Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 65 of 352
Found at i:20407636 original size:21 final size:21
Alignment explanation
Indices: 20407610--20407651 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
20407600 AAAGAGCTGA
20407610 TAAAATCCCATAGAAAGCCTG
1 TAAAATCCCATAGAAAGCCTG
20407631 TAAAATCCCATAGAAAGCCTG
1 TAAAATCCCATAGAAAGCCTG
20407652 CCATTTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (21 bp):
TAAAATCCCATAGAAAGCCTG
Found at i:20414294 original size:26 final size:26
Alignment explanation
Indices: 20414265--20414314 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
20414255 TAGGGTAAAT
20414265 TATATTGATA-TTCATTTAATTATTCG
1 TATATT-ATATTTCATTTAATTATTCG
* *
20414291 TATATTTTATTTTATTTAATTATT
1 TATATTATATTTCATTTAATTATT
20414315 TAATTATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (26 bp):
TATATTATATTTCATTTAATTATTCG
Found at i:20419889 original size:2 final size:2
Alignment explanation
Indices: 20419882--20419908 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20419872 CAAGAGAAAT
20419882 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
20419909 TACATACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:20431128 original size:16 final size:15
Alignment explanation
Indices: 20431098--20431141 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
20431088 CGTAGATCGG
20431098 CAAAAGCCAAAATGC
1 CAAAAGCCAAAATGC
*
20431113 CAAAATGCCGAAATGC
1 CAAAA-GCCAAAATGC
*
20431129 TGAAAAGCCAAAA
1 -CAAAAGCCAAAA
20431142 GTTTGGCTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 5 0.21
16 15 0.62
17 4 0.17
ACGTcount: A:0.52, C:0.23, G:0.16, T:0.09
Consensus pattern (15 bp):
CAAAAGCCAAAATGC
Found at i:20431384 original size:29 final size:29
Alignment explanation
Indices: 20431352--20431476 Score: 128
Period size: 29 Copynumber: 4.3 Consensus size: 29
20431342 GCGAGCATGA
* *
20431352 ATATGCATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGAATTGGGCCTAATGGGCC
* * * *
20431381 ATATGAATTTGAATTGGGCCTGATAGGCT
1 ATATGAATGTGAATTGGGCCTAATGGGCC
* * *
20431410 ATATAAATGTGAATTGGGCCTGATGGGCT
1 ATATGAATGTGAATTGGGCCTAATGGGCC
*
20431439 ATATGAATGAG-ATTGGGCC-AAGTGGGCC
1 ATATGAATGTGAATTGGGCCTAA-TGGGCC
*
20431467 ATATGCATGT
1 ATATGAATGT
20431477 ATGTAGGGGT
Statistics
Matches: 80, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
27 1 0.01
28 21 0.26
29 58 0.73
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.30
Consensus pattern (29 bp):
ATATGAATGTGAATTGGGCCTAATGGGCC
Found at i:20438412 original size:21 final size:20
Alignment explanation
Indices: 20438375--20438417 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
20438365 ATTAATAAGC
* *
20438375 ATGAATGTTTTATGATAGATT
1 ATGAATGTTTGACGATAG-TT
20438396 ATGAATGTTTGACGATAGTT
1 ATGAATGTTTGACGATAGTT
20438416 AT
1 AT
20438418 ACAAGTTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (20 bp):
ATGAATGTTTGACGATAGTT
Found at i:20448867 original size:21 final size:20
Alignment explanation
Indices: 20448841--20448879 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
20448831 ATGTATTTTG
20448841 ATGTTTGATGATAGATTATGA
1 ATGTTTGATGATAG-TTATGA
20448862 ATGTTTGATGATAGTTAT
1 ATGTTTGATGATAGTTAT
20448880 ACAAGTTTTG
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:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (20 bp):
ATGTTTGATGATAGTTATGA
Found at i:20448889 original size:21 final size:21
Alignment explanation
Indices: 20448841--20448887 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
20448831 ATGTATTTTG
*
20448841 ATGTTTGATGATAGATTATGA
1 ATGTTTGATGATAGATTATCA
20448862 ATGTTTGATGATAG-TTATACA
1 ATGTTTGATGATAGATTAT-CA
20448883 A-GTTT
1 ATGTTT
20448888 TGTTAAGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (21 bp):
ATGTTTGATGATAGATTATCA
Found at i:20451266 original size:38 final size:38
Alignment explanation
Indices: 20451205--20451279 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
20451195 ATACCTAAAA
20451205 TGACAAGTTGATAGTGTGACGATGCTCCAATGATCTCT
1 TGACAAGTTGATAGTGTGACGATGCTCCAATGATCTCT
* * *
20451243 TGACTAGTTGATAGTGTGTCGATGCTCTAATGATCTC
1 TGACAAGTTGATAGTGTGACGATGCTCCAATGATCTC
20451280 CAACCTTCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (38 bp):
TGACAAGTTGATAGTGTGACGATGCTCCAATGATCTCT
Found at i:20454487 original size:37 final size:37
Alignment explanation
Indices: 20454437--20454515 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
20454427 TTATTACGAA
* * *
20454437 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
20454474 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
20454511 GTCTT
1 GTCTT
20454516 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:20454712 original size:47 final size:47
Alignment explanation
Indices: 20454634--20455046 Score: 661
Period size: 47 Copynumber: 8.7 Consensus size: 47
20454624 CCCTTCGGGA
* * * * * *
20454634 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
20454681 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20454728 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20454775 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20454822 CTTATCACATATATATACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20454870 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20454919 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20454966 CTTATCACATATATACACTTTCA-ATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
20455012 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
20455047 AGAATCCTAA
Statistics
Matches: 348, Mismatches: 13, Indels: 10
0.94 0.04 0.03
Matches are distributed among these distances:
45 1 0.00
46 42 0.12
47 211 0.61
48 48 0.14
49 46 0.13
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:20454925 original size:144 final size:143
Alignment explanation
Indices: 20454634--20455025 Score: 657
Period size: 144 Copynumber: 2.8 Consensus size: 143
20454624 CCCTTCGGGA
* * * * * * * *
20454634 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
20454699 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
20454762 TCGGCCATTAGGC
131 TCGGCCATTAGGC
20454775 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
20454840 ACTTTCACATTCATCACATCGG-CATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
20454904 CATCGGCCATTAGGC
129 CATCGGCCATTAGGC
20454919 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
20454984 TTTCA-ATTCATCACATCGGCCATTAGGCCTTATCTCATATAT
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
20455026 GCATGTTCAC
Statistics
Matches: 237, Mismatches: 9, Indels: 9
0.93 0.04 0.04
Matches are distributed among these distances:
141 61 0.26
142 52 0.22
143 30 0.13
144 94 0.40
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (143 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:20455122 original size:191 final size:189
Alignment explanation
Indices: 20454634--20455046 Score: 570
Period size: 191 Copynumber: 2.2 Consensus size: 189
20454624 CCCTTCGGGA
* * ** * *
20454634 CTTATCAC-ATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCT-GTCAC--ATATAT
1 CTTATCACAATATATACACTTTCACATCCATCACATCAG-CA-TAGG-CCTAATCACATATATAT
* * *
20454695 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
63 ACACTTTCACATTCATCACATCAGCCATTAGGCCATACCACATATATACACTTTCACATTCATCA
20454760 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
128 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
20454822 CTTATCACATATATATACACTTTCACATTCATCACATCGGCATTAGGCCTTATCACATATATATA
1 CTTATCACA-ATATATACACTTTCACATCCATCACATCAGCA-TAGGCCTAATCACATATATATA
* * *
20454887 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
64 CACTTTCACATTCATCACATCAGCCATTAGGCCATACCACATATATACACTTTCACATTCATCAC
20454952 ATCGGCCATTAGGCCTTATCACATATATACACTTTCA-ATTCATCACATCGGCCATTAGGC
129 ATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
20455012 CTTATCTC-ATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACAATATATACACT-TTCACATCCATCACAT
20455047 AGAATCCTAA
Statistics
Matches: 209, Mismatches: 10, Indels: 12
0.90 0.04 0.05
Matches are distributed among these distances:
187 1 0.00
188 34 0.16
189 9 0.04
190 56 0.27
191 109 0.52
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (189 bp):
CTTATCACAATATATACACTTTCACATCCATCACATCAGCATAGGCCTAATCACATATATATACA
CTTTCACATTCATCACATCAGCCATTAGGCCATACCACATATATACACTTTCACATTCATCACAT
CGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:20458886 original size:40 final size:40
Alignment explanation
Indices: 20458854--20459285 Score: 630
Period size: 40 Copynumber: 10.8 Consensus size: 40
20458844 CCAGCATGAT
* * *
20458854 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
** *
20458894 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
20458934 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
20458974 TGCTCTTCGGGATTTAACCTGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
20459014 TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
20459054 TGCTCTTTGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * * *
20459094 TGCTCTTCAGAACTTAGTCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * *
20459134 TGCTATTCGGGATTTAACCTGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
20459174 TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
20459214 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
20459254 TGCTCTTCGGGACTTAGCCCGGATATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATATATCACT
20459286 CTCAATTCTC
Statistics
Matches: 343, Mismatches: 49, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 343 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:20459118 original size:160 final size:160
Alignment explanation
Indices: 20458854--20459285 Score: 729
Period size: 160 Copynumber: 2.7 Consensus size: 160
20458844 CCAGCATGAT
* * * * * ** *
20458854 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATA
1 TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
*
20458919 TATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTCTTCGG
66 TATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTATTCGG
20458984 GATTTAACCTGGATATATCACTAGCACGAA
131 GATTTAACCTGGATATATCACTAGCACGAA
*
20459014 TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCACGAATGCTCTTTGGGACTTAGCCCGGATA
1 TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
* *
20459079 TATCACTAGCACGAATGCTCTTCAGAACTTAGTCCGGATACATCACTAGCATGAATGCTATTCGG
66 TATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTATTCGG
20459144 GATTTAACCTGGATATATCACTAGCACGAA
131 GATTTAACCTGGATATATCACTAGCACGAA
20459174 TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
1 TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
* * *
20459239 TATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
66 TATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACT
20459286 CTCAATTCTC
Statistics
Matches: 255, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
160 255 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (160 bp):
TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
TATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTATTCGG
GATTTAACCTGGATATATCACTAGCACGAA
Found at i:20460550 original size:37 final size:37
Alignment explanation
Indices: 20460500--20460578 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
20460490 TTATTACGAA
* * *
20460500 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
20460537 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
20460574 GTCTT
1 GTCTT
20460579 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:20460775 original size:47 final size:47
Alignment explanation
Indices: 20460697--20461158 Score: 773
Period size: 47 Copynumber: 9.7 Consensus size: 47
20460687 CCCTTCGGGA
* * * * * *
20460697 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
20460744 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20460791 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20460838 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20460885 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20460934 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20460983 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20461030 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20461077 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
20461124 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
20461159 AGAATCCTAA
Statistics
Matches: 399, Mismatches: 13, Indels: 6
0.95 0.03 0.01
Matches are distributed among these distances:
46 1 0.00
47 302 0.76
49 96 0.24
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:20461127 original size:239 final size:237
Alignment explanation
Indices: 20460697--20461137 Score: 792
Period size: 239 Copynumber: 1.9 Consensus size: 237
20460687 CCCTTCGGGA
* * * *
20460697 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATTTATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
20460762 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
20460827 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
20460892 CATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
196 CATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
20460934 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACAT-T-TATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATAC
20460999 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
20461064 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
129 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
*
20461129 CTCATATAT
194 CACATATAT
20461138 GCATGTTCAC
Statistics
Matches: 194, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
237 10 0.05
238 1 0.01
239 183 0.94
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (237 bp):
CTTATCACATTTATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
CATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:20465411 original size:70 final size:70
Alignment explanation
Indices: 20465243--20465915 Score: 443
Period size: 70 Copynumber: 9.6 Consensus size: 70
20465233 TTAATCCTAC
* * * * * ** *
20465243 GAGCATTAATAATGACAGCTGAGAGCTTTCAACTCTCGCTAACTATTTTGGGGGTTGCAGTATAG
1 GAGCCTTAA-AATGACAACTGAGAGCTTTTAACTCTCGCTAACT-TTTAGGAGGTTGTGGTATTG
*
20465308 AACATGT
64 AACCTGT
* * * * *
20465315 GAGCTTTAGAATGAGAACTGAGAGCTTATAACTCTCGCTAACTTTTAAGAGGTTGTGGTATTGAA
1 GAGCCTTAAAATGACAACTGAGAGCTTTTAACTCTCGCTAACTTTTAGGAGGTTGTGGTATTGAA
*
20465380 CTTGT
66 CCTGT
* * * * * * *
20465385 GAGCCATAAAATGACAACTAAGAGCTTTTAACTCTTGGTAA-TTGTTAGGGGGCTGCGGTATTGA
1 GAGCCTTAAAATGACAACTGAGAGCTTTTAACTCTCGCTAACTT-TTAGGAGGTTGTGGTATTGA
20465449 ACCTGT
65 ACCTGT
* ** * * ** * * *
20465455 GAGCCTTAGAATGACAGTTGAGAGCTTTTAATTCTCACTAACTGTCAAGG-GGCTATGGTTTTGA
1 GAGCCTTAAAATGACAACTGAGAGCTTTTAACTCTCGCTAACT-TTTAGGAGGTTGTGGTATTGA
*
20465519 ACCTGC
65 ACCTGT
* * * * * *
20465525 GA-CCTTAGAATGACAAATG-GAAGCTTTTAATTCTCGCTAACTATTAGGAGGGTTATGGTTTTG
1 GAGCCTTAAAATGACAACTGAG-AGCTTTTAACTCTCGCTAACTTTTAGGA-GGTTGTGGTATTG
**
20465588 AACCTAC
64 AACCTGT
* * *
20465595 GAGCCTTAAAATGA-TAGTTAGTAG-TTTTAACTCTCGCTAACTGTTT-GGAGGTTGTGGTATTG
1 GAGCCTTAAAATGACAACTGAG-AGCTTTTAACTCTCGCTAACT-TTTAGGAGGTTGTGGTATTG
20465657 AACCTGT
64 AACCTGT
** * * * * * ** *
20465664 GAGCCTTAAAATGACAGTTGGGAGGTTTTAACTCTAGCTAACTGTTAGG-TGTTGCAGTTTTGAA
1 GAGCCTTAAAATGACAACTGAGAGCTTTTAACTCTCGCTAACTTTTAGGAGGTTGTGGTATTGAA
20465728 CCTG-
66 CCTGT
* * * * ** * *
20465732 GAAGCCTTATAATAACAACAGGGAGCTTTTAACTCTTACTAATTGTTTA-GAGGTTGTGATATTG
1 G-AGCCTTAAAATGACAACTGAGAGCTTTTAACTCTCGCTAACT-TTTAGGAGGTTGTGGTATTG
*
20465796 AACCTGC
64 AACCTGT
* * * ** * * * * * *
20465803 GTGCCTTATAATAACAGTTAAGAGCTTTTAATTCTCGTTAA-TTGTTA-GAGGGTTGTGCTTTTA
1 GAGCCTTAAAATGACAACTGAGAGCTTTTAACTCTCGCTAACTT-TTAGGA-GGTTGTGGTATTG
20465866 AACCTGT
64 AACCTGT
* * ** *
20465873 GAGCCTTAAATTGATAGTTGTGAGCTTTTAACTCTCGCTAACT
1 GAGCCTTAAAATGACAACTGAGAGCTTTTAACTCTCGCTAACT
20465916 ATTTGGGTTT
Statistics
Matches: 473, Mismatches: 109, Indels: 39
0.76 0.18 0.06
Matches are distributed among these distances:
68 6 0.01
69 126 0.27
70 282 0.60
71 51 0.11
72 8 0.02
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.34
Consensus pattern (70 bp):
GAGCCTTAAAATGACAACTGAGAGCTTTTAACTCTCGCTAACTTTTAGGAGGTTGTGGTATTGAA
CCTGT
Found at i:20465468 original size:140 final size:140
Alignment explanation
Indices: 20465198--20465915 Score: 504
Period size: 140 Copynumber: 5.1 Consensus size: 140
20465188 AGTTGGGAGT
* * * * * * * *
20465198 TTTTAACTCTCACTAACTATT-AGAGGGATGCGGT-TTTAATCCTACGAGCATTAATAATGACAG
1 TTTTAACTCTCGCTAACTTTTAAGA-GGTTGTGGTATTGAA-CCTGCGAGCCTTAA-AATGACAA
* * * * * * * * * *
20465261 CTGAGAGCTTTCAACTCTCGCTAACTATTTTGGGGGTTGCAGTATAGAACATGTGAGCTTTAGAA
63 TTAAGAGCTTTTAACTCTCGCTAACT-GTTAGGGGGTTGCGGTTTTGAACCTGTGAGCCTTAGAA
*
20465326 TGAGAACTGAGAGC
127 TGACAACTGAGAGC
* * * * *
20465340 TTATAACTCTCGCTAACTTTTAAGAGGTTGTGGTATTGAACTTGTGAGCCATAAAATGACAACTA
1 TTTTAACTCTCGCTAACTTTTAAGAGGTTGTGGTATTGAACCTGCGAGCCTTAAAATGACAATTA
* * * * *
20465405 AGAGCTTTTAACTCTTGGTAATTGTTAGGGGGCTGCGGTATTGAACCTGTGAGCCTTAGAATGAC
66 AGAGCTTTTAACTCTCGCTAACTGTTAGGGGGTTGCGGTTTTGAACCTGTGAGCCTTAGAATGAC
**
20465470 AGTTGAGAGC
131 AACTGAGAGC
* * * * * * * * * *
20465480 TTTTAATTCTCACTAACTGTCAAGGGGCTATGGTTTTGAACCTGCGA-CCTTAGAATGACAAAT-
1 TTTTAACTCTCGCTAACTTTTAAGAGGTTGTGGTATTGAACCTGCGAGCCTTAAAATGACAATTA
* * * ** ** *
20465543 GGAAGCTTTTAATTCTCGCTAACTATTAGGAGGGTTATGGTTTTGAACCTACGAGCCTTAAAATG
66 AG-AGCTTTTAACTCTCGCTAACTGTTAGG-GGGTTGCGGTTTTGAACCTGTGAGCCTTAGAATG
* * *
20465608 A-TAGTTAGTAG-
129 ACAACTGAG-AGC
* * *
20465619 TTTTAACTCTCGCTAACTGTTT-GGAGGTTGTGGTATTGAACCTGTGAGCCTTAAAATGACAGTT
1 TTTTAACTCTCGCTAACT-TTTAAGAGGTTGTGGTATTGAACCTGCGAGCCTTAAAATGACAATT
** * * * * * *
20465683 GGGAGGTTTTAACTCTAGCTAACTGTTA-GGTGTTGCAGTTTTGAACCTG-GAAGCCTTATAATA
65 AAGAGCTTTTAACTCTCGCTAACTGTTAGGGGGTTGCGGTTTTGAACCTGTG-AGCCTTAGAATG
* *
20465746 ACAACAGGGAGC
129 ACAACTGAGAGC
** * * * * * *
20465758 TTTTAACTCTTACTAA-TTGTTTAGAGGTTGTGATATTGAACCTGCGTGCCTTATAATAACAGTT
1 TTTTAACTCTCGCTAACTT-TTAAGAGGTTGTGGTATTGAACCTGCGAGCCTTAAAATGACAATT
* * * * * * *
20465822 AAGAGCTTTTAATTCTCGTTAATTGTTAGAGGGTTGTGCTTTTAAACCTGTGAGCCTTA-AATTG
65 AAGAGCTTTTAACTCTCGCTAACTGTTAGGGGGTTGCGGTTTTGAACCTGTGAGCCTTAGAA-TG
* ** *
20465886 ATAGTTGTGAGC
129 ACAACTGAGAGC
20465898 TTTTAACTCTCGCTAACT
1 TTTTAACTCTCGCTAACT
20465916 ATTTGGGTTT
Statistics
Matches: 443, Mismatches: 116, Indels: 35
0.75 0.20 0.06
Matches are distributed among these distances:
137 2 0.00
138 32 0.07
139 149 0.34
140 187 0.42
141 32 0.07
142 34 0.08
143 7 0.02
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (140 bp):
TTTTAACTCTCGCTAACTTTTAAGAGGTTGTGGTATTGAACCTGCGAGCCTTAAAATGACAATTA
AGAGCTTTTAACTCTCGCTAACTGTTAGGGGGTTGCGGTTTTGAACCTGTGAGCCTTAGAATGAC
AACTGAGAGC
Found at i:20465761 original size:209 final size:209
Alignment explanation
Indices: 20465337--20465915 Score: 523
Period size: 209 Copynumber: 2.8 Consensus size: 209
20465327 GAGAACTGAG
* * * * * * ** * *
20465337 AGCTTATAACTCTCGCTAACT-TTTAAGAGGTTGTGGTATTGAACTTGTGAGCCATAAAATGACA
1 AGCTTTTAACTCTCACTAACTGATT-AGAGGTTATGATATTGAACCTACGAGCCTTAAAATAACA
** * * * * * * *
20465401 ACTAAGAGCTTTTAACTCTTGGTAATTGTTAGGGGGCTGCGGTATTGAACCTGTGAGCCTTAGAA
65 GTTAAGAGCTTTTAACTCTCGCTAACTGTTAGAGGGTTGTGGTATTGAACCTGTGAGCCTTAAAA
*
20465466 TGACAGTTGAGAGCTTTTAATTCTCA-CTAACTGTCAAGGGGCTATGGTTTTGAACCTGCGACCT
130 TGACAGTTGAGAGCTTTTAACTCT-AGCTAACTGTCAAGGGGCTATGGTTTTGAACCTGCGACCT
*
20465530 TAGAATGACAAATGGA
194 TAGAATAACAAATGGA
* * * * * *
20465546 AGCTTTTAATTCTCGCTAACT-ATTAGGAGGGTTATGGTTTTGAACCTACGAGCCTTAAAATGAT
1 AGCTTTTAACTCTCACTAACTGATTA-GA-GGTTATGATATTGAACCTACGAGCCTTAAAATAAC
*
20465610 AGTT-AGTAG-TTTTAACTCTCGCTAACTGTTTG-GAGGTTGTGGTATTGAACCTGTGAGCCTTA
64 AGTTAAG-AGCTTTTAACTCTCGCTAACTGTTAGAG-GGTTGTGGTATTGAACCTGTGAGCCTTA
* * * *
20465672 AAATGACAGTTGGGAGGTTTTAACTCTAGCTAACTGT-TAGGTG-T-TGCAGTTTTGAACCTG-G
127 AAATGACAGTTGAGAGCTTTTAACTCTAGCTAACTGTCAAGGGGCTATG--GTTTTGAACCTGCG
* *
20465733 AAGCCTTATAATAACAACA-GGG
190 -A-CCTTAGAATAACAA-ATGGA
* * * * * * *
20465755 AGCTTTTAACTCTTACTAATTGTTTAGAGGTTGTGATATTGAACCTGCGTGCCTTATAATAACAG
1 AGCTTTTAACTCTCACTAACTGATTAGAGGTTATGATATTGAACCTACGAGCCTTAAAATAACAG
* * * * * * *
20465820 TTAAGAGCTTTTAATTCTCGTTAATTGTTAGAGGGTTGTGCTTTTAAACCTGTGAGCCTTAAATT
66 TTAAGAGCTTTTAACTCTCGCTAACTGTTAGAGGGTTGTGGTATTGAACCTGTGAGCCTTAAAAT
* * *
20465885 GATAGTTGTGAGCTTTTAACTCTCGCTAACT
131 GACAGTTGAGAGCTTTTAACTCTAGCTAACT
20465916 ATTTGGGTTT
Statistics
Matches: 304, Mismatches: 52, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
206 2 0.01
207 2 0.01
208 53 0.17
209 210 0.69
210 37 0.12
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (209 bp):
AGCTTTTAACTCTCACTAACTGATTAGAGGTTATGATATTGAACCTACGAGCCTTAAAATAACAG
TTAAGAGCTTTTAACTCTCGCTAACTGTTAGAGGGTTGTGGTATTGAACCTGTGAGCCTTAAAAT
GACAGTTGAGAGCTTTTAACTCTAGCTAACTGTCAAGGGGCTATGGTTTTGAACCTGCGACCTTA
GAATAACAAATGGA
Found at i:20473347 original size:31 final size:32
Alignment explanation
Indices: 20473301--20473370 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 32
20473291 GAAGAGAATG
*
20473301 AGGAGAAGGG-AAAAAAAGAGAAGAA-AAGAGA
1 AGGAAAAGGGAAAAAAAAGAGAA-AAGAAGAGA
20473332 AGGAAAAGGGGAAAAAAAAGAGAAAAGAAGAGA
1 AGGAAAA-GGGAAAAAAAAGAGAAAAGAAGAGA
20473365 AGGAAA
1 AGGAAA
20473371 GAAAAAAGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
31 6 0.17
32 5 0.14
33 24 0.69
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (32 bp):
AGGAAAAGGGAAAAAAAAGAGAAAAGAAGAGA
Found at i:20475100 original size:28 final size:28
Alignment explanation
Indices: 20475064--20475214 Score: 239
Period size: 28 Copynumber: 5.4 Consensus size: 28
20475054 TAAAAACTTG
* * *
20475064 GTAAAATAAGTGCAAAAATACAAACTTT
1 GTAATATAAATGCAAAAATACAAGCTTT
*
20475092 GTAATATAAATGAAAAAATACAAGCTTT
1 GTAATATAAATGCAAAAATACAAGCTTT
* *
20475120 GTTATATAAATGTAAAAATACAAGCTTT
1 GTAATATAAATGCAAAAATACAAGCTTT
*
20475148 GTAATATAAATGTAAAAATACAAGCTTT
1 GTAATATAAATGCAAAAATACAAGCTTT
20475176 GTAATATAAATGCAAAAATACAAGCTTT
1 GTAATATAAATGCAAAAATACAAGCTTT
20475204 GTAATATAAAT
1 GTAATATAAAT
20475215 TAGATGCATT
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 115 1.00
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (28 bp):
GTAATATAAATGCAAAAATACAAGCTTT
Found at i:20478151 original size:31 final size:31
Alignment explanation
Indices: 20478116--20478176 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
20478106 GGCACTAGTA
* * *
20478116 CTTTGGTGCCACCTTTCCCATGGGCACCACT
1 CTTTGGTACCACCTTTCCCATAGACACCACT
*
20478147 CTTTGGTACCGCCTTTCCCATAGACACCAC
1 CTTTGGTACCACCTTTCCCATAGACACCAC
20478177 CACCCAAACC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.16, C:0.39, G:0.16, T:0.28
Consensus pattern (31 bp):
CTTTGGTACCACCTTTCCCATAGACACCACT
Found at i:20479038 original size:143 final size:142
Alignment explanation
Indices: 20478771--20479043 Score: 485
Period size: 143 Copynumber: 1.9 Consensus size: 142
20478761 ATTTTTCGGT
* *
20478771 ATCTGATTTTCTTATTCCATTGTAGTACTTGAATTATTATTTTATTATATTTTTTGCCTCTAAAA
1 ATCTGATTTTCTTATTCCATTGTAGCACTTGAATTATTATTTTATTATATTTTTTGCCCCTAAAA
20478836 TTAACGGTATTAAAAAAAAAACCTCAAACAAACAAAATGCATGTGGCTGTTGACTTATGACATGT
66 TTAACGGTATTAAAAAAAAAACCTCAAACAAACAAAATGCATGTGGCTGTTGACTTATGACATGT
20478901 TTTCATATTGAC
131 TTTCATATTGAC
*
20478913 ATCTGATTTTCTTATTCCATTTTAGCACTTGAATTATTATTTTATTATACCTTTTTTGCCCCTAA
1 ATCTGATTTTCTTATTCCATTGTAGCACTTGAATTATTATTTTATTATA--TTTTTTGCCCCTAA
*
20478978 AATTAACGGTATT-AAAAAAAAACCTCAACCAAACAAAATGCATGTGGCTGTTGACTTATGACAT
64 AATTAACGGTATTAAAAAAAAAACCTCAAACAAACAAAATGCATGTGGCTGTTGACTTATGACAT
20479042 GT
129 GT
20479044 ACATTGATCA
Statistics
Matches: 125, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
142 47 0.38
143 52 0.42
144 26 0.21
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (142 bp):
ATCTGATTTTCTTATTCCATTGTAGCACTTGAATTATTATTTTATTATATTTTTTGCCCCTAAAA
TTAACGGTATTAAAAAAAAAACCTCAAACAAACAAAATGCATGTGGCTGTTGACTTATGACATGT
TTTCATATTGAC
Found at i:20481973 original size:30 final size:26
Alignment explanation
Indices: 20481918--20481969 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
20481908 GTAAAGCACA
20481918 CATAACACACTTAAGGCATGATTAGT
1 CATAACACACTTAAGGCATGATTAGT
20481944 CATAACACACTTAAGGCATGATTAGT
1 CATAACACACTTAAGGCATGATTAGT
20481970 TAGTGCAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (26 bp):
CATAACACACTTAAGGCATGATTAGT
Found at i:20483636 original size:21 final size:22
Alignment explanation
Indices: 20483598--20483640 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
20483588 ATTTTCAAAT
20483598 TATTATATAAATTTATATTTTA
1 TATTATATAAATTTATATTTTA
*
20483620 TATTGTATAAA-TTATATTTTA
1 TATTATATAAATTTATATTTTA
20483641 AAATAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TATTATATAAATTTATATTTTA
Found at i:20484856 original size:15 final size:15
Alignment explanation
Indices: 20484822--20484855 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
20484812 TAATTTTTGT
20484822 ATTTTAATTTGATCA
1 ATTTTAATTTGATCA
*
20484837 ATTTTAATTTTAT-A
1 ATTTTAATTTGATCA
20484851 ATTTT
1 ATTTT
20484856 TGAATTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
ATTTTAATTTGATCA
Found at i:20493158 original size:31 final size:31
Alignment explanation
Indices: 20493123--20493185 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
20493113 ACCGGTCAAA
20493123 TTGAGGATAGATGA-TCTAATTGATTTGATTT
1 TTGAGGATA-ATGAGTCTAATTGATTTGATTT
* *
20493154 TTGAGGATAATTAGTCTGATTGATTTGATTT
1 TTGAGGATAATGAGTCTAATTGATTTGATTT
20493185 T
1 T
20493186 GAAATCTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 3 0.10
31 26 0.90
ACGTcount: A:0.27, C:0.03, G:0.22, T:0.48
Consensus pattern (31 bp):
TTGAGGATAATGAGTCTAATTGATTTGATTT
Found at i:20493361 original size:14 final size:13
Alignment explanation
Indices: 20493342--20493396 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 13
20493332 TTTTAAAATT
20493342 AAATATAATTATA
1 AAATATAATTATA
20493355 AAA-AT-A-TATA
1 AAATATAATTATA
*
20493365 AAATATCAATTAAA
1 AAATAT-AATTATA
20493379 AAATATAATT-T-
1 AAATATAATTATA
20493390 AAATATA
1 AAATATA
20493397 TTTTAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
10 7 0.19
11 10 0.28
12 2 0.06
13 8 0.22
14 9 0.25
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (13 bp):
AAATATAATTATA
Found at i:20493380 original size:23 final size:23
Alignment explanation
Indices: 20493342--20493385 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
20493332 TTTTAAAATT
20493342 AAATATAATTATAAAAATATATA
1 AAATATAATTATAAAAATATATA
20493365 AAATATCAATTA-AAAAATATA
1 AAATAT-AATTATAAAAATATA
20493386 ATTTAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATATAATTATAAAAATATATA
Found at i:20496240 original size:10 final size:9
Alignment explanation
Indices: 20496221--20496293 Score: 60
Period size: 9 Copynumber: 7.9 Consensus size: 9
20496211 GTTGGATTCT
20496221 AAAAATTAA
1 AAAAATTAA
20496230 AAAAATATAA
1 AAAAAT-TAA
*
20496240 AAAAATT-C
1 AAAAATTAA
*
20496248 AAAACTTAA
1 AAAAATTAA
*
20496257 TAAAATCTATA
1 AAAAAT-TA-A
*
20496268 AAGAA-TAA
1 AAAAATTAA
20496276 AAAATATTAA
1 AAAA-ATTAA
20496286 AAAAATTA
1 AAAAATTA
20496294 CTTAAAATTG
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
8 10 0.20
9 18 0.36
10 18 0.36
11 4 0.08
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.25
Consensus pattern (9 bp):
AAAAATTAA
Found at i:20496466 original size:2 final size:2
Alignment explanation
Indices: 20496459--20496488 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20496449 GGTCTTTGCT
20496459 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20496489 CTCTTATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20497218 original size:22 final size:22
Alignment explanation
Indices: 20497193--20497234 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
20497183 TCTAGTGTTC
20497193 TATTCTATTCTA-TTTATTTTTT
1 TATT-TATTCTATTTTATTTTTT
*
20497215 TATTTATTTTATTTTATTTT
1 TATTTATTCTATTTTATTTT
20497235 ATTTCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TATTTATTCTATTTTATTTTTT
Found at i:20497227 original size:26 final size:26
Alignment explanation
Indices: 20497193--20497247 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
20497183 TCTAGTGTTC
*
20497193 TATTCTATTCTA-TTTATTTTTTTATT
1 TATTCTATTCTATTTTATTTCTTT-TT
* *
20497219 TATTTTATTTTATTTTATTTCTTTTT
1 TATTCTATTCTATTTTATTTCTTTTT
20497245 TAT
1 TAT
20497248 CTACGAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (26 bp):
TATTCTATTCTATTTTATTTCTTTTT
Found at i:20497244 original size:15 final size:13
Alignment explanation
Indices: 20497203--20497244 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 13
20497193 TATTCTATTC
20497203 TATTTA-TTTTTT
1 TATTTATTTTTTT
20497215 TATTTATTTTATTT
1 TATTTATTTT-TTT
20497229 TATTTTATTTCTTTT
1 TA-TTTATTT-TTTT
20497244 T
1 T
20497245 TATCTACGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.23
13 3 0.12
14 5 0.19
15 11 0.42
16 1 0.04
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (13 bp):
TATTTATTTTTTT
Found at i:20503011 original size:16 final size:15
Alignment explanation
Indices: 20502973--20503015 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
20502963 AATGAAACAT
20502973 ACAAATTGAAATAAA
1 ACAAATTGAAATAAA
* *
20502988 ACTTAATTGAGATAAA
1 AC-AAATTGAAATAAA
20503004 ATCAAATTGAAA
1 A-CAAATTGAAA
20503016 GGGGGCAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
15 2 0.09
16 19 0.86
17 1 0.05
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.26
Consensus pattern (15 bp):
ACAAATTGAAATAAA
Found at i:20507140 original size:15 final size:15
Alignment explanation
Indices: 20507117--20507147 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20507107 AAGGTTATAA
*
20507117 AAATCATATAAATAT
1 AAATAATATAAATAT
20507132 AAATAATATAAATAT
1 AAATAATATAAATAT
20507147 A
1 A
20507148 CTATAACCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATAATATAAATAT
Found at i:20511516 original size:96 final size:96
Alignment explanation
Indices: 20511386--20511631 Score: 284
Period size: 96 Copynumber: 2.5 Consensus size: 96
20511376 ATTTTTAAAT
** *
20511386 TTTAGGGTTTTAAGGAAAAAAAT-AAATAAATTAGGGTTTAGTGTTTGTTAATTAAATTAATTAC
1 TTTAGGGTTTTAAGGAAAAAAATCAAATAAATTAGGGTTTAG-GTTACTTAAGTAAATTAATTA-
*
20511450 T-AATTTT-AAAAAATTAGATTATGG-TTTAGTG
64 TAAATTTTAAAAAAATTAGATTA-GGATTTAGGG
* *
20511481 TTTATGGTTTTAAGGAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTAAGGAAAAAAATCAAATAAATTAGGGTTT-AGGTTACTTAAGTAAATTAATTAT
20511546 AAATTTTAAAAAAATTAGATTAGGATTTTAGGG
65 AAATTTTAAAAAAATTAGATTAGGA-TTTAGGG
*
20511579 TTTAGGGTTTTAGGGTATTTAAGAAAAAATCAAATAAATTAGGGTTTAAGGTT
1 TTTAGGGTTTTAAGG------A-AAAAAATCAAATAAATTAGGGTTT-AGGTT
20511632 TAGGGTAACT
Statistics
Matches: 130, Mismatches: 8, Indels: 16
0.84 0.05 0.10
Matches are distributed among these distances:
95 23 0.18
96 41 0.32
97 16 0.12
98 19 0.15
104 1 0.01
105 30 0.23
ACGTcount: A:0.41, C:0.02, G:0.18, T:0.39
Consensus pattern (96 bp):
TTTAGGGTTTTAAGGAAAAAAATCAAATAAATTAGGGTTTAGGTTACTTAAGTAAATTAATTATA
AATTTTAAAAAAATTAGATTAGGATTTAGGG
Found at i:20511589 original size:15 final size:15
Alignment explanation
Indices: 20511565--20511594 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20511555 AAAAATTAGA
20511565 TTAGGATTTTAGGGT
1 TTAGGATTTTAGGGT
*
20511580 TTAGGGTTTTAGGGT
1 TTAGGATTTTAGGGT
20511595 ATTTAAGAAA
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:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (15 bp):
TTAGGATTTTAGGGT
Found at i:20511896 original size:126 final size:126
Alignment explanation
Indices: 20511676--20512200 Score: 822
Period size: 126 Copynumber: 4.2 Consensus size: 126
20511666 AAAAGCTTCT
* *
20511676 ACGTGGACGCTCTTTTGCTACAATAGTCTCTGAAAAAATGAATTTGAGAAGACGTGTCTGTGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGTCTGTGCAA
*
20511741 ATAGTGTCAAAAACGCTTCAAGCATGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* *
20511802 ACGTGGATGCTCTTTTGCTACAGTAGTATCTGAAAAAATAAATTTGAGAAGACGTGTCTGTGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGTCTGTGCAA
* *
20511867 ATAGTGTAAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTTCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* * * *
20511928 ACGTGGACGCTCTTTTGCTACAGTAGTCTTTGAAAAAATAATTTTGAGAAGACGAGTCTGTACAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGTCTGTGCAA
* * * *
20511993 ATAGTGGT-AAAAACGCTTCAAGCAGGATGCATTTTCAGCAAAATTACTGGAAGAGGCTCCC
66 ATAGT-GTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* * *
20512054 ACGTGGATGCTCTTTTGCTACAGTGGTCTCTGAAAAAATAATTTTGAGAAGACGTGT-T-TGCAT
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGTCTGTGC--
*
20512117 AAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTTTCAGCAAAAGTACTGAAAGAAGCTCCC
64 AAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
*
20512180 ACGTGGACGCTATTTTGCTAC
1 ACGTGGACGCTCTTTTGCTAC
20512201 CATGGTTTTT
Statistics
Matches: 367, Mismatches: 28, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
124 2 0.01
125 3 0.01
126 360 0.98
127 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (126 bp):
ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGTCTGTGCAA
ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
Found at i:20515296 original size:55 final size:54
Alignment explanation
Indices: 20515237--20515532 Score: 190
Period size: 55 Copynumber: 5.2 Consensus size: 54
20515227 TACATGAAAT
20515237 AATATAAAAATATTCAAAATATTGCTTTATTTAAAATAATTTTCATTTTATTAAA
1 AATATAAAAATATTCAAAATATTGCTTTATTTAAAATAATTTT-ATTTTATTAAA
* * * * *
20515292 AATATAAAAGTA---AATTATAATTACTTTATTTAAAACAACCTTTTATATTATCACATGAAA
1 AATATAAAAATATTCAA-AAT-ATTGCTTTATTTAAAATAA--TTTTAT-TT-T---ATTAAA
** * *
20515352 TAATATAAATGTATTCAAAATGTTGCCTTATTTAAAATAATTTATATTTTATTAAA
1 -AATATAAAAATATTCAAAATATTGCTTTATTTAAAATAATTT-TATTTTATTAAA
* * * * *
20515408 AATATAAAAGTAAATT--ACA-ATTACTTTATTTAAAACAACCTTTTATCTAATTACATGAAA
1 AATATAAAA--ATATTCAAAATATTGCTTTATTTAAAATAA--TTTTAT-T--TT--ATTAAA
* * *
20515468 TAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTAAA
1 -AATATAAAAATATTCAAAATATTGCTTTATTTAAAATAATTT-TATTTTATTAAA
20515524 AATATAAAA
1 AATATAAAA
20515533 GTAAATTACA
Statistics
Matches: 184, Mismatches: 29, Indels: 56
0.68 0.11 0.21
Matches are distributed among these distances:
52 2 0.01
53 2 0.01
54 32 0.17
55 35 0.19
56 20 0.11
57 4 0.02
58 4 0.02
59 5 0.03
60 19 0.10
61 27 0.15
62 30 0.16
63 2 0.01
64 2 0.01
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (54 bp):
AATATAAAAATATTCAAAATATTGCTTTATTTAAAATAATTTTATTTTATTAAA
Found at i:20515386 original size:62 final size:61
Alignment explanation
Indices: 20515227--20515607 Score: 201
Period size: 54 Copynumber: 6.5 Consensus size: 61
20515217 TATATTTTAT
* * * *
20515227 TACATGAAATAATATAAAAATATTCAAAATATTGCTTTATTTAAAATAA--TTTTCAT-TT-
1 TACATGAAATAATATAAAAGTATTCAAAATGTTGCCTTATTTAAAACAACCTTTT-ATATTA
* * * *
20515285 T--ATTAAA-AATATAAAAGTAAATT-ATAA--TTACTTTATTTAAAACAACCTTTTATATTA
1 TACATGAAATAATATAAAAGT--ATTCAAAATGTTGCCTTATTTAAAACAACCTTTTATATTA
* *
20515342 TCACATGAAATAATATAAATGTATTCAAAATGTTGCCTTATTTAAAATAA---TTTATATT-
1 T-ACATGAAATAATATAAAAGTATTCAAAATGTTGCCTTATTTAAAACAACCTTTTATATTA
* * * * * * *
20515400 T-TATTAAA-AATATAAAAGTAAATT-ACAA--TTACTTTATTTAAAACAACCTTTTATCTAA
1 TACATGAAATAATATAAAAGT--ATTCAAAATGTTGCCTTATTTAAAACAACCTTTTATATTA
* * *
20515458 TTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAA--TTTCCAT-TT-
1 -TACATGAAATAATATAAAAGTATTCAAAATGTTGCCTTATTTAAAACAACCTTT-TATATTA
* * * * * * *
20515517 T--ATTAAA-AATATAAAAGTAAATT-ACAA--TTACTTTATTTAAAACAATCTTTTATCTAA
1 TACATGAAATAATATAAAAGT--ATTCAAAATGTTGCCTTATTTAAAACAACCTTTTATATTA
20515574 TTACATGAAATAATATAAAAAG-ATTCAAAATGTT
1 -TACATGAAATAATAT-AAAAGTATTCAAAATGTT
20515608 TGTACAAATA
Statistics
Matches: 244, Mismatches: 39, Indels: 76
0.68 0.11 0.21
Matches are distributed among these distances:
54 46 0.19
55 34 0.14
56 34 0.14
57 16 0.07
58 4 0.02
59 18 0.07
60 28 0.11
61 27 0.11
62 37 0.15
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.40
Consensus pattern (61 bp):
TACATGAAATAATATAAAAGTATTCAAAATGTTGCCTTATTTAAAACAACCTTTTATATTA
Found at i:20515401 original size:116 final size:115
Alignment explanation
Indices: 20515225--20515607 Score: 640
Period size: 116 Copynumber: 3.3 Consensus size: 115
20515215 TTTATATTTT
* *
20515225 ATTACATGAAATAATATAAAAATATTCAAAATATTGCTTTATTTAAAATAATTTTCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTT-ATTTTATTA
* * *
20515290 AAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACCTTTTATATT
65 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
* **
20515341 ATCACATGAAATAATATAAATGTATTCAAAATGTTGCCTTATTTAAAATAATTTATATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTT-TATTTTATTA
20515406 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
65 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
*
20515457 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTT-TATTTTATTA
*
20515522 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAATCTTTTATCTA
65 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
*
20515573 ATTACATGAAATAATATAAAAAGATTCAAAATGTT
1 ATTACATGAAATAATATAAAAATATTCAAAATGTT
20515608 TGTACAAATA
Statistics
Matches: 251, Mismatches: 15, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
116 250 1.00
117 1 0.00
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.40
Consensus pattern (115 bp):
ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTTATTTTATTAA
AAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
Found at i:20515473 original size:61 final size:60
Alignment explanation
Indices: 20515292--20515593 Score: 226
Period size: 61 Copynumber: 5.2 Consensus size: 60
20515282 TTTTATTAAA
* * * *
20515292 AATATAAAAGTAAATTATAATTACTTTATTTAAAACAACCTTTTATATTATCACATGAAAT
1 AATATAAAAGTAAATTACAATTACTTTATTTAAAACAA-CTTTTATCTAATTACATGAAAT
* * * * * *
20515353 AATATAAATGT--ATTCAAAATGTTGCCTTATTTAAAATAA-TTTATAT-T--TT--ATTAAA-
1 AATATAAAAGTAAATT-ACAA--TTACTTTATTTAAAACAACTTT-TATCTAATTACATGAAAT
20515408 AATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTAATTACATGAAAT
1 AATATAAAAGTAAATTACAATTACTTTATTTAAAACAA-CTTTTATCTAATTACATGAAAT
* * * * * * *
20515469 AATATAAAA--ATATTCAAAATGTTGCCTTATTTAAAATAA-TTTCCAT-T--TT--ATTAAA-
1 AATATAAAAGTAAATT-ACAA--TTACTTTATTTAAAACAACTTT-TATCTAATTACATGAAAT
20515524 AATATAAAAGTAAATTACAATTACTTTATTTAAAACAATCTTTTATCTAATTACATGAAAT
1 AATATAAAAGTAAATTACAATTACTTTATTTAAAACAA-CTTTTATCTAATTACATGAAAT
20515585 AATATAAAA
1 AATATAAAA
20515594 AGATTCAAAA
Statistics
Matches: 186, Mismatches: 27, Indels: 56
0.69 0.10 0.21
Matches are distributed among these distances:
54 30 0.16
55 24 0.13
56 24 0.13
57 7 0.04
58 7 0.04
59 7 0.04
60 24 0.13
61 33 0.18
62 30 0.16
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (60 bp):
AATATAAAAGTAAATTACAATTACTTTATTTAAAACAACTTTTATCTAATTACATGAAAT
Found at i:20516018 original size:18 final size:18
Alignment explanation
Indices: 20515992--20516034 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
20515982 GACTAGAAAA
* * *
20515992 AGGAAACATATAAGGGCT
1 AGGATACATAAAAGGGAT
20516010 AGGATACATAAAAGGGAT
1 AGGATACATAAAAGGGAT
20516028 AGGATAC
1 AGGATAC
20516035 GTACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGATACATAAAAGGGAT
Found at i:20516122 original size:30 final size:30
Alignment explanation
Indices: 20516088--20516153 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
20516078 GTTGAACTAT
*
20516088 TGGGCCCGGTGACTGTGTAGGTCCTGTTGC
1 TGGGCCCGGTGACTGTGTAGGTCCTGTTGA
* * * **
20516118 TGGGCCGGGTGATTGTGTGGGTGTTGTTGA
1 TGGGCCCGGTGACTGTGTAGGTCCTGTTGA
20516148 TGGGCC
1 TGGGCC
20516154 TGCGTCGTCG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.06, C:0.17, G:0.45, T:0.32
Consensus pattern (30 bp):
TGGGCCCGGTGACTGTGTAGGTCCTGTTGA
Found at i:20517785 original size:15 final size:15
Alignment explanation
Indices: 20517765--20517795 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20517755 TTTTTATTTT
*
20517765 AAAAAATAAATTTAG
1 AAAAAATAAAATTAG
20517780 AAAAAATAAAATTAG
1 AAAAAATAAAATTAG
20517795 A
1 A
20517796 GCTTTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (15 bp):
AAAAAATAAAATTAG
Found at i:20517839 original size:11 final size:11
Alignment explanation
Indices: 20517823--20517874 Score: 81
Period size: 11 Copynumber: 4.9 Consensus size: 11
20517813 TAACAAGAGT
*
20517823 TTTGAGAGGAA
1 TTTGAGAGAAA
20517834 TTTGAGAGAAA
1 TTTGAGAGAAA
20517845 TTT--GAGAAA
1 TTTGAGAGAAA
20517854 TTTGAGAGAAA
1 TTTGAGAGAAA
20517865 TTTGAGAGAA
1 TTTGAGAGAA
20517875 TATTGAAAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
9 9 0.24
11 29 0.76
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (11 bp):
TTTGAGAGAAA
Found at i:20517855 original size:20 final size:20
Alignment explanation
Indices: 20517832--20517871 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
20517822 TTTTGAGAGG
20517832 AATTTGAGAGAAATTTGAGA
1 AATTTGAGAGAAATTTGAGA
20517852 AATTTGAGAGAAATTTGAGA
1 AATTTGAGAGAAATTTGAGA
20517872 GAATATTGAA
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:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (20 bp):
AATTTGAGAGAAATTTGAGA
Found at i:20517880 original size:11 final size:11
Alignment explanation
Indices: 20517824--20517880 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
20517814 AACAAGAGTT
20517824 TTGAGAGGAAT-
1 TTGAGA-GAATA
20517835 TTGAGAGAA-A
1 TTGAGAGAATA
20517845 TTTGAGA-AAT-
1 -TTGAGAGAATA
20517855 TTGAGAGAA-A
1 TTGAGAGAATA
20517865 TTTGAGAGAATA
1 -TTGAGAGAATA
20517877 TTGA
1 TTGA
20517881 AAGATTGAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
9 6 0.15
10 7 0.18
11 25 0.64
12 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.30
Consensus pattern (11 bp):
TTGAGAGAATA
Found at i:20519620 original size:40 final size:40
Alignment explanation
Indices: 20519565--20519645 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
20519555 GAAGCCAGAA
20519565 AAAACCTCCCATGTTTCATCCT-TCGAGAAAGAATTAGCCC
1 AAAACCTCCCATGTTTCATCCTCT-GAGAAAGAATTAGCCC
20519605 AAAACCTCCCATGTTTCATCCTCTGAGAAAGAATTAGCCC
1 AAAACCTCCCATGTTTCATCCTCTGAGAAAGAATTAGCCC
20519645 A
1 A
20519646 CTCTACGCGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 39 0.98
41 1 0.03
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.25
Consensus pattern (40 bp):
AAAACCTCCCATGTTTCATCCTCTGAGAAAGAATTAGCCC
Found at i:20519773 original size:96 final size:95
Alignment explanation
Indices: 20519605--20519799 Score: 300
Period size: 96 Copynumber: 2.0 Consensus size: 95
20519595 GAATTAGCCC
* * *
20519605 AAAACCTCCCATGTTTCATCCTCTGAGAAAGAATTAGCCCACTCTACGCGAACCTCAGTGACTGC
1 AAAACCTCCCATGTTTCATCCTCTGAGAAAGAATTAGCCCACTCCACGCAAACCTCAGTCACTGC
* * *
20519670 ATTATGACATCTCTTATAAATATGTTTATCT
66 ATGATGACATCTCTT-TAAATACGCTTATCT
* *
20519701 AAAACCTCCCATGTTTCATCCTCTGGGAAAGAATTAGCCCACTCCACGTAAACCTCAGTCACTGC
1 AAAACCTCCCATGTTTCATCCTCTGAGAAAGAATTAGCCCACTCCACGCAAACCTCAGTCACTGC
*
20519766 ATGATGACCTCTCTTTAAATACGCTTATCT
66 ATGATGACATCTCTTTAAATACGCTTATCT
20519796 AAAA
1 AAAA
20519800 TTCGAGCTGG
Statistics
Matches: 90, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
95 17 0.19
96 73 0.81
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (95 bp):
AAAACCTCCCATGTTTCATCCTCTGAGAAAGAATTAGCCCACTCCACGCAAACCTCAGTCACTGC
ATGATGACATCTCTTTAAATACGCTTATCT
Found at i:20523198 original size:21 final size:19
Alignment explanation
Indices: 20523164--20523225 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 19
20523154 TAAGTTATAT
20523164 ATAATAATATAATATGAATAAA
1 ATAATAA-A-AATAT-AATAAA
20523186 AT-ATAAGGAAATATAATATAAA
1 ATAATAA--AAATAT-A-ATAAA
20523208 ATAATAAAAATATAATAA
1 ATAATAAAAATATAATAA
20523226 GTAATTTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 4 0.11
20 1 0.03
21 16 0.46
22 10 0.29
23 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
ATAATAAAAATATAATAAA
Found at i:20523275 original size:21 final size:22
Alignment explanation
Indices: 20523249--20523290 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
20523239 AAAATATAGT
*
20523249 AAAATAAATAGTATA-AAAAAC
1 AAAATAAATAATATATAAAAAC
20523270 AAAATAAATAATATATAAAAA
1 AAAATAAATAATATATAAAAA
20523291 TATAAGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAATAAATAATATATAAAAAC
Found at i:20523656 original size:12 final size:11
Alignment explanation
Indices: 20523609--20523689 Score: 54
Period size: 12 Copynumber: 6.9 Consensus size: 11
20523599 ACAATTTTAT
20523609 AAAAATATATA
1 AAAAATATATA
20523620 AAGAAATATATA
1 AA-AAATATATA
* *
20523632 AAATAAAAAATA
1 AAA-AATATATA
20523644 AAAAATAATATA
1 AAAAAT-ATATA
*** *
20523656 ATTTATAGATA
1 AAAAATATATA
*
20523667 AAATATATGATA
1 AAAAATAT-ATA
20523679 AAATAATATAT
1 AAA-AATATAT
20523690 TGGATAATAA
Statistics
Matches: 53, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
11 14 0.26
12 35 0.66
13 4 0.08
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (11 bp):
AAAAATATATA
Found at i:20524380 original size:21 final size:20
Alignment explanation
Indices: 20524347--20524385 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
20524337 GTCCTTCCAC
*
20524347 ATGTAACTCTTTTTCTTTTGA
1 ATGTAACTATTTTT-TTTTGA
*
20524368 ATGTTACTATTTTTTTTT
1 ATGTAACTATTTTTTTTT
20524386 AAAAAACAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.18, C:0.10, G:0.08, T:0.64
Consensus pattern (20 bp):
ATGTAACTATTTTTTTTTGA
Found at i:20525922 original size:206 final size:207
Alignment explanation
Indices: 20525328--20526021 Score: 1176
Period size: 207 Copynumber: 3.4 Consensus size: 207
20525318 GGTCTGCTTC
*
20525328 AGCCAAATCAGCTATATCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATC
1 AGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATC
*
20525393 TTGCTTCAGTATAAACATCTGAAGGCCATATCTGCTATGTGTCTGCTCTCCGTCGAATATGGAGA
66 TTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCTCTCCGTCGAATATGGAGA
*
20525458 CGCCAAACTTCGATTTGTTCTCTGAGAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCG
131 CGCCAAACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCG
20525523 TAAGCACGTGAA
196 TAAGCACGTGAA
* * * *
20525535 AGCCAAATCAGCTATGTCTTCGATTTGTTCTTTGTAAGTACGAGGATGCCAAATCATCTTGGATC
1 AGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATC
* *
20525600 TTGCTTCAGTATAAACATTTGAAGGCTAGATCTGCTATGTGTCTGCTCTCCGTCGAATATGGAGA
66 TTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCTCTCCGTCGAATATGGAGA
* * *
20525665 CGCCAAACTTCGATTTGTTCTCTGACAAAACACAGATGCCAAATTATCTTAGATTTGCTTCATCG
131 CGCCAAACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCG
20525730 TAAGCACGTGAA
196 TAAGCACGTGAA
* *
20525742 AGCCAAATCAGCTATGAT-TTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATCATCTTGGAT
1 AGCCAAATCAGCTATG-TCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
* *
20525806 C-TGCTTCAGTCTAATCATCTGAAGGCCAGATCTGCTATGTGTCTGCTCTCCGTCGAATATGGAG
65 CTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCTCTCCGTCGAATATGGAG
* *
20525870 ACGCCAAACTTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTACTTCATC
130 ACGCCAAACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATC
20525935 GTAAGCACGTGAA
195 GTAAGCACGTGAA
**
20525948 AGCCAAATTGGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATC
1 AGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATC
*
20526013 TTGTTTCAG
66 TTGCTTCAG
20526022 CCAGATCTGC
Statistics
Matches: 454, Mismatches: 30, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
205 1 0.00
206 191 0.42
207 261 0.57
208 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (207 bp):
AGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATC
TTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCTCTCCGTCGAATATGGAGA
CGCCAAACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCG
TAAGCACGTGAA
Found at i:20538365 original size:14 final size:13
Alignment explanation
Indices: 20538333--20538408 Score: 57
Period size: 12 Copynumber: 5.6 Consensus size: 13
20538323 ATACAATTTT
20538333 ATAAAATATATAA
1 ATAAAATATATAA
*
20538346 A-GAAATATATAA
1 ATAAAATATATAA
20538358 ACTAAAATATATAA
1 A-TAAAATATATAA
* *
20538372 TATAATATAATTTATAG
1 -AT-A-A-AATATATAA
*
20538389 ATAAAATATAT-G
1 ATAAAATATATAA
20538401 ATAAAATA
1 ATAAAATA
20538409 ATGTATTGGA
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
12 20 0.38
13 7 0.13
14 12 0.23
15 3 0.06
16 3 0.06
17 7 0.13
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (13 bp):
ATAAAATATATAA
Found at i:20544088 original size:43 final size:43
Alignment explanation
Indices: 20544037--20544122 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
20544027 TATGGTAAGG
** * * *
20544037 GAGGCTTTTTGTAAGGAATAGTGGAAAAAGCGTCAATAATATC
1 GAGGCTTTTCATAAGAAATAATGGAAAAAGCATCAATAATATC
20544080 GAGGCTTTTCATAAGAAATAATGGAAAAAGCATCAATAATATC
1 GAGGCTTTTCATAAGAAATAATGGAAAAAGCATCAATAATATC
20544123 TTTGATTGCC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (43 bp):
GAGGCTTTTCATAAGAAATAATGGAAAAAGCATCAATAATATC
Found at i:20545860 original size:31 final size:32
Alignment explanation
Indices: 20545814--20545877 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
20545804 AGAAATATTC
*
20545814 CTCTCTAAAAAAAATGAAAAGCAAAGTTGGAG
1 CTCTCTAAAAAAAATGAAAAGCAAAGTTAGAG
* *
20545846 CTCTC-AAAATAAATGAAAAGCAATGTTAGAG
1 CTCTCTAAAAAAAATGAAAAGCAAAGTTAGAG
20545877 C
1 C
20545878 GATGATTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 24 0.83
32 5 0.17
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.20
Consensus pattern (32 bp):
CTCTCTAAAAAAAATGAAAAGCAAAGTTAGAG
Found at i:20551122 original size:25 final size:25
Alignment explanation
Indices: 20551093--20551144 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
20551083 AAGAATAATT
20551093 TGAATATT-TGATATTGCCTAATAAA
1 TGAAT-TTCTGATATTGCCTAATAAA
* *
20551118 TGAATTTCTGATATTGCTTAGTAAA
1 TGAATTTCTGATATTGCCTAATAAA
20551143 TG
1 TG
20551145 TCAAGCCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (25 bp):
TGAATTTCTGATATTGCCTAATAAA
Found at i:20552662 original size:17 final size:17
Alignment explanation
Indices: 20552639--20552702 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 17
20552629 AGCCAAGGAA
*
20552639 AAAGAAAAAGAAAAAGG
1 AAAGAAAAAGAAAAAAG
*
20552656 GAAG-AAAAGAAAAAAG
1 AAAGAAAAAGAAAAAAG
* ***
20552672 AAAGAAAATGAGGGAA-
1 AAAGAAAAAGAAAAAAG
20552688 AAAGAAAAAGAAAAA
1 AAAGAAAAAGAAAAA
20552703 GAGGTACAAA
Statistics
Matches: 35, Mismatches: 11, Indels: 3
0.71 0.22 0.06
Matches are distributed among these distances:
16 25 0.71
17 10 0.29
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (17 bp):
AAAGAAAAAGAAAAAAG
Found at i:20552701 original size:5 final size:6
Alignment explanation
Indices: 20552636--20552704 Score: 54
Period size: 6 Copynumber: 11.3 Consensus size: 6
20552626 GGCAGCCAAG
** *
20552636 GAAAAA GAAAAA GAAAAA G-GGAA G-AAAA GAAAAA -AGAAA GAAAATGA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA--A
20552683 GGGAAAAA GAAAAA GAAAAA GA
1 --GAAAAA GAAAAA GAAAAA GA
20552705 GGTACAAAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
5 10 0.20
6 34 0.67
8 2 0.04
10 5 0.10
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (6 bp):
GAAAAA
Found at i:20552714 original size:22 final size:22
Alignment explanation
Indices: 20552635--20552706 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 22
20552625 TGGCAGCCAA
20552635 GGAAAAAGAAAAAGAAAAAG-G
1 GGAAAAAGAAAAAGAAAAAGAG
*
20552656 GAAGAAAAGAAAAAAGAAAGAAAATGAG
1 GGA-AAAAG-AAAAAG--A-AAAA-GAG
20552684 GGAAAAAGAAAAAGAAAAAGAG
1 GGAAAAAGAAAAAGAAAAAGAG
20552706 G
1 G
20552707 TACAAAGAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
21 2 0.05
22 9 0.21
23 10 0.24
24 1 0.02
25 1 0.02
26 10 0.24
27 6 0.14
28 3 0.07
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (22 bp):
GGAAAAAGAAAAAGAAAAAGAG
Found at i:20559929 original size:19 final size:17
Alignment explanation
Indices: 20559905--20559942 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
20559895 AATTAATTAT
20559905 GAAATTAAACATAATATAA
1 GAAATTAAA-ATAATA-AA
20559924 GAAATTAAAATAATAAA
1 GAAATTAAAATAATAAA
20559941 GA
1 GA
20559943 TAATATATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 6 0.32
19 9 0.47
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.24
Consensus pattern (17 bp):
GAAATTAAAATAATAAA
Found at i:20563761 original size:19 final size:20
Alignment explanation
Indices: 20563739--20563785 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
20563729 AATATTATAT
20563739 TATATTTTAAATATT-TGTA
1 TATATTTTAAATATTCTGTA
* *
20563758 TATATTAT-AATATTCTTTA
1 TATATTTTAAATATTCTGTA
*
20563777 AATATTTTA
1 TATATTTTA
20563786 CCTTTAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
TATATTTTAAATATTCTGTA
Found at i:20567777 original size:24 final size:25
Alignment explanation
Indices: 20567741--20567793 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
20567731 ATATTAAAAG
*
20567741 ATAT-ATATATAAAATGTATACATA
1 ATATAATATATAAAATATATACATA
* *
20567765 ATATAATAT-TAAAATATTTACATG
1 ATATAATATATAAAATATATACATA
20567789 ATATA
1 ATATA
20567794 TACATAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (25 bp):
ATATAATATATAAAATATATACATA
Found at i:20567829 original size:48 final size:48
Alignment explanation
Indices: 20567730--20567867 Score: 126
Period size: 48 Copynumber: 2.9 Consensus size: 48
20567720 ATAAAAATAC
* * *
20567730 AATATTA-AAAGATATATATATAA-AATGTATACATAATATAATATTAA
1 AATATTACATAGATATATACATAATAATGTA-ACAAAATATAATATTAA
20567777 AATATTTACAT-GATATATACATAATAATGTAA-AAAATA-AACTATTAA
1 AATA-TTACATAGATATATACATAATAATGTAACAAAATATAA-TATTAA
* * *
20567824 TAATATTATATAAATATATACAT-ATAATAGTAATAATAATATAA
1 -AATATTACATAGATATATACATAATAAT-GTAACAA-AATATAA
20567868 AGGTATTTCA
Statistics
Matches: 76, Mismatches: 5, Indels: 16
0.78 0.05 0.16
Matches are distributed among these distances:
46 2 0.03
47 25 0.33
48 34 0.45
49 9 0.12
50 4 0.05
51 2 0.03
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (48 bp):
AATATTACATAGATATATACATAATAATGTAACAAAATATAATATTAA
Found at i:20568354 original size:39 final size:39
Alignment explanation
Indices: 20568291--20568369 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
20568281 AAAAAAGCTG
* * *
20568291 ATCCCACTCCCCTATGCTATTTTGTTTTATTATTAATTA
1 ATCCCACTCCCCCATGCCACTTTGTTTTATTATTAATTA
20568330 ATCCCACTCCCCCATGCCACTTTGTTTTATTATTAATTA
1 ATCCCACTCCCCCATGCCACTTTGTTTTATTATTAATTA
20568369 A
1 A
20568370 AACCATAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.24, C:0.27, G:0.05, T:0.44
Consensus pattern (39 bp):
ATCCCACTCCCCCATGCCACTTTGTTTTATTATTAATTA
Found at i:20569862 original size:44 final size:44
Alignment explanation
Indices: 20569797--20570591 Score: 1169
Period size: 44 Copynumber: 18.1 Consensus size: 44
20569787 AGGAACACCG
* * **
20569797 ATCTGTTATTTTCGATCTGCTCTCTGCCAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* * * *
20569841 ATCTGTCATCTTCGATTTGCTCTCCACCACTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
20569885 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* * *
20569929 ATCTATTATCTTCGATTTGCTCTCCGCCGCTACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
20569973 ATCTGCTATCTTCGATCTGCTCTCCACCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
**
20570017 ATCTGTTATCTTCGATCTGCTCTTTGCCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
*
20570061 ATCT-TCTATCTTTGATCTGCTCTCCGCCGCTACAGAGACGCCAA
1 ATCTGT-TATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* * *
20570105 ATCTGCTATCTTTGATCTGCTCTCCACCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
20570149 ATCTGCTACCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
20570193 ATCTGCTATCTTTGATCTGCTCTCCGCCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* * * * * *
20570237 ATCTATTATTTTTGACCTGCTCTCCACAGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* * * * *
20570281 ATCTGTTATCTTCGACCTGCTCTTCACCGCTGCAGAGACGCTAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
** *
20570325 ATCTACTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
20570369 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
20570413 ATCTGTTATCTTCGACCTGCTCTCTGCCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
**
20570457 ATCTGTTATCTTCGATCTGCTCTCCATCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
20570501 ATCTGTTATCTTCGATTTGCTCTCCGCCGCTACAGAGACACCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
**
20570545 ATCTGTTATCTTCGATCTGCTCTCTACCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
20570589 ATC
1 ATC
20570592 ATCTTGGATT
Statistics
Matches: 679, Mismatches: 70, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
43 1 0.00
44 678 1.00
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.28
Consensus pattern (44 bp):
ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
Found at i:20570677 original size:132 final size:129
Alignment explanation
Indices: 20569827--20570678 Score: 816
Period size: 132 Copynumber: 6.5 Consensus size: 129
20569817 TCTCTGCCAA
* * * * * *
20569827 TACAGAGACGCCAAATCTGTCATCTTCGATTTGCTCTCCACCACTACAGAGACGCCAAATCTGTT
1 TACAGAGAAGCCAAATCAGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* ** * * ***
20569892 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTATTATCTTCGATTTGCTCTCCGCC
66 ATCTTCGACCTGCTCTCTACCGCTACAGAGACGCCAAATC---TATCTTCGATCTGATCTCAATC
20569957 GC
128 GC
* * * *
20569959 TACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCACCGCTACAGAGACGCCAAATCTGTT
1 TACAGAGAAGCCAAATCAGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* * * * * ***
20570024 ATCTTCGATCTGCTCTTTGCCGCTACAGAGACGCCAAATCTTCTATCTTTGATCTGCTCTCCGCC
66 ATCTTCGACCTGCTCTCTACCGCTACAGAGACGCCAAA---TCTATCTTCGATCTGATCTCAATC
20570089 GC
128 GC
* * * * * *
20570091 TACAGAGACGCCAAATCTGCTATCTTTGATCTGCTCTCCACCGCTACAGAGACGCCAAATCTGCT
1 TACAGAGAAGCCAAATCAGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* * ** * * ***
20570156 ACCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGCTATCTTTGATCTGCTCTCCGCC
66 ATCTTCGACCTGCTCTCTACCGCTACAGAGACGCCAAA--T-CTATCTTCGATCTGATCTCAATC
20570221 GC
128 GC
* * * * * *
20570223 TACAGAGACGCCAAATCTA-TTATTTTTGACCTGCTCTCCACAGCTACAGAGACGCCAAATCTGT
1 TACAGAGAAGCCAAATC-AGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGT
* * * **
20570287 TATCTTCGACCTGCTCT-TCACCGCTGCAGAGACGCTAAATCTACTATCTTCGATCTGCTCTCTG
65 TATCTTCGACCTGCTCTCT-ACCGCTACAGAGACGCCAAA--T-CTATCTTCGATCTGATCTCAA
*
20570351 CCGC
126 TCGC
* *
20570355 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
1 TACAGAGAAGCCAAATCAGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* * *
20570420 ATCTTCGACCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCATC
66 ATCTTCGACCTGCTCTCTACCGCTACAGAGACGCCAAATC---TATCTTCGATCTGATCTCAATC
20570485 GC
128 GC
* * * *
20570487 TACAGAGACGCCAAATCTGTTATCTTCGATTTGCTCTCCGCCGCTACAGAGACACCAAATCTGTT
1 TACAGAGAAGCCAAATCAGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* * *
20570552 ATCTTCGATCTGCTCTCTACCGCTACAGAGACGCCAAATC-ATCTTGGATTTGAT-TCAAT-G-
66 ATCTTCGACCTGCTCTCTACCGCTACAGAGACGCCAAATCTATCTTCGATCTGATCTCAATCGC
* * * * *
20570612 TAAACACGTGAAAGCCAAATCAGCTATGTCTTCGATCTGCTCCCCGCCTGATACAGAGATGCCAA
1 T--ACA-GAG-AAGCCAAATCAG-T-TATCTTCGATCTGCTCTCCGCC-GCTACAGAGACGCCAA
20570677 AT
59 AT
20570679 TATCTTAGAT
Statistics
Matches: 641, Mismatches: 61, Indels: 36
0.87 0.08 0.05
Matches are distributed among these distances:
125 1 0.00
126 1 0.00
127 7 0.01
128 13 0.02
129 11 0.02
130 2 0.00
131 20 0.03
132 583 0.91
133 1 0.00
135 2 0.00
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (129 bp):
TACAGAGAAGCCAAATCAGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
ATCTTCGACCTGCTCTCTACCGCTACAGAGACGCCAAATCTATCTTCGATCTGATCTCAATCGC
Found at i:20570916 original size:61 final size:64
Alignment explanation
Indices: 20570798--20570920 Score: 191
Period size: 61 Copynumber: 2.0 Consensus size: 64
20570788 TCATGTATCC
20570798 ATGCTTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAAATGTG
1 ATGCTTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAAATGTG
* *
20570862 ATGCTTTATGTCAAATAATTAGGATG-T-T-A-TGAAATGAATCAAATGTTCCTAACTAAATG
1 ATGC-TTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAAATG
20570921 AATGGTTATG
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
61 29 0.52
62 1 0.02
63 1 0.02
64 5 0.09
65 20 0.36
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.33
Consensus pattern (64 bp):
ATGCTTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAAATGTG
Found at i:20581429 original size:17 final size:17
Alignment explanation
Indices: 20581407--20581450 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
20581397 AAAAATATAA
20581407 TAATAATATAATAGTAG
1 TAATAATATAATAGTAG
** *
20581424 TAATAACGTAATAGTAT
1 TAATAATATAATAGTAG
*
20581441 TAAAAATATA
1 TAATAATATA
20581451 CGATATATAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (17 bp):
TAATAATATAATAGTAG
Found at i:20582269 original size:39 final size:39
Alignment explanation
Indices: 20582226--20582304 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
20582216 AAAAAAGCTG
* *
20582226 ATCCCACTCCCCCATGCTATTTTGTTTTATTATTAATTA
1 ATCCCACTCCCCCATGCCACTTTGTTTTATTATTAATTA
20582265 ATCCCACTCCCCCATGCCACTTTGTTTTATTATTAATTA
1 ATCCCACTCCCCCATGCCACTTTGTTTTATTATTAATTA
20582304 A
1 A
20582305 AACCATATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.24, C:0.28, G:0.05, T:0.43
Consensus pattern (39 bp):
ATCCCACTCCCCCATGCCACTTTGTTTTATTATTAATTA
Found at i:20585203 original size:12 final size:11
Alignment explanation
Indices: 20585166--20585233 Score: 55
Period size: 12 Copynumber: 5.7 Consensus size: 11
20585156 TTATGTACAC
20585166 ATTATTTATATT
1 ATTA-TTATATT
* *
20585178 ATTTTTACTACT
1 ATTATTA-TATT
20585190 ATTATTATATCT
1 ATTATTATAT-T
20585202 ATTATTAGTATT
1 ATTATTA-TATT
*
20585214 AGTATTATAATT
1 ATTATTAT-ATT
*
20585226 ACTATTAT
1 ATTATTAT
20585234 TACACTTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
11 6 0.13
12 37 0.80
13 3 0.07
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTATTATATT
Found at i:20585432 original size:25 final size:24
Alignment explanation
Indices: 20585373--20585557 Score: 118
Period size: 25 Copynumber: 7.8 Consensus size: 24
20585363 GTAACATTAT
* *
20585373 TATTAT-TAT-TATTTTTAATGTG
1 TATTATGTATATATTTTTAATATA
* *
20585395 TATGTATTATATATATTTTTAAAACTA
1 TAT-TA-TGTATATATTTTTAATA-TA
*
20585422 TATTATGTATATA-TTATATATATA
1 TATTATGTATATATTTTTA-ATATA
* * *
20585446 TATT-TTTATATATATTTATTATA
1 TATTATGTATATATTTTTAATATA
*
20585469 TTTTTATGTATATATTTTTAATATCA
1 -TATTATGTATATATTTTTAATAT-A
20585495 TATTAT-TCATATA-TTTT--T-TA
1 TATTATGT-ATATATTTTTAATATA
* * *
20585515 TATTATGTAAAGATTTTCAATACTA
1 TATTATGTATATATTTTTAATA-TA
*
20585540 CATTATGTATATATTTTT
1 TATTATGTATATATTTTT
20585558 GTCTATATTG
Statistics
Matches: 124, Mismatches: 22, Indels: 31
0.70 0.12 0.18
Matches are distributed among these distances:
20 10 0.08
21 5 0.04
22 4 0.03
23 14 0.11
24 22 0.18
25 53 0.43
26 12 0.10
27 4 0.03
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (24 bp):
TATTATGTATATATTTTTAATATA
Found at i:20585436 original size:11 final size:11
Alignment explanation
Indices: 20585420--20585509 Score: 50
Period size: 11 Copynumber: 8.5 Consensus size: 11
20585410 TTTTTAAAAC
*
20585420 TATATTATGTA
1 TATATTATATA
20585431 TATATTATATA
1 TATATTATATA
20585442 TATA-TAT-T-
1 TATATTATATA
*
20585450 TTTA-TATATA
1 TATATTATATA
* *
20585460 TTTATTATATT
1 TATATTATATA
*
20585471 TTTATGTATATA
1 TATAT-TATATA
*
20585483 T-TTTTA-ATA
1 TATATTATATA
20585492 TCATATTAT-TCA
1 T-ATATTATAT-A
20585504 TATATT
1 TATATT
20585510 TTTTATATTA
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
8 6 0.09
9 6 0.09
10 9 0.14
11 36 0.55
12 8 0.12
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (11 bp):
TATATTATATA
Found at i:20585457 original size:10 final size:10
Alignment explanation
Indices: 20585442--20585475 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
20585432 ATATTATATA
20585442 TATATATTTT
1 TATATATTTT
*
20585452 TATATATATT
1 TATATATTTT
20585462 TATTATATTTT
1 TA-TATATTTT
20585473 TAT
1 TAT
20585476 GTATATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TATATATTTT
Found at i:20585457 original size:14 final size:14
Alignment explanation
Indices: 20585435--20585517 Score: 58
Period size: 14 Copynumber: 6.4 Consensus size: 14
20585425 TATGTATATA
20585435 TTATATATATATATT
1 TTATATATATAT-TT
20585450 TT-TATATATA---
1 TTATATATATATTT
20585460 TT-TAT-TATATTT
1 TTATATATATATTT
*
20585472 TTATGTATATATTT
1 TTATATATATATTT
*
20585486 TTA-ATATCATATTA
1 TTATATAT-ATATTT
*
20585500 TT-CATATAT-TTT
1 TTATATATATATTT
20585512 TTATAT
1 TTATAT
20585518 TATGTAAAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
9 4 0.07
10 5 0.09
12 6 0.11
13 9 0.16
14 29 0.53
15 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (14 bp):
TTATATATATATTT
Found at i:20585477 original size:48 final size:48
Alignment explanation
Indices: 20585424--20585518 Score: 124
Period size: 48 Copynumber: 2.0 Consensus size: 48
20585414 TAAAACTATA
*
20585424 TTATGTATATA-TTATATATAT-ATATT-TTTATATATATTTATTATATTT
1 TTATGTATATATTTATA-ATATCATATTATTCATATAT-TTT-TTATATTT
*
20585472 TTATGTATATATTTTTAATATCATATTATTCATATATTTTTTATATT
1 TTATGTATATATTTATAATATCATATTATTCATATATTTTTTATATT
20585519 ATGTAAAGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
48 22 0.52
49 12 0.29
50 8 0.19
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (48 bp):
TTATGTATATATTTATAATATCATATTATTCATATATTTTTTATATTT
Found at i:20585835 original size:26 final size:26
Alignment explanation
Indices: 20585805--20585856 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
20585795 ATTATGTATA
*
20585805 TATTTTTAATACTACGTATACATTTT
1 TATTTCTAATACTACGTATACATTTT
* * *
20585831 TATTTCTATTATTACGTATATATTTT
1 TATTTCTAATACTACGTATACATTTT
20585857 AATACATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.58
Consensus pattern (26 bp):
TATTTCTAATACTACGTATACATTTT
Found at i:20597382 original size:16 final size:16
Alignment explanation
Indices: 20597361--20597428 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
20597351 TTTGGTTCGC
20597361 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
20597377 TGTATTGGATTAGAGA
1 TGTATTGGATTAGAGG
20597393 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
20597409 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
20597425 TGTA
1 TGTA
20597429 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:20597685 original size:18 final size:17
Alignment explanation
Indices: 20597664--20597698 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20597654 TTATTATTAA
*
20597664 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
20597682 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
20597699 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:20597805 original size:18 final size:17
Alignment explanation
Indices: 20597784--20597818 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20597774 TTATTATTAA
*
20597784 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
20597802 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
20597819 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:20597905 original size:120 final size:120
Alignment explanation
Indices: 20597647--20597894 Score: 496
Period size: 120 Copynumber: 2.1 Consensus size: 120
20597637 ATCATATTTA
20597647 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
20597712 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
20597767 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
20597832 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
20597887 AACATAAT
1 AACATAAT
20597895 AATATATAAA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 128 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:20601271 original size:88 final size:87
Alignment explanation
Indices: 20601169--20601547 Score: 238
Period size: 88 Copynumber: 4.3 Consensus size: 87
20601159 ATCTAGGCTT
*
20601169 CCTGATGTTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGG
1 CCTGAAGTTGCAGTGAAGCAGATTTAAGCCA-CATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGG
20601234 CTGAAGATTGTAGATCTTGTTTC
65 CTGAAGATTGTAGATCTTGTTTC
* * * * ** * *
20601257 CCTG-AGATTGCAGTGGAGCAGATCAAATATAG-CAAATCTTATTTCCCTGAAGTTGCAGTGGAA
1 CCTGAAG-TTGCAGTGAAGCAGAT---TTA-AGCCACATCCTAGCTCCCTAAAGTTGTAGTGG--
* ** * *
20601320 CAGATTAAAGCT-AA-ATTACAGATCTTATATC
59 -AG--T-AGGCTGAAGATTGTAGATCTTGTTTC
* * * ** * * * *
20601351 TCTGAAGTTGCAGT-AGAGTAGA-TCAAAACAGAT-CTTGTCTCCCTGAAGTTGTAGTGGAATA-
1 CCTGAAGTTGCAGTGA-AGCAGATTTAAGCCACATCCTAG-CTCCCTAAAGTTGTAGTGGAGTAG
* ** * *
20601412 GATCGAAGACGGTAAATCTTGCCTT-
64 GCT-GAAGATTGTAGATCTTG-TTTC
* * *
20601437 CCTGAAGTTGTAGTGAAGCAGATTTAAGCTACCATCCTAACTCCCTAAAGTTGTAGTGGAGTAGG
1 CCTGAAGTTGCAGTGAAGCAGATTTAAGCCA-CATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGG
20601502 CTGAAGATTGTAGATCTTGTTTC
65 CTGAAGATTGTAGATCTTGTTTC
*
20601525 CCTG-AGATTGCAGTGGAGCAGAT
1 CCTGAAG-TTGCAGTGAAGCAGAT
20601548 CAAATATAGC
Statistics
Matches: 210, Mismatches: 55, Indels: 52
0.66 0.17 0.16
Matches are distributed among these distances:
83 2 0.01
84 1 0.00
85 3 0.01
86 24 0.11
87 12 0.06
88 74 0.35
89 6 0.03
90 43 0.20
91 4 0.02
92 2 0.01
93 2 0.01
94 28 0.13
95 5 0.02
96 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (87 bp):
CCTGAAGTTGCAGTGAAGCAGATTTAAGCCACATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGC
TGAAGATTGTAGATCTTGTTTC
Found at i:20601386 original size:90 final size:89
Alignment explanation
Indices: 20601264--20601682 Score: 302
Period size: 90 Copynumber: 4.6 Consensus size: 89
20601254 TTCCCTGAGA
* * * * * *
20601264 TTGCAGTGGAGCAGATCAAATATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAA
1 TTGCAGTAGAGCAGATC-AA-A-A-CAGATCTTATCTCCCTGAAGTTGTAGTGGAATAGATTGAA
20601329 GCTAAATTACAGATCTTATATCTCTGAAG
62 GCTAAATTACAGATCTTAT-TCTCTGAAG
* * *
20601358 TTGCAGTAGAGTAGATCAAAACAGATCTTGTCTCCCTGAAGTTGTAGTGGAATAGATCGAAG--A
1 TTGCAGTAGAGCAGATCAAAACAGATCTTATCTCCCTGAAGTTGTAGTGGAATAGATTGAAGCTA
*** *
20601421 CGGTA-A-ATCTTGCCTTC-CTGAAG
66 AATTACAGATCTT--ATTCTCTGAAG
* ** * * * * * * **
20601444 TTGTAGT-GAAGCAGATTTAAGCTACCATCCTAACTCCCTAAAGTTGTAGTGGAGTAGGCTGAAG
1 TTGCAGTAG-AGCAGATCAAAAC-A-GATCTTATCTCCCTGAAGTTGTAGTGGAATAGATTGAAG
** * *
20601508 ----ATTGTAGATCTTGTTTCCCTG-AG
63 CTAAATTACAGATCTT-ATTCTCTGAAG
* * * *
20601531 ATTGCAGTGGAGCAGATCAAATATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAATAGATTGA
1 -TTGCAGTAGAGCAGATC-AA-A-A-CAGATCTTATCTCCCTGAAGTTGTAGTGGAATAGATTGA
20601596 AGCTAAATTACAGATCTTATCTCTCTGAAG
61 AGCTAAATTACAGATCTTAT-TCTCTGAAG
* *
20601626 TTACAGTAGAGCAGATCAAAACAGATCTTGTCTCCCTGAAGTTGTAGTGGAATAGAT
1 TTGCAGTAGAGCAGATCAAAACAGATCTTATCTCCCTGAAGTTGTAGTGGAATAGAT
20601683 CGAATACGAT
Statistics
Matches: 250, Mismatches: 55, Indels: 44
0.72 0.16 0.13
Matches are distributed among these distances:
85 1 0.00
86 27 0.11
87 10 0.04
88 55 0.22
89 2 0.01
90 97 0.39
91 3 0.01
92 3 0.01
93 5 0.02
94 45 0.18
95 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (89 bp):
TTGCAGTAGAGCAGATCAAAACAGATCTTATCTCCCTGAAGTTGTAGTGGAATAGATTGAAGCTA
AATTACAGATCTTATTCTCTGAAG
Found at i:20601397 original size:41 final size:41
Alignment explanation
Indices: 20601337--20601415 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
20601327 AAGCTAAATT
* *
20601337 ACAGATCTTATATCTCTGAAGTTGCAGTAGAGTAGATCAAA
1 ACAGATCTTATATCCCTGAAGTTGCAGTAGAATAGATCAAA
* * * *
20601378 ACAGATCTTGTCTCCCTGAAGTTGTAGTGGAATAGATC
1 ACAGATCTTATATCCCTGAAGTTGCAGTAGAATAGATC
20601416 GAAGACGGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (41 bp):
ACAGATCTTATATCCCTGAAGTTGCAGTAGAATAGATCAAA
Found at i:20601415 original size:135 final size:135
Alignment explanation
Indices: 20601245--20601733 Score: 437
Period size: 135 Copynumber: 3.6 Consensus size: 135
20601235 TGAAGATTGT
* * *
20601245 AGATCTTGTTTCCCTGAGATTGCAGTGGAGCAGATCAAATATAGCAAATCTT-ATTTCCCTGAAG
1 AGATCTTGTCTCCCTGAGATTGCAGTGGAACAGATCAAATATAGCAAATCTTGACTT-CCTGAAG
20601309 TTGCAGTGGAACAGATTAAAGCTAAATTACAGATCTTATATCTCTGAAGTTGCAGTAGAGTAGAT
65 TTGCAGTGGAACAGATTAAAGCTAAATTACAGATCTTATATCTCTGAAGTTGCAGTAGAGTAGAT
20601374 CAAAAC
130 CAAAAC
* * * * ** * *
20601380 AGATCTTGTCTCCCTGA-AGTTGTAGTGGAATAGATCGAAGACGGTAAATCTTGCCTTCCTGAAG
1 AGATCTTGTCTCCCTGAGA-TTGCAGTGGAACAGATCAAATATAGCAAATCTTGACTTCCTGAAG
* * * * * * * *
20601444 TTGTAGT-GAAGCAGATTTAAGC-----TAC-CATCCTA-ACTCCCTAAAGTTGTAGTGGAGTAG
65 TTGCAGTGGAA-CAGATTAAAGCTAAATTACAGATCTTATA-TCTCTGAAGTTGCAGTAGAGTA-
* * **
20601501 GCTGAAGATTGT
127 GATCAA-A--AC
* * *
20601513 AGATCTTGTTTCCCTGAGATTGCAGTGGAGCAGATCAAATATAGCAAATCTT-ATTTCCCTGAAG
1 AGATCTTGTCTCCCTGAGATTGCAGTGGAACAGATCAAATATAGCAAATCTTGACTT-CCTGAAG
* * * * *
20601577 TTGCAGTGGAATAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGAT
65 TTGCAGTGGAACAGATTAAAGCTAAATTACAGATCTTATATCTCTGAAGTTGCAGTAGAGTAGAT
20601642 CAAAAC
130 CAAAAC
* * * * * *
20601648 AGATCTTGTCTCCCTGA-AGTTGTAGTGGAATAGATCGAATA-CGATAAATCTTGCCTTCCTGAA
1 AGATCTTGTCTCCCTGAGA-TTGCAGTGGAACAGATCAAATATAG-CAAATCTTGACTTCCTGAA
* *
20601711 GTTGCAGTGAAACAGATTCAAGC
64 GTTGCAGTGGAACAGATTAAAGC
20601734 CACCAAGCCT
Statistics
Matches: 271, Mismatches: 62, Indels: 42
0.72 0.17 0.11
Matches are distributed among these distances:
128 1 0.00
129 23 0.08
130 7 0.03
131 1 0.00
132 2 0.01
133 63 0.23
134 10 0.04
135 131 0.48
136 4 0.01
137 1 0.00
138 7 0.03
139 21 0.08
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (135 bp):
AGATCTTGTCTCCCTGAGATTGCAGTGGAACAGATCAAATATAGCAAATCTTGACTTCCTGAAGT
TGCAGTGGAACAGATTAAAGCTAAATTACAGATCTTATATCTCTGAAGTTGCAGTAGAGTAGATC
AAAAC
Found at i:20601562 original size:133 final size:133
Alignment explanation
Indices: 20601112--20601584 Score: 478
Period size: 133 Copynumber: 3.5 Consensus size: 133
20601102 TCAATTCTAC
* * * * * * *
20601112 AGATCTTGTTTCCCTGAGATTGCAGTGGAGTAGATCGAAGATGGCGAATCTAGGCTTCCTGATGT
1 AGATCTTGTTTCCCTGAGATTGCAGTGGAGCAGATCAAAGATAGCAAATCTTGACTTCCTGAAGT
* *
20601177 TGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAGAT
66 TGCAGTGAAGCAGATTTAAGCTACCATCCTAACTCCCTAAAGTTGTAGTGGAGTAGGCTGAAGAT
20601242 TGT
131 TGT
* *
20601245 AGATCTTGTTTCCCTGAGATTGCAGTGGAGCAGATCAAATATAGCAAATCTT-ATTTCCCTGAAG
1 AGATCTTGTTTCCCTGAGATTGCAGTGGAGCAGATCAAAGATAGCAAATCTTGACTT-CCTGAAG
* * * * * * *
20601309 TTGCAGTGGAA-CAGATTAAAGCTAAATTACAGATCTTATA-TCTCTGAAGTTGCAGTAGAGTA-
65 TTGCAGT-GAAGCAGATTTAAGC-----TAC-CATCCTA-ACTCCCTAAAGTTGTAGTGGAGTAG
* * **
20601371 GATCAA-A--AC
122 GCTGAAGATTGT
* * ** * ** * *
20601380 AGATCTTGTCTCCCTGA-AGTTGTAGTGGAATAGATCGAAGACGGTAAATCTTGCCTTCCTGAAG
1 AGATCTTGTTTCCCTGAGA-TTGCAGTGGAGCAGATCAAAGATAGCAAATCTTGACTTCCTGAAG
*
20601444 TTGTAGTGAAGCAGATTTAAGCTACCATCCTAACTCCCTAAAGTTGTAGTGGAGTAGGCTGAAGA
65 TTGCAGTGAAGCAGATTTAAGCTACCATCCTAACTCCCTAAAGTTGTAGTGGAGTAGGCTGAAGA
20601509 TTGT
130 TTGT
* *
20601513 AGATCTTGTTTCCCTGAGATTGCAGTGGAGCAGATCAAATATAGCAAATCTT-ATTTCCCTGAAG
1 AGATCTTGTTTCCCTGAGATTGCAGTGGAGCAGATCAAAGATAGCAAATCTTGACTT-CCTGAAG
20601577 TTGCAGTG
65 TTGCAGTG
20601585 GAATAGATTG
Statistics
Matches: 264, Mismatches: 57, Indels: 38
0.74 0.16 0.11
Matches are distributed among these distances:
128 1 0.00
129 23 0.09
130 7 0.03
131 1 0.00
132 4 0.02
133 124 0.47
134 8 0.03
135 64 0.24
136 2 0.01
137 1 0.00
138 6 0.02
139 23 0.09
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (133 bp):
AGATCTTGTTTCCCTGAGATTGCAGTGGAGCAGATCAAAGATAGCAAATCTTGACTTCCTGAAGT
TGCAGTGAAGCAGATTTAAGCTACCATCCTAACTCCCTAAAGTTGTAGTGGAGTAGGCTGAAGAT
TGT
Found at i:20601587 original size:268 final size:268
Alignment explanation
Indices: 20601110--20601738 Score: 1053
Period size: 268 Copynumber: 2.3 Consensus size: 268
20601100 GATCAATTCT
* * * * ** * *
20601110 ACAGATCTTGTTTCCCTG-AGATTGCAGTGGAGTAGATCGAAGATGGCGAATCTAGGCTTCCTGA
1 ACAGATCTTGTCTCCCTGAAG-TTGTAGTGGAATAGATCGAAGACGGTAAATCTTGCCTTCCTGA
* *
20601174 TGTTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAA
65 AGTTGCAGTGAAGCAGATTTAAGCCACCATCCTAACTCCCTAAAGTTGTAGTGGAGTAGGCTGAA
20601239 GATTGTAGATCTTGTTTCCCTGAGATTGCAGTGGAGCAGATCAAATATAGCAAATCTTATTTCCC
130 GATTGTAGATCTTGTTTCCCTGAGATTGCAGTGGAGCAGATCAAATATAGCAAATCTTATTTCCC
*
20601304 TGAAGTTGCAGTGGAACAGATTAAAGCTAAATTACAGATCTTATATCTCTGAAGTTGCAGTAGAG
195 TGAAGTTGCAGTGGAACAGATTAAAGCTAAATTACAGATCTTATATCTCTGAAGTTACAGTAGAG
*
20601369 TAGATCAAA
260 CAGATCAAA
20601378 ACAGATCTTGTCTCCCTGAAGTTGTAGTGGAATAGATCGAAGACGGTAAATCTTGCCTTCCTGAA
1 ACAGATCTTGTCTCCCTGAAGTTGTAGTGGAATAGATCGAAGACGGTAAATCTTGCCTTCCTGAA
* *
20601443 GTTGTAGTGAAGCAGATTTAAGCTACCATCCTAACTCCCTAAAGTTGTAGTGGAGTAGGCTGAAG
66 GTTGCAGTGAAGCAGATTTAAGCCACCATCCTAACTCCCTAAAGTTGTAGTGGAGTAGGCTGAAG
20601508 ATTGTAGATCTTGTTTCCCTGAGATTGCAGTGGAGCAGATCAAATATAGCAAATCTTATTTCCCT
131 ATTGTAGATCTTGTTTCCCTGAGATTGCAGTGGAGCAGATCAAATATAGCAAATCTTATTTCCCT
* * *
20601573 GAAGTTGCAGTGGAATAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTACAGTAGAGC
196 GAAGTTGCAGTGGAACAGATTAAAGCTAAATTACAGATCTTATATCTCTGAAGTTACAGTAGAGC
20601638 AGATCAAA
261 AGATCAAA
* *
20601646 ACAGATCTTGTCTCCCTGAAGTTGTAGTGGAATAGATCGAATACGATAAATCTTGCCTTCCTGAA
1 ACAGATCTTGTCTCCCTGAAGTTGTAGTGGAATAGATCGAAGACGGTAAATCTTGCCTTCCTGAA
* *
20601711 GTTGCAGTGAAACAGATTCAAGCCACCA
66 GTTGCAGTGAAGCAGATTTAAGCCACCA
20601739 AGCCTTAATC
Statistics
Matches: 337, Mismatches: 23, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
268 335 0.99
269 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (268 bp):
ACAGATCTTGTCTCCCTGAAGTTGTAGTGGAATAGATCGAAGACGGTAAATCTTGCCTTCCTGAA
GTTGCAGTGAAGCAGATTTAAGCCACCATCCTAACTCCCTAAAGTTGTAGTGGAGTAGGCTGAAG
ATTGTAGATCTTGTTTCCCTGAGATTGCAGTGGAGCAGATCAAATATAGCAAATCTTATTTCCCT
GAAGTTGCAGTGGAACAGATTAAAGCTAAATTACAGATCTTATATCTCTGAAGTTACAGTAGAGC
AGATCAAA
Found at i:20601797 original size:89 final size:89
Alignment explanation
Indices: 20601693--20601867 Score: 298
Period size: 89 Copynumber: 2.0 Consensus size: 89
20601683 CGAATACGAT
*
20601693 AAATCTTGCCTTCCTGAAGTTGCAGTGAAACAGATTCAAGCCACCAAGCCTTAATCC-CCTAAGC
1 AAATCTTACCTTCCTGAAGTTGCAGTGAAACAGATTCAAGCCACCAAGCCTTAA-CCTCCTAAGC
*
20601757 AGTAGGGTAATAGGCTGAAAATTAC
65 AATAGGGTAATAGGCTGAAAATTAC
* *
20601782 AAATCTTACCTTCCTGAAGTTGCAGTGAAGCAGATTCAAGCCACCAAGCCTTAACCTCCTAAGTA
1 AAATCTTACCTTCCTGAAGTTGCAGTGAAACAGATTCAAGCCACCAAGCCTTAACCTCCTAAGCA
20601847 ATAGGGTAATAGGCTGAAAAT
66 ATAGGGTAATAGGCTGAAAAT
20601868 CACTAGTCTT
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
88 2 0.02
89 79 0.98
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (89 bp):
AAATCTTACCTTCCTGAAGTTGCAGTGAAACAGATTCAAGCCACCAAGCCTTAACCTCCTAAGCA
ATAGGGTAATAGGCTGAAAATTAC
Found at i:20601878 original size:89 final size:89
Alignment explanation
Indices: 20601693--20601888 Score: 295
Period size: 89 Copynumber: 2.2 Consensus size: 89
20601683 CGAATACGAT
*
20601693 AAATCTTGCCTTCCTGAAGTTGCAGTGAAACAGATTCAAGCCACCAAGCCTTAATCCCCTAAGCA
1 AAATCTTACCTTCCTGAAGTTGCAGTGAAACAGATTCAAGCCACCAAGCCTTAATCCCCTAAGCA
* *
20601758 GTAGGGTAATAGGCTGAAAATTAC
66 ATAGGGTAATAGGCTGAAAATCAC
* *
20601782 AAATCTTACCTTCCTGAAGTTGCAGTGAAGCAGATTCAAGCCACCAAGCCTTAA-CCTCCTAAGT
1 AAATCTTACCTTCCTGAAGTTGCAGTGAAACAGATTCAAGCCACCAAGCCTTAATCC-CCTAAGC
20601846 AATAGGGTAATAGGCTGAAAATCAC
65 AATAGGGTAATAGGCTGAAAATCAC
* * * *
20601871 TAGTCTTATCTCCCTGAA
1 AAATCTTACCTTCCTGAA
20601889 ATTGAGCAGA
Statistics
Matches: 97, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
88 2 0.02
89 95 0.98
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (89 bp):
AAATCTTACCTTCCTGAAGTTGCAGTGAAACAGATTCAAGCCACCAAGCCTTAATCCCCTAAGCA
ATAGGGTAATAGGCTGAAAATCAC
Found at i:20603602 original size:12 final size:11
Alignment explanation
Indices: 20603565--20603632 Score: 55
Period size: 12 Copynumber: 5.7 Consensus size: 11
20603555 TTATGTACAC
20603565 ATTATTTATATT
1 ATTA-TTATATT
* *
20603577 ATTTTTACTACT
1 ATTATTA-TATT
20603589 ATTATTATATCT
1 ATTATTATAT-T
20603601 ATTATTAGTATT
1 ATTATTA-TATT
*
20603613 AGTATTATAATT
1 ATTATTAT-ATT
*
20603625 ACTATTAT
1 ATTATTAT
20603633 TACACTTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
11 6 0.13
12 37 0.80
13 3 0.07
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTATTATATT
Found at i:20603837 original size:19 final size:20
Alignment explanation
Indices: 20603813--20603868 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
20603803 TTTTTAAAAC
20603813 TATATTATGTATATATA-TA
1 TATATTATGTATATATATTA
* *
20603832 TATATTATATATATTTATTA
1 TATATTATGTATATATATTA
*
20603852 TATTTTTATGTATATAT
1 TA-TATTATGTATATAT
20603869 TTTTAATATC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 15 0.50
20 4 0.13
21 11 0.37
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (20 bp):
TATATTATGTATATATATTA
Found at i:20603840 original size:13 final size:13
Alignment explanation
Indices: 20603824--20603854 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
20603814 ATATTATGTA
20603824 TATATATATATAT
1 TATATATATATAT
*
20603837 TATATATATTTAT
1 TATATATATATAT
20603850 TATAT
1 TATAT
20603855 TTTTATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATATATATATAT
Found at i:20603840 original size:15 final size:14
Alignment explanation
Indices: 20603792--20603893 Score: 64
Period size: 15 Copynumber: 7.7 Consensus size: 14
20603782 AATGTGTATG
20603792 TATTATATATAT-T
1 TATTATATATATAT
*
20603805 T-TTA-AAACTATAT
1 TATTATATA-TATAT
20603818 TATGTATATATATAT
1 TAT-TATATATATAT
20603833 ATATTATATATAT-T
1 -TATTATATATATAT
20603847 TATTATAT-T-T-T
1 TATTATATATATAT
*
20603858 TA-TGTATATAT-T
1 TATTATATATATAT
20603870 T-TTA-ATATCATAT
1 TATTATATAT-ATAT
20603883 TATTCATATAT
1 TATT-ATATAT
20603894 TTTTTATATT
Statistics
Matches: 71, Mismatches: 4, Indels: 25
0.71 0.04 0.25
Matches are distributed among these distances:
10 4 0.06
11 11 0.15
12 13 0.18
13 13 0.18
14 4 0.06
15 17 0.24
16 9 0.13
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (14 bp):
TATTATATATATAT
Found at i:20603882 original size:14 final size:14
Alignment explanation
Indices: 20603795--20603902 Score: 56
Period size: 14 Copynumber: 8.2 Consensus size: 14
20603785 GTGTATGTAT
20603795 TATATATATTTTTA
1 TATATATATTTTTA
* *
20603809 -AAACTATATTATGTA
1 TATA-TATATT-TTTA
*
20603824 TATATATA--TATA
1 TATATATATTTTTA
*
20603836 T-TATATA-TATT-
1 TATATATATTTTTA
20603847 TAT-TATATTTTTA
1 TATATATATTTTTA
*
20603860 TGTATATATTTTTA
1 TATATATATTTTTA
*
20603874 -ATATCATATTATT-
1 TATAT-ATATTTTTA
*
20603887 CATATAT-TTTTTA
1 TATATATATTTTTA
20603900 TAT
1 TAT
20603903 TATGTAAATA
Statistics
Matches: 71, Mismatches: 12, Indels: 23
0.67 0.11 0.22
Matches are distributed among these distances:
11 11 0.15
12 13 0.18
13 11 0.15
14 27 0.38
15 7 0.10
16 2 0.03
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (14 bp):
TATATATATTTTTA
Found at i:20603885 original size:25 final size:25
Alignment explanation
Indices: 20603857--20603942 Score: 78
Period size: 25 Copynumber: 3.6 Consensus size: 25
20603847 TATTATATTT
20603857 TTATGTATATATTTTTAATATCATA
1 TTATGTATATATTTTTAATATCATA
20603882 TTAT-TCATATA-TTTT--T-T-ATA
1 TTATGT-ATATATTTTTAATATCATA
* * *
20603902 TTATGTAAATATTTTCAATA-CTACA
1 TTATGTATATATTTTTAATATC-ATA
20603927 TTATGTATATATTTTT
1 TTATGTATATATTTTT
20603943 GTCTATATTG
Statistics
Matches: 48, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
20 11 0.23
21 5 0.10
22 1 0.02
23 1 0.02
24 5 0.10
25 25 0.52
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (25 bp):
TTATGTATATATTTTTAATATCATA
Found at i:20603900 original size:40 final size:40
Alignment explanation
Indices: 20603817--20603897 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 40
20603807 TAAAACTATA
* *
20603817 TTATGTATATATATATATATTATATATATTTATTATATTT
1 TTATGTATATATATATATATCATATATATTCATTATATTT
* *
20603857 TTATGTATATATTTTTAATATCATAT-TATTCA-TATATTT
1 TTATGTATATATATAT-ATATCATATATATTCATTATATTT
20603896 TT
1 TT
20603898 TATATTATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 9 0.25
40 19 0.53
41 8 0.22
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (40 bp):
TTATGTATATATATATATATCATATATATTCATTATATTT
Found at i:20603930 original size:45 final size:45
Alignment explanation
Indices: 20603839--20603942 Score: 113
Period size: 45 Copynumber: 2.2 Consensus size: 45
20603829 ATATATATTA
* * * *
20603839 TATATATTTATTATATTTTTATGTATATATTTTTAATATCATATTAT-
1 TATATATTT-TT-TA-TATTATGTAAATATTTTCAATATCACATTATG
20603886 TCATATATTTTTTATATTATGTAAATATTTTCAATA-CTACATTATG
1 T-ATATATTTTTTATATTATGTAAATATTTTCAATATC-ACATTATG
20603932 TATATATTTTT
1 TATATATTTTT
20603943 GTCTATATTG
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
44 1 0.02
45 35 0.70
46 3 0.06
47 3 0.06
48 8 0.16
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.59
Consensus pattern (45 bp):
TATATATTTTTTATATTATGTAAATATTTTCAATATCACATTATG
Found at i:20604219 original size:26 final size:26
Alignment explanation
Indices: 20604189--20604240 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
20604179 ATTATGTATA
*
20604189 TATTTTTAATACTACGTATACATTTT
1 TATTTCTAATACTACGTATACATTTT
* * *
20604215 TATTTCTATTATTACGTATATATTTT
1 TATTTCTAATACTACGTATACATTTT
20604241 AATACATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.58
Consensus pattern (26 bp):
TATTTCTAATACTACGTATACATTTT
Found at i:20609950 original size:17 final size:16
Alignment explanation
Indices: 20609924--20609959 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
20609914 TAATCTAATT
20609924 TATTTGATATATTCAAA
1 TATTTGATATATT-AAA
*
20609941 TATTTTATATATTAAA
1 TATTTGATATATTAAA
20609957 TAT
1 TAT
20609960 ATTCAAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (16 bp):
TATTTGATATATTAAA
Found at i:20610195 original size:19 final size:19
Alignment explanation
Indices: 20610157--20610199 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
20610147 AAACAGATCC
*
20610157 TTAAATTGTAACTCTTATT
1 TTAAATTGTAACTCTAATT
20610176 TTAAATTGTAAC-CTGAATT
1 TTAAATTGTAACTCT-AATT
20610195 TTAAA
1 TTAAA
20610200 GTATTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (19 bp):
TTAAATTGTAACTCTAATT
Found at i:20610392 original size:17 final size:17
Alignment explanation
Indices: 20610355--20610393 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
20610345 GTGTAGCGTT
20610355 TAAAA-TAAAAATAAAA
1 TAAAACTAAAAATAAAA
* *
20610371 AAAAACTAAAAATAAAG
1 TAAAACTAAAAATAAAA
20610388 TAAAAC
1 TAAAAC
20610394 CGAAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (17 bp):
TAAAACTAAAAATAAAA
Found at i:20613562 original size:37 final size:36
Alignment explanation
Indices: 20613511--20613580 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
20613501 ATTCCAAAAA
*
20613511 TAATATTATTTTAATAGT-TTATTATTAAATTAAATT
1 TAATATTATCTTAATAGTATT-TTATTAAATTAAATT
*
20613547 TAATAATTATCTTAATAGTATTTTATTAATTTAA
1 TAAT-ATTATCTTAATAGTATTTTATTAAATTAA
20613581 TATTAAAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 4 0.13
37 24 0.80
38 2 0.07
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (36 bp):
TAATATTATCTTAATAGTATTTTATTAAATTAAATT
Found at i:20613690 original size:23 final size:24
Alignment explanation
Indices: 20613657--20613706 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
20613647 TTTTAATAAG
*
20613657 ATTTAATATTAAATTTAATCTAAT
1 ATTTAATATTAAATTAAATCTAAT
* *
20613681 ATTT-ATATTAGATTAAATTTAAT
1 ATTTAATATTAAATTAAATCTAAT
20613704 ATT
1 ATT
20613707 AAAGTGATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
ATTTAATATTAAATTAAATCTAAT
Found at i:20616268 original size:33 final size:33
Alignment explanation
Indices: 20616177--20616386 Score: 199
Period size: 33 Copynumber: 6.4 Consensus size: 33
20616167 TTTTTGATGG
* * * * * *
20616177 ACCTTTCCTTTTCCAGTTGTACACTCGAGGTAT
1 ACCTTTCCTTTTCAAGTGGTATACACAAAGTAT
* * * *
20616210 ACGTTT-ATTTTCGAGTGGTACACACAAAGTAT
1 ACCTTTCCTTTTCAAGTGGTATACACAAAGTAT
* * *
20616242 GCCTTTCCTTTTCAAATGATATACACAAAGTAT
1 ACCTTTCCTTTTCAAGTGGTATACACAAAGTAT
** * * *
20616275 ACCTAACCTTTCCAAGT-GTACACACAAAGTGT
1 ACCTTTCCTTTTCAAGTGGTATACACAAAGTAT
* * *
20616307 ACATATCCTTTTCAATTGGTATACACAAAGTAT
1 ACCTTTCCTTTTCAAGTGGTATACACAAAGTAT
* *
20616340 ACCTTTCATTTTCTAGTGGTATACACAAAGTAT
1 ACCTTTCCTTTTCAAGTGGTATACACAAAGTAT
20616373 ACCTTTCCTTTTCA
1 ACCTTTCCTTTTCA
20616387 CATTCGATAG
Statistics
Matches: 140, Mismatches: 35, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
32 49 0.35
33 91 0.65
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (33 bp):
ACCTTTCCTTTTCAAGTGGTATACACAAAGTAT
Found at i:20616275 original size:65 final size:64
Alignment explanation
Indices: 20616206--20616386 Score: 202
Period size: 65 Copynumber: 2.8 Consensus size: 64
20616196 TACACTCGAG
* *
20616206 GTATACGTTTATTTTCGAGTGGTACACACAAAGTATGCCTTTCCTTTTCAAATGATATACACAAA
1 GTATAC-TTTATTTTCAAGTGGTACACACAAAGTATACCTTTCCTTTTCAAATGATATACACAAA
* * * * * * * *
20616271 GTATACCTAACCTTTCCAAGT-GTACACACAAAGTGTACATATCCTTTTCAATTGGTATACACAA
1 GTATACTTTA--TTTTCAAGTGGTACACACAAAGTATACCTTTCCTTTTCAAATGATATACACAA
20616335 A
64 A
* *
20616336 GTATACCTTTCATTTTCTAGTGGTATACACAAAGTATACCTTTCCTTTTCA
1 GTATA-CTTT-ATTTTCAAGTGGTACACACAAAGTATACCTTTCCTTTTCA
20616387 CATTCGATAG
Statistics
Matches: 93, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
64 2 0.02
65 56 0.60
66 34 0.37
67 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (64 bp):
GTATACTTTATTTTCAAGTGGTACACACAAAGTATACCTTTCCTTTTCAAATGATATACACAAA
Found at i:20616424 original size:29 final size:29
Alignment explanation
Indices: 20616379--20616506 Score: 211
Period size: 29 Copynumber: 4.4 Consensus size: 29
20616369 GTATACCTTT
20616379 CCTTTTCACATTCGATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
*
20616408 CCTTTTCACATTTGATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
20616437 CCTTTTCACATTCGATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
* * **
20616466 CTTTTTCACATTCAATAGTAGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
20616495 CCTTTTCACATT
1 CCTTTTCACATT
20616507 GTACACACAA
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 92 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (29 bp):
CCTTTTCACATTCGATAGCCGAAGCTATC
Found at i:20617976 original size:21 final size:21
Alignment explanation
Indices: 20617952--20618021 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
20617942 TAAGTTCATG
*
20617952 AATAAACCACTAGTATTTGCA
1 AATAAACCACTAGTGTTTGCA
* *
20617973 AATAAACCACCAATGTTTGCA
1 AATAAACCACTAGTGTTTGCA
* *
20617994 GATAAACCACTAGTGTTTGTA
1 AATAAACCACTAGTGTTTGCA
*
20618015 GATAAAC
1 AATAAAC
20618022 TGCTTGTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (21 bp):
AATAAACCACTAGTGTTTGCA
Found at i:20628035 original size:17 final size:17
Alignment explanation
Indices: 20628015--20628113 Score: 144
Period size: 17 Copynumber: 5.6 Consensus size: 17
20628005 TAATGATATG
20628015 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
20628032 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
20628050 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
20628067 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
20628085 CAATCTTAGATATGATATA
1 CAATCTTAGATATG--ATA
20628104 CAATCTTAGA
1 CAATCTTAGA
20628114 AGATATGATT
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
17 31 0.42
18 31 0.42
19 11 0.15
20 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:20628053 original size:35 final size:35
Alignment explanation
Indices: 20628007--20628113 Score: 187
Period size: 35 Copynumber: 3.0 Consensus size: 35
20627997 ATAATCTTTA
20628007 ATGATATGCAATCTTAGATATGATACAATCTTAGAT
1 ATGAT-TGCAATCTTAGATATGATACAATCTTAGAT
20628043 ATGATTGCAATCTTAGATATGATACAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATACAATCTTAGAT
20628078 ATGATTGCAATCTTAGATATGATATACAATCTTAGA
1 ATGATTGCAATCTTAGATATG--ATACAATCTTAGA
20628114 AGATATGATT
Statistics
Matches: 69, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
35 51 0.74
36 5 0.07
37 13 0.19
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (35 bp):
ATGATTGCAATCTTAGATATGATACAATCTTAGAT
Found at i:20628055 original size:18 final size:18
Alignment explanation
Indices: 20628015--20628113 Score: 157
Period size: 18 Copynumber: 5.6 Consensus size: 18
20628005 TAATGATATG
20628015 CAATCTTAGATATGA-TA
1 CAATCTTAGATATGATTA
*
20628032 CAATCTTAGATATGATTG
1 CAATCTTAGATATGATTA
20628050 CAATCTTAGATATGA-TA
1 CAATCTTAGATATGATTA
*
20628067 CAATCTTAGATATGATTG
1 CAATCTTAGATATGATTA
20628085 CAATCTTAGATATGATATA
1 CAATCTTAGATATGAT-TA
20628104 CAATCTTAGA
1 CAATCTTAGA
20628114 AGATATGATT
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
17 31 0.41
18 33 0.44
19 11 0.15
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (18 bp):
CAATCTTAGATATGATTA
Found at i:20628678 original size:26 final size:26
Alignment explanation
Indices: 20628630--20628679 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
20628620 TTATAAATAT
* * * *
20628630 ATTTTTTATTATATATTATATTTTAA
1 ATTTATTATTAAATATCACATTTTAA
20628656 ATTTATTATTAAATATCACATTTT
1 ATTTATTATTAAATATCACATTTT
20628680 TTTATATGCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTATTATTAAATATCACATTTTAA
Found at i:20631706 original size:26 final size:25
Alignment explanation
Indices: 20631677--20631734 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
20631667 AGAAGATAAG
*
20631677 GAAAAGGAAAGGAAAAAGAATAGAAA
1 GAAAAGAAAAGGAAAAAGAAT-GAAA
* * *
20631703 GAAAAAAAAATGAAAAGGAATGAAA
1 GAAAAGAAAAGGAAAAAGAATGAAA
20631728 GAAAAGA
1 GAAAAGA
20631735 GAATAAGGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.05
Consensus pattern (25 bp):
GAAAAGAAAAGGAAAAAGAATGAAA
Found at i:20632052 original size:28 final size:29
Alignment explanation
Indices: 20632021--20632079 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
20632011 TTGAAAATAT
* *
20632021 AATAAAAAGTGATTAT-ATTAAAATTAAA
1 AATAAAAAGTAATTATGATTAAAAATAAA
*
20632049 AATAAAATGTAATTATGATTAAAAATAAA
1 AATAAAAAGTAATTATGATTAAAAATAAA
20632078 AA
1 AA
20632080 AAATATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.31
Consensus pattern (29 bp):
AATAAAAAGTAATTATGATTAAAAATAAA
Found at i:20638705 original size:35 final size:34
Alignment explanation
Indices: 20638639--20638705 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 34
20638629 TAATTAATAA
** *
20638639 TTATTTTTTTAAATTCTTTTTATTTACTAATTTG
1 TTATTTTTTTAAATTCTTTGCATATACTAATTTG
20638673 TTATTTTTTTAAAAATTCTTTGCATATA-TAATT
1 TTATTTTTTT--AAATTCTTTGCATATACTAATT
20638706 AATGATTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 10 0.36
35 5 0.18
36 13 0.46
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (34 bp):
TTATTTTTTTAAATTCTTTGCATATACTAATTTG
Found at i:20645772 original size:32 final size:30
Alignment explanation
Indices: 20645707--20645777 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 30
20645697 TAGATAAAAC
* * *
20645707 AATTCATTATAATTTTTTTATTATCATATA
1 AATTCATTATAAATTTTTTAATATAATATA
20645737 AATTCATTTAATAAATTTTTTAATATAATCA-A
1 AATTCA-TT-ATAAATTTTTTAATATAAT-ATA
20645769 AATTC-TTAT
1 AATTCATTAT
20645778 TTGTAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
29 2 0.06
30 8 0.23
31 2 0.06
32 22 0.63
33 1 0.03
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (30 bp):
AATTCATTATAAATTTTTTAATATAATATA
Done.