6327559 AATTCGACAATGAATATCTATATACAAATCA
1 AATTCGACAATGTATATCTATATACAAATCA
6327590 AATTCGACAATGTATATCTATATACAAATCA
1 AATTCGACAATGTATATCTATATACAAATCA
6327621 AATTCGGA-AATGTATA
1 AATTC-GACAATGTATA
6327637 AAACATATAC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 70 0.97
32 2 0.03
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (31 bp):
AATTCGACAATGTATATCTATATACAAATCA
Found at i:6331870 original size:6 final size:6
Alignment explanation
Indices: 6331861--6331925 Score: 64
Period size: 6 Copynumber: 11.3 Consensus size: 6
6331851 CTAAGAAAAT
* * * * *
6331861 AATAAA AAT--A ACTAAA AATAAC AATAAA CATAAT CAT-AA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
6331906 AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AA
6331926 AACTTAATGG
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
4 3 0.06
5 3 0.06
6 42 0.88
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:6331922 original size:23 final size:23
Alignment explanation
Indices: 6331861--6331924 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
6331851 CTAAGAAAAT
** *
6331861 AATAAAAATAACTA-AAAATAAC
1 AATAAAAATAAAAATAAAATAAA
* **
6331883 AATAAACATAATCATAAAATAAA
1 AATAAAAATAAAAATAAAATAAA
6331906 AATAAAAATAAAAATAAAA
1 AATAAAAATAAAAATAAAA
6331925 AAACTTAATG
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 11 0.32
23 23 0.68
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (23 bp):
AATAAAAATAAAAATAAAATAAA
Found at i:6333775 original size:12 final size:12
Alignment explanation
Indices: 6333760--6333791 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
6333750 TAAAAGACAA
6333760 AAAAAAAAAAAG
1 AAAAAAAAAAAG
*
6333772 AAAAAGAAAAAG
1 AAAAAAAAAAAG
6333784 AAAAAAAA
1 AAAAAAAA
6333792 GCTGAAGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:6333775 original size:21 final size:21
Alignment explanation
Indices: 6333751--6333792 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6333741 GTTGACCTCT
6333751 AAAAGACAAAAAAAAAAAAAGA
1 AAAAGA-AAAAAAAAAAAAAGA
*
6333773 AAAAGAAAAAGAAAAAAAAG
1 AAAAGAAAAAAAAAAAAAAG
6333793 CTGAAGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAAAAAAAAAAAGA
Found at i:6337749 original size:15 final size:15
Alignment explanation
Indices: 6337729--6337757 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6337719 TAAATCCATT
6337729 TTTATATTTAAGTAC
1 TTTATATTTAAGTAC
6337744 TTTATATTTAAGTA
1 TTTATATTTAAGTA
6337758 TTTGTACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.55
Consensus pattern (15 bp):
TTTATATTTAAGTAC
Found at i:6337794 original size:13 final size:13
Alignment explanation
Indices: 6337776--6337800 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6337766 ATAAATATTC
6337776 TTAAATATTTTTT
1 TTAAATATTTTTT
6337789 TTAAATATTTTT
1 TTAAATATTTTT
6337801 ATACGGGTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTAAATATTTTTT
Found at i:6340958 original size:31 final size:32
Alignment explanation
Indices: 6340899--6340963 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
6340889 GGCAAATTAC
6340899 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
6340931 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
6340962 AA
1 AA
6340964 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:6341757 original size:15 final size:15
Alignment explanation
Indices: 6341726--6341780 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
6341716 CATCATCATC
*
6341726 ATAATAATAAATGAA
1 ATAATAATAAATAAA
6341741 ATAATTAATAAA-AAA
1 ATAA-TAATAAATAAA
*
6341756 ATATAGTATTAAATAAA
1 ATA-A-TAATAAATAAA
6341773 ATAA-AATA
1 ATAATAATA
6341781 CAATGAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
14 3 0.09
15 9 0.27
16 15 0.45
17 6 0.18
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (15 bp):
ATAATAATAAATAAA
Found at i:6346453 original size:22 final size:22
Alignment explanation
Indices: 6346424--6346477 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
6346414 GATATGCAAG
6346424 GGTT-GAATGCCCTAATGTTTT
1 GGTTCGAATGCCCTAATGTTTT
6346445 GGTTCGAATGCCCTAATGTTTT
1 GGTTCGAATGCCCTAATGTTTT
*
6346467 GGGTCGAATGC
1 GGTTCGAATGC
6346478 TCGATTTGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.37
Consensus pattern (22 bp):
GGTTCGAATGCCCTAATGTTTT
Found at i:6347772 original size:63 final size:63
Alignment explanation
Indices: 6347694--6347817 Score: 176
Period size: 63 Copynumber: 2.0 Consensus size: 63
6347684 GAATCAGGCC
* * * * *
6347694 GTGTAATTCATTGTTTATGAATTAGGGTCACATAGGCTAGGGACACAAGTGTGTTTCCAAGCT
1 GTGTAACTCACTGTTTATGAATTAGGGTCACATAGGCCAGAGACACAAGTGTGTGTCCAAGCT
* * *
6347757 GTGTAACTCACTGTTTTTGAATTAGTGTCACATGGGCCAGAGACACAAGTGTGTGTCCAAG
1 GTGTAACTCACTGTTTATGAATTAGGGTCACATAGGCCAGAGACACAAGTGTGTGTCCAAG
6347818 ACATGTGAGA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (63 bp):
GTGTAACTCACTGTTTATGAATTAGGGTCACATAGGCCAGAGACACAAGTGTGTGTCCAAGCT
Found at i:6351284 original size:23 final size:23
Alignment explanation
Indices: 6351258--6351301 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
6351248 TAATTAGTAA
*
6351258 TTTAAT-ATTTTTTATTTTTTATT
1 TTTAATAATTTATT-TTTTTTATT
6351281 TTTAATAATTTATTTTTTTTA
1 TTTAATAATTTATTTTTTTTA
6351302 AATTGATCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTAATAATTTATTTTTTTTATT
Found at i:6351407 original size:27 final size:27
Alignment explanation
Indices: 6351358--6351416 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
6351348 AGTGAATTCA
* * *
6351358 AAATATATTTTAATTAGGAAATTGATT
1 AAATTTATTTTAATTAGAAAATTAATT
6351385 AAATTTATTTTAATTA-AACAATTAATT
1 AAATTTATTTTAATTAGAA-AATTAATT
*
6351412 TAATT
1 AAATT
6351417 AAAATATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (27 bp):
AAATTTATTTTAATTAGAAAATTAATT
Found at i:6351415 original size:17 final size:17
Alignment explanation
Indices: 6351393--6351432 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
6351383 TTAAATTTAT
6351393 TTTAATTAAACA-ATTAA
1 TTTAATTAAA-ATATTAA
6351410 TTTAATTAAAATATTAA
1 TTTAATTAAAATATTAA
6351427 -TTAATT
1 TTTAATT
6351433 GGATTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAATTAAAATATTAA
Found at i:6352419 original size:17 final size:17
Alignment explanation
Indices: 6352399--6352435 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
6352389 AATTTTTGAA
6352399 TTAGTGAATTCTGTGAT
1 TTAGTGAATTCTGTGAT
*
6352416 TTAGTGAATTTTGTGAT
1 TTAGTGAATTCTGTGAT
6352433 TTA
1 TTA
6352436 AAAAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (17 bp):
TTAGTGAATTCTGTGAT
Found at i:6353715 original size:46 final size:46
Alignment explanation
Indices: 6353662--6353801 Score: 253
Period size: 46 Copynumber: 3.0 Consensus size: 46
6353652 CCATTGCAAA
*
6353662 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAATCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
6353708 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* *
6353754 TTGTGAAAAGTATGTATGGTATTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
6353800 TT
1 TT
6353802 ATAGCATTGT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 91 1.00
ACGTcount: A:0.35, C:0.08, G:0.26, T:0.31
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:6360965 original size:17 final size:17
Alignment explanation
Indices: 6360936--6360968 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6360926 ATGAATAAAA
6360936 AATAATAATTTTTTTTG
1 AATAATAATTTTTTTTG
6360953 AATAA-AATATTTTTTT
1 AATAATAAT-TTTTTTT
6360969 ATATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
AATAATAATTTTTTTTG
Found at i:6361119 original size:19 final size:19
Alignment explanation
Indices: 6361092--6361296 Score: 144
Period size: 19 Copynumber: 10.7 Consensus size: 19
6361082 AGAGGCGCCA
6361092 ATGAATATTGTAATTTTGT
1 ATGAATATTGTAATTTTGT
* *
6361111 ATTAATATTGTAATTATTTT
1 ATGAATATTGTAATT-TTGT
6361131 AT-AATTAAATTTGT-ATTTATAGTT
1 ATGAA-T--A-TTGTAATTT-T-G-T
* * *
6361155 TTGGAT-TAGT-ATTTTGT
1 ATGAATATTGTAATTTTGT
6361172 ATGAATATTGTAATTTTTGT
1 ATGAATATTGTAA-TTTTGT
6361192 ATGAATATTGTAATTTTGT
1 ATGAATATTGTAATTTTGT
*
6361211 ATGAATATTGTAATTTTTT
1 ATGAATATTGTAATTTTGT
*
6361230 ATGAATATTGTAA-TAT-T
1 ATGAATATTGTAATTTTGT
* *
6361247 AT-AATTTTGTATGAATATTG-
1 ATGAATATTG--T-AATTTTGT
6361267 -T-AATATTGTAA-TTTGT
1 ATGAATATTGTAATTTTGT
6361283 ATGAATATTGTAAT
1 ATGAATATTGTAAT
6361297 GTCGGGATAT
Statistics
Matches: 149, Mismatches: 16, Indels: 42
0.72 0.08 0.20
Matches are distributed among these distances:
15 3 0.02
16 8 0.05
17 10 0.07
18 17 0.11
19 64 0.43
20 33 0.22
21 1 0.01
22 5 0.03
23 4 0.03
24 3 0.02
25 1 0.01
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (19 bp):
ATGAATATTGTAATTTTGT
Found at i:6361193 original size:27 final size:27
Alignment explanation
Indices: 6361163--6361296 Score: 112
Period size: 27 Copynumber: 4.9 Consensus size: 27
6361153 TTTTGGATTA
*
6361163 GTATTTTGTATGAATATTGTAATTTTT
1 GTATTTTGTATGAATATTGTAATTATT
*** * *
6361190 GTA-TGAATATTGTAATTTTGTATGAATATT
1 GTATTTTGTA-TG-AATATTGTA--ATTATT
*
6361220 GTAATTTTTTATGAATATTGTAA-TATT
1 GT-ATTTTGTATGAATATTGTAATTATT
*
6361247 ATAATTTTGTATGAATATTGTAA-TATT
1 GT-ATTTTGTATGAATATTGTAATTATT
*
6361274 GTAATTTGTATGAATATTGTAAT
1 GTATTTTGTATGAATATTGTAAT
6361297 GTCGGGATAT
Statistics
Matches: 86, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
26 22 0.26
27 35 0.41
28 9 0.10
30 14 0.16
31 3 0.03
32 3 0.03
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (27 bp):
GTATTTTGTATGAATATTGTAATTATT
Found at i:6361208 original size:39 final size:38
Alignment explanation
Indices: 6361165--6361351 Score: 152
Period size: 39 Copynumber: 4.7 Consensus size: 38
6361155 TTGGATTAGT
6361165 ATTTTGTATGAATATTGTAATTTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTAATTTTT-TATGAATATTGTA
6361204 ATTTTGTATGAATATTGTAATTTTTTATGAATATTGTA
1 ATTTTGTATGAATATTGTAATTTTTTATGAATATTGTA
* * ***
6361242 A-TAT-TAT-AATTTTGT-A-TGAATATTGTAATATTGTA
1 ATTTTGTATGAATATTGTAATTTTTTA-TG-AATATTGTA
* *
6361277 A-TTTGTATGAATATTGTAATGTCGGGATATATTGTAATATTGTA
1 ATTTTGTATGAATATTGTAAT-T----TTTTA-TG-AATATTGTA
6361321 ATTTTTTGTATGAATATTGTAATTATTTTAT
1 A--TTTTGTATGAATATTGTAATT-TTTTAT
6361352 AATTAATTTG
Statistics
Matches: 122, Mismatches: 12, Indels: 25
0.77 0.08 0.16
Matches are distributed among these distances:
33 3 0.02
34 3 0.02
35 19 0.16
36 6 0.05
37 9 0.07
38 15 0.12
39 25 0.20
40 1 0.01
42 1 0.01
43 3 0.02
44 17 0.14
46 1 0.01
47 19 0.16
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (38 bp):
ATTTTGTATGAATATTGTAATTTTTTATGAATATTGTA
Found at i:6361246 original size:8 final size:8
Alignment explanation
Indices: 6361233--6361322 Score: 56
Period size: 8 Copynumber: 10.4 Consensus size: 8
6361223 ATTTTTTATG
6361233 AATATTGT
1 AATATTGT
*
6361241 AATATTAT
1 AATATTGT
*
6361249 AATTTTGTAT
1 AATATTG--T
6361259 GAATATTGT
1 -AATATTGT
6361268 AATATTGT
1 AATATTGT
6361276 AAT-TTGTAT
1 AATATTG--T
6361285 GAATATTGT
1 -AATATTGT
* * *
6361294 AATGTCGGG
1 AATAT-TGT
6361303 ATATATTGT
1 A-ATATTGT
6361312 AATATTGT
1 AATATTGT
6361320 AAT
1 AAT
6361323 TTTTTGTATG
Statistics
Matches: 63, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
7 3 0.05
8 37 0.59
9 7 0.11
10 7 0.11
11 9 0.14
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.48
Consensus pattern (8 bp):
AATATTGT
Found at i:6361272 original size:73 final size:72
Alignment explanation
Indices: 6361195--6361343 Score: 203
Period size: 73 Copynumber: 2.0 Consensus size: 72
6361185 TTTTTGTATG
* * *
6361195 AATATTGTAATTTTGTATGAATATTGTAATTTTTTATGA-ATATTGTAATATTATAA-TTTTGTA
1 AATATTGTAA-TTTGTATGAATATTGTAA--TGTCAGGATATATTGTAATATTATAATTTTTGTA
6361258 TGAATATTGT
63 TGAATATTGT
* *
6361268 AATATTGTAATTTGTATGAATATTGTAATGTCGGGATATATTGTAATATTGTAATTTTTTGTATG
1 AATATTGTAATTTGTATGAATATTGTAATGTCAGGATATATTGTAATATTATAA-TTTTTGTATG
6361333 AATATTGT
65 AATATTGT
6361341 AAT
1 AAT
6361344 TATTTTATAA
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
70 4 0.06
71 16 0.24
72 18 0.26
73 30 0.44
ACGTcount: A:0.34, C:0.01, G:0.15, T:0.51
Consensus pattern (72 bp):
AATATTGTAATTTGTATGAATATTGTAATGTCAGGATATATTGTAATATTATAATTTTTGTATGA
ATATTGT
Found at i:6361337 original size:65 final size:65
Alignment explanation
Indices: 6361175--6361344 Score: 200
Period size: 71 Copynumber: 2.5 Consensus size: 65
6361165 ATTTTGTATG
****
6361175 AATATTGTAA-TTTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTTTTTATGAATATT
1 AATATTGTAATTTTTTGTATGAATATTGTAA-TTTGTATGAATATTGTAATTCGGGAT-AATATT
6361239 GT
64 GT
*
6361241 AATATTATAATTTTGTATGAATATTGTAATATTGTAATTTGTATGAATATTGTAATGTCGGGAT-
1 AATATTGTAATTTT-T-TG--TA-TG-AATATTGTAATTTGTATGAATATTGTAAT-TCGGGATA
6361305 ATATTGT
59 ATATTGT
6361312 AATATTGTAATTTTTTGTATGAATATTGTAATT
1 AATATTGTAATTTTTTGTATGAATATTGTAATT
6361345 ATTTTATAAT
Statistics
Matches: 90, Mismatches: 6, Indels: 17
0.80 0.05 0.15
Matches are distributed among these distances:
65 12 0.13
66 11 0.12
67 5 0.06
68 1 0.01
69 4 0.04
70 1 0.01
71 22 0.24
72 21 0.23
73 13 0.14
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.52
Consensus pattern (65 bp):
AATATTGTAATTTTTTGTATGAATATTGTAATTTGTATGAATATTGTAATTCGGGATAATATTGT
Found at i:6361525 original size:16 final size:16
Alignment explanation
Indices: 6361482--6361525 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
6361472 AAAATCAAAT
*
6361482 AAAATTTAATTATATA
1 AAAATTAAATTATATA
* *
6361498 AAAGTTACATTATATA
1 AAAATTAAATTATATA
6361514 AAAATTAAATTA
1 AAAATTAAATTA
6361526 GTTAACAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAATTAAATTATATA
Found at i:6361601 original size:38 final size:37
Alignment explanation
Indices: 6361558--6361638 Score: 144
Period size: 38 Copynumber: 2.2 Consensus size: 37
6361548 AAAAAGTCAG
6361558 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAA-TTTT
*
6361596 TTATAATTAAACTTTTAATAAGATGATTTTTAATTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTT
6361633 TTATAA
1 TTATAA
6361639 ACTTTATATG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 10 0.24
38 32 0.76
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (37 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTT
Found at i:6361747 original size:60 final size:60
Alignment explanation
Indices: 6361671--6361792 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 60
6361661 ATATTAAACT
* * * * *
6361671 AAACACAACAACTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTAC
*
6361731 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
6361791 AA
1 AA
6361793 TATTAATACA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 4 0.07
60 51 0.93
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:6361820 original size:8 final size:8
Alignment explanation
Indices: 6361807--6361943 Score: 76
Period size: 8 Copynumber: 15.4 Consensus size: 8
6361797 AATACAAAAA
6361807 ATTACAAT
1 ATTACAAT
6361815 ATTACAAT
1 ATTACAAT
* * *
6361823 ATATCCCGAC
1 AT-T-ACAAT
6361833 ATTACAAT
1 ATTACAAT
*
6361841 ATTCATACAAA
1 A-T--TACAAT
6361852 ATTACAAT
1 ATTACAAT
6361860 ATTACAAT
1 ATTACAAT
*
6361868 ATTCATACAAA
1 A-T--TACAAT
6361879 ATTACAAT
1 ATTACAAT
6361887 ATTACAAT
1 ATTACAAT
*
6361895 ATTCATACAAA
1 A-T--TACAAT
*
6361906 ATTATAAT
1 ATTACAAT
6361914 ATTACAAT
1 ATTACAAT
*
6361922 ATTCATACAAA
1 A-T--TACAAT
6361933 ATTACAAT
1 ATTACAAT
6361941 ATT
1 ATT
6361944 CATACAAAAA
Statistics
Matches: 99, Mismatches: 16, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
8 61 0.62
9 6 0.06
10 8 0.08
11 24 0.24
ACGTcount: A:0.50, C:0.15, G:0.01, T:0.34
Consensus pattern (8 bp):
ATTACAAT
Found at i:6361869 original size:27 final size:27
Alignment explanation
Indices: 6361833--6362157 Score: 249
Period size: 27 Copynumber: 12.8 Consensus size: 27
6361823 ATATCCCGAC
6361833 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
6361860 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
*
6361887 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
6361914 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
6361941 ATT-C-ATA--CA-A-AAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
* * * *
6361962 ATT-CATATAAAATACTAATCCAAAACTATAA-
1 ATTACA-AT---AT--TCATACAAAATTACAAT
** *
6361993 A-TACAA-ATT--TA-ATTA-TAAAAT
1 ATTACAATATTCATACAAAATTACAAT
6362014 AATTACAATATTCATACAAAAAATTACAAT
1 -ATTACAATATTCATAC--AAAATTACAAT
* * *
6362044 ATTACAATA-T-AT-C------CCGAC
1 ATTACAATATTCATACAAAATTACAAT
*
6362062 ATTACAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAATTACAAT
*
6362089 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
6362116 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
6362138 A-TACAATATTCATACAAAAT
1 ATTACAATATTCATACAAAAT
6362158 ACTAATCCAA
Statistics
Matches: 244, Mismatches: 21, Indels: 70
0.73 0.06 0.21
Matches are distributed among these distances:
18 11 0.05
19 1 0.00
20 6 0.02
21 32 0.13
22 7 0.03
23 11 0.05
24 5 0.02
25 3 0.01
26 10 0.04
27 127 0.52
28 1 0.00
29 11 0.05
30 8 0.03
31 3 0.01
32 8 0.03
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAT
Found at i:6361904 original size:46 final size:47
Alignment explanation
Indices: 6361854--6362157 Score: 180
Period size: 46 Copynumber: 6.2 Consensus size: 47
6361844 CATACAAAAT
* *
6361854 TACAATATTACAATATTCATACAAAAT-TACAATATTACAATATTCA
1 TACAAAATTACAATATTCATACAAAATATACAAAATTACAATATTCA
* *
6361900 TACAAAATTATAATA-T--TACAATATTCATACAAAATTACAATATTCA
1 TACAAAATTACAATATTCATACAA-AAT-ATACAAAATTACAATATTCA
*
6361946 TACAAAAAATTACAATATTCATATAAAATACTAATCCAAAACTATAAATACAAATTTAATT-A
1 TAC--AAAATTACAATATTCATACAAAATA-T-A--C-AAA--AT---TAC-AA--T-ATTCA
* * *
6362008 TAAAATAATTACAATATTCATACAAAAAATTACAATATTACAATA-T-A
1 TACAA-AATTACAATATTCATACAAAATA-TACAAAATTACAATATTCA
* * *
6362055 TCCCGACATTACAATATTCATACAAAAT-TACAAAATTACAATATTCA
1 T-ACAAAATTACAATATTCATACAAAATATACAAAATTACAATATTCA
* * *
6362102 TACAAAATTATAATA-T--TACAATATTCATACAAAAAAATACAATATTCA
1 TACAAAATTACAATATTCATACAA-AAT-ATAC--AAAATTACAATATTCA
6362150 TACAAAAT
1 TACAAAAT
6362158 ACTAATCCAA
Statistics
Matches: 203, Mismatches: 24, Indels: 60
0.71 0.08 0.21
Matches are distributed among these distances:
43 10 0.05
44 4 0.02
45 16 0.08
46 48 0.24
47 25 0.12
48 36 0.18
49 3 0.01
50 3 0.01
51 7 0.03
52 3 0.01
53 1 0.00
54 3 0.01
55 2 0.01
56 2 0.01
57 2 0.01
58 1 0.00
59 3 0.01
60 5 0.02
61 22 0.11
62 4 0.02
63 3 0.01
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (47 bp):
TACAAAATTACAATATTCATACAAAATATACAAAATTACAATATTCA
Found at i:6362142 original size:21 final size:21
Alignment explanation
Indices: 6362086--6362156 Score: 79
Period size: 21 Copynumber: 3.1 Consensus size: 21
6362076 ACAAAATTAC
*
6362086 AAAATTACAATATTCATACAAA
1 AAAAATACAATATTCATAC-AA
6362108 ATTATAATATTACAATATTCATACAA
1 A--A-AA-A-TACAATATTCATACAA
6362134 AAAAATACAATATTCATACAA
1 AAAAATACAATATTCATACAA
6362155 AA
1 AA
6362157 TACTAATCCA
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
21 18 0.42
22 2 0.05
23 2 0.05
24 2 0.05
25 2 0.05
26 3 0.07
27 14 0.33
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAATACAATATTCATACAA
Found at i:6362264 original size:27 final size:27
Alignment explanation
Indices: 6362226--6362292 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
6362216 AATTACAATA
6362226 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
*
6362253 TTCATTGGCGCCTCTCTGTGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
6362280 TTCATTGGCGCCT
1 TTCATTGGCGCCT
6362293 ACTTGATAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.12, C:0.33, G:0.24, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATGAGGCACC
Found at i:6364032 original size:24 final size:24
Alignment explanation
Indices: 6364003--6364051 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
6363993 AAATGGAAAG
6364003 TTAGCTTCGAAGAGGGATATTAGT
1 TTAGCTTCGAAGAGGGATATTAGT
6364027 TTAGCTTCGAAGAGGGATATTAGT
1 TTAGCTTCGAAGAGGGATATTAGT
6364051 T
1 T
6364052 ATAATGCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.35
Consensus pattern (24 bp):
TTAGCTTCGAAGAGGGATATTAGT
Found at i:6366769 original size:4 final size:4
Alignment explanation
Indices: 6366760--6366787 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
6366750 CACATGAGAT
6366760 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
6366788 AAATGAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:6368352 original size:30 final size:29
Alignment explanation
Indices: 6368287--6368352 Score: 123
Period size: 29 Copynumber: 2.2 Consensus size: 29
6368277 CTTATGTCTG
6368287 TAACAGAGCTATTGTTTTCCGTTATTGAC
1 TAACAGAGCTATTGTTTTCCGTTATTGAC
6368316 TAACAGAGCTATTGTTTTCCGTTATTGAC
1 TAACAGAGCTATTGTTTTCCGTTATTGAC
6368345 TTAACAGA
1 -TAACAGA
6368353 AATGTCACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 29 0.81
30 7 0.19
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (29 bp):
TAACAGAGCTATTGTTTTCCGTTATTGAC
Found at i:6368478 original size:16 final size:17
Alignment explanation
Indices: 6368453--6368485 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6368443 TGTCTCCCCC
*
6368453 TCTTCCCCAT-ATTCCT
1 TCTTCACCATCATTCCT
6368469 TCTTCACCATCATTCCT
1 TCTTCACCATCATTCCT
6368486 CTCACCCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.15, C:0.42, G:0.00, T:0.42
Consensus pattern (17 bp):
TCTTCACCATCATTCCT
Found at i:6372032 original size:18 final size:18
Alignment explanation
Indices: 6372011--6372047 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
6372001 TGAGTTTTCG
6372011 AATTCGAATAATTTAAAT
1 AATTCGAATAATTTAAAT
*
6372029 AATTCGAATAATTTGAAT
1 AATTCGAATAATTTAAAT
6372047 A
1 A
6372048 TCAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (18 bp):
AATTCGAATAATTTAAAT
Found at i:6376185 original size:14 final size:15
Alignment explanation
Indices: 6376166--6376197 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
6376156 TTTTGATCAC
6376166 ATAAAATT-AAATTA
1 ATAAAATTAAAATTA
6376180 ATAAAATTAAAATTA
1 ATAAAATTAAAATTA
6376195 ATA
1 ATA
6376198 TAATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAAAATTAAAATTA
Found at i:6376720 original size:17 final size:17
Alignment explanation
Indices: 6376674--6376724 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 17
6376664 ATAGTATTTT
*
6376674 ATTAATTTGATATTAAA
1 ATTAATTTAATATTAAA
*
6376691 GTTATTATCTTAATATTAAA
1 ATTA--AT-TTAATATTAAA
6376711 ATTAATTTAATATT
1 ATTAATTTAATATT
6376725 TATCTTGTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 11 0.39
18 2 0.07
19 2 0.07
20 13 0.46
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (17 bp):
ATTAATTTAATATTAAA
Found at i:6382098 original size:34 final size:34
Alignment explanation
Indices: 6382055--6382122 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
6382045 GCATTTTTGA
* *
6382055 CACTGTACTGAGATGGGC-TAGGGCCCAA-ACTGT
1 CACTGTACTGAAAAGGGCTTA-GGCCCAAGACTGT
6382088 CACTGATACTGAAAAGGGCTTAGGCCCAAGACTGT
1 CACTG-TACTGAAAAGGGCTTAGGCCCAAGACTGT
6382123 TCAACTGTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 5 0.17
34 18 0.60
35 7 0.23
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.21
Consensus pattern (34 bp):
CACTGTACTGAAAAGGGCTTAGGCCCAAGACTGT
Found at i:6384916 original size:17 final size:17
Alignment explanation
Indices: 6384890--6384988 Score: 59
Period size: 17 Copynumber: 5.8 Consensus size: 17
6384880 ATTTATCTAC
*
6384890 AAATTAAATATTAAATT
1 AAATTTAATATTAAATT
6384907 AAATTTAATATTAAGA-T
1 AAATTTAATATTAA-ATT
6384924 AACCACTTTAATATTAAATTT
1 AA--A-TTTAATATTAAA-TT
* *
6384945 AAA---AA-ATTACTATC
1 AAATTTAATATTA-AATT
6384959 AAA--TAAGTATTAAATT
1 AAATTTAA-TATTAAATT
6384975 AAATTTAATATTAA
1 AAATTTAATATTAA
6384989 TTTATTAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 24
0.69 0.05 0.26
Matches are distributed among these distances:
14 8 0.12
15 5 0.08
16 5 0.08
17 26 0.40
18 4 0.06
19 3 0.05
20 11 0.17
21 3 0.05
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (17 bp):
AAATTTAATATTAAATT
Found at i:6388208 original size:14 final size:14
Alignment explanation
Indices: 6388170--6388202 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
6388160 TACATGTATG
*
6388170 TAATTTAACAAATA
1 TAATCTAACAAATA
6388184 TAATCTAACAAATA
1 TAATCTAACAAATA
6388198 TAATC
1 TAATC
6388203 ATACAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATCTAACAAATA
Found at i:6390541 original size:27 final size:29
Alignment explanation
Indices: 6390511--6390566 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
6390501 GCAAAGTCAC
*
6390511 ATGTGCATATTTG-AC-AATCAAAATTTT
1 ATGTGCATAATTGCACAAATCAAAATTTT
*
6390538 ATGTTCATAATTGCACAAAATCAAAATTT
1 ATGTGCATAATTGCAC-AAATCAAAATTT
6390567 ACAAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.46
28 2 0.08
30 11 0.46
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (29 bp):
ATGTGCATAATTGCACAAATCAAAATTTT
Found at i:6403133 original size:6 final size:6
Alignment explanation
Indices: 6403122--6403146 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6403112 AGATATGCCG
6403122 ATATGT ATATGT ATATGT ATATGT A
1 ATATGT ATATGT ATATGT ATATGT A
6403147 CGTATGTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (6 bp):
ATATGT
Found at i:6404544 original size:2 final size:2
Alignment explanation
Indices: 6404537--6404583 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
6404527 ATACATACAT
* * *
6404537 AC AC AC AC AC GC AC GC AC GC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
6404579 GC AC A
1 AC AC A
6404584 TACATACATG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.43, C:0.49, G:0.09, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6406318 original size:9 final size:9
Alignment explanation
Indices: 6406300--6406348 Score: 80
Period size: 9 Copynumber: 5.4 Consensus size: 9
6406290 TTTGGTTAAA
*
6406300 AATTAACCG
1 AATTACCCG
6406309 AATTACCCG
1 AATTACCCG
6406318 AATTACCCG
1 AATTACCCG
*
6406327 AATTAACCG
1 AATTACCCG
6406336 AATTACCCG
1 AATTACCCG
6406345 AATT
1 AATT
6406349 GAATCATTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:6406557 original size:38 final size:39
Alignment explanation
Indices: 6406513--6406590 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
6406503 ACTTAAGAGT
*
6406513 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
*
6406551 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTATTTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
6406590 T
1 T
6406591 TGGGTTGGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 27 0.73
39 10 0.27
ACGTcount: A:0.17, C:0.03, G:0.28, T:0.53
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:6406605 original size:17 final size:18
Alignment explanation
Indices: 6406572--6406609 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
6406562 TTTAGTTTTA
*
6406572 TTGGGTTGGGTATTTGGG
1 TTGGGTTGGGTAATTGGG
6406590 TTGGGTT-GGTAATTGGG
1 TTGGGTTGGGTAATTGGG
6406607 TTG
1 TTG
6406610 AGTAATTGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.08, C:0.00, G:0.47, T:0.45
Consensus pattern (18 bp):
TTGGGTTGGGTAATTGGG
Found at i:6406607 original size:12 final size:13
Alignment explanation
Indices: 6406590--6406621 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
6406580 GGTATTTGGG
6406590 TTGGGTTG-GTAA
1 TTGGGTTGAGTAA
6406602 TTGGGTTGAGTAA
1 TTGGGTTGAGTAA
6406615 TTGGGTT
1 TTGGGTT
6406622 TGGTTGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.16, C:0.00, G:0.41, T:0.44
Consensus pattern (13 bp):
TTGGGTTGAGTAA
Found at i:6406607 original size:30 final size:31
Alignment explanation
Indices: 6406571--6406634 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
6406561 TTTTAGTTTT
* *
6406571 ATTGGGTTGGGTATTTGGGTTGGGTTGG-TA
1 ATTGGGTTGAGTAATTGGGTTGGGTTGGATA
*
6406601 ATTGGGTTGAGTAATTGGGTTTGGTTGGATA
1 ATTGGGTTGAGTAATTGGGTTGGGTTGGATA
6406632 ATT
1 ATT
6406635 TTATTTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.16, C:0.00, G:0.41, T:0.44
Consensus pattern (31 bp):
ATTGGGTTGAGTAATTGGGTTGGGTTGGATA
Found at i:6407274 original size:9 final size:9
Alignment explanation
Indices: 6407247--6407283 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
6407237 TGAGTTTTTG
6407247 AATTCGAAT
1 AATTCGAAT
* *
6407256 AACTCAAAT
1 AATTCGAAT
6407265 AATTCGAAT
1 AATTCGAAT
6407274 AATTCGAAT
1 AATTCGAAT
6407283 A
1 A
6407284 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:6414140 original size:124 final size:125
Alignment explanation
Indices: 6413975--6414235 Score: 418
Period size: 124 Copynumber: 2.1 Consensus size: 125
6413965 TGTTACACAG
*
6413975 TAGGTCCT-GAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTAGC
1 TAGGTCCTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* * *
6414039 AGAATGCTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGAAC-AACTTTTGCTACAA
66 AGAATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGAACGAACTTTTGCTACAA
*
6414098 TAGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
1 TAGGTCCTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* * ** *
6414163 AGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
66 AGAATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGAACGAACTTTTGCTACAA
6414223 TAGGTCCTGGAAA
1 TAGGTCCTGGAAA
6414236 TTGAGAGGAA
Statistics
Matches: 125, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
123 8 0.06
124 94 0.75
125 23 0.18
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (125 bp):
TAGGTCCTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
AGAATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGAACGAACTTTTGCTACAA
Found at i:6420860 original size:16 final size:17
Alignment explanation
Indices: 6420841--6420877 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
6420831 TGCTTGATAG
6420841 AGAAAAGAAAA-TAAAA
1 AGAAAAGAAAAGTAAAA
6420857 AGAAAAGAAAAGTTAAAA
1 AGAAAAGAAAAG-TAAAA
6420875 AGA
1 AGA
6420878 GGGAGGCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.58
18 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (17 bp):
AGAAAAGAAAAGTAAAA
Found at i:6431502 original size:27 final size:27
Alignment explanation
Indices: 6431445--6431502 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
6431435 AATGTCAAAT
* ***
6431445 TTTTTAATATTTATTGGATTAGATTTT
1 TTTTTAATATTTATGGGATTAGATCAA
* *
6431472 TTTTTAATATTTGTGGGATTAGGTCAA
1 TTTTTAATATTTATGGGATTAGATCAA
6431499 TTTT
1 TTTT
6431503 CTCATTCTCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.24, C:0.02, G:0.16, T:0.59
Consensus pattern (27 bp):
TTTTTAATATTTATGGGATTAGATCAA
Found at i:6437983 original size:11 final size:13
Alignment explanation
Indices: 6437972--6438014 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
6437962 ATTATAATAT
6437972 ATAA-ATGTTATA
1 ATAATATGTTATA
*
6437984 ATAAGTATATTATA
1 ATAA-TATGTTATA
*
6437998 TTAATATGTTATA
1 ATAATATGTTATA
6438011 ATAA
1 ATAA
6438015 ACATTAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
12 4 0.16
13 11 0.44
14 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
ATAATATGTTATA
Found at i:6438020 original size:25 final size:26
Alignment explanation
Indices: 6437968--6438020 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
6437958 TATTATTATA
*
6437968 ATATATAAATGTTATAATAAGTATATT
1 ATATATAAATGTTATAATAAG-ACATT
6437995 ATAT-TAATATGTTATAATAA-ACATT
1 ATATATAA-ATGTTATAATAAGACATT
6438020 A
1 A
6438021 AAAGAAAGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.21
26 3 0.12
27 16 0.67
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (26 bp):
ATATATAAATGTTATAATAAGACATT
Found at i:6438947 original size:43 final size:42
Alignment explanation
Indices: 6438885--6439009 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 42
6438875 GGACTCTGAT
**
6438885 ATGTGTTTTTGTGTAAGACCACGTCTGGGACGTCGGCATCGAC
1 ATGTGTTTACGTGTAAGACCACGTCTGGGACGT-GGCATCGAC
* **
6438928 CTGTGTTTACGTGTAAGACC-CTGTCTGGGACAGTGGCATCGGT
1 ATGTGTTTACGTGTAAGACCAC-GTCTGGGAC-GTGGCATCGAC
* *
6438971 ATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 ATGTGTTTACGTGTAAGACCACGTCTGGGACG-TGGCAT
6439010 TGTACGAGCT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
42 2 0.03
43 65 0.93
44 3 0.04
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (42 bp):
ATGTGTTTACGTGTAAGACCACGTCTGGGACGTGGCATCGAC
Found at i:6444400 original size:18 final size:18
Alignment explanation
Indices: 6444379--6444418 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6444369 GATTGAGAGT
* * *
6444379 GAAAAGGAATGTGAAACA
1 GAAAAGAAAAGTGAAAAA
6444397 GAAAAGAAAAGTGAAAAA
1 GAAAAGAAAAGTGAAAAA
6444415 GAAA
1 GAAA
6444419 TTGAAGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.25, T:0.07
Consensus pattern (18 bp):
GAAAAGAAAAGTGAAAAA
Found at i:6446859 original size:10 final size:10
Alignment explanation
Indices: 6446841--6446870 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
6446831 TTTTTCCCAA
6446841 TTTTC-TTTT
1 TTTTCTTTTT
6446850 TTTTCTTTTT
1 TTTTCTTTTT
6446860 TTTTCTTTTT
1 TTTTCTTTTT
6446870 T
1 T
6446871 CTTTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.25
10 15 0.75
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:6446880 original size:10 final size:9
Alignment explanation
Indices: 6446841--6446880 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
6446831 TTTTTCCCAA
6446841 TTTTCTTTT
1 TTTTCTTTT
6446850 TTTTCTTTT
1 TTTTCTTTT
*
6446859 TTTT-TCTT
1 TTTTCTTTT
6446867 TTTTCTTTT
1 TTTTCTTTT
6446876 ATTTT
1 -TTTT
6446881 AGTTACTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 7 0.26
9 16 0.59
10 4 0.15
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:6446880 original size:17 final size:17
Alignment explanation
Indices: 6446848--6446880 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6446838 CAATTTTCTT
*
6446848 TTTTTTCTTTTTTTTTC
1 TTTTTTCTTTTATTTTC
6446865 TTTTTTCTTTTATTTT
1 TTTTTTCTTTTATTTT
6446881 AGTTACTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTTCTTTTATTTTC
Found at i:6452675 original size:13 final size:13
Alignment explanation
Indices: 6452637--6452714 Score: 60
Period size: 13 Copynumber: 6.3 Consensus size: 13
6452627 AGCACTTACA
*
6452637 ATTTATGCATTTT
1 ATTTATACATTTT
*
6452650 ATTT-T-TA-TTT
1 ATTTATACATTTT
6452660 ATTTATACATTTT
1 ATTTATACATTTT
*
6452673 ATTT-TATCAATTT
1 ATTTATA-CATTTT
*
6452686 A-CTATATCA-TTT
1 ATTTATA-CATTTT
6452698 ATTTATACATTTT
1 ATTTATACATTTT
6452711 ATTT
1 ATTT
6452715 TATTTTATCC
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
10 7 0.13
11 2 0.04
12 11 0.21
13 33 0.62
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.63
Consensus pattern (13 bp):
ATTTATACATTTT
Found at i:6452685 original size:22 final size:23
Alignment explanation
Indices: 6452635--6452686 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
6452625 TTAGCACTTA
*
6452635 CAATTTATGCATTTTATTTTTAT
1 CAATTTATACATTTTATTTTTAT
**
6452658 TTATTTATACATTTTA-TTTTAT
1 CAATTTATACATTTTATTTTTAT
6452680 CAATTTA
1 CAATTTA
6452687 CTATATCATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.62
Consensus pattern (23 bp):
CAATTTATACATTTTATTTTTAT
Found at i:6452918 original size:16 final size:15
Alignment explanation
Indices: 6452899--6452928 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6452889 TCTTCATCTA
6452899 TTTATTTATTCATTTG
1 TTTATTTA-TCATTTG
6452915 TTTATTTATCATTT
1 TTTATTTATCATTT
6452929 TAACGCCATC
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:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTATTTATCATTTG
Found at i:6454565 original size:30 final size:31
Alignment explanation
Indices: 6454529--6454586 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
6454519 GGTTACCCAC
**
6454529 ACGGCCTGGTGACACGGCCGTGT-GCGGCAT
1 ACGGCCTGGACACACGGCCGTGTCGCGGCAT
*
6454559 ACGGCCTGGACACACGGGCGTGTCGCGG
1 ACGGCCTGGACACACGGCCGTGTCGCGG
6454587 GCCGTGTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.14, C:0.31, G:0.41, T:0.14
Consensus pattern (31 bp):
ACGGCCTGGACACACGGCCGTGTCGCGGCAT
Done.