Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 202 of 378
Found at i:59750958 original size:324 final size:324
Alignment explanation
Indices: 59750369--59751000 Score: 1183
Period size: 324 Copynumber: 2.0 Consensus size: 324
59750359 CCTTTTTAGC
59750369 CATTTTCACTAGAAATCACTTAGTAAAAGATGTTTATCACACATCAAACATTCATATTCTGTAAC
1 CATTTTCACTAGAAATCACTTAGTAAAAGATGTTTATCACACATCAAACATTCATATTCTGTAAC
59750434 GCCCCAAATTTGGGGCCTGGAAGTATTAGGTCTTGAGCACGGAAACAATTAGGAGGTTGCACATA
66 GCCCCAAATTTGGGGCCTGGAAGTATTAGGTCTTGAGCACGGAAACAATTAGGAGGTTGCACATA
* *
59750499 AATGTTTAGTTGTGCAAGAAAGTGACACAATTGTCTGTTTGCCTCAGTGTTTATGTGTTTTGGGA
131 AATGTTTAGTTGTGCAAGAAAGTGACACAATTGTCTGTCTGCCTCACTGTTTATGTGTTTTGGGA
*
59750564 AGTGTTTGAGAAGTCTTGGGTTCAAGCCTGGGGATGTGCAAAAAGTTTTGTTTTTAAAGGTTAAA
196 AGTGTTTGAGAAGTCTTGGGTTCAAGCCTGGGGATGTGAAAAAAGTTTTGTTTTTAAAGGTTAAA
*
59750629 GCTCTATCGATAGTTAATAGGCTTATAAATAAACGTGGGTCAAAGATGTTTATCGCACATCAAA
261 GCTCTATCGATAGTTAATAGGCTTATAAATAAACGTGGGTAAAAGATGTTTATCGCACATCAAA
59750693 CATTTTCACTAGAAATCACTTAGTAAAAGATGTTTATCACACATCAAACATTCATATTCTGTAAC
1 CATTTTCACTAGAAATCACTTAGTAAAAGATGTTTATCACACATCAAACATTCATATTCTGTAAC
* *
59750758 GCCCCAAATTTGGGGCCTGGAAGTATTAGGTCTTGAGCATGGGAACAATTAGGAGGTTGCACATA
66 GCCCCAAATTTGGGGCCTGGAAGTATTAGGTCTTGAGCACGGAAACAATTAGGAGGTTGCACATA
59750823 AATGTTTAGTTGTGCAAGAAAGTGACACAATTGTCTGTCTGCCTCACTGTTTATGTGTTTTGGGA
131 AATGTTTAGTTGTGCAAGAAAGTGACACAATTGTCTGTCTGCCTCACTGTTTATGTGTTTTGGGA
*
59750888 AGTGTTTGAGAAGTCTTGGGTTCAAGCCTGGGGATGTGAAAAAAGTTTTGTTTTTAATGGTTAAA
196 AGTGTTTGAGAAGTCTTGGGTTCAAGCCTGGGGATGTGAAAAAAGTTTTGTTTTTAAAGGTTAAA
* *
59750953 GCTCTATCGATAGTTAGTAGGCTTATAAATAAATGTGGGTAAAAGATG
261 GCTCTATCGATAGTTAATAGGCTTATAAATAAACGTGGGTAAAAGATG
59751001 ATAGAAAGGG
Statistics
Matches: 299, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
324 299 1.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.33
Consensus pattern (324 bp):
CATTTTCACTAGAAATCACTTAGTAAAAGATGTTTATCACACATCAAACATTCATATTCTGTAAC
GCCCCAAATTTGGGGCCTGGAAGTATTAGGTCTTGAGCACGGAAACAATTAGGAGGTTGCACATA
AATGTTTAGTTGTGCAAGAAAGTGACACAATTGTCTGTCTGCCTCACTGTTTATGTGTTTTGGGA
AGTGTTTGAGAAGTCTTGGGTTCAAGCCTGGGGATGTGAAAAAAGTTTTGTTTTTAAAGGTTAAA
GCTCTATCGATAGTTAATAGGCTTATAAATAAACGTGGGTAAAAGATGTTTATCGCACATCAAA
Found at i:59755406 original size:17 final size:18
Alignment explanation
Indices: 59755364--59755412 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
59755354 AGTTGAAAAG
59755364 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
59755383 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
59755400 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
59755413 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:59756301 original size:40 final size:40
Alignment explanation
Indices: 59756235--59756401 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
59756225 AAATTGAATG
* * *
59756235 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
59756274 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
59756314 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
59756354 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
59756394 ATATCCGG
1 ATATCCGG
59756402 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:59766679 original size:17 final size:18
Alignment explanation
Indices: 59766637--59766685 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
59766627 AGTTGAAAAG
59766637 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
59766656 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
59766673 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
59766686 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:59767572 original size:40 final size:40
Alignment explanation
Indices: 59767506--59767672 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
59767496 AAATTGAATG
* * *
59767506 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
59767545 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
59767585 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
59767625 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
59767665 ATATCCGG
1 ATATCCGG
59767673 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:59775077 original size:55 final size:54
Alignment explanation
Indices: 59774948--59775144 Score: 263
Period size: 54 Copynumber: 3.6 Consensus size: 54
59774938 TTGGTAAGAT
* * *
59774948 AAGGATATCATGTAAGACCATGACAAGACATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTCTATAAGGC
* * *
59775002 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGCTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAG-TTCTATAAGGC
* * * * *
59775057 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGATTTC-ATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTCTATAAGGC
59775110 AAGGATACCATGTAAGACCATGTCAAGACATGGCA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCA
59775145 ATGGTAAGCT
Statistics
Matches: 125, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
52 4 0.03
53 34 0.27
54 42 0.34
55 41 0.33
56 4 0.03
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTCTATAAGGC
Found at i:59777630 original size:27 final size:26
Alignment explanation
Indices: 59777600--59777691 Score: 123
Period size: 27 Copynumber: 3.5 Consensus size: 26
59777590 AACAAAGCTG
*
59777600 CTAGTAACAATATATGTGGCAAAGCCA
1 CTAGTAACAGTA-ATGTGGCAAAGCCA
*
59777627 CTAGTATCAGTAAATGTGGCAAAGCCA
1 CTAGTAACAGT-AATGTGGCAAAGCCA
59777654 CTAGTAACAGTAATTGTGGCAAAGCCA
1 CTAGTAACAGTAA-TGTGGCAAAGCCA
*
59777681 CCAGT-ACAGTA
1 CTAGTAACAGTA
59777692 CTTCCTCCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
26 8 0.14
27 50 0.85
28 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.22
Consensus pattern (26 bp):
CTAGTAACAGTAATGTGGCAAAGCCA
Found at i:59783582 original size:30 final size:31
Alignment explanation
Indices: 59783541--59783601 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
59783531 TTTCTGAGCC
* *
59783541 TAGGGGCAAAATCGTAATTCTGT-AAAGTTT
1 TAGGGGAAAAATCATAATTCTGTCAAAGTTT
* *
59783571 TAGGGGAAAAATTATAATTTTGTCAAAGTTT
1 TAGGGGAAAAATCATAATTCTGTCAAAGTTT
59783602 GAGTTAGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (31 bp):
TAGGGGAAAAATCATAATTCTGTCAAAGTTT
Found at i:59785342 original size:27 final size:27
Alignment explanation
Indices: 59785304--59785590 Score: 385
Period size: 27 Copynumber: 10.6 Consensus size: 27
59785294 TCAATTTACC
59785304 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * * *
59785331 AAATCACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
59785358 AAATCACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* **
59785385 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
59785412 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * * *
59785439 AAATTACTAAAATACCCTTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
59785466 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
59785493 AAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
59785520 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
59785547 AAATTACCAAAATACCCCCGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
*
59785574 AAATTACTAAAATACCC
1 AAATTACCAAAATACCC
59785591 TCGACCTGTA
Statistics
Matches: 229, Mismatches: 31, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 229 1.00
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:59785604 original size:27 final size:27
Alignment explanation
Indices: 59785304--59785643 Score: 192
Period size: 27 Copynumber: 12.6 Consensus size: 27
59785294 TCAATTTACC
* **
59785304 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACTAAAATACCCTC-GACTTGTA
* * ** *
59785331 AAATCACTAAAATACCCTTGGTTTATA
1 AAATTACTAAAATACCCTCGACTTGTA
* * **
59785358 AAATCACCAAAATACCC-CTGGTTTGTA
1 AAATTACTAAAATACCCTC-GACTTGTA
* * ** **
59785385 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACTAAAATACCCTCGACTTGTA
* * *
59785412 AAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACTAAAATACCCTCGA-CTTGTA
* * *
59785439 AAATTACTAAAATACCCTTTG-TTTATA
1 AAATTACTAAAATACCC-TCGACTTGTA
* **
59785466 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACTAAAATACCCTC-GACTTGTA
* *
59785493 AAATTA-TCAAAATACCC-CTAGTTTGTA
1 AAATTACT-AAAATACCCTCGA-CTTGTA
* * *
59785520 AAATTACCAAAATACCC-CTGATTTGTG
1 AAATTACTAAAATACCCTC-GACTTGTA
* * * *
59785547 AAATTACCAAAATACCCCCGATTTGTG
1 AAATTACTAAAATACCCTCGACTTGTA
*
59785574 AAATTACTAAAATACCCTCGACCTGTA
1 AAATTACTAAAATACCCTCGACTTGTA
* *
59785601 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACTAAAATACCCTCGACTTGTA
*
59785628 AAATTACTAAAGTACC
1 AAATTACTAAAATACC
59785644 ATTGATTTAC
Statistics
Matches: 260, Mismatches: 40, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
26 1 0.00
27 257 0.99
28 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
AAATTACTAAAATACCCTCGACTTGTA
Found at i:59785614 original size:81 final size:81
Alignment explanation
Indices: 59785304--59785643 Score: 366
Period size: 81 Copynumber: 4.2 Consensus size: 81
59785294 TCAATTTACC
* * * *
59785304 AAATTACCAAAATACCCCTGGTTTGTAAAATCACTAAAATACCCTTG-GTTTATAAAATCACCAA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCC-CGAGTTTGTAAAATTACCAA
*
59785368 AATACCCCTGGTTTGTA
65 AATACCCCTGATTTGTA
* ** * * *
59785385 AAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCCGAGTTTGTAAAATTACCAAA
* *
59785450 ATACCCTTTG-TTTATA
66 ATACCC-CTGATTTGTA
*
59785466 AAATTACCAAAATACCCCTGGTTTGTAAAATTA-TCAAAATACCCCTAGTTTGTAAAATTACCAA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACT-AAAATACCCCGAGTTTGTAAAATTACCAA
*
59785530 AATACCCCTGATTTGTG
65 AATACCCCTGATTTGTA
* * * ** ***
59785547 AAATTACCAAAATACCCCCGATTTGTGAAATTACTAAAATACCCTCGA-CCTGTAAAATTATTGA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCC-CGAGTTTGTAAAATTACCAA
*
59785611 AATA-CCCTCGACTTGTA
65 AATACCCCT-GATTTGTA
* *
59785628 AAATTACTAAAGTACC
1 AAATTACCAAAATACC
59785644 ATTGATTTAC
Statistics
Matches: 219, Mismatches: 33, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
80 6 0.03
81 208 0.95
82 5 0.02
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (81 bp):
AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCCGAGTTTGTAAAATTACCAAA
ATACCCCTGATTTGTA
Found at i:59785716 original size:27 final size:27
Alignment explanation
Indices: 59785686--59785900 Score: 308
Period size: 27 Copynumber: 8.0 Consensus size: 27
59785676 TTTACAAAAT
59785686 TACCGAAATACCCTTGTAGGGTAGAAA
1 TACCGAAATACCCTTGTAGGGTAGAAA
59785713 TACCGAAATACCCTTGTAGGGTAGAAA
1 TACCGAAATACCCTTGTAGGGTAGAAA
* *
59785740 TACCGAAATACCCCTGTAGGGTAGAAT
1 TACCGAAATACCCTTGTAGGGTAGAAA
** * * *
59785767 TATTGAAATACCCCTGTAGGATAGAAT
1 TACCGAAATACCCTTGTAGGGTAGAAA
*
59785794 TACCGAAATACCCTTGTAGGGTAGAAT
1 TACCGAAATACCCTTGTAGGGTAGAAA
59785821 TACCGAAATACCCTTGTAGGGTAGAAA
1 TACCGAAATACCCTTGTAGGGTAGAAA
* * *
59785848 TACCGAAATACCCCTGTAGGATAGAAT
1 TACCGAAATACCCTTGTAGGGTAGAAA
*
59785875 TACCGAGATA-CCTTGTAGGGTA-AAA
1 TACCGAAATACCCTTGTAGGGTAGAAA
59785900 T
1 T
59785901 TACCATTTTA
Statistics
Matches: 171, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
25 3 0.02
26 10 0.06
27 158 0.92
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (27 bp):
TACCGAAATACCCTTGTAGGGTAGAAA
Found at i:59786642 original size:27 final size:26
Alignment explanation
Indices: 59786554--59786655 Score: 105
Period size: 27 Copynumber: 3.8 Consensus size: 26
59786544 ATTCTGTTAA
* *
59786554 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTCTGCCACAATATCTG-TTCTG
* *
59786581 GTGGCTATGCCACAAATATCTGTTCTA
1 GTGGCTCTGCCAC-AATATCTGTTCTG
*
59786608 GTGGCTCTGCCACAATATCTGTATATG
1 GTGGCTCTGCCACAATATCTGT-TCTG
* **
59786635 GTGACTCTATCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
59786656 ATAACTGAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
26 9 0.14
27 48 0.75
28 7 0.11
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.36
Consensus pattern (26 bp):
GTGGCTCTGCCACAATATCTGTTCTG
Found at i:59786649 original size:54 final size:53
Alignment explanation
Indices: 59786553--59786655 Score: 125
Period size: 54 Copynumber: 1.9 Consensus size: 53
59786543 TATTCTGTTA
* * * * * *
59786553 AGTGGCTTTGCCACATTATCTGTTTCTGGTGGCTATGCCACAAATATCTGTTCT
1 AGTGGCTCTGCCACAATATCTGTATATGGTGACTATACCAC-AATATCTGTTCT
* *
59786607 AGTGGCTCTGCCACAATATCTGTATATGGTGACTCTATCACAATATCTG
1 AGTGGCTCTGCCACAATATCTGTATATGGTGACTATACCACAATATCTG
59786656 ATAACTGAGC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
53 8 0.20
54 33 0.80
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (53 bp):
AGTGGCTCTGCCACAATATCTGTATATGGTGACTATACCACAATATCTGTTCT
Found at i:59786830 original size:6 final size:6
Alignment explanation
Indices: 59786815--59786939 Score: 60
Period size: 6 Copynumber: 20.3 Consensus size: 6
59786805 ATTCTGTTAC
* * * *
59786815 CTGATA CTGATT CTGATT TTGATT CTG-TT ACCTGATA CCGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT CTGATT --CTGATT CTGATT CTGATT
* * * * * *
59786864 TTGATT CTG-TCAC CTAATA CTGATT AC-GATT CTGATT CT-ATCAC CTAATT
1 CTGATT CTGAT--T CTGATT CTGATT -CTGATT CTGATT CTGAT--T CTGATT
*
59786914 CTGATT CTGATT CTAATT CTGATT CT
1 CTGATT CTGATT CTGATT CTGATT CT
59786940 AGTTTTGATA
Statistics
Matches: 89, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
5 6 0.07
6 71 0.80
7 8 0.09
8 4 0.04
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.45
Consensus pattern (6 bp):
CTGATT
Found at i:59786843 original size:31 final size:31
Alignment explanation
Indices: 59786792--59786934 Score: 162
Period size: 31 Copynumber: 4.6 Consensus size: 31
59786782 TTGCATTCAC
* * *
59786792 ATTCTGATTTTTAATTCTGTTACCTGATACTG
1 ATTCTGA-TTTTGATTCTGTCACCTAATACTG
* * *
59786824 ATTCTGATTTTGATTCTGTTACCTGATACCG
1 ATTCTGATTTTGATTCTGTCACCTAATACTG
59786855 ATTCTGATTTTGATTCTGTCACCTAATACTG
1 ATTCTGATTTTGATTCTGTCACCTAATACTG
* * *
59786886 ATTAC-GATTCTGATTCTATCACCTAATTCTG
1 ATT-CTGATTTTGATTCTGTCACCTAATACTG
* *
59786917 ATTCTGATTCTAATTCTG
1 ATTCTGATTTTGATTCTG
59786935 ATTCTAGTTT
Statistics
Matches: 99, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
30 1 0.01
31 90 0.91
32 8 0.08
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.46
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTCACCTAATACTG
Found at i:59787689 original size:55 final size:53
Alignment explanation
Indices: 59787595--59787744 Score: 185
Period size: 55 Copynumber: 2.8 Consensus size: 53
59787585 GTGTTACACT
* *
59787595 ATAAGGCAAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGATAC
1 ATAAGGCAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAG-TAC
* * * * * *
59787649 TGTAAGGCAAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC
1 -ATAAGGC-AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTAC
*
59787703 ATAAGGCAAGGATACCACGTAAGACCATGTCAAGACATGGCA
1 ATAAGGCAAGGATACCATGTAAGACCATGTCAAGACATGGCA
59787745 ATGGTAAGTT
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
52 4 0.05
53 32 0.40
54 2 0.03
55 38 0.47
56 4 0.05
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (53 bp):
ATAAGGCAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTAC
Found at i:59787731 original size:53 final size:54
Alignment explanation
Indices: 59787593--59787754 Score: 193
Period size: 53 Copynumber: 3.0 Consensus size: 54
59787583 GGGTGTTACA
* * * *
59787593 CTATAAGGCAAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGATA
1 CTATAAGGCAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTGAG-TT
* * * *
59787648 CTGTAAGGCAAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTT
1 CTATAAGGC-AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTGAGTT
* * *
59787702 C-ATAAGGCAAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 CTATAAGGCAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTGAGTT
59787755 TAAAATGGAA
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
52 4 0.04
53 40 0.44
54 2 0.02
55 40 0.44
56 4 0.04
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (54 bp):
CTATAAGGCAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTGAGTT
Found at i:59789890 original size:17 final size:17
Alignment explanation
Indices: 59789868--59789901 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
59789858 AGGTCGATCG
59789868 AGGAAAATGAAAGGTTT
1 AGGAAAATGAAAGGTTT
59789885 AGGAAAATGAAAGGTTT
1 AGGAAAATGAAAGGTTT
59789902 CGAAATAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (17 bp):
AGGAAAATGAAAGGTTT
Found at i:59792587 original size:29 final size:28
Alignment explanation
Indices: 59792555--59792657 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
59792545 GTGACGAGAT
* *
59792555 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* *
59792584 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
59792613 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
59792642 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
59792658 TGATTGAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 58 0.94
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Found at i:59800384 original size:29 final size:28
Alignment explanation
Indices: 59800352--59800454 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
59800342 GTGACGAGAT
* *
59800352 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* *
59800381 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
59800410 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
59800439 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
59800455 TGATTGAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 58 0.94
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Found at i:59803299 original size:27 final size:27
Alignment explanation
Indices: 59803269--59803445 Score: 192
Period size: 27 Copynumber: 6.6 Consensus size: 27
59803259 ATAGAATAAA
*
59803269 TGTTTTGCCCTTATGTGGTAAAATGAC
1 TGTTTTGCCCTTATGCGGTAAAATGAC
* *
59803296 TGTTTTGCCCTTATACGATAAAATGAC
1 TGTTTTGCCCTTATGCGGTAAAATGAC
* *
59803323 TATTTTGCCCTTATACGGTAAAATGAC
1 TGTTTTGCCCTTATGCGGTAAAATGAC
* * * *
59803350 TATTTTTCCCTTATGAGGTAAAATGAT
1 TGTTTTGCCCTTATGCGGTAAAATGAC
* *
59803377 TGTTTGGCCCTTATGCGGTAAAATGAT
1 TGTTTTGCCCTTATGCGGTAAAATGAC
* * ** *
59803404 TGTTTTGCCTTTTTATGGTAAGATGAC
1 TGTTTTGCCCTTATGCGGTAAAATGAC
* *
59803431 TGTTTTACCCCTATG
1 TGTTTTGCCCTTATG
59803446 TGATGTATGT
Statistics
Matches: 125, Mismatches: 25, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 125 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (27 bp):
TGTTTTGCCCTTATGCGGTAAAATGAC
Found at i:59803315 original size:54 final size:54
Alignment explanation
Indices: 59803249--59803412 Score: 188
Period size: 54 Copynumber: 3.0 Consensus size: 54
59803239 CGTACCTGGA
* * *
59803249 CCCTTA-ATCGATAGAATAAATGTTTTGCCCTTATGTGGTAAAATGACTGTTTTG
1 CCCTTATA-CGATAAAATGAATGTTTTGCCCTTATGCGGTAAAATGACTGTTTTG
* * * * *
59803303 CCCTTATACGATAAAATGACTATTTTGCCCTTATACGGTAAAATGACTATTTTT
1 CCCTTATACGATAAAATGAATGTTTTGCCCTTATGCGGTAAAATGACTGTTTTG
* * * *
59803357 CCCTTATGA-GGTAAAATGATTGTTTGGCCCTTATGCGGTAAAATGATTGTTTTG
1 CCCTTAT-ACGATAAAATGAATGTTTTGCCCTTATGCGGTAAAATGACTGTTTTG
59803411 CC
1 CC
59803413 TTTTTATGGT
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
54 90 0.98
55 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (54 bp):
CCCTTATACGATAAAATGAATGTTTTGCCCTTATGCGGTAAAATGACTGTTTTG
Found at i:59803387 original size:81 final size:81
Alignment explanation
Indices: 59803271--59803445 Score: 215
Period size: 81 Copynumber: 2.2 Consensus size: 81
59803261 AGAATAAATG
* * *
59803271 TTTTGCCCTTATGTGGTAAAATGACTGTTTTGCCCTTATACGATAAAATGACTATTTTGCCCTTA
1 TTTTACCCTTATGAGGTAAAATGACTGTTTGGCCCTTATACGATAAAATGACTATTTTGCCCTTA
59803336 TACGGTAAAATGACTA
66 TACGGTAAAATGACTA
* * * * * * * *
59803352 TTTTTCCCTTATGAGGTAAAATGATTGTTTGGCCCTTATGCGGTAAAATGATTGTTTTGCCTTTT
1 TTTTACCCTTATGAGGTAAAATGACTGTTTGGCCCTTATACGATAAAATGACTATTTTGCCCTTA
* * *
59803417 TATGGTAAGATGACTG
66 TACGGTAAAATGACTA
*
59803433 TTTTACCCCTATG
1 TTTTACCCTTATG
59803446 TGATGTATGT
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (81 bp):
TTTTACCCTTATGAGGTAAAATGACTGTTTGGCCCTTATACGATAAAATGACTATTTTGCCCTTA
TACGGTAAAATGACTA
Found at i:59803745 original size:18 final size:18
Alignment explanation
Indices: 59803722--59803783 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 18
59803712 AGGACTTGCA
* *
59803722 TACTGTTACTGCACGGTT
1 TACTGTTACTACACTGTT
*
59803740 TACTGTTATTACACTG-T
1 TACTGTTACTACACTGTT
*
59803757 TACTATTACTACACTGTT
1 TACTGTTACTACACTGTT
*
59803775 TATTGTTAC
1 TACTGTTAC
59803784 CACAATGGGC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 15 0.42
18 21 0.58
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (18 bp):
TACTGTTACTACACTGTT
Found at i:59803769 original size:17 final size:17
Alignment explanation
Indices: 59803739--59803774 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
59803729 ACTGCACGGT
* *
59803739 TTACTGTTATTACACTG
1 TTACTATTACTACACTG
59803756 TTACTATTACTACACTG
1 TTACTATTACTACACTG
59803773 TT
1 TT
59803775 TATTGTTACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.47
Consensus pattern (17 bp):
TTACTATTACTACACTG
Found at i:59806953 original size:27 final size:27
Alignment explanation
Indices: 59806923--59807080 Score: 181
Period size: 27 Copynumber: 5.9 Consensus size: 27
59806913 TAATTGATAG
59806923 AATGACTATTTTGCCCTTATGTGGTAA
1 AATGACTATTTTGCCCTTATGTGGTAA
* * *
59806950 AATGACTGTTTTGCCCTTATGAGGTGA
1 AATGACTATTTTGCCCTTATGTGGTAA
* * * *
59806977 AATGAATTTTTTGCTCTTATGAGGTAA
1 AATGACTATTTTGCCCTTATGTGGTAA
*
59807004 AATGACTATTTTGCCCTTATATGGTAA
1 AATGACTATTTTGCCCTTATGTGGTAA
* * *
59807031 AATGACTATTTTTCCCTTTTATGGTAA
1 AATGACTATTTTGCCCTTATGTGGTAA
* * * *
59807058 GATGACTGTTTTACCCCTATGTG
1 AATGACTATTTTGCCCTTATGTG
59807081 ATGTATGTTT
Statistics
Matches: 111, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 111 1.00
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (27 bp):
AATGACTATTTTGCCCTTATGTGGTAA
Found at i:59818843 original size:48 final size:48
Alignment explanation
Indices: 59818773--59818885 Score: 183
Period size: 48 Copynumber: 2.4 Consensus size: 48
59818763 CTCTCACACT
* * *
59818773 AAGTGCCAATATCTTGGCCCGAAGCCAAATCAATGTAACACT-CACTCG
1 AAGTGCTAATATCATGGACCGAAGCCAAATCAATGTAACA-TGCACTCG
59818821 AAGTGCTAATATCATGGACCGAAGCCAAATCAATGTAACATGCACTCG
1 AAGTGCTAATATCATGGACCGAAGCCAAATCAATGTAACATGCACTCG
59818869 AAGTGCTAATATCATGG
1 AAGTGCTAATATCATGG
59818886 CCTAAATCCA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
47 1 0.02
48 60 0.98
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (48 bp):
AAGTGCTAATATCATGGACCGAAGCCAAATCAATGTAACATGCACTCG
Found at i:59818897 original size:48 final size:47
Alignment explanation
Indices: 59818773--59818906 Score: 180
Period size: 48 Copynumber: 2.8 Consensus size: 47
59818763 CTCTCACACT
* *
59818773 AAGTGCCAATATCTTGGCCCGAAGCCAAATCAATGTAACACTCACTCG
1 AAGTGCTAATATCATGG-CCGAAGCCAAATCAATGTAACACTCACTCG
59818821 AAGTGCTAATATCATGGACCGAAGCCAAATCAATGTAACA-TGCACTCG
1 AAGTGCTAATATCATGG-CCGAAGCCAAATCAATGTAACACT-CACTCG
* * *
59818869 AAGTGCTAATATCATGGCCTAAATCCAAAGCAATGTAA
1 AAGTGCTAATATCATGGCC-GAAGCCAAATCAATGTAA
59818907 AAATCCAAAG
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
47 3 0.04
48 75 0.96
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (47 bp):
AAGTGCTAATATCATGGCCGAAGCCAAATCAATGTAACACTCACTCG
Found at i:59818912 original size:18 final size:18
Alignment explanation
Indices: 59818889--59818924 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
59818879 ATCATGGCCT
59818889 AAATCCAAAGCAATGTAA
1 AAATCCAAAGCAATGTAA
59818907 AAATCCAAAGCAATGTAA
1 AAATCCAAAGCAATGTAA
59818925 CTCACACCCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.17, G:0.11, T:0.17
Consensus pattern (18 bp):
AAATCCAAAGCAATGTAA
Found at i:59818951 original size:66 final size:66
Alignment explanation
Indices: 59818845--59818970 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 66
59818835 TGGACCGAAG
* * * * *
59818845 CCAAATCAATGTAACATGCACTCGAAGTGCTAATATCATGGCCTAAATCCAAAGCAATGTAAAAA
1 CCAAAGCAATGTAACATACACCCGAAGTGCTAATATCATGGCCCAAAGCCAAAGCAATGTAAAAA
59818910 T
66 T
*
59818911 CCAAAGCAATGTAAC-TCACACCCGAAGTGCTAATATCATGGCCCAAAGCCAAATCAATGT
1 CCAAAGCAATGTAACAT-ACACCCGAAGTGCTAATATCATGGCCCAAAGCCAAAGCAATGT
59818971 TCCTTAATGA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 1 0.02
66 52 0.98
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.21
Consensus pattern (66 bp):
CCAAAGCAATGTAACATACACCCGAAGTGCTAATATCATGGCCCAAAGCCAAAGCAATGTAAAAA
T
Found at i:59819563 original size:21 final size:20
Alignment explanation
Indices: 59819539--59819577 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
59819529 TTGTATAACT
*
59819539 ATCATCAAACATTCAAAATCA
1 ATCATAAAACA-TCAAAATCA
59819560 ATCATAAAACATCAAAAT
1 ATCATAAAACATCAAAAT
59819578 ACTCATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.56, C:0.21, G:0.00, T:0.23
Consensus pattern (20 bp):
ATCATAAAACATCAAAATCA
Found at i:59821619 original size:68 final size:66
Alignment explanation
Indices: 59821547--59821718 Score: 170
Period size: 67 Copynumber: 2.6 Consensus size: 66
59821537 CATCATGTGT
* * * *
59821547 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
59821610 TGTAG
62 TGTAG
** * *
59821615 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
59821680 AG
65 AG
* * * *
59821682 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG
59821719 GGTGGTACTG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 24 0.27
65 3 0.03
66 17 0.19
67 32 0.36
68 13 0.15
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:59821652 original size:64 final size:64
Alignment explanation
Indices: 59821571--59821754 Score: 203
Period size: 67 Copynumber: 2.8 Consensus size: 64
59821561 AGACATTATG
* * *
59821571 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
59821635 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
59821700 AA
63 AA
* * *
59821702 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
59821755 CAAACTATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
66 21 0.21
67 33 0.33
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:59824450 original size:25 final size:25
Alignment explanation
Indices: 59824417--59824467 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
59824407 ATGAAAGATA
*
59824417 AAAAGTACATTAAGAGGTACTTTCT
1 AAAAGTACATTAAGAAGTACTTTCT
59824442 AAAAGTACATTAAGAAGTACTTTCT
1 AAAAGTACATTAAGAAGTACTTTCT
59824467 A
1 A
59824468 TAGTCAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (25 bp):
AAAAGTACATTAAGAAGTACTTTCT
Found at i:59827349 original size:21 final size:21
Alignment explanation
Indices: 59827325--59827373 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
59827315 ACGAACTCGG
59827325 ACTCAACTCAACGAGTTCGAA
1 ACTCAACTCAACGAGTTCGAA
*
59827346 ACTCAACTCAACGAGTTTGAA
1 ACTCAACTCAACGAGTTCGAA
59827367 ACTCAAC
1 ACTCAAC
59827374 CATCCTAGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (21 bp):
ACTCAACTCAACGAGTTCGAA
Found at i:59829118 original size:68 final size:70
Alignment explanation
Indices: 59829046--59829243 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
59829036 ACACCCTGTA
* * * *
59829046 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
59829108 ATAAAT
65 ATAAAT
*
59829114 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
59829179 ATAAAT
65 ATAAAT
*
59829185 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
59829244 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:59829157 original size:41 final size:41
Alignment explanation
Indices: 59829112--59829229 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
59829102 TGAAAGATAA
59829112 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
59829153 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
59829183 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
59829224 ATGTAG
1 ATGTAG
59829230 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:59829169 original size:71 final size:71
Alignment explanation
Indices: 59829080--59829243 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
59829070 GAGATGTATC
59829080 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
59829145 AGGACA
66 AGGACA
59829151 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
59829216 AGGACA
66 AGGACA
59829222 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
59829244 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:59833313 original size:36 final size:36
Alignment explanation
Indices: 59833272--59833343 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
59833262 CACATCCTAA
59833272 GCCATTTCGAGAAGCATCACTATACACCACAAATTC
1 GCCATTTCGAGAAGCATCACTATACACCACAAATTC
59833308 GCCATTTCGAGAAGCATCACTATACACCACAAATTC
1 GCCATTTCGAGAAGCATCACTATACACCACAAATTC
59833344 TTTACCTGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.31, G:0.11, T:0.22
Consensus pattern (36 bp):
GCCATTTCGAGAAGCATCACTATACACCACAAATTC
Found at i:59842126 original size:18 final size:18
Alignment explanation
Indices: 59842103--59842140 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
59842093 TGTTATGAAA
59842103 ATCCATATTATAATATTT
1 ATCCATATTATAATATTT
59842121 ATCCATATTATAATATTT
1 ATCCATATTATAATATTT
59842139 AT
1 AT
59842141 TTTTATACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (18 bp):
ATCCATATTATAATATTT
Found at i:59842373 original size:30 final size:28
Alignment explanation
Indices: 59842333--59842400 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
59842323 TATCTTATAT
* *
59842333 TATA-TATATAAGATCAAAATCCATTAATA
1 TATATTATATAACAT-AAAAT-CATGAATA
* *
59842362 TATATTATATAACATAAAGTCATGCATA
1 TATATTATATAACATAAAATCATGAATA
59842390 TATATTATATA
1 TATATTATATA
59842401 GAATAAAGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 17 0.50
29 8 0.24
30 9 0.26
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (28 bp):
TATATTATATAACATAAAATCATGAATA
Found at i:59842429 original size:30 final size:28
Alignment explanation
Indices: 59842359--59842428 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
59842349 AAATCCATTA
*
59842359 ATATATATTATATAACATAAAGTCATGC
1 ATATATATTATATAACATAAAGCCATGC
59842387 ATATATATTATATAGA-ATAAAGCCATGC
1 ATATATATTATATA-ACATAAAGCCATGC
* *
59842415 ATACATATAATATA
1 ATATATATTATATA
59842429 TGTATAATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 37 0.97
29 1 0.03
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (28 bp):
ATATATATTATATAACATAAAGCCATGC
Found at i:59842483 original size:34 final size:34
Alignment explanation
Indices: 59842445--59842557 Score: 107
Period size: 32 Copynumber: 3.5 Consensus size: 34
59842435 ATCACCCACG
59842445 TATATATATGTATATATATACAACTCCACTCATA
1 TATATATATGTATATATATACAACTCCACTCATA
* * *
59842479 TATAT-TATATATGTATATTACCAACTCC-CCCAT-
1 TATATATATGTATATATA-TA-CAACTCCACTCATA
*
59842512 T-TATATAT-TATATATATA-ACAC-CCACTAATA
1 TATATATATGTATATATATACA-ACTCCACTCATA
59842543 TATATAT-TGTATATA
1 TATATATATGTATATA
59842558 AAATAAAGTC
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
29 3 0.05
30 5 0.08
31 4 0.06
32 21 0.32
33 14 0.22
34 11 0.17
35 7 0.11
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.41
Consensus pattern (34 bp):
TATATATATGTATATATATACAACTCCACTCATA
Found at i:59842524 original size:36 final size:37
Alignment explanation
Indices: 59842447--59842526 Score: 103
Period size: 36 Copynumber: 2.2 Consensus size: 37
59842437 CACCCACGTA
*
59842447 TATATATGTATATATATACAACTCCACTCATATATAT
1 TATATATGTATATATATACAACTCCACCCATATATAT
*
59842484 TATATATGTATAT-TA-CCAACTCC-CCCATTTATATAT
1 TATATATGTATATATATACAACTCCACCCA--TATATAT
59842520 TATATAT
1 TATATAT
59842527 ATAACACCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
34 3 0.08
35 7 0.18
36 16 0.41
37 13 0.33
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.42
Consensus pattern (37 bp):
TATATATGTATATATATACAACTCCACCCATATATAT
Found at i:59843842 original size:15 final size:15
Alignment explanation
Indices: 59843822--59843851 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
59843812 CTATTATTAA
*
59843822 CTAATTATTTGTTTT
1 CTAATTATTTATTTT
59843837 CTAATTATTTATTTT
1 CTAATTATTTATTTT
59843852 ATCTTATTTT
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:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (15 bp):
CTAATTATTTATTTT
Found at i:59843970 original size:65 final size:65
Alignment explanation
Indices: 59843886--59844016 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
59843876 AAAATTCGAT
* *
59843886 TTTTCTCTCAAACCCATAATCTAATGTCCAATTCTACTAACTCGATTTTCGAGATGTGATATTTG
1 TTTTCTCTCAAACCCATAATCTAATGTCCAATTCTACTAACCCGATTTTCGAGATGTGACATTTG
*
59843951 TTTTCTCTCAAACCTATAATCTAATGTCCAATTCTACTAACCCGATTTTCGAGATGTGACATTTG
1 TTTTCTCTCAAACCCATAATCTAATGTCCAATTCTACTAACCCGATTTTCGAGATGTGACATTTG
59844016 T
1 T
59844017 ATCCAAATCA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (65 bp):
TTTTCTCTCAAACCCATAATCTAATGTCCAATTCTACTAACCCGATTTTCGAGATGTGACATTTG
Found at i:59844661 original size:51 final size:51
Alignment explanation
Indices: 59844605--59844712 Score: 148
Period size: 51 Copynumber: 2.1 Consensus size: 51
59844595 CCAAACATCT
* * *
59844605 ATTCATATGAAATAAT-AGTTCTTACCAAATGAC-ATCTCATTCAAAATAATA
1 ATTCATATGAAAT-ATCAGTTCATACCAAATAACAAT-TCATGCAAAATAATA
*
59844656 GTTCATATGAAATATCAGTTCATACCAAATAACAATTCATGCAAAATAATA
1 ATTCATATGAAATATCAGTTCATACCAAATAACAATTCATGCAAAATAATA
59844707 ATTCAT
1 ATTCAT
59844713 GCTCCATCAT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
50 2 0.04
51 46 0.92
52 2 0.04
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.32
Consensus pattern (51 bp):
ATTCATATGAAATATCAGTTCATACCAAATAACAATTCATGCAAAATAATA
Found at i:59844713 original size:17 final size:17
Alignment explanation
Indices: 59844682--59844714 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
59844672 AGTTCATACC
59844682 AAATAACAATTCATGCA
1 AAATAACAATTCATGCA
*
59844699 AAATAATAATTCATGC
1 AAATAACAATTCATGC
59844715 TCCATCATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (17 bp):
AAATAACAATTCATGCA
Found at i:59845090 original size:19 final size:19
Alignment explanation
Indices: 59845061--59845098 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
59845051 GACTAAACCG
59845061 AAAACTTTAG-AAATTTTT
1 AAAACTTTAGAAAATTTTT
59845079 AAAACATTTAGAAAATTTTT
1 AAAAC-TTTAGAAAATTTTT
59845099 CATCAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 5 0.28
20 8 0.44
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (19 bp):
AAAACTTTAGAAAATTTTT
Found at i:59847563 original size:39 final size:40
Alignment explanation
Indices: 59847420--59847634 Score: 359
Period size: 40 Copynumber: 5.5 Consensus size: 40
59847410 CGGATGATAA
59847420 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
59847460 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
59847500 -CGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTAC-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
59847537 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
59847577 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
59847617 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
59847635 TACTTGGTTT
Statistics
Matches: 168, Mismatches: 3, Indels: 9
0.93 0.02 0.05
Matches are distributed among these distances:
37 4 0.02
38 33 0.20
39 50 0.30
40 81 0.48
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:59855481 original size:40 final size:40
Alignment explanation
Indices: 59855400--59855535 Score: 208
Period size: 40 Copynumber: 3.5 Consensus size: 40
59855390 CGGATGATAA
59855400 CCGGGCTAAGTCCCGAAGGCATTTGT--GAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
59855438 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
59855478 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
59855518 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
59855536 TACTTGGTTT
Statistics
Matches: 92, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
38 26 0.28
39 17 0.18
40 49 0.53
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:59859275 original size:79 final size:82
Alignment explanation
Indices: 59859135--59859319 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
59859125 TCGAATGATG
* * *
59859135 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
*
59859199 CGTGCGAGTTAATA-AA
66 CGTGCGAGTCAATATAA
* **
59859215 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCAT
*
59859277 TCGTGCGAGTCACTATAA
65 TCGTGCGAGTCAATATAA
**
59859295 -CCGGGCTTCGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
59859320 AGCGAGTCGT
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 34 0.37
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (82 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTCAATATAA
Found at i:59859327 original size:40 final size:40
Alignment explanation
Indices: 59859136--59859327 Score: 151
Period size: 40 Copynumber: 4.8 Consensus size: 40
59859126 CGAATGATGT
* * * * *
59859136 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTCACTAAAC
** * * * * *
59859176 CCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAAT
1 CCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTCACTAAAC
* * *
59859216 CCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTACTAAAC
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC
*
59859255 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCACTATAA-
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTA-AAC
* *
59859295 CCGGGCTT-CGTCCCGAAGGCATTTGAGCGAGTC
1 CCGGG-TTAAGTCCCGAAGGCATTTGTGCGAGTC
59859328 GTTATATCCG
Statistics
Matches: 126, Mismatches: 20, Indels: 12
0.80 0.13 0.08
Matches are distributed among these distances:
39 33 0.26
40 82 0.65
41 11 0.09
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC
Found at i:59859350 original size:79 final size:79
Alignment explanation
Indices: 59859135--59859352 Score: 183
Period size: 79 Copynumber: 2.7 Consensus size: 79
59859125 TCGAATGATG
* * * * ** *
59859135 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGA-TCCGAAGGCAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGAGC-AAGTCACTAAACCCGGGTTA-AATTCCGAAGGCAT
*
59859198 TCGTGCGAGTTAATAAA
63 TCGTGCGAGTCAATAAA
* * * *
59859215 TCCGGGCTAAGCCCGAAGGCATTTGTGCAAGTTACTAAACCCGGGTTAAGTCCCGAAGGCATTCG
1 TCCGGGCTAAGCCCGAAGGCATTTGAGCAAGTCACTAAACCCGGGTTAAATTCCGAAGGCATTCG
*
59859280 TGCGAGTCACTATAA
66 TGCGAGTCAATA-AA
** * ** * *
59859295 -CCGGGCTTCGTCCCGAAGGCATTTGAGCGAGTCGTTATATCC-GGTTAAATTCCGAAGG
1 TCCGGGCTAAG-CCCGAAGGCATTTGAGCAAGTCACTAAACCCGGGTTAAATTCCGAAGG
59859353 TACGTGATTC
Statistics
Matches: 113, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
79 69 0.61
80 44 0.39
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGCTAAGCCCGAAGGCATTTGAGCAAGTCACTAAACCCGGGTTAAATTCCGAAGGCATTCG
TGCGAGTCAATAAA
Found at i:59864916 original size:29 final size:29
Alignment explanation
Indices: 59864883--59864947 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
59864873 GTGACGAGAT
*
59864883 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
59864912 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
*
59864941 CGGCACT
1 TGGCACT
59864948 GGGTGTGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAAAATA
Found at i:59871595 original size:24 final size:24
Alignment explanation
Indices: 59871555--59871616 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
59871545 GATTATGTAG
59871555 AAAGAATAAAGAAATGAA-AAAAAA
1 AAAGAA-AAAGAAATGAAGAAAAAA
* *
59871579 AAAGAAAGAGAATATGAAGAAAAAC
1 AAAGAAAAAGAA-ATGAAGAAAAAA
*
59871604 AAAGAAAAGGAAA
1 AAAGAAAAAGAAA
59871617 AAAAAAGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 5 0.16
24 12 0.38
25 15 0.47
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.06
Consensus pattern (24 bp):
AAAGAAAAAGAAATGAAGAAAAAA
Found at i:59872815 original size:29 final size:29
Alignment explanation
Indices: 59872782--59872846 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
59872772 GTGACGAGAT
*
59872782 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
59872811 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
*
59872840 CGGCACT
1 TGGCACT
59872847 GGGTGTGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAAAATA
Found at i:59875143 original size:23 final size:21
Alignment explanation
Indices: 59875107--59875151 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
59875097 ATTTTAATAT
59875107 TTTAATTAATTAATTCCTAATTA
1 TTTAATTAATTAA-T-CTAATTA
59875130 TTTAATT-ATATAATCTAATTA
1 TTTAATTAAT-TAATCTAATTA
59875151 T
1 T
59875152 AGTTTTCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 8 0.38
22 3 0.14
23 10 0.48
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTAATTAATTAATCTAATTA
Found at i:59875149 original size:32 final size:31
Alignment explanation
Indices: 59875080--59875150 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
59875070 CCTAATAAAA
*
59875080 AATT-ATTAATTCTAATTATTTTAATATTTT
1 AATTAATTAATTCTAATTATTTTAATATTAT
59875110 AATTAATTAATTCCTAATTA-TTTAAT-TATAT
1 AATTAATTAATT-CTAATTATTTTAATAT-TAT
59875141 AATCTAATTA
1 AAT-TAATTA
59875151 TAGTTTTCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 5 0.14
31 18 0.50
32 13 0.36
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (31 bp):
AATTAATTAATTCTAATTATTTTAATATTAT
Found at i:59877125 original size:28 final size:28
Alignment explanation
Indices: 59877079--59877152 Score: 123
Period size: 28 Copynumber: 2.6 Consensus size: 28
59877069 TGGCCCCTTT
*
59877079 AGGCCCAATCTCATTCATATGGCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
59877107 -GGCCCTAATCACATTCATATGGCCCATC
1 AGGCCC-AATCACATTCATATGGCCCATC
59877135 AGGCCCAATCACATTCAT
1 AGGCCCAATCACATTCAT
59877153 GGTCATGCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
27 5 0.12
28 33 0.77
29 5 0.12
ACGTcount: A:0.27, C:0.35, G:0.14, T:0.24
Consensus pattern (28 bp):
AGGCCCAATCACATTCATATGGCCCATC
Found at i:59891236 original size:17 final size:18
Alignment explanation
Indices: 59891214--59891249 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
59891204 CACATTGAAG
59891214 TGTTTT-ATCGAAAACCC
1 TGTTTTCATCGAAAACCC
*
59891231 TGTTTTCATTGAAAACCC
1 TGTTTTCATCGAAAACCC
59891249 T
1 T
59891250 TCAAAAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (18 bp):
TGTTTTCATCGAAAACCC
Found at i:59894490 original size:11 final size:11
Alignment explanation
Indices: 59894454--59894509 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
59894444 CATGGTATGT
59894454 ATGATATGCAC
1 ATGATATGCAC
* *
59894465 ATGACATG--T
1 ATGATATGCAC
59894474 ATGATATGCAC
1 ATGATATGCAC
*
59894485 ATGATATG--T
1 ATGATATGCAC
59894494 ATGATATGCAC
1 ATGATATGCAC
59894505 ATGAT
1 ATGAT
59894510 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:59894509 original size:20 final size:20
Alignment explanation
Indices: 59894443--59894509 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
59894433 ATTTTGATAA
*
59894443 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
59894463 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
59894483 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
59894503 ACATGAT
1 ACATGAT
59894510 GTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:59894586 original size:24 final size:24
Alignment explanation
Indices: 59894559--59894750 Score: 271
Period size: 24 Copynumber: 8.0 Consensus size: 24
59894549 GAGGAAGTGA
*
59894559 AAAAGGGCTTATGCCCCAATTATC
1 AAAAGGGCTTATGCCCCAGTTATC
59894583 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
*
59894607 AAAAGGGCTTATGCCCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATC
*
59894631 AAAAGGGCTTATGCCCCAATTA-C
1 AAAAGGGCTTATGCCCCAGTTATC
*
59894654 TAAAAGGGCTTATGCCCCAGTTATT
1 -AAAAGGGCTTATGCCCCAGTTATC
*
59894679 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* *
59894703 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
59894727 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
59894751 TGATAAAGCA
Statistics
Matches: 155, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
24 144 0.93
25 11 0.07
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:59902801 original size:20 final size:20
Alignment explanation
Indices: 59902778--59902816 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
59902768 TAAACATGGT
59902778 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
59902798 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
59902817 TGTATTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:59902893 original size:24 final size:24
Alignment explanation
Indices: 59902866--59903034 Score: 243
Period size: 24 Copynumber: 7.0 Consensus size: 24
59902856 GGAGGAAGTG
59902866 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
59902890 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
59902914 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
59902938 AAAAAGGGCTTATGCCCCAGTTA-
1 CAAAAGGGCTTATGCCCCAGTTAT
*
59902961 CTAAAAGGGCTTATGCCCCTGTTAT
1 C-AAAAGGGCTTATGCCCCAGTTAT
* *
59902986 TAAAAGGGCTTATGCCCCTGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
59903010 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 CAAAAG-GGCTTATGCC-CCAGTTAT
59903035 TTGATAAAGT
Statistics
Matches: 135, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
24 125 0.93
25 10 0.07
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:59912055 original size:42 final size:43
Alignment explanation
Indices: 59911949--59912057 Score: 114
Period size: 42 Copynumber: 2.6 Consensus size: 43
59911939 CAAGTACAAT
* * * *
59911949 GTCGATGTCTCAGACCTGGTCTTACATGTAATTCAATATCGAT
1 GTCGATGTCCCAGACATGGTCTTACATGTAAATCAATATCGAA
* ** * *
59911992 GCCTCTGTCCTAGACAAGGTCTTACATG-AAATCAGATA-CGAA
1 GTCGATGTCCCAGACATGGTCTTACATGTAAATCA-ATATCGAA
59912034 GTCGATGTCCCAGACATGGTCTTA
1 GTCGATGTCCCAGACATGGTCTTA
59912058 TACATAAATC
Statistics
Matches: 51, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
42 27 0.53
43 24 0.47
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
GTCGATGTCCCAGACATGGTCTTACATGTAAATCAATATCGAA
Found at i:59913355 original size:28 final size:28
Alignment explanation
Indices: 59913320--59913393 Score: 123
Period size: 28 Copynumber: 2.6 Consensus size: 28
59913310 CAGCCCCTTT
*
59913320 AGGCCCAATCTCATTCATATGGCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
59913348 -GGCCCCAATCACATTCATATGGCCCATC
1 AGG-CCCAATCACATTCATATGGCCCATC
59913376 AGGCCCAATCACATTCAT
1 AGGCCCAATCACATTCAT
59913394 GGTCATGCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
27 2 0.05
28 39 0.91
29 2 0.05
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.23
Consensus pattern (28 bp):
AGGCCCAATCACATTCATATGGCCCATC
Found at i:59916833 original size:40 final size:40
Alignment explanation
Indices: 59916763--59916980 Score: 334
Period size: 40 Copynumber: 5.5 Consensus size: 40
59916753 AAACCAAGTA
* *
59916763 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
59916802 CCTTCGGGACTTAGCTCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
59916842 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
59916882 CCTTCGGGACTTAGCCCGAATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
59916922 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
59916962 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
59916981 TTACCATCCG
Statistics
Matches: 167, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 15 0.09
40 152 0.91
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:59918720 original size:20 final size:20
Alignment explanation
Indices: 59918692--59918730 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
59918682 AAACATACAT
* *
59918692 TTCACATACAATTTAATCAA
1 TTCAAATACAATTCAATCAA
59918712 TTCAAATACAATTCAATCA
1 TTCAAATACAATTCAATCA
59918731 CAACCAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (20 bp):
TTCAAATACAATTCAATCAA
Found at i:59923042 original size:29 final size:29
Alignment explanation
Indices: 59923009--59923073 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
59922999 GTGACGAGAT
*
59923009 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
59923038 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
*
59923067 CGGCACT
1 TGGCACT
59923074 GGGTGTGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAAAATA
Found at i:59927486 original size:16 final size:16
Alignment explanation
Indices: 59927467--59927497 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59927457 TTCTATCAAA
*
59927467 ATCACTTAATAAAATC
1 ATCACATAATAAAATC
59927483 ATCACATAATAAAAT
1 ATCACATAATAAAAT
59927498 AAGAACTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (16 bp):
ATCACATAATAAAATC
Found at i:59928778 original size:3 final size:3
Alignment explanation
Indices: 59928764--59928798 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
59928754 TTCACGTACA
*
59928764 AAC AAT AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
59928799 TAATAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.69, C:0.29, G:0.00, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:59930185 original size:16 final size:16
Alignment explanation
Indices: 59930164--59930196 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
59930154 GTTTACATTA
59930164 TACT-AATATTATATAT
1 TACTAAATATT-TATAT
59930180 TACTAAATATTTATAT
1 TACTAAATATTTATAT
59930196 T
1 T
59930197 TTGTGTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
TACTAAATATTTATAT
Found at i:59932649 original size:4 final size:4
Alignment explanation
Indices: 59932640--59932670 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
59932630 TCCTTTTATT
59932640 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
59932671 TTTTGAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:59936329 original size:29 final size:30
Alignment explanation
Indices: 59936296--59936367 Score: 74
Period size: 37 Copynumber: 2.2 Consensus size: 30
59936286 TCTTTTCTTT
59936296 TCATTTC-TTTTTTCGATTTGTATCTTATC
1 TCATTTCTTTTTTTCGATTTGTATCTTATC
59936325 TCATTATGTTCTTTTTTTTTTCGATTTGTATCTTATC
1 TC---AT-TTC---TTTTTTTCGATTTGTATCTTATC
59936362 TCATTT
1 TCATTT
59936368 TAGAGGCTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
29 2 0.06
32 2 0.06
33 5 0.14
34 2 0.06
37 24 0.69
ACGTcount: A:0.14, C:0.15, G:0.07, T:0.64
Consensus pattern (30 bp):
TCATTTCTTTTTTTCGATTTGTATCTTATC
Found at i:59937293 original size:19 final size:22
Alignment explanation
Indices: 59937247--59937292 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
59937237 AAGTAGGTTG
59937247 TATATTATTTTTTGTAATATTA
1 TATATTATTTTTTGTAATATTA
59937269 TATATTATTTTTAT-TAAT-TTA
1 TATATTATTTTT-TGTAATATTA
59937290 TAT
1 TAT
59937293 TTTAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.26
22 16 0.70
23 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TATATTATTTTTTGTAATATTA
Found at i:59937345 original size:21 final size:20
Alignment explanation
Indices: 59937316--59937355 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
59937306 ATATTAAGAA
59937316 TATTATTAAATTATATATTAT
1 TATTATTAAATTATA-ATTAT
*
59937337 TATTGTTAAATTATAATTA
1 TATTATTAAATTATAATTA
59937356 ATAATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TATTATTAAATTATAATTAT
Found at i:59937418 original size:61 final size:59
Alignment explanation
Indices: 59937265--59937423 Score: 185
Period size: 61 Copynumber: 2.6 Consensus size: 59
59937255 TTTTTGTAAT
* *** **
59937265 ATTATATATTATTTTTATTAATTTATATTTTAATAATTGCTATATTAAGAATATTATTAA
1 ATTATATATTATTTTTATTAAATTATA-TTTAATAATAAATATATTAAGAATAGGATTAA
* * * *
59937325 ATTATATATTATTATTGTTAAATTATAATTAATAATAAATTTATTAA-AATAGGATTAA
1 ATTATATATTATTTTTATTAAATTATATTTAATAATAAATATATTAAGAATAGGATTAA
59937383 ATTATGTATTATTATTTTTATTAAATTATATTTAATAATAA
1 ATTA--TA-TATTATTTTTATTAAATTATATTTAATAATAA
59937424 TCCTATTAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
58 13 0.16
59 15 0.18
60 26 0.31
61 29 0.35
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (59 bp):
ATTATATATTATTTTTATTAAATTATATTTAATAATAAATATATTAAGAATAGGATTAA
Found at i:59937642 original size:32 final size:32
Alignment explanation
Indices: 59937596--59937665 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
59937586 TTAAATTGCT
** *
59937596 ATTACAGTTCTATTCTGTTACAACTCTATTCC
1 ATTACAGTTCTATTCCATTACAACCCTATTCC
*
59937628 ATTATAGTTCTATTCCATTACAACCCTATTCC
1 ATTACAGTTCTATTCCATTACAACCCTATTCC
59937660 ATTACA
1 ATTACA
59937666 CTGAACCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.29, C:0.26, G:0.04, T:0.41
Consensus pattern (32 bp):
ATTACAGTTCTATTCCATTACAACCCTATTCC
Found at i:59937656 original size:16 final size:16
Alignment explanation
Indices: 59937613--59937665 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
59937603 TTCTATTCTG
59937613 TTACAACTCTATTCCA
1 TTACAACTCTATTCCA
* **
59937629 TTATAGTTCTATTCCA
1 TTACAACTCTATTCCA
*
59937645 TTACAACCCTATTCCA
1 TTACAACTCTATTCCA
59937661 TTACA
1 TTACA
59937666 CTGAACCAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.30, C:0.28, G:0.02, T:0.40
Consensus pattern (16 bp):
TTACAACTCTATTCCA
Found at i:59941337 original size:14 final size:15
Alignment explanation
Indices: 59941307--59941344 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
59941297 GCCTCTTTTG
59941307 CATTT-CATTTCATT
1 CATTTGCATTTCATT
59941321 CATTTGCATTTCA-T
1 CATTTGCATTTCATT
*
59941335 CATATGCATT
1 CATTTGCATT
59941345 AAGTTTCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.24, C:0.21, G:0.05, T:0.50
Consensus pattern (15 bp):
CATTTGCATTTCATT
Found at i:59947505 original size:26 final size:26
Alignment explanation
Indices: 59947469--59947520 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
59947459 TGATAAAAGG
59947469 ACATTGAGAAGGCTGGCTAGTGACTA
1 ACATTGAGAAGGCTGGCTAGTGACTA
*
59947495 ACATTGAGAAGGTTGGCTAGTGACTA
1 ACATTGAGAAGGCTGGCTAGTGACTA
59947521 TGAATTAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (26 bp):
ACATTGAGAAGGCTGGCTAGTGACTA
Found at i:59949634 original size:44 final size:45
Alignment explanation
Indices: 59949570--59949696 Score: 141
Period size: 44 Copynumber: 2.8 Consensus size: 45
59949560 ATCTACCATG
* * *
59949570 GCGAATCTTTTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-TC
1 GCGAATCTTATCTACCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * **
59949614 GCGAACCTTATCTACCTGAAGTTTCAGTGGAGCAGGCTGAAGATA
1 GCGAATCTTATCTACCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * *
59949659 GCAAATCTTAT-TTCTCTGAAGTTGCAGTGGAACAGATT
1 GCGAATCTTATCTAC-CTGAAGTTGCAGTGGAGCAGATT
59949697 AAAGCTACGA
Statistics
Matches: 67, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
44 38 0.57
45 29 0.43
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (45 bp):
GCGAATCTTATCTACCTGAAGTTGCAGTGGAGCAGATTGAAGATA
Found at i:59949687 original size:45 final size:44
Alignment explanation
Indices: 59949584--59949694 Score: 125
Period size: 45 Copynumber: 2.5 Consensus size: 44
59949574 ATCTTTTCTC
* * *
59949584 CCTGAAGTTGCAGTGGAGCAGATTGAAGTCGCGAACCTTATCTA
1 CCTGAAGTTGCAGTGGAGCAGACTGAAGTAGCAAACCTTATCTA
* * * *
59949628 CCTGAAGTTTCAGTGGAGCAGGCTGAAGATAGCAAATCTTAT-TT
1 CCTGAAGTTGCAGTGGAGCAGACTGAAG-TAGCAAACCTTATCTA
*
59949672 CTCTGAAGTTGCAGTGGAACAGA
1 C-CTGAAGTTGCAGTGGAGCAGA
59949695 TTAAAGCTAC
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
44 27 0.49
45 28 0.51
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (44 bp):
CCTGAAGTTGCAGTGGAGCAGACTGAAGTAGCAAACCTTATCTA
Found at i:59949949 original size:189 final size:184
Alignment explanation
Indices: 59949523--59950082 Score: 640
Period size: 189 Copynumber: 3.0 Consensus size: 184
59949513 AGAAATCAAA
** *
59949523 AATCCTATACAGCTGAAGTTGTAGTAGGTCGGATCAAATCTACCATGGCGAATCTTTTCTCCCTG
1 AATCCTATACCTCTGAAGTTGTAGTAGGTCGGATCAAATCTACCATGGCGAATCTTATCTCCCTG
* * * * * * *
59949588 AAGTTGCAGTGGAGCAGATTGAAGTCGCGAACCTTATCTACCTGAAGTTTCAGTGGAGCAGGCTG
66 AAGTTGCAGTAGAGCAGATTGAAGCCACAAACCTTATCT-CCTGAAGTTGCAGTGGAGCAAGTTG
* *
59949653 AAGATAGCAAATCTTATTTCTCTGAAGTTGCAGTGGAACAGATTAAAGCTACGAGTTAC
130 AAGATAGCAAATCTTATTTCTCTGAAGTTGCAGTAGAATAGATTAAAGCT---AG-TAC
* * * * *
59949712 AAGTCCTATACCTCTGAAGTTGTAATAGGTCAGATCAAATCGACCATGGCGAATCTTGTCTCTCT
1 AA-TCCTATACCTCTGAAGTTGTAGTAGGTCGGATCAAATCTACCATGGCGAATCTTATCTCCCT
* * *
59949777 GAAGTTGCAGAAGAGCAAATTAAAGCCACAAACAACAAATCTCATCTCCTTGAAGTTGCAGTGGA
65 GAAGTTGCAGTAGAGCAGATTGAAGCCACAAAC--C---T-T-ATCTCC-TGAAGTTGCAGTGGA
* * * *
59949842 GCAAGTTGAAGTTA-CAAGTCTTATCTCTCTGAAGTTGCAGTAGAATAGATTAAAGCTA-T-G
122 GCAAGTTGAAGATAGCAAATCTTATTTCTCTGAAGTTGCAGTAGAATAGATTAAAGCTAGTAC
* * * *
59949902 AATCCTATACCTCTGAAGTTGCAGCAGGTTGGATCAAATCTACCATGGCCAATCTTATCTCCCTG
1 AATCCTATACCTCTGAAGTTGTAGTAGGTCGGATCAAATCTACCATGGCGAATCTTATCTCCCTG
* * * * *
59949967 AAGTTACAGTAGAGCAGATTGAAGCCCCAAACCTTATCTCCCTGAAGTTGCAGTGAAGTAAATTG
66 AAGTTGCAGTAGAGCAGATTGAAGCCACAAACCTTATCT-CCTGAAGTTGCAGTGGAGCAAGTTG
* * *
59950032 AAGATAGCAAATATTATTTCCCTGAAGTTGCAGTAGAATAGACTAAAGCTA
130 AAGATAGCAAATCTTATTTCTCTGAAGTTGCAGTAGAATAGATTAAAGCTA
59950083 CAGATTACAA
Statistics
Matches: 314, Mismatches: 46, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
182 29 0.09
183 42 0.13
184 1 0.00
187 1 0.00
189 83 0.26
190 83 0.26
191 1 0.00
192 1 0.00
193 1 0.00
195 1 0.00
196 42 0.13
197 29 0.09
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (184 bp):
AATCCTATACCTCTGAAGTTGTAGTAGGTCGGATCAAATCTACCATGGCGAATCTTATCTCCCTG
AAGTTGCAGTAGAGCAGATTGAAGCCACAAACCTTATCTCCTGAAGTTGCAGTGGAGCAAGTTGA
AGATAGCAAATCTTATTTCTCTGAAGTTGCAGTAGAATAGATTAAAGCTAGTAC
Found at i:59950202 original size:11 final size:11
Alignment explanation
Indices: 59950186--59950216 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
59950176 TACTCAAAGA
59950186 AAAGAAGCACC
1 AAAGAAGCACC
59950197 AAAGAAGCACC
1 AAAGAAGCACC
59950208 AAAGAAGCA
1 AAAGAAGCA
59950217 AAGATTCAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.58, C:0.23, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAGAAGCACC
Found at i:59952292 original size:46 final size:47
Alignment explanation
Indices: 59952175--59952298 Score: 112
Period size: 46 Copynumber: 2.7 Consensus size: 47
59952165 ATTTTTCACA
* * * *
59952175 TATTATTTATTTTAGACTTTCTA-TGTTTTCTTTTAAATTGTTATATG
1 TATTAATTATTTTAGACTTT-TATTATTTTATTTTAAATTATTATATG
* ** * *
59952222 TATT-ATTCATTTTA-AGTTGCATTATTTTATTTTAAATTATTTTGTG
1 TATTAATT-ATTTTAGACTTTTATTATTTTATTTTAAATTATTATATG
*
59952268 TATTAATTATTTTAGA-TTTTATTATATTATT
1 TATTAATTATTTTAGACTTTTATTATTTTATT
59952299 CCCTTTAAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
45 1 0.02
46 46 0.75
47 14 0.23
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.62
Consensus pattern (47 bp):
TATTAATTATTTTAGACTTTTATTATTTTATTTTAAATTATTATATG
Found at i:59953725 original size:12 final size:12
Alignment explanation
Indices: 59953708--59953732 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59953698 TTTAAAGGGA
59953708 TAAAAATTTTAC
1 TAAAAATTTTAC
59953720 TAAAAATTTTAC
1 TAAAAATTTTAC
59953732 T
1 T
59953733 TTTAATAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAATTTTAC
Found at i:59956360 original size:18 final size:18
Alignment explanation
Indices: 59956339--59956384 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
59956329 CATGTAACAT
59956339 CCTGAGGCCGCGTGATAG
1 CCTGAGGCCGCGTGATAG
59956357 CCTGAGGCCGCGTGATAG
1 CCTGAGGCCGCGTGATAG
59956375 CCTGAGGCCG
1 CCTGAGGCCG
59956385 TGTGGTGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.15
Consensus pattern (18 bp):
CCTGAGGCCGCGTGATAG
Found at i:59961716 original size:16 final size:17
Alignment explanation
Indices: 59961684--59961716 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
59961674 CATCAAGAAG
59961684 GGTTTTCAATGAAAACAT
1 GGTTTTCAA-GAAAACAT
59961702 GGTTTTCAA-AAAACA
1 GGTTTTCAAGAAAACA
59961717 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (17 bp):
GGTTTTCAAGAAAACAT
Found at i:59963504 original size:40 final size:40
Alignment explanation
Indices: 59963449--59963670 Score: 333
Period size: 40 Copynumber: 5.6 Consensus size: 40
59963439 TATTCGAATG
* *
59963449 ATATCCGGGCTAAGTCCTGTAGGCATTTGTGCT-TGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAT-TGACT
*
59963489 ATATCCGAGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
*
59963529 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
59963569 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
* * *
59963609 ATATCCGGGCAAAGACCCGAAGGCATTTGTGCAAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-TTGACT
*
59963649 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
59963671 TACTTGGGTT
Statistics
Matches: 168, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
39 13 0.08
40 151 0.90
41 4 0.02
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
Found at i:59971555 original size:40 final size:40
Alignment explanation
Indices: 59971493--59971714 Score: 322
Period size: 40 Copynumber: 5.6 Consensus size: 40
59971483 TATTCGAATG
*
59971493 ATATCCAGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
59971533 ATATTCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
59971573 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
59971613 ATATCCAGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * **
59971653 ATATTCGGGCTAAGACCCGAAGGCATTTGTGGGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
* *
59971693 ATATCC-GGCTAAATCCTGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
59971715 TACTTGGGTT
Statistics
Matches: 164, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 13 0.08
40 149 0.91
41 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:59973822 original size:17 final size:18
Alignment explanation
Indices: 59973800--59973834 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
59973790 CATAACAGCC
59973800 CACATTTTCCT-TCCTTT
1 CACATTTTCCTATCCTTT
*
59973817 CACATTTTTCTATCCTTT
1 CACATTTTCCTATCCTTT
59973835 TCTACAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.14, C:0.31, G:0.00, T:0.54
Consensus pattern (18 bp):
CACATTTTCCTATCCTTT
Found at i:59988852 original size:10 final size:10
Alignment explanation
Indices: 59988839--59988863 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
59988829 ATTTGGTCCA
59988839 TTTTGTCCCT
1 TTTTGTCCCT
59988849 TTTTGTCCCT
1 TTTTGTCCCT
59988859 TTTTG
1 TTTTG
59988864 GCTCGTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.12, T:0.64
Consensus pattern (10 bp):
TTTTGTCCCT
Found at i:59988872 original size:11 final size:11
Alignment explanation
Indices: 59988846--59988883 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
59988836 CCATTTTGTC
*
59988846 CCTTTTTGTC-
1 CCTTTTTGGCT
59988856 CCTTTTTGGCT
1 CCTTTTTGGCT
*
59988867 CGTTTTTGGCT
1 CCTTTTTGGCT
59988878 CCTTTT
1 CCTTTT
59988884 GACTCTTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.00, C:0.26, G:0.16, T:0.58
Consensus pattern (11 bp):
CCTTTTTGGCT
Found at i:59990724 original size:6 final size:6
Alignment explanation
Indices: 59990715--59990747 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
59990705 AATAAAATTG
*
59990715 AAATGA AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAA
59990748 GATAAGAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:59996153 original size:13 final size:13
Alignment explanation
Indices: 59996135--59996163 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
59996125 GGTTGTTTAT
59996135 TAAACTAATTAAC
1 TAAACTAATTAAC
59996148 TAAACTAATTAAC
1 TAAACTAATTAAC
59996161 TAA
1 TAA
59996164 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:59997654 original size:2 final size:2
Alignment explanation
Indices: 59997647--59997697 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
59997637 ACCATTGACG
* *
59997647 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59997689 TA TA -A TA TA
1 TA TA TA TA TA
59997698 CAAACCAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:60004539 original size:30 final size:29
Alignment explanation
Indices: 60004505--60004564 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
60004495 TCCTTAACTC
60004505 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTAC-ATTTTGCCCCT
* * * *
60004535 AAACTTTTGCATATTTACATTTTGCCCCT
1 AAACTTTGGAAAAATTACATTTTGCCCCT
60004564 A
1 A
60004565 GGCTCTGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (29 bp):
AAACTTTGGAAAAATTACATTTTGCCCCT
Found at i:60005550 original size:22 final size:22
Alignment explanation
Indices: 60005524--60005567 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
60005514 AAAAACTAGC
60005524 AAATTAAAATAAAAAGAAAAAT
1 AAATTAAAATAAAAAGAAAAAT
* *
60005546 AAATTACAATAAAAATAAAAAT
1 AAATTAAAATAAAAAGAAAAAT
60005568 GGCTACAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (22 bp):
AAATTAAAATAAAAAGAAAAAT
Found at i:60008272 original size:35 final size:34
Alignment explanation
Indices: 60008229--60008304 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
60008219 CCATCTCAGT
* *
60008229 ACAGTATCAAATATGTAGTAGCGACTTAGCCCATC
1 ACAGTATC-AATATGCAGTAGCGACTTAACCCATC
* * * *
60008264 ACAGTATCAGTATGCATTAGGGCCTTAACCCATC
1 ACAGTATCAATATGCAGTAGCGACTTAACCCATC
60008298 ACAGTAT
1 ACAGTAT
60008305 TAGTAGCAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
34 27 0.77
35 8 0.23
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (34 bp):
ACAGTATCAATATGCAGTAGCGACTTAACCCATC
Found at i:60011726 original size:47 final size:47
Alignment explanation
Indices: 60011654--60011905 Score: 378
Period size: 47 Copynumber: 5.3 Consensus size: 47
60011644 CCCTTCGAGA
* * * * * * *
60011654 CTTATCACATTTATACACTTCCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
60011701 CCTATCACATATATACACTTTCACATTCATCACATTGGCTATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
60011748 CTTATCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
60011795 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
60011842 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATAT--ACACTTTCACATTCATCACATCGGCCATTAGGC
60011891 CTTATCACATATATA
1 CTTATCACATATATA
60011906 TATCTCATAC
Statistics
Matches: 190, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
47 143 0.75
49 47 0.25
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:60019754 original size:23 final size:24
Alignment explanation
Indices: 60019703--60019755 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
60019693 GCAAGAGAAT
60019703 AAAGA-AAAATGGATGAGAAATGA
1 AAAGAGAAAATGGATGAGAAATGA
* *
60019726 AGAGAGAAAATTGA-GAGAGAA-GA
1 AAAGAGAAAATGGATGAGA-AATGA
60019749 AAAGAGA
1 AAAGAGA
60019756 TGAGAAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.60, C:0.00, G:0.30, T:0.09
Consensus pattern (24 bp):
AAAGAGAAAATGGATGAGAAATGA
Found at i:60020348 original size:10 final size:10
Alignment explanation
Indices: 60020297--60020343 Score: 76
Period size: 10 Copynumber: 4.7 Consensus size: 10
60020287 GCAAATCTGC
*
60020297 CAAAAATAAT
1 CAAAATTAAT
60020307 CAAAATTAAT
1 CAAAATTAAT
60020317 CAAAATTAAT
1 CAAAATTAAT
60020327 CAAAATTAAT
1 CAAAATTAAT
*
60020337 TAAAATT
1 CAAAATT
60020344 CATTATGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 35 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.30
Consensus pattern (10 bp):
CAAAATTAAT
Found at i:60024374 original size:40 final size:40
Alignment explanation
Indices: 60024259--60024465 Score: 285
Period size: 40 Copynumber: 5.2 Consensus size: 40
60024249 TCTTCGGAAT
* ** *
60024259 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* * *
60024298 TTAACCCGGGTATAGCAACTC-CACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
60024337 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
60024377 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* * * *
60024417 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTTGGGAC
1 TTAGCCCGGATATAA-CAACTCGCACAAATGCCTTCGGGTC
60024457 TTAGCCCGG
1 TTAGCCCGG
60024466 GTATCATTCA
Statistics
Matches: 151, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 38 0.25
40 112 0.74
41 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
Found at i:60032431 original size:40 final size:40
Alignment explanation
Indices: 60032358--60032525 Score: 180
Period size: 40 Copynumber: 4.2 Consensus size: 40
60032348 TCTTCGGAAT
* ** *
60032358 TTAA-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAACCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* * * *
60032397 TTAACCCGGGTATAGCAACTCCCACAAATGCCTTCGAGTC
1 TTAACCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
60032437 TTAGA-CCGGATATAACAACTCGCACAAATGCCTTCGGGTC
1 TTA-ACCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* * * *
60032477 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGAC
1 TTAACCCGGATATAA-CAACTCGCACAAATGCCTTCGGGTC
*
60032517 TTAGCCCGG
1 TTAACCCGG
60032526 GTATCATTCA
Statistics
Matches: 109, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
39 4 0.04
40 103 0.94
41 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (40 bp):
TTAACCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
Found at i:60035509 original size:40 final size:40
Alignment explanation
Indices: 60035424--60035574 Score: 141
Period size: 40 Copynumber: 3.8 Consensus size: 40
60035414 AATTGAATGA
* * * *
60035424 TATCCGGGCTAAGCCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
60035464 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
60035505 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
60035544 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
60035575 ACGTGGTTAT
Statistics
Matches: 92, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 80 0.87
41 3 0.03
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:60035588 original size:40 final size:40
Alignment explanation
Indices: 60035461--60035590 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
60035451 ATGCTGGAAA
* * *
60035461 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * ***
60035501 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGACA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
60035541 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
60035581 TTATATCCGG
1 TTATATCCGG
60035591 TTATATTCCG
Statistics
Matches: 72, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
39 1 0.01
40 71 0.99
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:60035589 original size:80 final size:80
Alignment explanation
Indices: 60035423--60035590 Score: 207
Period size: 80 Copynumber: 2.1 Consensus size: 80
60035413 AAATTGAATG
* *
60035423 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCA
60035488 ATTGTGCTAGTGGCT
66 ATTGTGCTAGTGGCT
* * * * *
60035503 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATTCTATCCGGGCTAAGACCCGAAGG
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTG-GAAATTATATCCGGGCTAAGACCCGAAGG
* *
60035566 CATTTGTGC-ACGTGGTT
64 CAATTGTGCTA-GTGGCT
60035583 ATATCCGG
1 ATATCCGG
60035591 TTATATTCCG
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
79 5 0.07
80 70 0.93
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCA
ATTGTGCTAGTGGCT
Found at i:60037859 original size:26 final size:27
Alignment explanation
Indices: 60037809--60037859 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
60037799 AGTTCATAAA
*
60037809 TTCTCTTTGAGTTTTCTTTTTAAGAAT
1 TTCTCTTTGAGTTTTCTTTTGAAGAAT
60037836 TTCTC-TTGAG-TTTCTTTTAGAAGA
1 TTCTCTTTGAGTTTTCTTTT-GAAGA
60037860 GTTTTAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 9 0.41
27 5 0.23
ACGTcount: A:0.20, C:0.12, G:0.14, T:0.55
Consensus pattern (27 bp):
TTCTCTTTGAGTTTTCTTTTGAAGAAT
Found at i:60040262 original size:49 final size:49
Alignment explanation
Indices: 60040198--60040383 Score: 214
Period size: 49 Copynumber: 3.8 Consensus size: 49
60040188 ATCATAGTTA
* * * *
60040198 ATGAGATCTCGTGTAAGACTATGTCTGGGACATGGCATCGACATTCGAG
1 ATGAGATCCCATGTAAGACCATATCTGGGACATGGCATCGACATTCGAG
* *
60040247 ATGAGATCCCATGTAAGACCATATCTGGGACATGGCATTGACATCCGAG
1 ATGAGATCCCATGTAAGACCATATCTGGGACATGGCATCGACATTCGAG
* ** * * *
60040296 ATGAGAGCCGGTGTAAGACCATATCTGGGACATGGCATCGTCGTT-GAT
1 ATGAGATCCCATGTAAGACCATATCTGGGACATGGCATCGACATTCGAG
* * *
60040344 ATGTG-TGCTAGTGTAAGACCATATCTGGGACATGGCATCG
1 ATGAGATCCCA-TGTAAGACCATATCTGGGACATGGCATCG
60040384 GCACCAATAT
Statistics
Matches: 117, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
47 1 0.01
48 35 0.30
49 81 0.69
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (49 bp):
ATGAGATCCCATGTAAGACCATATCTGGGACATGGCATCGACATTCGAG
Found at i:60040409 original size:48 final size:48
Alignment explanation
Indices: 60040260--60040568 Score: 213
Period size: 48 Copynumber: 6.6 Consensus size: 48
60040250 AGATCCCATG
* * * * * ** *
60040260 TAAGACCATATCTGGGACATGGCATTGACATCCGAGATGAGAGCCGGTG
1 TAAGACCATATCTGGGACATGGCATCGGCA-CCGATATGTGATCTTGTA
* *** * *
60040309 TAAGACCATATCTGGGACATGGCATCGTCGTTGATATGTG-TGCTAGTG
1 TAAGACCATATCTGGGACATGGCATCGGCACCGATATGTGAT-CTTGTA
* *
60040357 TAAGACCATATCTGGGACATGGCATCGGCACCAATATGTCATCTTGTA
1 TAAGACCATATCTGGGACATGGCATCGGCACCGATATGTGATCTTGTA
** * * * * * *
60040405 TAAGACCATATCAAGGATATGGCTTCGGCATCGTTAAGTGATTTTGTA
1 TAAGACCATATCTGGGACATGGCATCGGCACCGATATGTGATCTTGTA
* * * **
60040453 TAAGACCATGTCT-GGACATGGCAT---CA---ATATGAGGTCCCGTA
1 TAAGACCATATCTGGGACATGGCATCGGCACCGATATGTGATCTTGTA
* * * *
60040494 TAAGACCATGTCTGGGATATGGCATCGGCACTGATATGAGA-CTTCGTA
1 TAAGACCATATCTGGGACATGGCATCGGCACCGATATGTGATCTT-GTA
* *
60040542 TAAGACCATATTTGGGATATGGCATCG
1 TAAGACCATATCTGGGACATGGCATCG
60040569 ATATACGGGC
Statistics
Matches: 205, Mismatches: 45, Indels: 21
0.76 0.17 0.08
Matches are distributed among these distances:
41 21 0.10
42 10 0.05
44 2 0.01
45 2 0.01
47 10 0.05
48 132 0.64
49 28 0.14
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (48 bp):
TAAGACCATATCTGGGACATGGCATCGGCACCGATATGTGATCTTGTA
Found at i:60040606 original size:90 final size:89
Alignment explanation
Indices: 60040450--60040615 Score: 208
Period size: 90 Copynumber: 1.9 Consensus size: 89
60040440 AAGTGATTTT
* * * * *
60040450 GTATAAGACCATGTCTGGACATGGCATCAATATGAGGTCCCGTATAAGACCATGTCTGGGATATG
1 GTATAAGACCATATCTGGACATGGCATCAATATGAGGGCCCATATAAGACCATATCTGGGACATG
60040515 GCATCGGCACTGATATGAGACTTC
66 GCATCGGCACTGATATGAGACTTC
* * * *
60040539 GTATAAGACCATATTTGGGATATGGCATCGATAT-ACGGGCCCATGTAAGACCATATCTGGGACA
1 GTATAAGACCATATCT-GGACATGGCATCAATATGA-GGGCCCATATAAGACCATATCTGGGACA
* *
60040603 TGGCTTTGGCACT
64 TGGCATCGGCACT
60040616 CTATTTGGTG
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
89 15 0.23
90 49 0.77
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (89 bp):
GTATAAGACCATATCTGGACATGGCATCAATATGAGGGCCCATATAAGACCATATCTGGGACATG
GCATCGGCACTGATATGAGACTTC
Found at i:60042335 original size:25 final size:24
Alignment explanation
Indices: 60042294--60042356 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
60042284 GATTATGTAG
60042294 AAAGAATAAAGAAATGAAAAAAAAA
1 AAAGAA-AAAGAAATGAAAAAAAAA
* * *
60042319 AAAGAAAGAGAATATGAAGAAAAAC
1 AAAGAAAAAGAA-ATGAAAAAAAAA
*
60042344 AAAGAAAAGGAAA
1 AAAGAAAAAGAAA
60042357 AAAAAAGTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 6 0.19
25 26 0.81
ACGTcount: A:0.75, C:0.02, G:0.17, T:0.06
Consensus pattern (24 bp):
AAAGAAAAAGAAATGAAAAAAAAA
Found at i:60043556 original size:29 final size:29
Alignment explanation
Indices: 60043523--60043587 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
60043513 GTGACGAGAT
*
60043523 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
60043552 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
*
60043581 CGGCACT
1 TGGCACT
60043588 GGGTGTGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAAAATA
Found at i:60050231 original size:19 final size:19
Alignment explanation
Indices: 60050183--60050252 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
60050173 GTTAGTGGAT
* *
60050183 TATGTAGAAAGAATAAAGAA
1 TATGAAGAAA-AAAAAAGAA
*
60050203 -ATGAAAAAAAAAAAAGAA
1 TATGAAGAAAAAAAAAGAA
*
60050221 TATGAAGAAAAACAAAGAA
1 TATGAAGAAAAAAAAAGAA
* *
60050240 AAGGAA-AAAAAAA
1 TATGAAGAAAAAAA
60050253 GTGTTCATTC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 14 0.34
19 27 0.66
ACGTcount: A:0.73, C:0.01, G:0.16, T:0.10
Consensus pattern (19 bp):
TATGAAGAAAAAAAAAGAA
Found at i:60051446 original size:29 final size:29
Alignment explanation
Indices: 60051413--60051477 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
60051403 GTGACGAGAT
*
60051413 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
60051442 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
*
60051471 CGGCACT
1 TGGCACT
60051478 GGGTGTGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAAAATA
Found at i:60055408 original size:28 final size:29
Alignment explanation
Indices: 60055377--60055439 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 29
60055367 TAATTTTTAA
60055377 AAATTGGTT-GAAGAAA-ATAAAAAAT-ATT
1 AAATT-GTTGGAA-AAATATAAAAAATAATT
*
60055405 AAATT-TTGGAAAAATATTAAAAATAATT
1 AAATTGTTGGAAAAATATAAAAAATAATT
60055433 AAATTGT
1 AAATTGT
60055440 AAAAGAAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 5 0.17
27 11 0.37
28 13 0.43
29 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (29 bp):
AAATTGTTGGAAAAATATAAAAAATAATT
Done.