Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 43 of 97
Found at i:17531137 original size:29 final size:28
Alignment explanation
Indices: 17530987--17531160 Score: 206
Period size: 28 Copynumber: 6.1 Consensus size: 28
17530977 AACCCTTACA
* *
17530987 ATGGCTTTTAACGGGTTCAACCACAAACCA
1 ATGG-TTTTAACGAGTTC-ACCACAAACCC
*
17531017 ATGGTTTTAACGAGTTCACCTCAAACCC
1 ATGGTTTTAACGAGTTCACCACAAACCC
* *
17531045 ATGGTTTTAACAAGTTCACTACAAACCC
1 ATGGTTTTAACGAGTTCACCACAAACCC
* * *
17531073 ATGGTTTTAACAAGTTCATCACAACCCC
1 ATGGTTTTAACGAGTTCACCACAAACCC
*
17531101 ATGGTTTTAACGGGTTCACCACAAACCC
1 ATGGTTTTAACGAGTTCACCACAAACCC
* *
17531129 ATGGTTTTTAACTG-GATCAGCACAAACCC
1 ATGG-TTTTAAC-GAGTTCACCACAAACCC
17531158 ATG
1 ATG
17531161 CTAATTTTTC
Statistics
Matches: 127, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
28 87 0.69
29 35 0.28
30 5 0.04
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (28 bp):
ATGGTTTTAACGAGTTCACCACAAACCC
Found at i:17532963 original size:34 final size:34
Alignment explanation
Indices: 17532875--17532964 Score: 110
Period size: 34 Copynumber: 2.6 Consensus size: 34
17532865 AGTTAAGAGA
*
17532875 TTATGCTTGATCCTTGAAAAAGGCATTCTAAAGG
1 TTATGCTTGATCCTTGGAAAAGGCATTCTAAAGG
* * *
17532909 TTGTGCATGATCCTTTGAAAAGGCATTGC-AAAGG
1 TTATGCTTGATCCTTGGAAAAGGCATT-CTAAAGG
* *
17532943 TTATGCTTAAGCCTTGGAAAAG
1 TTATGCTTGATCCTTGGAAAAG
17532965 TAATTTCCAT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
34 45 0.98
35 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.31
Consensus pattern (34 bp):
TTATGCTTGATCCTTGGAAAAGGCATTCTAAAGG
Found at i:17534350 original size:88 final size:88
Alignment explanation
Indices: 17534201--17534378 Score: 257
Period size: 88 Copynumber: 2.0 Consensus size: 88
17534191 TTCATAAACA
*
17534201 TATAGTTCTTTAAATAAGCTAAAAATTTATACAAAACCTTTAGGAAAAACAAGGAAGTTGTACCT
1 TATAGTTATTTAAATAAGCTAAAAATTTATACAAAACCTTTAGGAAAAACAAGGAAGTTGTACCT
* * *
17534266 TACTTGTGGCATTGAATCCTCCC
66 CACCTGTGGCATCGAATCCTCCC
* * * * *
17534289 TATAGTTATTTAAATAAGCTGAACATTTATGCAAAACTTTTAGGTAAAACAAGGAAGTTGTACCT
1 TATAGTTATTTAAATAAGCTAAAAATTTATACAAAACCTTTAGGAAAAACAAGGAAGTTGTACCT
* *
17534354 CACCTGTGGTATCGGATCCTCCC
66 CACCTGTGGCATCGAATCCTCCC
17534377 TA
1 TA
17534379 AAGGAAACAA
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 79 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (88 bp):
TATAGTTATTTAAATAAGCTAAAAATTTATACAAAACCTTTAGGAAAAACAAGGAAGTTGTACCT
CACCTGTGGCATCGAATCCTCCC
Found at i:17539059 original size:22 final size:22
Alignment explanation
Indices: 17539023--17539065 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17539013 AAATCCTACC
17539023 TTTTTCACTTGTTTTCCTTGAT
1 TTTTTCACTTGTTTTCCTTGAT
*
17539045 TTTTCTCACTT-TTTTTCTTGA
1 TTTT-TCACTTGTTTTCCTTGA
17539066 AATTCTCCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.09, C:0.19, G:0.07, T:0.65
Consensus pattern (22 bp):
TTTTTCACTTGTTTTCCTTGAT
Found at i:17539060 original size:23 final size:21
Alignment explanation
Indices: 17539023--17539065 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
17539013 AAATCCTACC
17539023 TTTTTCACTTGTTTTCCTTGAT
1 TTTTTCACTTGTTTT-CTTGAT
*
17539045 TTTTCTCACTTTTTTTCTTGA
1 TTTT-TCACTTGTTTTCTTGA
17539066 AATTCTCCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.09, C:0.19, G:0.07, T:0.65
Consensus pattern (21 bp):
TTTTTCACTTGTTTTCTTGAT
Found at i:17543421 original size:21 final size:22
Alignment explanation
Indices: 17543397--17543440 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
17543387 TTTAAAACAA
17543397 ATTTAAAA-CAAAAGCTCTGAT
1 ATTTAAAACCAAAAGCTCTGAT
*
17543418 ATTTAAAACCAAATGCTCTGAT
1 ATTTAAAACCAAAAGCTCTGAT
17543440 A
1 A
17543441 CCAATCGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (22 bp):
ATTTAAAACCAAAAGCTCTGAT
Found at i:17549676 original size:36 final size:36
Alignment explanation
Indices: 17549573--17549711 Score: 116
Period size: 36 Copynumber: 3.9 Consensus size: 36
17549563 CTTATACATG
* * * *
17549573 TGTGGTACAACACCCCATATCTAGCCATATTAAACA
1 TGTGGTATAACACCCCACATCTAGCCACATTACACA
** * * *
17549609 TGTGGTATAACGTCCCTCATCTAGTCTCATTACACA
1 TGTGGTATAACACCCCACATCTAGCCACATTACACA
* * ***
17549645 TGTGGTATAACACCCCACATTTGGCCACATTACTGG
1 TGTGGTATAACACCCCACATCTAGCCACATTACACA
** * *
17549681 TGTGGTATAATGCCCCACATTTGGCCACATT
1 TGTGGTATAACACCCCACATCTAGCCACATT
17549712 GTTCACATAG
Statistics
Matches: 82, Mismatches: 21, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 82 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (36 bp):
TGTGGTATAACACCCCACATCTAGCCACATTACACA
Found at i:17565720 original size:19 final size:19
Alignment explanation
Indices: 17565698--17565749 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 19
17565688 AAATTTTTTG
17565698 AATAAATTAATATTTTATT
1 AATAAATTAATATTTTATT
17565717 AAT-AA--AATA--TTATT
1 AATAAATTAATATTTTATT
17565731 AA-AATATTAATATTTTATT
1 AATAA-ATTAATATTTTATT
17565750 CAGTTTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 12
0.69 0.00 0.31
Matches are distributed among these distances:
14 8 0.30
15 1 0.04
16 4 0.15
17 4 0.15
18 2 0.07
19 8 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATAAATTAATATTTTATT
Found at i:17565727 original size:11 final size:11
Alignment explanation
Indices: 17565713--17565742 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
17565703 ATTAATATTT
17565713 TATTAATAAAA
1 TATTAATAAAA
*
17565724 TATTATTAAAA
1 TATTAATAAAA
17565735 TATTAATA
1 TATTAATA
17565743 TTTTATTCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAATAAAA
Found at i:17567929 original size:19 final size:19
Alignment explanation
Indices: 17567891--17567929 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
17567881 AAAATTTTGG
**
17567891 AATAAAATAATATTTTATT
1 AATAAAATAATATTAAATT
*
17567910 AATAAAATATTATTAAATT
1 AATAAAATAATATTAAATT
17567929 A
1 A
17567930 TTAATATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATAAAATAATATTAAATT
Found at i:17568424 original size:18 final size:19
Alignment explanation
Indices: 17568389--17568425 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
17568379 GCTAATTTTC
17568389 TTTCATTTTCTTTCCTTGT
1 TTTCATTTTCTTTCCTTGT
17568408 TTTC-TTTTCATTT-CTTGT
1 TTTCATTTTC-TTTCCTTGT
17568426 CTCTTCTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.05, C:0.19, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTCATTTTCTTTCCTTGT
Found at i:17569664 original size:42 final size:42
Alignment explanation
Indices: 17569596--17569830 Score: 323
Period size: 42 Copynumber: 5.6 Consensus size: 42
17569586 TGTTGATATG
* * *
17569596 GACCCAGCTATGTGCAAGTAGGAGTGCACATAAGCTGTTACT
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCTGTTGCT
*
17569638 GACCCGGCTATGTGCGAGT-GAAAGTGCACATAAGCTGTTGCT
1 GACCCGGCTATGTGCGAGTAG-GAGTGCACATAAGCTGTTGCT
* *
17569680 -ACCCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTACT
1 GA-CCCGGCTATGTGCGAGTAGGAGTGCACATAAGCTGTTGCT
*
17569722 GACCCGGCTATGTGCGAGTAGAAGTGCACATAAG-TCGTTGCT
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCT-GTTGCT
* *
17569764 GACCCGGCTATGTGTGAGTGGGAGTGCACATAAGCTGTTGCT
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCTGTTGCT
* *
17569806 GACCCGGCTATATGCGAGTGGGAGT
1 GACCCGGCTATGTGCGAGTAGGAGT
17569831 ACGTGTTAGC
Statistics
Matches: 172, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
41 2 0.01
42 167 0.97
43 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.31, T:0.23
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCTGTTGCT
Found at i:17569822 original size:126 final size:126
Alignment explanation
Indices: 17569596--17569830 Score: 357
Period size: 126 Copynumber: 1.9 Consensus size: 126
17569586 TGTTGATATG
*
17569596 GACCCAGCTATGTGCAAGTAGGAGTGCACATAAGCTGTTACTGACCCGGCTATGTGCGAGTGAAA
1 GACCCAGCTATGTGCAAGTAGAAGTGCACATAAGCTGTTACTGACCCGGCTATGTGCGAGTGAAA
*
17569661 GTGCACATAAGCTGTTGCTACCCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTACT
66 GTGCACATAAGCTGTTGCTACCCCGGCTATATGCGAGTAGGAGTGCACATAAGCCGTTACT
* * * * **
17569722 GACCCGGCTATGTGCGAGTAGAAGTGCACATAAG-TCGTTGCTGACCCGGCTATGTGTGAGTGGG
1 GACCCAGCTATGTGCAAGTAGAAGTGCACATAAGCT-GTTACTGACCCGGCTATGTGCGAGTGAA
*
17569786 AGTGCACATAAGCTGTTGCTGA-CCCGGCTATATGCGAGTGGGAGT
65 AGTGCACATAAGCTGTTGCT-ACCCCGGCTATATGCGAGTAGGAGT
17569831 ACGTGTTAGC
Statistics
Matches: 98, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
125 1 0.01
126 96 0.98
127 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.31, T:0.23
Consensus pattern (126 bp):
GACCCAGCTATGTGCAAGTAGAAGTGCACATAAGCTGTTACTGACCCGGCTATGTGCGAGTGAAA
GTGCACATAAGCTGTTGCTACCCCGGCTATATGCGAGTAGGAGTGCACATAAGCCGTTACT
Found at i:17570827 original size:15 final size:15
Alignment explanation
Indices: 17570807--17570835 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17570797 TTCATAACTC
17570807 AATCATAAACTTTGA
1 AATCATAAACTTTGA
17570822 AATCATAAACTTTG
1 AATCATAAACTTTG
17570836 TTCAAGTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (15 bp):
AATCATAAACTTTGA
Found at i:17572365 original size:16 final size:16
Alignment explanation
Indices: 17572335--17572364 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17572325 CCAAAAATTA
17572335 GATTTTGATTCTTTTG
1 GATTTTGATTCTTTTG
17572351 GATTTTGATT-TTTT
1 GATTTTGATTCTTTT
17572365 TTTATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.03, G:0.17, T:0.67
Consensus pattern (16 bp):
GATTTTGATTCTTTTG
Found at i:17574386 original size:20 final size:20
Alignment explanation
Indices: 17574314--17574386 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
17574304 TTTTGTGTGA
**
17574314 AATGTATCGATACATTTTACT
1 AATGTATCGATACA-TTTAAG
* * *
17574335 AATGTATCAATAGATTTATG
1 AATGTATCGATACATTTAAG
* * *
17574355 AAAGTATTGATACATTCAAG
1 AATGTATCGATACATTTAAG
17574375 AATGTATCGATA
1 AATGTATCGATA
17574387 GTTTTGGCAT
Statistics
Matches: 40, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
20 28 0.70
21 12 0.30
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (20 bp):
AATGTATCGATACATTTAAG
Found at i:17579285 original size:35 final size:35
Alignment explanation
Indices: 17579236--17579332 Score: 104
Period size: 35 Copynumber: 2.7 Consensus size: 35
17579226 GCTATCTTGT
* ** *
17579236 AAGGTTATCACTTGATCTTGTAAAAAACTATTATA
1 AAGGTTATCGCTTGATCTCATAAAAAACCATTATA
* *
17579271 AAGGTTATCGCTTGATCCCATAAAAAACCATTGTA
1 AAGGTTATCGCTTGATCTCATAAAAAACCATTATA
* * *
17579306 AGGGTTTTCGCTTAATCTCACTAAAAA
1 AAGGTTATCGCTTGATCTCA-TAAAAA
17579333 GAAAGAATCC
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
35 45 0.88
36 6 0.12
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.33
Consensus pattern (35 bp):
AAGGTTATCGCTTGATCTCATAAAAAACCATTATA
Found at i:17584082 original size:35 final size:35
Alignment explanation
Indices: 17584019--17584089 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
17584009 TTAATTATTG
* *
17584019 GGTTTTGGTTGATCTTGGTAAAAACCATTGTGAAA
1 GGTTTTGGTTGATCTTAGTAAAAACCATTGTAAAA
* *
17584054 GGTTTTGGTTGA-CTCTAGTCAAAGCCATTGTAAAA
1 GGTTTTGGTTGATCT-TAGTAAAAACCATTGTAAAA
17584089 G
1 G
17584090 CTTGGTGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 2 0.06
35 29 0.94
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.35
Consensus pattern (35 bp):
GGTTTTGGTTGATCTTAGTAAAAACCATTGTAAAA
Found at i:17596036 original size:21 final size:21
Alignment explanation
Indices: 17595994--17596036 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
17595984 CTTGTACCGG
*
17595994 TGGTGGAACTAAAGGAGTAAC
1 TGGTGGAACTAAAGGAGGAAC
* * *
17596015 TGGTGGTACTATAGGTGGAAC
1 TGGTGGAACTAAAGGAGGAAC
17596036 T
1 T
17596037 TGACCAGTCG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.09, G:0.35, T:0.26
Consensus pattern (21 bp):
TGGTGGAACTAAAGGAGGAAC
Found at i:17603318 original size:17 final size:17
Alignment explanation
Indices: 17603296--17603331 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17603286 AAGTAAAATA
17603296 AGCACAAACTAAGGGGG
1 AGCACAAACTAAGGGGG
* *
17603313 AGCACACACTTAGGGGG
1 AGCACAAACTAAGGGGG
17603330 AG
1 AG
17603332 AAATTCTCAT
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:0.36, C:0.19, G:0.36, T:0.08
Consensus pattern (17 bp):
AGCACAAACTAAGGGGG
Found at i:17608330 original size:17 final size:19
Alignment explanation
Indices: 17608296--17608330 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
17608286 TATGTGGACA
17608296 TGCATGTGAAATTCATTAT
1 TGCATGTGAAATTCATTAT
17608315 TGCATG-GAAA-TCATTA
1 TGCATGTGAAATTCATTA
17608331 CATGCAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (19 bp):
TGCATGTGAAATTCATTAT
Found at i:17608336 original size:18 final size:20
Alignment explanation
Indices: 17608293--17608336 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
17608283 GATTATGTGG
17608293 ACATGCATGTGAAATTCATT
1 ACATGCATGTGAAATTCATT
*
17608313 A-TTGCATG-GAAA-TCATT
1 ACATGCATGTGAAATTCATT
17608330 ACATGCA
1 ACATGCA
17608337 AAAAAAAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 6 0.29
18 8 0.38
19 6 0.29
20 1 0.05
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (20 bp):
ACATGCATGTGAAATTCATT
Found at i:17608870 original size:14 final size:14
Alignment explanation
Indices: 17608853--17608900 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
17608843 AGAAAAAAAG
17608853 AGAAAGGAGAAGAA
1 AGAAAGGAGAAGAA
*
17608867 AGAAAGAAGAA-AA
1 AGAAAGGAGAAGAA
17608880 TAGAAAGGA-AAGGAA
1 -AGAAAGGAGAA-GAA
17608895 AGAAAG
1 AGAAAG
17608901 AAAAAGAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 4 0.14
14 23 0.79
15 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (14 bp):
AGAAAGGAGAAGAA
Found at i:17608873 original size:28 final size:28
Alignment explanation
Indices: 17608841--17608921 Score: 107
Period size: 28 Copynumber: 3.0 Consensus size: 28
17608831 CACCCATAAC
17608841 AAAGAAAAAAAGAGAAAGGAGAA-GAAAG
1 AAAGAAAAAAAGAGAAAGGA-AAGGAAAG
* *
17608869 AAAGAAGAAAATAGAAAGGAAAGGAAAG
1 AAAGAAAAAAAGAGAAAGGAAAGGAAAG
17608897 AAAG--AAAAAGAGAAAGG-AAGGAAAG
1 AAAGAAAAAAAGAGAAAGGAAAGGAAAG
17608922 GCTTGGTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
25 8 0.17
26 11 0.23
27 2 0.04
28 27 0.56
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (28 bp):
AAAGAAAAAAAGAGAAAGGAAAGGAAAG
Found at i:17608913 original size:21 final size:20
Alignment explanation
Indices: 17608883--17608921 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
17608873 AAGAAAATAG
17608883 AAAGGAAAGGAAAGAAAGAA
1 AAAGGAAAGGAAAGAAAGAA
*
17608903 AAAGAGAAAGGAAGGAAAG
1 AAAG-GAAAGGAAAGAAAG
17608922 GCTTGGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
AAAGGAAAGGAAAGAAAGAA
Found at i:17613165 original size:43 final size:43
Alignment explanation
Indices: 17613109--17613227 Score: 148
Period size: 43 Copynumber: 2.8 Consensus size: 43
17613099 GTAATGACAT
* * * *
17613109 TGACTCGGCTATGTGTGAGTAAGAAGTGCGCATAAGTCAATGA
1 TGACTTGGCTATGTGCGAGTAAGGAGTGCGCATAACTCAATGA
* **
17613152 TGACTTGGTTATGTGCGAGTAAGGAGTGCGCATAACTCGGTGA
1 TGACTTGGCTATGTGCGAGTAAGGAGTGCGCATAACTCAATGA
* * *
17613195 TGACCTAGCCATGTGCGAGTAAGGAGTGCGCAT
1 TGACTTGGCTATGTGCGAGTAAGGAGTGCGCAT
17613228 GAGTTGGGGA
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.25
Consensus pattern (43 bp):
TGACTTGGCTATGTGCGAGTAAGGAGTGCGCATAACTCAATGA
Found at i:17617984 original size:60 final size:60
Alignment explanation
Indices: 17617891--17618038 Score: 262
Period size: 60 Copynumber: 2.5 Consensus size: 60
17617881 CCATAACTGG
* * *
17617891 TTCTCGCTGCAACGAAAAACTTTCTATTTCTGGGTAACAATTTCGTTGCAGCGAAATTCA
1 TTCTCGCTGCAGCGAAAAACTTTCTGTTTCTGGGTAACAATTTCGTTGCAGCGAAATTAA
17617951 TTCTCGCTGCAGCGAAAAACTTTCTGTTTCTGGGTAACAATTTCGTTGCAGCGAAATTAA
1 TTCTCGCTGCAGCGAAAAACTTTCTGTTTCTGGGTAACAATTTCGTTGCAGCGAAATTAA
17618011 TTCTCGCTGCAGC-AAAAACTTTCTGTTT
1 TTCTCGCTGCAGCGAAAAACTTTCTGTTT
17618039 TGTCTCCTAT
Statistics
Matches: 85, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
59 15 0.18
60 70 0.82
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (60 bp):
TTCTCGCTGCAGCGAAAAACTTTCTGTTTCTGGGTAACAATTTCGTTGCAGCGAAATTAA
Found at i:17619753 original size:27 final size:27
Alignment explanation
Indices: 17619723--17619777 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
17619713 AAAAAGAAGT
17619723 AGGAATGATGTACACTAAAGGTATTGC
1 AGGAATGATGTACACTAAAGGTATTGC
17619750 AGGAATGATGTACACTAAAGGTATTGC
1 AGGAATGATGTACACTAAAGGTATTGC
17619777 A
1 A
17619778 TTTGAATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.25
Consensus pattern (27 bp):
AGGAATGATGTACACTAAAGGTATTGC
Found at i:17621366 original size:42 final size:42
Alignment explanation
Indices: 17621293--17621411 Score: 139
Period size: 42 Copynumber: 2.8 Consensus size: 42
17621283 TGTTGATGTG
* * *
17621293 GACCTGGCTATGTGCGAGTAGGAATGGACATAAGCCATTACT
1 GACCTGGCTATGTGCGAGTGGGAGTGCACATAAGCCATTACT
* * * **
17621335 GACCCGGCTATGTGCTAGTGGGAGTGCACATAAGCCGTTGTT
1 GACCTGGCTATGTGCGAGTGGGAGTGCACATAAGCCATTACT
* * *
17621377 GACCTAGCTATGTGCGAATGGGAGTGCGCATAAGC
1 GACCTGGCTATGTGCGAGTGGGAGTGCACATAAGC
17621412 TGTTACATAT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (42 bp):
GACCTGGCTATGTGCGAGTGGGAGTGCACATAAGCCATTACT
Found at i:17624478 original size:19 final size:20
Alignment explanation
Indices: 17624427--17624484 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
17624417 AAAAACTAAT
*
17624427 AAATAACAATGAAATTAAAAG
1 AAATAAC-ATAAAATTAAAAG
17624448 AAATAACATAAAATTAAAA-
1 AAATAACATAAAATTAAAAG
* * *
17624467 AATTAACTTAAAAATAAA
1 AAATAACATAAAATTAAA
17624485 CTAACTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 15 0.45
20 11 0.33
21 7 0.21
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.22
Consensus pattern (20 bp):
AAATAACATAAAATTAAAAG
Found at i:17629750 original size:28 final size:29
Alignment explanation
Indices: 17629718--17629780 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
17629708 CATAACCAAG
* * *
17629718 AAGAAAATAGAAAAGAGAGGAAAGAAA-A
1 AAGAAAAGAGAAAAGAAAGGAAAAAAAGA
*
17629746 AAGAAAAGAGAAAGGAAAGGAAAAAAAGA
1 AAGAAAAGAGAAAAGAAAGGAAAAAAAGA
17629775 AAGAAA
1 AAGAAA
17629781 GAAAAAAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 23 0.77
29 7 0.23
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (29 bp):
AAGAAAAGAGAAAAGAAAGGAAAAAAAGA
Found at i:17629770 original size:18 final size:17
Alignment explanation
Indices: 17629749--17629803 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
17629739 AAGAAAAAAG
17629749 AAAAGAGAAAGGAAAGGA
1 AAAAGAGAAA-GAAAGGA
* *
17629767 AAAAAAGAAAGAAAGAAA
1 AAAAGAGAAAGAAAG-GA
17629785 AAAAGAGAAATG-AAGGA
1 AAAAGAGAAA-GAAAGGA
17629802 AA
1 AA
17629804 GGATCGGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 8 0.26
18 22 0.71
19 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (17 bp):
AAAAGAGAAAGAAAGGA
Found at i:17629789 original size:25 final size:26
Alignment explanation
Indices: 17629742--17629794 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
17629732 GAGAGGAAAG
* *
17629742 AAAAAAGAAAAGAGAAAGGAAAG-GA
1 AAAAAAGAAAAAAGAAAGAAAAGAGA
17629767 AAAAAAGAAAGAAAGAAA-AAAAGAGA
1 AAAAAAGAAA-AAAGAAAGAAAAGAGA
17629793 AA
1 AA
17629795 TGAAGGAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (26 bp):
AAAAAAGAAAAAAGAAAGAAAAGAGA
Found at i:17632432 original size:30 final size:30
Alignment explanation
Indices: 17632376--17632436 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
17632366 CCCACTCCTT
*
17632376 TTTTTTTTTCTTCTTCTTCTTCTTTCTTTC
1 TTTTTTTTTCTTCTTCTTCTCCTTTCTTTC
17632406 TTTTTTTTTCTTTCTT-TTC-CCATTTCTTTC
1 TTTTTTTTTC-TTCTTCTTCTCC-TTTCTTTC
17632436 T
1 T
17632437 CTCTCTCTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 1 0.04
30 22 0.79
31 5 0.18
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (30 bp):
TTTTTTTTTCTTCTTCTTCTCCTTTCTTTC
Found at i:17635174 original size:88 final size:88
Alignment explanation
Indices: 17635002--17635176 Score: 208
Period size: 88 Copynumber: 2.0 Consensus size: 88
17634992 TTCATAAACA
* * *
17635002 TATAGTTCTTTAAATAACCTGAAAATTTTTACAAAACCTTTAGGAAAAACAAGGAAGTTGTACCT
1 TATAGTTATTTAAATAACCTGAAAATTTATACAAAACCTTTAGGAAAAACAAGGAAATTGTACCT
* *
17635067 TACTTATGGCATGGAATCCTCCT
66 CACCTATGGCATGGAATCCTCCT
* * * * * * *
17635090 TATAGTTATTTGAATAAGCTGAACATTTATGCAAAACTTTTAGGTAACACAAGGAAATTGTACCT
1 TATAGTTATTTAAATAACCTGAAAATTTATACAAAACCTTTAGGAAAAACAAGGAAATTGTACCT
* *
17635155 CACCTGTGGTATCGG-ATCCTCC
66 CACCTATGGCAT-GGAATCCTCC
17635177 CTAAGGGAAA
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
88 70 0.97
89 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (88 bp):
TATAGTTATTTAAATAACCTGAAAATTTATACAAAACCTTTAGGAAAAACAAGGAAATTGTACCT
CACCTATGGCATGGAATCCTCCT
Found at i:17644842 original size:23 final size:23
Alignment explanation
Indices: 17644792--17644844 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
17644782 AGTTCCAGTT
* * *
17644792 AGAGAGAGAATGAGAGAGGGAGA
1 AGAGAGAGAAAGAGAAAGGGAAA
17644815 AGAGAGAGAAAGA-AAAGGGAAA
1 AGAGAGAGAAAGAGAAAGGGAAA
17644837 ATGAGAGA
1 A-GAGAGA
17644845 AAAAAAGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.04
Consensus pattern (23 bp):
AGAGAGAGAAAGAGAAAGGGAAA
Found at i:17645201 original size:25 final size:25
Alignment explanation
Indices: 17645173--17645227 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
17645163 CAGTATAATT
17645173 GAAACCAATATAATTACATTGGCTA
1 GAAACCAATATAATTACATTGGCTA
17645198 GAAACCAATATAATTACATTGGCTA
1 GAAACCAATATAATTACATTGGCTA
17645223 GAAAC
1 GAAAC
17645228 ACAAGTGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.25
Consensus pattern (25 bp):
GAAACCAATATAATTACATTGGCTA
Found at i:17651985 original size:22 final size:22
Alignment explanation
Indices: 17651957--17652000 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
17651947 GTCATTTTTT
17651957 TTCTTCTTTACAAACAAAGATC
1 TTCTTCTTTACAAACAAAGATC
17651979 TTCTTCTTTACAAACAAAGATC
1 TTCTTCTTTACAAACAAAGATC
17652001 GATCAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (22 bp):
TTCTTCTTTACAAACAAAGATC
Found at i:17652389 original size:49 final size:49
Alignment explanation
Indices: 17652329--17652423 Score: 163
Period size: 49 Copynumber: 1.9 Consensus size: 49
17652319 TTACTATTTT
* * *
17652329 CTTTACTTGCACACCAAGTAGGTTTAGGTTTAGTTGGCTATTATAATTA
1 CTTTACTTGCACACCAAGTAAGTTTAAGTTTAGTTAGCTATTATAATTA
17652378 CTTTACTTGCACACCAAGTAAGTTTAAGTTTAGTTAGCTATTATAA
1 CTTTACTTGCACACCAAGTAAGTTTAAGTTTAGTTAGCTATTATAA
17652424 AAAGCCCTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (49 bp):
CTTTACTTGCACACCAAGTAAGTTTAAGTTTAGTTAGCTATTATAATTA
Found at i:17655225 original size:105 final size:105
Alignment explanation
Indices: 17655043--17655248 Score: 331
Period size: 105 Copynumber: 2.0 Consensus size: 105
17655033 ACATTTTGGG
* * * * *
17655043 AAAAGTGTTCAACAATGTTGTGATAGTATTCATGAAATTGAGAGTGAGTTAGTTCTTCTTGCAAG
1 AAAAGTGTTCAACAATGTCGTGATAGTATTCATGAAATTGAGAGTGAGTTAGTTATTCCTACAAA
*
17655108 TGAATCAGGTGCTTCCATTACAAAGTCCTCAAAATTTAGA
66 TGAATCAGGTGCTTCCATTACAAAGTACTCAAAATTTAGA
*
17655148 AAAAGTGTTCAACGATGTCGTGATAGTATTCATGAAATTGAGAGTGAGTTAGTTATTCCTACAAA
1 AAAAGTGTTCAACAATGTCGTGATAGTATTCATGAAATTGAGAGTGAGTTAGTTATTCCTACAAA
* *
17655213 TGAATCAGGTGCTTCTATTACAGAGTACTCAAAATT
66 TGAATCAGGTGCTTCCATTACAAAGTACTCAAAATT
17655249 GCCCATGCCT
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 92 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (105 bp):
AAAAGTGTTCAACAATGTCGTGATAGTATTCATGAAATTGAGAGTGAGTTAGTTATTCCTACAAA
TGAATCAGGTGCTTCCATTACAAAGTACTCAAAATTTAGA
Found at i:17657296 original size:49 final size:49
Alignment explanation
Indices: 17657242--17657336 Score: 163
Period size: 49 Copynumber: 1.9 Consensus size: 49
17657232 TTACTATTTT
* *
17657242 CTTTACTTACACACCAAGTAGGTTTAGGTTTAGTTGGCTATTATAATTA
1 CTTTACTTACACACCAAATAGGTTTAGGTTTAGTTAGCTATTATAATTA
*
17657291 CTTTACTTGCACACCAAATAGGTTTAGGTTTAGTTAGCTATTATAA
1 CTTTACTTACACACCAAATAGGTTTAGGTTTAGTTAGCTATTATAA
17657337 ATAGCCCTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (49 bp):
CTTTACTTACACACCAAATAGGTTTAGGTTTAGTTAGCTATTATAATTA
Found at i:17661464 original size:10 final size:10
Alignment explanation
Indices: 17661449--17661496 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
17661439 GTGTTGTTGA
17661449 TGATAATGTT
1 TGATAATGTT
17661459 TGATAATGTT
1 TGATAATGTT
17661469 TGTTTAATAATGTT
1 TG----ATAATGTT
*
17661483 TGATAATGCT
1 TGATAATGTT
17661493 TGAT
1 TGAT
17661497 TGAGGAGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 23 0.70
14 10 0.30
ACGTcount: A:0.29, C:0.02, G:0.19, T:0.50
Consensus pattern (10 bp):
TGATAATGTT
Found at i:17661478 original size:14 final size:14
Alignment explanation
Indices: 17661455--17661484 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17661445 TTGATGATAA
*
17661455 TGTTTGATAATGTT
1 TGTTTAATAATGTT
17661469 TGTTTAATAATGTT
1 TGTTTAATAATGTT
17661483 TG
1 TG
17661485 ATAATGCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (14 bp):
TGTTTAATAATGTT
Found at i:17662827 original size:360 final size:358
Alignment explanation
Indices: 17661921--17662903 Score: 1278
Period size: 360 Copynumber: 2.8 Consensus size: 358
17661911 GTGTTATAAT
* * * *
17661921 TAATTAAGCAATTAATTATATTAGTAAATTTATATAATATCTTATCTATTTAAACTAATTCAGGG
1 TAATTAAGCAATTAATTAAATTAGTAAATTTATATAATATCTTATTTATTTAAATTAATTTAGGG
* * * * *
17661986 -TT------TCAA-CAA-ATTC-AAGTAATTACAAAGAATCATGTGTTAGTAATTAATCAGTTAA
66 TTTAGGGAATTAATCAATAATCAAAGTAATTATAAAGAATCATGTATTAGTAATTAATCAATTAA
* * * * *
17662041 TCAAATTAGAAAATTTATGGTTTTTAAAAATTATTTAAATTAATT-A--AGGTTTTATTAAATTA
131 TTAAATTAGTAAATTTAGGGTTTTT-TAAATTATTTGAATTAATTAATTAGGTTTTATTAAATTA
* ** * *
17662103 ATTAAAGAATTTAACTAATCAAATGAAAAAAATGCT-TTAGTTAATAAGAAATTAATTAAATTAG
195 ATTAAAGAATTAAACTAATCAAATGAAAAAAATATTATTA-TTTA-AAGCAATTAATTAAATTAG
* * *
17662167 TAATATTATTTAATTT-AAAAAATATTTAAATTAATTGAGGTGTGAATGAGTGAATAAAAAATAT
258 TAATATTATTTAATTTAAAAAAATATTTAAATTAATTAAGGTGTGAATAAGTCAATAAAAAATAT
* ** *
17662231 TTATATAATTAAGCAACGTAATTTGTTATAATTAAT
323 TTATACAATTAAGCAACGTAACGTGTTATAATTAAG
* * * *
17662267 TAATTAAGAAATTATTTAAATTAGTAAAATTATATAATATCTTA-TTATCTAAATTAATTTAGGG
1 TAATTAAGCAATTAATTAAATTAGTAAATTTATATAATATCTTATTTATTTAAATTAATTTAGGG
* * * *
17662331 TTTAGGGAATTAATTATATAATTAAAATAATTATAAAGAATCATGTATTAGTAATTAATCATTTA
66 TTTAGGGAATTAATCA-ATAATCAAAGTAATTATAAAGAATCATGTATTAGTAATTAATCAATTA
* * *
17662396 ATTAAATTAGTAAATTTAGGGTTTTTTCAAATTCTTGGAATTAATTAATTAGGTTTTATTAAATC
130 ATTAAATTAGTAAATTTAGGGTTTTTT-AAATTATTTGAATTAATTAATTAGGTTTTATTAAATT
* * * *
17662461 AATTAAATAATTAAACTAATCAAATGAAAAAAAAATTATTATTTAAAGCATTTAATGAAATTAGT
194 AATTAAAGAATTAAACTAATCAAATGAAAAAAATATTATTATTTAAAGCAATTAATTAAATTAGT
*
17662526 AATATTATTTAATTTAAAAAAATATTTAAATTAATTAAGGTGTGAATAAGTCAATTAAAAATATT
259 AATATTATTTAATTTAAAAAAATATTTAAATTAATTAAGGTGTGAATAAGTCAATAAAAAATATT
* ** *
17662591 TTTACAATTAAGTTATGTAACGTGTTATAATTAAG
324 TATACAATTAAGCAACGTAACGTGTTATAATTAAG
17662626 TAATTAAGCAATTAATTAAATTAGTAAATTTATATAATATCTTATTTATTTAAATTAATTTAGGG
1 TAATTAAGCAATTAATTAAATTAGTAAATTTATATAATATCTTATTTATTTAAATTAATTTAGGG
* * * *
17662691 TTTAGGGAATTAATCACATAATCAAAGTAATTATAAAGAGTAATGTATTAGTAGTTAAGCAATTA
66 TTTAGGGAATTAATCA-ATAATCAAAGTAATTATAAAGAATCATGTATTAGTAATTAATCAATTA
*
17662756 ATTAAATTAGTAAATTTAGGGTTTTCTTAAATTGTTTGAATTAATTAATTAGGTTTTATTAAATT
130 ATTAAATTAGTAAATTTAGGGTTTT-TTAAATTATTTGAATTAATTAATTAGGTTTTATTAAATT
* * * *
17662821 AATTAAAGAATTAAACTAATCAAATGAAAAATTATTTTATGATTTAATGCAATTAATTAAATTAG
194 AATTAAAGAATTAAACTAATCAAATGAAAAA-AATATTATTATTTAAAGCAATTAATTAAATTAG
*
17662886 TAATATTATTTAAATTAA
258 TAATATTATTTAATTTAA
17662904 TTAACCTATG
Statistics
Matches: 547, Mismatches: 70, Indels: 25
0.85 0.11 0.04
Matches are distributed among these distances:
345 16 0.03
346 42 0.08
352 3 0.01
353 1 0.00
354 1 0.00
355 2 0.00
356 75 0.14
357 1 0.00
358 32 0.06
359 162 0.30
360 167 0.31
361 45 0.08
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (358 bp):
TAATTAAGCAATTAATTAAATTAGTAAATTTATATAATATCTTATTTATTTAAATTAATTTAGGG
TTTAGGGAATTAATCAATAATCAAAGTAATTATAAAGAATCATGTATTAGTAATTAATCAATTAA
TTAAATTAGTAAATTTAGGGTTTTTTAAATTATTTGAATTAATTAATTAGGTTTTATTAAATTAA
TTAAAGAATTAAACTAATCAAATGAAAAAAATATTATTATTTAAAGCAATTAATTAAATTAGTAA
TATTATTTAATTTAAAAAAATATTTAAATTAATTAAGGTGTGAATAAGTCAATAAAAAATATTTA
TACAATTAAGCAACGTAACGTGTTATAATTAAG
Found at i:17669771 original size:40 final size:40
Alignment explanation
Indices: 17669674--17669776 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 40
17669664 ATAATGCCCG
* *
17669674 TGTGCACGATGTGGGGGGATGTC-CACGATGGCACTGACTA
1 TGTGCACGATGTGGGGGGATG-CACACGATGACACCGACTA
* *
17669714 --TGCACGATGTGGGGGGATGCACACGATGACTCCGGCTA
1 TGTGCACGATGTGGGGGGATGCACACGATGACACCGACTA
*
17669752 TGTGCACGATGTGGAGGGATGCACA
1 TGTGCACGATGTGGGGGGATGCACA
17669777 TGAGCTGGGT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
37 1 0.02
38 32 0.58
40 22 0.40
ACGTcount: A:0.21, C:0.20, G:0.38, T:0.20
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGCACACGATGACACCGACTA
Found at i:17675956 original size:42 final size:42
Alignment explanation
Indices: 17675897--17675977 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
17675887 GTGATAATTA
* *
17675897 TGACCCAGTCATGTGCGGTGTAGG-AGTGCACATGAGCTGTGC
1 TGACCCAGCCATGTGCGGTGT-GGTAGTGCACATAAGCTGTGC
*
17675939 TGACCCGGCCATGTGCGGTGTGGTAGTGCACATAAGCTG
1 TGACCCAGCCATGTGCGGTGTGGTAGTGCACATAAGCTG
17675978 AGAAAGAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 2 0.06
42 33 0.94
ACGTcount: A:0.19, C:0.22, G:0.36, T:0.23
Consensus pattern (42 bp):
TGACCCAGCCATGTGCGGTGTGGTAGTGCACATAAGCTGTGC
Found at i:17684239 original size:35 final size:35
Alignment explanation
Indices: 17684169--17684417 Score: 272
Period size: 35 Copynumber: 7.1 Consensus size: 35
17684159 CACTTGATTA
* *
17684169 AAATTGTTTAATTAAG---TTGTGCCTAATTAACT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
17684201 AAATTGTTTAATTGAA-TCATTGGGCCTAATTAATT
1 AAATTGTTTAATT-AAGTCATTGGGCCTAATTAATT
* *
17684236 AAATTATTTAATTAAGTCATTGGCCCTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
*** * *
17684271 AAATTAAATAATTAAGTTATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* * *
17684306 AAATTTGTTTAATTAAGTCATTAGGCCTAGTTGATT
1 AAA-TTGTTTAATTAAGTCATTGGGCCTAATTAATT
* ** *
17684342 AAAATTGTTTAATTAAATTGTTGGGCTTAATTAATT
1 -AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* * *
17684378 AAATTATTTAATTAAGTTATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
17684413 AAATT
1 AAATT
17684418 AAACAATTAA
Statistics
Matches: 183, Mismatches: 27, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
32 13 0.07
33 2 0.01
34 2 0.01
35 112 0.61
36 51 0.28
37 3 0.02
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
Found at i:17684381 original size:107 final size:106
Alignment explanation
Indices: 17684189--17684417 Score: 309
Period size: 107 Copynumber: 2.2 Consensus size: 106
17684179 ATTAAGTTGT
* * * *
17684189 GCCTAATTAACTAAA-TTGTTTAATTGAATCATTGGGCCTAATTAATTAAATTATTTAATTAAGT
1 GCCTAATTGATTAAATTTGTTTAATTGAATCATTAGGCCTAATTAATTAAATTATTTAATTAAAT
17684253 CATTGGCCCTAATTAATTAAATTAAATAATTAAGTTATTGG
66 CATTGGCCCTAATTAATTAAATTAAATAATTAAGTTATTGG
* * *
17684294 GCCTAATTGATTAAATTTGTTTAATT-AAGTCATTAGGCCTAGTTGATTAAAATTGTTTAATTAA
1 GCCTAATTGATTAAATTTGTTTAATTGAA-TCATTAGGCCTAATTAATT-AAATTATTTAATTAA
** * * **
17684358 ATTGTTGGGCTTAATTAATTAAATTATTTAATTAAGTTATTGG
64 ATCATTGGCCCTAATTAATTAAATTAAATAATTAAGTTATTGG
17684401 GCCTAATTGATTAAATT
1 GCCTAATTGATTAAATT
17684418 AAACAATTAA
Statistics
Matches: 108, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
105 15 0.14
106 26 0.24
107 67 0.62
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (106 bp):
GCCTAATTGATTAAATTTGTTTAATTGAATCATTAGGCCTAATTAATTAAATTATTTAATTAAAT
CATTGGCCCTAATTAATTAAATTAAATAATTAAGTTATTGG
Found at i:17688565 original size:42 final size:42
Alignment explanation
Indices: 17688505--17688618 Score: 160
Period size: 42 Copynumber: 2.7 Consensus size: 42
17688495 TGGACTGGGT
17688505 TATGTGCGAGT-AGAAGTGCACATAAGCCGTTGCTGA-CTCGGC
1 TATGTGCGAGTGAG-AGTGCACATAAGCCGTTGCTGACCT-GGC
*
17688547 TATGTGCGAGTGAGAGTGCACATAAGCAGTTGCTGACCTGGC
1 TATGTGCGAGTGAGAGTGCACATAAGCCGTTGCTGACCTGGC
* * *
17688589 TATGTACGAGTGGGAGTGCGCATAAGCCGT
1 TATGTGCGAGTGAGAGTGCACATAAGCCGT
17688619 GGCATATAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
42 61 0.94
43 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (42 bp):
TATGTGCGAGTGAGAGTGCACATAAGCCGTTGCTGACCTGGC
Found at i:17697817 original size:586 final size:586
Alignment explanation
Indices: 17696705--17697879 Score: 2206
Period size: 586 Copynumber: 2.0 Consensus size: 586
17696695 TGTTCACACA
17696705 GAGGCACATAATCTAGATCTTGTGAACTAGAGTAAACCCATTCCTCGGATTGTGCTCGTTCCCTA
1 GAGGCACATAATCTAGATCTTGTGAACTAGAGTAAACCCATTCCTCGGATTGTGCTCGTTCCCTA
17696770 TTGTGAAAATCAGCGAATTCATTAGCCAAACTTTACAACCCAACTACCAAATCTTCTAGGGTGAC
66 TTGTGAAAATCAGCGAATTCATTAGCCAAACTTTACAACCCAACTACCAAATCTTCTAGGGTGAC
*
17696835 ACCTCTTCCTATAGGGTAGTCATTCCTGGCTCCCATATCCTCACCACCATTTGGCACATAACAAG
131 ACCTCTTCCTATAGGGTAGTCATTCCTGGCTCCCATATCCTCACCACCAGTTGGCACATAACAAG
* * * *
17696900 GTTACGCATTTCGAGCGTGTCTAGCTAGTTTCCTTTTACCACGGTTCCTTGACGTGGACATTCGT
196 GTTACGCATTTCGAGCGTGTCTAGCTACTTTACTTCTACCACGGTTCCTTGACCTGGACATTCGT
* * *
17696965 GGTAGTTCCGTAGACTCATCTGGGGCAACTTGCTTTCCCGTGGCTCTAGAGGCAGCTCTCATTTC
261 CGTAGTTCCATAGACTCATCTGGGGCAACTTGCTTTCCCGTGGCTCTAGAGGCAACTCTCATTTC
*
17697030 AGGCAGCATCTTATACCAAGACTAAGTAATACCATGTTCAAAATCAAAATTCCAAAATCTTATGG
326 AGGCAGCATCTTATACCAAGACGAAGTAATACCATGTTCAAAATCAAAATTCCAAAATCTTATGG
17697095 GTAGGTTTACTAAGACTTGGGAGTTCATGCAGCCTCTTGCTCATAATTAATGCTGTAGTGATAAA
391 GTAGGTTTACTAAGACTTGGGAGTTCATGCAGCCTCTTGCTCATAATTAATGCTGTAGTGATAAA
17697160 CCATGAACAAGATTCTACACTAATCCCGACACTCCACTAATAGACTTAAGATAACCTAGGACACT
456 CCATGAACAAGATTCTACACTAATCCCGACACTCCACTAATAGACTTAAGATAACCTAGGACACT
*
17697225 CTAAACCTAGGCACTTTAATACCAACTTTATCATGACCCAAACCTAGGGGTCCATGACCTACGTA
521 CTAAACCTAGGCACTTTAATACCAACTTTATCATGACCCAAACCTAGGGGTCCATGACCGACGTA
17697290 T
586 T
* *
17697291 GAGGCACATAATCTAGATCTTGTGAACTAGAGTAAACCCATTCCTCGGATTGTGCTTGTTCCTTA
1 GAGGCACATAATCTAGATCTTGTGAACTAGAGTAAACCCATTCCTCGGATTGTGCTCGTTCCCTA
17697356 TTGTGAAAATCAGCGAATTCATTAGCCAAACTTTACAACCCAACTACCAAATCTTCTAGGGTGAC
66 TTGTGAAAATCAGCGAATTCATTAGCCAAACTTTACAACCCAACTACCAAATCTTCTAGGGTGAC
17697421 ACCTCTTCCTATAGGGTAGTCATTCCTGGCTCCCATATCCTCACCACCAGTTGGCACATAACAAG
131 ACCTCTTCCTATAGGGTAGTCATTCCTGGCTCCCATATCCTCACCACCAGTTGGCACATAACAAG
*
17697486 GTTACGTATTTCGAGCGTGTCTAGCTACTTTACTTCTACCACGGTTCCTTGACCTGGACATTCGT
196 GTTACGCATTTCGAGCGTGTCTAGCTACTTTACTTCTACCACGGTTCCTTGACCTGGACATTCGT
17697551 CGTAGTTCCATAGACTCATCTGGGGCAACTTGCTTTCCCGTGGCTCTAGAGGCAACTCTCATTTC
261 CGTAGTTCCATAGACTCATCTGGGGCAACTTGCTTTCCCGTGGCTCTAGAGGCAACTCTCATTTC
* *
17697616 AGGCAGCATCTTATACCAAGACGAAGTAATATCATGTTCAAAATTAAAATTCCAAAATCTTATGG
326 AGGCAGCATCTTATACCAAGACGAAGTAATACCATGTTCAAAATCAAAATTCCAAAATCTTATGG
17697681 GTAGGTTTACTAAGACTTGGGAGTTCATGCAGCCTCTTGCTCATAATTAATGCTGTAGTGATAAA
391 GTAGGTTTACTAAGACTTGGGAGTTCATGCAGCCTCTTGCTCATAATTAATGCTGTAGTGATAAA
17697746 CCATGAACAAGATTCTACACTAATCCCGACACTCCACTAATAGACTTAAGATAACCTAGGACACT
456 CCATGAACAAGATTCTACACTAATCCCGACACTCCACTAATAGACTTAAGATAACCTAGGACACT
*
17697811 CTAAACCTAGGCACTTTAATACCAACTTTATCATGACCCAAACCTAGGGGTCCATGACCGATGTA
521 CTAAACCTAGGCACTTTAATACCAACTTTATCATGACCCAAACCTAGGGGTCCATGACCGACGTA
17697876 T
586 T
17697877 GAG
1 GAG
17697880 CCTAGTAAGC
Statistics
Matches: 573, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
586 573 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (586 bp):
GAGGCACATAATCTAGATCTTGTGAACTAGAGTAAACCCATTCCTCGGATTGTGCTCGTTCCCTA
TTGTGAAAATCAGCGAATTCATTAGCCAAACTTTACAACCCAACTACCAAATCTTCTAGGGTGAC
ACCTCTTCCTATAGGGTAGTCATTCCTGGCTCCCATATCCTCACCACCAGTTGGCACATAACAAG
GTTACGCATTTCGAGCGTGTCTAGCTACTTTACTTCTACCACGGTTCCTTGACCTGGACATTCGT
CGTAGTTCCATAGACTCATCTGGGGCAACTTGCTTTCCCGTGGCTCTAGAGGCAACTCTCATTTC
AGGCAGCATCTTATACCAAGACGAAGTAATACCATGTTCAAAATCAAAATTCCAAAATCTTATGG
GTAGGTTTACTAAGACTTGGGAGTTCATGCAGCCTCTTGCTCATAATTAATGCTGTAGTGATAAA
CCATGAACAAGATTCTACACTAATCCCGACACTCCACTAATAGACTTAAGATAACCTAGGACACT
CTAAACCTAGGCACTTTAATACCAACTTTATCATGACCCAAACCTAGGGGTCCATGACCGACGTA
T
Found at i:17700462 original size:70 final size:70
Alignment explanation
Indices: 17700324--17700514 Score: 188
Period size: 70 Copynumber: 2.7 Consensus size: 70
17700314 CTCTTTTCCC
* ** *
17700324 CTTCACAGGATCGACTATAGAGGGTCTATAGTCGATCTTGGACCAAAATGTCCATTTTTATTCTA
1 CTTCACAAGATCGACTATAGAGGGTCTATAGTCGATCTTGGACCAAAATGTCCACATTTATTCCA
17700389 TTTTG
66 TTTTG
* * * * * * *
17700394 CTTCACAAGATTGACTATGGAGGGTCTGTAGTCGATCTTGGACTAGAATGTTCACATTTCTTCCA
1 CTTCACAAGATCGACTATAGAGGGTCTATAGTCGATCTTGGACCAAAATGTCCACATTTATTCCA
*
17700459 TTTTTC
66 -TTTTG
* ** * *
17700465 CTTC-CTAAGATCAACTATAGAGGACCTATAGTCAAAT-TTGGGCCAAAATG
1 CTTCAC-AAGATCGACTATAGAGGGTCTATAGTC-GATCTTGGACCAAAATG
17700515 CATGACTTCC
Statistics
Matches: 96, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
70 55 0.57
71 39 0.41
72 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (70 bp):
CTTCACAAGATCGACTATAGAGGGTCTATAGTCGATCTTGGACCAAAATGTCCACATTTATTCCA
TTTTG
Found at i:17704404 original size:2 final size:2
Alignment explanation
Indices: 17704397--17704427 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17704387 NNNNNNNNNN
*
17704397 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17704428 GTAAATGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:17716262 original size:73 final size:73
Alignment explanation
Indices: 17716183--17716384 Score: 253
Period size: 72 Copynumber: 2.8 Consensus size: 73
17716173 GAATATGGTT
* * * *
17716183 GGTTCAGAGATAAAGACGACTTAATCGACTAAGAAGCATCGTTAGTCGACTAAGAGCTTACTTCT
1 GGTTCAGAGATAAAGACGACTTAATCGACTAAGAAGCATAGTTAGTCGACTAAGAGCTCACTGCC
17716248 AGAAACTA
66 AGAAACTA
* * * * * *
17716256 GGTTCAGAGAT-AAGATGACTTAATCGACTAAGAAGTATTGTTAGTGGGCAAAGAGCTCACTGCC
1 GGTTCAGAGATAAAGACGACTTAATCGACTAAGAAGCATAGTTAGTCGACTAAGAGCTCACTGCC
*
17716320 AGAAACTG
66 AGAAACTA
* * * * *
17716328 GGTTCAGAGACAGAGACAACTTAATCAACTAAGAAGCATAGTTAGTCAACTAAGAGC
1 GGTTCAGAGATAAAGACGACTTAATCGACTAAGAAGCATAGTTAGTCGACTAAGAGC
17716385 ATTTTGTTTG
Statistics
Matches: 107, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
72 61 0.57
73 46 0.43
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (73 bp):
GGTTCAGAGATAAAGACGACTTAATCGACTAAGAAGCATAGTTAGTCGACTAAGAGCTCACTGCC
AGAAACTA
Found at i:17725269 original size:73 final size:73
Alignment explanation
Indices: 17725181--17725383 Score: 253
Period size: 73 Copynumber: 2.8 Consensus size: 73
17725171 GAAGATGGTC
* * *
17725181 GGTTCAAAGATAGAGACGACTTAATTGACTAAAAAGCATCGTTAGTCGACTAAGAGCTTACTGCC
1 GGTTCAAAGATAGAGACGACTTAATTGACTAAGAAGCATAGTTAGTCGACTAAGAGCTTACTACC
*
17725246 AAAAATTA
66 AAAAACTA
* * * *
17725254 GGTTCAAAGACAGAGATGACTTAATTGACTAAGAAGTATTGTTAGTCGACTAAGAGCTTACTACC
1 GGTTCAAAGATAGAGACGACTTAATTGACTAAGAAGCATAGTTAGTCGACTAAGAGCTTACTACC
*
17725319 AGAAACTA
66 AAAAACTA
* * * * * * * *
17725327 GGTTTAGAGATAAAGACAACTTAATCGGCTAAGAAGCATAGTTTGTCTACTAAGAGC
1 GGTTCAAAGATAGAGACGACTTAATTGACTAAGAAGCATAGTTAGTCGACTAAGAGC
17725384 ATTTTGTCTG
Statistics
Matches: 110, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
73 110 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (73 bp):
GGTTCAAAGATAGAGACGACTTAATTGACTAAGAAGCATAGTTAGTCGACTAAGAGCTTACTACC
AAAAACTA
Found at i:17728360 original size:29 final size:28
Alignment explanation
Indices: 17728328--17728471 Score: 137
Period size: 29 Copynumber: 5.0 Consensus size: 28
17728318 AAATATTTGA
* *
17728328 TCTTGTCTAAATTTGAGACAAATATGTAT
1 TCTTGTCTAAA-TTAAGACAAATATGTTT
* *
17728357 TCTTGTCTAGATTAAGATAAAAAATAT-TTT
1 TCTTGTCTAAATTAAG---ACAAATATGTTT
* *
17728387 TCTTGTCTTAAATTAAGACAAACATATTT
1 TCTTGTC-TAAATTAAGACAAATATGTTT
*
17728416 TCTTATCTAAATTAAGACCAAATATGTTT
1 TCTTGTCTAAATTAAGA-CAAATATGTTT
* * *
17728445 ACTTTTCTAAATTAAGACAAACATGTT
1 TCTTGTCTAAATTAAGACAAATATGTT
17728472 AAAGCAGCCA
Statistics
Matches: 96, Mismatches: 13, Indels: 13
0.79 0.11 0.11
Matches are distributed among these distances:
28 29 0.30
29 43 0.45
30 9 0.09
31 15 0.16
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAATATGTTT
Found at i:17728373 original size:60 final size:59
Alignment explanation
Indices: 17728306--17728468 Score: 179
Period size: 59 Copynumber: 2.8 Consensus size: 59
17728296 TCTTGTCCGT
* * * *
17728306 AATTAAGACAAAAAATATTTGATCTTGTC-TAAATTTGAGACAAATATGTATTCTTGTCTA
1 AATTAAGACAAAAAATATTT-ATCTTGTCTTAAA-TTAAGACAAACATATATTCTTATCTA
* * * *
17728366 GATTAAGATAAAAAATATTTTTCTTGTCTTAAATTAAGACAAACATATTTTCTTATCTA
1 AATTAAGACAAAAAATATTTATCTTGTCTTAAATTAAGACAAACATATATTCTTATCTA
* * * *
17728425 AATTAAGACCAAATATGTTTA-CTTTTC-TAAATTAAGACAAACAT
1 AATTAAGACAAAAAATATTTATCTTGTCTTAAATTAAGACAAACAT
17728469 GTTAAAGCAG
Statistics
Matches: 87, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
57 17 0.20
58 5 0.06
59 43 0.49
60 22 0.25
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.39
Consensus pattern (59 bp):
AATTAAGACAAAAAATATTTATCTTGTCTTAAATTAAGACAAACATATATTCTTATCTA
Found at i:17732924 original size:18 final size:19
Alignment explanation
Indices: 17732901--17732936 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
17732891 AAATCCATTT
17732901 TCGCTGCAACGA-AATTCC
1 TCGCTGCAACGAGAATTCC
*
17732919 TCGCTGCAGCGAGAATTC
1 TCGCTGCAACGAGAATTC
17732937 TTTTTCACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.22
Consensus pattern (19 bp):
TCGCTGCAACGAGAATTCC
Found at i:17733297 original size:37 final size:35
Alignment explanation
Indices: 17733195--17733318 Score: 185
Period size: 35 Copynumber: 3.5 Consensus size: 35
17733185 CACACCACCC
* *
17733195 CACTTCATTCATCGTCATGTGCACTCCCTACTCGCA
1 CACTTCA-ACATCATCATGTGCACTCCCTACTCGCA
*
17733231 CACTTCAACATCATCATGTGCACTCCCTACTCACA
1 CACTTCAACATCATCATGTGCACTCCCTACTCGCA
*
17733266 CACTTGAACATCATCATGTGTGCACTCCCTACTCGCA
1 CACTTCAACATCATCA--TGTGCACTCCCTACTCGCA
17733303 CACTTCAACATCATCA
1 CACTTCAACATCATCA
17733319 CACAACATTA
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
35 40 0.50
36 7 0.09
37 33 0.41
ACGTcount: A:0.26, C:0.38, G:0.09, T:0.27
Consensus pattern (35 bp):
CACTTCAACATCATCATGTGCACTCCCTACTCGCA
Found at i:17738188 original size:29 final size:29
Alignment explanation
Indices: 17738156--17738299 Score: 127
Period size: 29 Copynumber: 5.0 Consensus size: 29
17738146 AAATATTTAA
* *
17738156 TCTTGTCTAAATTTGAGACAAATATGTAT
1 TCTTGTCTAAATTTAAGACAAATATGTTT
* *
17738185 TCTTGTCTAGA-TTAAGATAAAAAATAT-TTT
1 TCTTGTCTAAATTTAAG---ACAAATATGTTT
* *
17738215 TCTTGTCTTAAA-TTAAGACAAACATATTT
1 TCTTGTC-TAAATTTAAGACAAATATGTTT
*
17738244 TCTTGTCTAAA-TTAAGACCAAACATGTTT
1 TCTTGTCTAAATTTAAGA-CAAATATGTTT
* *
17738273 TCTTGTCTAAA-TTAAGAAAAACATGTT
1 TCTTGTCTAAATTTAAGACAAATATGTT
17738300 AAAGTTGTCA
Statistics
Matches: 100, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
28 29 0.29
29 47 0.47
30 9 0.09
31 15 0.15
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (29 bp):
TCTTGTCTAAATTTAAGACAAATATGTTT
Found at i:17738236 original size:59 final size:58
Alignment explanation
Indices: 17738134--17738298 Score: 197
Period size: 59 Copynumber: 2.8 Consensus size: 58
17738124 TCTTATCCGT
* * *
17738134 AATTAAGATAAAAAATATTTAATCTTGTCTAAATTTGAGACAAATATGTATTCTTGTCTA
1 AATTAAGATAAAAAATATTT-TTCTTGTCTAAA-TTAAGACAAACATGTATTCTTGTCTA
* * *
17738194 GATTAAGATAAAAAATATTTTTCTTGTCTTAAATTAAGACAAACATATTTTCTTGTCTA
1 AATTAAGATAAAAAATATTTTTCTTGTC-TAAATTAAGACAAACATGTATTCTTGTCTA
** * * *
17738253 AATTAAGACCAAACAT-GTTTTCTTGTCTAAATTAAGAAAAACATGT
1 AATTAAGATAAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGT
17738299 TAAAGTTGTC
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
57 17 0.19
58 10 0.11
59 41 0.45
60 23 0.25
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (58 bp):
AATTAAGATAAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGTATTCTTGTCTA
Found at i:17745665 original size:2 final size:2
Alignment explanation
Indices: 17745658--17745692 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
17745648 AAGATGAAAT
17745658 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
17745693 AGAAAAGAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17745745 original size:2 final size:2
Alignment explanation
Indices: 17745738--17745775 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
17745728 NNNNNNNNNN
17745738 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG TAG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG A
17745776 AAAAAGAGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:17747194 original size:33 final size:33
Alignment explanation
Indices: 17747156--17747232 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
17747146 TCATGGAGAG
* *
17747156 CTTTGACAAGTCTGCAAACTTTGTCTTTGCTAG
1 CTTTGACAAGTCTGCAAACTATGTCTTTGCTAA
*
17747189 TTTTGACAAGTCTGCAAACTATGTCTTTGCTAA
1 CTTTGACAAGTCTGCAAACTATGTCTTTGCTAA
17747222 CTTTGACAAGT
1 CTTTGACAAGT
17747233 ACACATTGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (33 bp):
CTTTGACAAGTCTGCAAACTATGTCTTTGCTAA
Found at i:17749353 original size:30 final size:31
Alignment explanation
Indices: 17749301--17749378 Score: 101
Period size: 30 Copynumber: 2.6 Consensus size: 31
17749291 ATTTAAAAAT
17749301 ATTTAAATAAATTTTT-TATTTTT-TATT-A
1 ATTTAAATAAATTTTTATATTTTTATATTGA
* *
17749329 CATTTAATTAAATTTTTATATTTTTATTTTGA
1 -ATTTAAATAAATTTTTATATTTTTATATTGA
17749361 A-TTAAATAAATTTTTATA
1 ATTTAAATAAATTTTTATA
17749379 ACTAATGGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 15 0.35
30 23 0.53
31 4 0.09
32 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (31 bp):
ATTTAAATAAATTTTTATATTTTTATATTGA
Found at i:17749659 original size:32 final size:30
Alignment explanation
Indices: 17749621--17749716 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
17749611 TAAGAATAGC
17749621 TATTTGACTTAAAATATAAAAATATAAAAATT
1 TATTTGA-TTAAAA-ATAAAAATATAAAAATT
**
17749653 TATTTGATTTCAAATAAAAATATAAAAATT
1 TATTTGATTAAAAATAAAAATATAAAAATT
* * ** *
17749683 TAATTGAAT-GTAATAAAAATATAAAAGTT
1 TATTTGATTAAAAATAAAAATATAAAAATT
17749712 TATTT
1 TATTT
17749717 AAAATTTTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
29 21 0.38
30 24 0.43
31 4 0.07
32 7 0.12
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (30 bp):
TATTTGATTAAAAATAAAAATATAAAAATT
Found at i:17749672 original size:30 final size:29
Alignment explanation
Indices: 17749636--17749716 Score: 110
Period size: 30 Copynumber: 2.8 Consensus size: 29
17749626 GACTTAAAAT
*
17749636 ATAAAAATATAAAAATTTATTTG-ATTTCAA
1 ATAAAAATATAAAAATTTATTTGAATGT--A
*
17749666 ATAAAAATATAAAAATTTAATTGAATGTA
1 ATAAAAATATAAAAATTTATTTGAATGTA
*
17749695 ATAAAAATATAAAAGTTTATTT
1 ATAAAAATATAAAAATTTATTT
17749717 AAAATTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 21 0.46
30 22 0.48
31 3 0.07
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (29 bp):
ATAAAAATATAAAAATTTATTTGAATGTA
Found at i:17753128 original size:67 final size:66
Alignment explanation
Indices: 17752992--17753156 Score: 167
Period size: 67 Copynumber: 2.5 Consensus size: 66
17752982 AATATTAATC
* * *
17752992 TAACTAGTT-CAATTCAAGCATATAATGTAGCTGAATTAGCTGTGTGCTTACAAAGCACATTCTA
1 TAACTAGTTGC-A-TCAAGCATATAATTTAGCTGAATTAGCTGTGTGCTTACAAAACACATTCGA
17753056 ATA
64 ATA
* * *
17753059 TAACT-GATTGCTGTCAAGCATATAATTTAGCTGAATTAGCCT-TGTGCGTT-CAAAATAGATTC
1 TAACTAG-TTGC-ATCAAGCATATAATTTAGCTGAATTAG-CTGTGTGC-TTACAAAACACATTC
*
17753121 GATTA
62 GAATA
* *
17753126 TAACTAGTTGCATCTAGCATATACTTTAGCT
1 TAACTAGTTGCATCAAGCATATAATTTAGCT
17753157 TTATTAGTCA
Statistics
Matches: 82, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
66 18 0.22
67 58 0.71
68 6 0.07
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (66 bp):
TAACTAGTTGCATCAAGCATATAATTTAGCTGAATTAGCTGTGTGCTTACAAAACACATTCGAAT
A
Found at i:17754722 original size:2 final size:2
Alignment explanation
Indices: 17754715--17754741 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17754705 TTAAGAAAAT
17754715 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
17754742 GAGGATCTAC
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17757316 original size:17 final size:18
Alignment explanation
Indices: 17757282--17757327 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
17757272 TACCAATCAG
17757282 CTAAATAAA-CAAATATT
1 CTAAATAAAGCAAATATT
*
17757299 CTAAATAAAGTAAA-ATT
1 CTAAATAAAGCAAATATT
17757316 CAATAAATAAAG
1 C--TAAATAAAG
17757328 ATGTGATACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 13 0.52
18 3 0.12
19 9 0.36
ACGTcount: A:0.61, C:0.09, G:0.04, T:0.26
Consensus pattern (18 bp):
CTAAATAAAGCAAATATT
Found at i:17762745 original size:20 final size:20
Alignment explanation
Indices: 17762706--17762745 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
17762696 AAATATATTT
** *
17762706 TCTATTTTTCATTTGCCTAA
1 TCTATTTTTCATACGACTAA
17762726 TCTATTTTTCATACGACTAA
1 TCTATTTTTCATACGACTAA
17762746 ATATATTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (20 bp):
TCTATTTTTCATACGACTAA
Found at i:17762869 original size:21 final size:20
Alignment explanation
Indices: 17762845--17762895 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 20
17762835 TACTTGGATC
17762845 TATTTTTTACTACT-AAATATT
1 TATTTTTT-CT-CTCAAATATT
*
17762866 TATTTATTTCTCTCATATATT
1 TATTT-TTTCTCTCAAATATT
17762887 TATATTTTT
1 TAT-TTTTT
17762896 TAAAAAAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.08
21 19 0.73
22 5 0.19
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTTTTCTCTCAAATATT
Found at i:17778207 original size:12 final size:12
Alignment explanation
Indices: 17778190--17778217 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
17778180 ATATTTAAAT
17778190 TACATATATATA
1 TACATATATATA
17778202 TACATATATATA
1 TACATATATATA
17778214 TACA
1 TACA
17778218 CACACATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (12 bp):
TACATATATATA
Found at i:17781697 original size:13 final size:13
Alignment explanation
Indices: 17781679--17781704 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17781669 TTTCAGAAAA
17781679 TTTATAAAATCAT
1 TTTATAAAATCAT
17781692 TTTATAAAATCAT
1 TTTATAAAATCAT
17781705 AATTTCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:17783786 original size:13 final size:13
Alignment explanation
Indices: 17783768--17783801 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
17783758 TAAGAAGTGT
17783768 TATATAAAAAAGG
1 TATATAAAAAAGG
17783781 TATATAAAAAAGG
1 TATATAAAAAAGG
17783794 TATATAAA
1 TATATAAA
17783802 TTTGATCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (13 bp):
TATATAAAAAAGG
Found at i:17792534 original size:18 final size:19
Alignment explanation
Indices: 17792494--17792539 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
17792484 GTAAAAGGAA
17792494 AAAAATAAAAATCAGCAAAT
1 AAAAAT-AAAATCAGCAAAT
* *
17792514 AAAAATAAAAT-TGCAAGT
1 AAAAATAAAATCAGCAAAT
17792532 AAAAATAA
1 AAAAATAA
17792540 CTCTAACTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 13 0.54
19 5 0.21
20 6 0.25
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.17
Consensus pattern (19 bp):
AAAAATAAAATCAGCAAAT
Found at i:17798817 original size:28 final size:28
Alignment explanation
Indices: 17798785--17798861 Score: 118
Period size: 28 Copynumber: 2.8 Consensus size: 28
17798775 CTGGTGGTGG
* *
17798785 AAAATTACAATTTTGCCCCTAGAGCAGC
1 AAAATTACCATTTTACCCCTAGAGCAGC
**
17798813 AAAATTACCATTTTACCCCTAGAGTGGC
1 AAAATTACCATTTTACCCCTAGAGCAGC
17798841 AAAATTACCATTTTACCCCTA
1 AAAATTACCATTTTACCCCTA
17798862 TACTCCAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.35, C:0.26, G:0.10, T:0.29
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCTAGAGCAGC
Found at i:17798877 original size:28 final size:28
Alignment explanation
Indices: 17798785--17798870 Score: 95
Period size: 28 Copynumber: 3.1 Consensus size: 28
17798775 CTGGTGGTGG
* * *
17798785 AAAATTACAATTTTGCCCCTAGAGCAG-C
1 AAAATTACCATTTTACCCCTAGA-CTGCC
* *
17798813 AAAATTACCATTTTACCCCTAGAGTGGC
1 AAAATTACCATTTTACCCCTAGACTGCC
*
17798841 AAAATTACCATTTTACCCCTATACT-CC
1 AAAATTACCATTTTACCCCTAGACTGCC
17798868 AAA
1 AAA
17798871 TTATACCGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
27 5 0.10
28 45 0.90
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.28
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCTAGACTGCC
Found at i:17815209 original size:25 final size:25
Alignment explanation
Indices: 17815159--17815204 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
17815149 CTTCAACCAC
*
17815159 CAAAATTTCCACACACTTTCTCTCA
1 CAAAATTTCCACACACTCTCTCTCA
*
17815184 CAAAATTTTC-CA-ACTCTCTCT
1 CAAAATTTCCACACACTCTCTCT
17815205 TTCACTCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 2 0.11
25 9 0.47
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (25 bp):
CAAAATTTCCACACACTCTCTCTCA
Found at i:17816573 original size:2 final size:2
Alignment explanation
Indices: 17816566--17816676 Score: 100
Period size: 2 Copynumber: 54.0 Consensus size: 2
17816556 TGTACATGAA
17816566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * * * * **
17816609 GT AC GT AC GT AGT AGT AGT AGT NG A- AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T A-T A-T A-T AT AT AT AT AT AT AT AT AT AT AT
17816651 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
17816677 GGTTGCCTAG
Statistics
Matches: 92, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
1 2 0.02
2 79 0.86
3 11 0.12
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.44
Consensus pattern (2 bp):
AT
Found at i:17819839 original size:63 final size:63
Alignment explanation
Indices: 17819772--17819929 Score: 230
Period size: 63 Copynumber: 2.5 Consensus size: 63
17819762 TGATGTAACC
*
17819772 GTGCATGTGCGGAGTGGGCAGTGCATATGCC-AGTTGAATGACGATGTTGTGACAAC-TACAACT
1 GTGCATGTGCGGAGTGGGCAGTGCATATGCCGA-TCGAATGACGATGTTGTGAC-ACTTACAACT
* * * *
17819835 GTGCATATGCGGAGTGGGTAGTGCCTATGCCGATCGAATGATGATGTTGTGACACTTACAACT
1 GTGCATGTGCGGAGTGGGCAGTGCATATGCCGATCGAATGACGATGTTGTGACACTTACAACT
*
17819898 GTGCATGTGCGGAGTGGGCAGTGCACATGCCG
1 GTGCATGTGCGGAGTGGGCAGTGCATATGCCG
17819930 GTAATGATGT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
62 2 0.02
63 81 0.96
64 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (63 bp):
GTGCATGTGCGGAGTGGGCAGTGCATATGCCGATCGAATGACGATGTTGTGACACTTACAACT
Found at i:17823911 original size:43 final size:43
Alignment explanation
Indices: 17823863--17823985 Score: 158
Period size: 43 Copynumber: 2.9 Consensus size: 43
17823853 CACCATCCCA
* * * **
17823863 TCATCACCAGCTCATGCACACTCTCTACTCGCACAT-GGCTGGG
1 TCATCACCAGCTTATGCGCACTCCCTACTCGCACATAATC-GGG
*
17823906 TCATCACCAGTTTATGCGCACTCCCTACTCGCACATAATCGGG
1 TCATCACCAGCTTATGCGCACTCCCTACTCGCACATAATCGGG
* *
17823949 TCATCATCGGCTTATGCGCACTCCCTACTCGCACATA
1 TCATCACCAGCTTATGCGCACTCCCTACTCGCACATA
17823986 GCCGAGTCCA
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
43 69 0.99
44 1 0.01
ACGTcount: A:0.22, C:0.37, G:0.16, T:0.25
Consensus pattern (43 bp):
TCATCACCAGCTTATGCGCACTCCCTACTCGCACATAATCGGG
Found at i:17829038 original size:19 final size:20
Alignment explanation
Indices: 17829014--17829052 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
17829004 ACAAAATATA
17829014 TGCC-AATGTATCGATACAT
1 TGCCAAATGTATCGATACAT
17829033 TGCCAAATGTATCGATACAT
1 TGCCAAATGTATCGATACAT
17829053 CACTAAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (20 bp):
TGCCAAATGTATCGATACAT
Found at i:17829673 original size:2 final size:2
Alignment explanation
Indices: 17829666--17829695 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17829656 TAAATATGAA
17829666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17829696 GGTTACCTAG
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):
AT
Found at i:17831017 original size:74 final size:73
Alignment explanation
Indices: 17830936--17831197 Score: 278
Period size: 73 Copynumber: 3.6 Consensus size: 73
17830926 AAAAATAGAG
* * * *
17830936 AAGACTTAGTCAACTAAGAAGTATCT-TTAGTCAACTACGAGCTTACTGCTAGAAATTTGGATT-
1 AAGACTTAATCGACTAAGAAGTAT-TGTTAGTCAACTAAGAGCTTACTGCCAGAAA-TTGGATTC
17830999 ACGAGACAAA-
64 A-GAGACAAAT
* * * * *
17831009 AAGAACTTAATCGACTAAGAAGCATTGTTAGTCAACCAAGAGCTTACTGCCAAAAACTGGGTTCA
1 AAG-ACTTAATCGACTAAGAAGTATTGTTAGTCAACTAAGAGCTTACTGCCAGAAATTGGATTCA
17831074 GAGACAAAT
65 GAGACAAAT
* * * * *
17831083 ACGACTTAATTGACTAAGAAGTATTGTTAGTCGACTAAGAGCTCACTGCCAGAAATTGGATTCAA
1 AAGACTTAATCGACTAAGAAGTATTGTTAGTCAACTAAGAGCTTACTGCCAGAAATTGGATTCAG
* *
17831148 AGACAGAG
66 AGACAAAT
* ** * *
17831156 AATACTTAATCGACTAAGAAACATAGTTAGTCGACTAAGAGC
1 AAGACTTAATCGACTAAGAAGTATTGTTAGTCAACTAAGAGC
17831198 ATTCTATCTG
Statistics
Matches: 158, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
73 112 0.71
74 46 0.29
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.24
Consensus pattern (73 bp):
AAGACTTAATCGACTAAGAAGTATTGTTAGTCAACTAAGAGCTTACTGCCAGAAATTGGATTCAG
AGACAAAT
Found at i:17831710 original size:35 final size:35
Alignment explanation
Indices: 17831605--17831725 Score: 113
Period size: 35 Copynumber: 3.5 Consensus size: 35
17831595 ATTGATCCCA
* * * *
17831605 TGAAAAATCATTGTTAAATGTTGTGGTTGAGGCTT
1 TGAAAAACCATTGTTAAAGGTTGTGGTTGAGACTG
* * * ** *
17831640 TGAAAAGCCATT-TT--TGGTTTTGGTTGATCCCG
1 TGAAAAACCATTGTTAAAGGTTGTGGTTGAGACTG
17831672 TGAAAAACCATTGTTAAAGGTTGTGGTTGAGACTG
1 TGAAAAACCATTGTTAAAGGTTGTGGTTGAGACTG
* *
17831707 TGAAAAGCCATTGTAAAAG
1 TGAAAAACCATTGTTAAAG
17831726 CTTGGTGGGA
Statistics
Matches: 66, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
32 22 0.33
33 2 0.03
34 2 0.03
35 40 0.61
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.35
Consensus pattern (35 bp):
TGAAAAACCATTGTTAAAGGTTGTGGTTGAGACTG
Found at i:17836355 original size:31 final size:31
Alignment explanation
Indices: 17836297--17836355 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
17836287 GATGGGTGTC
* * *
17836297 AAATCTGCAAGCTCACATTGAGCAAGAAAAA
1 AAATCTGCAAGCTCACAATCAGAAAGAAAAA
17836328 AAATCTGCAAGCTC-CAATCAGGAAAGAA
1 AAATCTGCAAGCTCACAATCA-GAAAGAA
17836356 CAGAAAGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.47, C:0.20, G:0.17, T:0.15
Consensus pattern (31 bp):
AAATCTGCAAGCTCACAATCAGAAAGAAAAA
Found at i:17841327 original size:76 final size:76
Alignment explanation
Indices: 17841201--17841354 Score: 254
Period size: 76 Copynumber: 2.0 Consensus size: 76
17841191 TCATTGTAGT
* **
17841201 TGACTTTGAAAGCTATTGTAACTTGTGTTTCTTTGTGCTTAGTTCCAATTACTTTCAATCCATGG
1 TGACTTTGAAAGCTATTATAACTTGTGTTTCTTTGTGCTTAACTCCAATTACTTTCAATCCATGG
17841266 TCATGAATTCA
66 TCATGAATTCA
* * *
17841277 TGACTTTGGAAGTTATTATAACTTGTGTTTCTTTGTGCTTAACTCCAATTACTTTCAGTCCATGG
1 TGACTTTGAAAGCTATTATAACTTGTGTTTCTTTGTGCTTAACTCCAATTACTTTCAATCCATGG
17841342 TCATGAATTCA
66 TCATGAATTCA
17841353 TG
1 TG
17841355 TACATGTCTT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.44
Consensus pattern (76 bp):
TGACTTTGAAAGCTATTATAACTTGTGTTTCTTTGTGCTTAACTCCAATTACTTTCAATCCATGG
TCATGAATTCA
Found at i:17856494 original size:29 final size:28
Alignment explanation
Indices: 17856449--17856590 Score: 185
Period size: 29 Copynumber: 4.9 Consensus size: 28
17856439 GGCAGCTTTG
17856449 ACATGTTTGTCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
17856477 ACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATGTTT-GTCTTAATTTAGACAAGAAA
* *
17856506 ATATGTTTGCCTTAATTTAAGACAAGAAAA
1 ACATGTTTGTCTTAATTT-AGACAAG-AAA
* * *
17856536 ATATTTTTTGTCTTAATTTAGTCAAGAAA
1 ACA-TGTTTGTCTTAATTTAGACAAGAAA
* *
17856565 ACATATTTGTCTCAATTTAGACAAGA
1 ACATGTTTGTCTTAATTTAGACAAGA
17856591 TAAAATATTT
Statistics
Matches: 101, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
28 37 0.37
29 39 0.39
30 12 0.12
31 13 0.13
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAGACAAGAAA
Found at i:17856562 original size:59 final size:58
Alignment explanation
Indices: 17856449--17856623 Score: 226
Period size: 59 Copynumber: 3.0 Consensus size: 58
17856439 GGCAGCTTTG
* * *
17856449 ACATGTTTGTCTTAATTTAGACAAG-AAAACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
* * *
17856506 ATATGTTTGCCTTAATTTAAGACAAGAAAAATATTTTTTGTCTTAATTTAGTCAAGAAA
1 ACATGTTTGTCTTAATTT-AGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
* * *
17856565 ACATATTTGTCTCAATTTAGACAAGATAAAATATTTTTTTGTCTTAATTACAGACAAGA
1 ACATGTTTGTCTTAATTTAGACAAGA-AAAATA-TTTTTTGTCTTAATT-TAGACAAGA
17856624 GTTGTCTTAA
Statistics
Matches: 101, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
57 16 0.16
58 15 0.15
59 48 0.48
60 15 0.15
61 7 0.07
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (58 bp):
ACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
Found at i:17856598 original size:28 final size:28
Alignment explanation
Indices: 17856449--17856600 Score: 173
Period size: 28 Copynumber: 5.3 Consensus size: 28
17856439 GGCAGCTTTG
*
17856449 ACATGTTTGTCTTAATTTAGACAAGAAA
1 ACATATTTGTCTTAATTTAGACAAGAAA
*
17856477 ACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATATTT-GTCTTAATTTAGACAAGAAA
* * *
17856506 ATATGTTTGCCTTAATTTAAGACAAGAAA
1 ACATATTTGTCTTAATTT-AGACAAGAAA
*
17856535 A-ATATTTTTTGTCTTAATTTAGTCAAGAAA
1 ACATA---TTTGTCTTAATTTAGACAAGAAA
*
17856565 ACATATTTGTCTCAATTTAGACAAGATAA
1 ACATATTTGTCTTAATTTAGACAAGA-AA
17856594 A-ATATTT
1 ACATATTT
17856601 TTTTGTCTTA
Statistics
Matches: 110, Mismatches: 7, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
28 44 0.40
29 41 0.37
30 10 0.09
31 15 0.14
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.38
Consensus pattern (28 bp):
ACATATTTGTCTTAATTTAGACAAGAAA
Found at i:17856787 original size:17 final size:17
Alignment explanation
Indices: 17856765--17856797 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17856755 ATAATAATAA
17856765 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
17856782 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
17856798 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:17861962 original size:23 final size:23
Alignment explanation
Indices: 17861933--17861999 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
17861923 ACAAATATAT
17861933 TTTTATTATAATTTAATAATA-C
1 TTTTATTATAATTTAATAATACC
* **
17861955 TTTGTATTAGAAGATAATTAA-ACC
1 TTT-TATTATAATTTAA-TAATACC
*
17861979 TTTTATTATAATTAAATAATA
1 TTTTATTATAATTTAATAATA
17862000 TTTAAAATTA
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
22 6 0.18
23 21 0.62
24 7 0.21
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (23 bp):
TTTTATTATAATTTAATAATACC
Found at i:17862091 original size:32 final size:32
Alignment explanation
Indices: 17862052--17862122 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
17862042 TAAAACTAAG
*
17862052 TAATATTCTTTATTACATTTATTATA-TTCAAA
1 TAATATTCTTTATAACATTTATTATAGTT-AAA
* *
17862084 TAATATTCTTTATAATATTTGTTATAGTTAAA
1 TAATATTCTTTATAACATTTATTATAGTTAAA
17862116 TAATATT
1 TAATATT
17862123 AATATATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.54
Consensus pattern (32 bp):
TAATATTCTTTATAACATTTATTATAGTTAAA
Found at i:17862869 original size:11 final size:12
Alignment explanation
Indices: 17862841--17862874 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17862831 TTAAGCTTGT
17862841 TGAAAAAGAAAC
1 TGAAAAAGAAAC
*
17862853 TGAAAAAGACAC
1 TGAAAAAGAAAC
*
17862865 TAAAAAAGAA
1 TGAAAAAGAA
17862875 GTTGAGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.09, G:0.15, T:0.09
Consensus pattern (12 bp):
TGAAAAAGAAAC
Found at i:17867094 original size:16 final size:16
Alignment explanation
Indices: 17867073--17867117 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
17867063 TTAGTCTTAG
*
17867073 TTTAATTTTAGTTTTC
1 TTTAATTTTAGTTATC
17867089 TTTAATTTTCAG-TATC
1 TTTAATTTT-AGTTATC
*
17867105 TTTAAATTTAGTT
1 TTTAATTTTAGTT
17867118 GTTTGAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 2 0.08
16 21 0.84
17 2 0.08
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (16 bp):
TTTAATTTTAGTTATC
Found at i:17870118 original size:34 final size:35
Alignment explanation
Indices: 17870054--17870135 Score: 121
Period size: 34 Copynumber: 2.4 Consensus size: 35
17870044 AAAGGTAGAG
*
17870054 AGGTTGTGCTTGATCTTTGTGAAAAAGCATTGTGA
1 AGGTTGTGCTTGATCTTTGTGAAAAAGCATTGTAA
*
17870089 AGGTTGTGCTTGATCTTT-TGAAAAGGCATTGTAA
1 AGGTTGTGCTTGATCTTTGTGAAAAAGCATTGTAA
* *
17870123 AGATTATGCTTGA
1 AGGTTGTGCTTGA
17870136 GCCTTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 25 0.58
35 18 0.42
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.38
Consensus pattern (35 bp):
AGGTTGTGCTTGATCTTTGTGAAAAAGCATTGTAA
Found at i:17870147 original size:34 final size:34
Alignment explanation
Indices: 17870075--17870147 Score: 85
Period size: 34 Copynumber: 2.2 Consensus size: 34
17870065 GATCTTTGTG
* * * * *
17870075 AAAAA-GCATTGTGAAGGTTGTGCTTGATCTTTT
1 AAAAAGGCATTGTAAAGATTATGCTTGAGCCTTT
*
17870108 GAAAAGGCATTGTAAAGATTATGCTTGAGCCTTT
1 AAAAAGGCATTGTAAAGATTATGCTTGAGCCTTT
17870142 AAAAAG
1 AAAAAG
17870148 TATTCTTCAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
33 4 0.12
34 28 0.88
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (34 bp):
AAAAAGGCATTGTAAAGATTATGCTTGAGCCTTT
Found at i:17870626 original size:20 final size:21
Alignment explanation
Indices: 17870601--17870643 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
17870591 TTTGACCCCA
*
17870601 TTTGACTTATTGGAGTAT-AT
1 TTTGACTTATTGAAGTATGAT
*
17870621 TTTGACTTTTTGAAGTATGAT
1 TTTGACTTATTGAAGTATGAT
17870642 TT
1 TT
17870644 GAGGTTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.23, C:0.05, G:0.19, T:0.53
Consensus pattern (21 bp):
TTTGACTTATTGAAGTATGAT
Found at i:17873321 original size:16 final size:16
Alignment explanation
Indices: 17873300--17873331 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17873290 TTTGATATTT
17873300 TCACATTATTATTGAG
1 TCACATTATTATTGAG
17873316 TCACATTATTATTGAG
1 TCACATTATTATTGAG
17873332 CTAACATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (16 bp):
TCACATTATTATTGAG
Found at i:17873725 original size:27 final size:27
Alignment explanation
Indices: 17873690--17873747 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
17873680 ACAGGAATGA
*
17873690 AATACAATTGTTATTCTGTGAGAATAG
1 AATAAAATTGTTATTCTGTGAGAATAG
*
17873717 AATAAAATTGTTATTCTGTGGGAATAG
1 AATAAAATTGTTATTCTGTGAGAATAG
17873744 AATA
1 AATA
17873748 GAATAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (27 bp):
AATAAAATTGTTATTCTGTGAGAATAG
Found at i:17873757 original size:27 final size:27
Alignment explanation
Indices: 17873700--17873758 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
17873690 AATACAATTG
**
17873700 TTATTCTGTGAGAATAGAATAAAATTG
1 TTATTCTGTGAGAATAGAATAAAATAA
* *
17873727 TTATTCTGTGGGAATAGAATAGAATAA
1 TTATTCTGTGAGAATAGAATAAAATAA
17873754 TTATT
1 TTATT
17873759 ACTTTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (27 bp):
TTATTCTGTGAGAATAGAATAAAATAA
Found at i:17876369 original size:35 final size:35
Alignment explanation
Indices: 17876280--17876347 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
17876270 GGGAAGATGT
* *
17876280 GTGAGAGCGGTTGAGAGAGAGGGGCAGACCCACAG
1 GTGAGAGCGGCTGAGAGAGAGGGGAAGACCCACAG
17876315 GTGAGAGCGGCTGAGAGAGAGGGGAAGACCCAC
1 GTGAGAGCGGCTGAGAGAGAGGGGAAGACCCAC
17876348 TGTTGAGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.29, C:0.18, G:0.46, T:0.07
Consensus pattern (35 bp):
GTGAGAGCGGCTGAGAGAGAGGGGAAGACCCACAG
Found at i:17876369 original size:37 final size:35
Alignment explanation
Indices: 17876280--17876369 Score: 108
Period size: 35 Copynumber: 2.5 Consensus size: 35
17876270 GGGAAGATGT
* * *
17876280 GTGAGAGCGGTTGAGAGAGAGGGGCAGACCCACAG
1 GTGAGAGCGGCTAAGAGAGAGGGGAAGACCCACAG
* *
17876315 GTGAGAGCGGCTGAGAGAGAGGGGAAGACCCACTG
1 GTGAGAGCGGCTAAGAGAGAGGGGAAGACCCACAG
*
17876350 TTGAGAACGCGGCTAAGAGA
1 GTGAG-A-GCGGCTAAGAGA
17876370 AAGGAAGAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 36 0.75
36 1 0.02
37 11 0.23
ACGTcount: A:0.30, C:0.17, G:0.43, T:0.10
Consensus pattern (35 bp):
GTGAGAGCGGCTAAGAGAGAGGGGAAGACCCACAG
Found at i:17876464 original size:33 final size:33
Alignment explanation
Indices: 17876384--17876507 Score: 149
Period size: 33 Copynumber: 3.6 Consensus size: 33
17876374 AAGAAGACCA
* * * *
17876384 GCTGAGAGAAGAGATGAAGCCGGGGGAAGGTCAACTG
1 GCTGACAGAGGAGATGAAGACAGGGGAAGG-C--C-G
*
17876421 GCTGAGAGAGGAGATGAAGACAGGGGAAGGCCG
1 GCTGACAGAGGAGATGAAGACAGGGGAAGGCCG
17876454 GCTGACAGAGGAGATGAAGACAGGGGAAGGCCG
1 GCTGACAGAGGAGATGAAGACAGGGGAAGGCCG
* *
17876487 GCTGACAAAGGAGAGGAAGAC
1 GCTGACAGAGGAGATGAAGAC
17876508 GGTCAAAGAT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
33 52 0.64
34 1 0.01
36 1 0.01
37 27 0.33
ACGTcount: A:0.35, C:0.14, G:0.44, T:0.07
Consensus pattern (33 bp):
GCTGACAGAGGAGATGAAGACAGGGGAAGGCCG
Found at i:17879802 original size:60 final size:59
Alignment explanation
Indices: 17879709--17879829 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 59
17879699 AATAAAGAGA
* * * *
17879709 GACCTGAAGCCACGACTTATATTTAGTGGTGTGGAGAGTTCCCACGAGTAGGTAAAAGGG
1 GACCTAAAGCCACAACTCATATTTAGTGGTGTGGAGAGTTCCCACGAGTA-GAAAAAGGG
* * *
17879769 GACCTAAAGCCCCAACTCATATTT-GATGGTGTGGGGAGTTCTCACGAGTAGAAAAAGGG
1 GACCTAAAGCCACAACTCATATTTAG-TGGTGTGGAGAGTTCCCACGAGTAGAAAAAGGG
17879828 GA
1 GA
17879830 ATTGAATCCC
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 11 0.21
60 42 0.79
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.22
Consensus pattern (59 bp):
GACCTAAAGCCACAACTCATATTTAGTGGTGTGGAGAGTTCCCACGAGTAGAAAAAGGG
Found at i:17880473 original size:28 final size:27
Alignment explanation
Indices: 17880441--17880894 Score: 190
Period size: 28 Copynumber: 16.7 Consensus size: 27
17880431 CAACAACAAA
17880441 ACGTGTAACAACTACATATTTTAACATC
1 ACGTGTAACAACTACAT-TTTTAACATC
* *
17880469 ACGTGTAACAACTAAATTTTTCAACATG
1 ACGTGTAACAACTACATTTTT-AACATC
* * * * **
17880497 ATGTGTAGCATCTA-ATTCTTCAACAAA
1 ACGTGTAACAACTACATT-TTTAACATC
17880524 ACGTGTAACAACTACATTTTTTAACATC
1 ACGTGTAACAACTACA-TTTTTAACATC
* * ** * *
17880552 ACATGTAACAACTAAATTTCCAATATG
1 ACGTGTAACAACTACATTTTTAACATC
* * *
17880579 ATGTGTAACAGCTACATTTTTCAACATGG
1 ACGTGTAACAACTACATTTTT-AACAT-C
* * *
17880608 A-GTATAATAACTAAATTTTTAACAT-
1 ACGTGTAACAACTACATTTTTAACATC
* * * *
17880633 AGCGTGT---AACTAAATCTTCAACATG
1 A-CGTGTAACAACTACATTTTTAACATC
* * * * * **
17880658 ATGTGTAATAATTAAATTTTCAACAAG
1 ACGTGTAACAACTACATTTTTAACATC
* *
17880685 ATGTGTAACAACTACATTTTTCAACATG
1 ACGTGTAACAACTACATTTTT-AACATC
** * * * *
17880713 GGGTGTAACAATTAAATTTTTTAGCATG
1 ACGTGTAACAACTACA-TTTTTAACATC
* * *
17880741 ATGTGTAATAACTACATTTTCAACAT-
1 ACGTGTAACAACTACATTTTTAACATC
* * * *
17880767 AGCGTGT---AACTAAATCTTCAACATG
1 A-CGTGTAACAACTACATTTTTAACATC
* * * **
17880792 ACGTGTAATAACTAAATTTTCAACAAG
1 ACGTGTAACAACTACATTTTTAACATC
* *
17880819 ATGTGTAACAACTACATTTTTCAACATG
1 ACGTGTAACAACTACATTTTT-AACATC
** * * *
17880847 GGGTGTAACAATTAAATTTTTTAACATG
1 ACGTGTAACAACTACA-TTTTTAACATC
* *
17880875 ATGTGTAATAACTACATTTT
1 ACGTGTAACAACTACATTTT
17880895 CAGCGCTTGA
Statistics
Matches: 331, Mismatches: 74, Indels: 43
0.74 0.17 0.10
Matches are distributed among these distances:
24 39 0.12
25 3 0.01
26 1 0.00
27 133 0.40
28 141 0.43
29 14 0.04
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (27 bp):
ACGTGTAACAACTACATTTTTAACATC
Found at i:17880528 original size:55 final size:55
Alignment explanation
Indices: 17880443--17880896 Score: 351
Period size: 55 Copynumber: 8.4 Consensus size: 55
17880433 ACAACAAAAC
*
17880443 GTGTAACAACTACATATTTT-AACATCACGTGTAACAACTAAATTTTTCAACATGAT
1 GTGTAACAACTA-A-ATTTTCAACATGACGTGTAACAACTAAATTTTTCAACATGAT
* * ** * * * *
17880499 GTGTAGCATCT-AATTCTTCAACAAAACGTGTAACAACTACATTTTTTAACATCAC
1 GTGTAACAACTAAATT-TTCAACATGACGTGTAACAACTAAATTTTTCAACATGAT
* * * * * *
17880554 ATGTAACAACTAAATTTCCAATATGATGTGTAACAGCTACATTTTTCAACATGGA-
1 GTGTAACAACTAAATTTTCAACATGACGTGTAACAACTAAATTTTTCAACAT-GAT
* * * *
17880609 GTATAATAACTAAATTTTTAACAT-AGCGTGT---AACTAAA-TCTTCAACATGAT
1 GTGTAACAACTAAATTTTCAACATGA-CGTGTAACAACTAAATTTTTCAACATGAT
* * * * * **
17880660 GTGTAATAATTAAATTTTCAACAAGATGTGTAACAACTACATTTTTCAACATGGG
1 GTGTAACAACTAAATTTTCAACATGACGTGTAACAACTAAATTTTTCAACATGAT
* * * * * * *
17880715 GTGTAACAATTAAATTTTTTAGCATGATGTGTAATAACTACA-TTTTCAACAT-AGC
1 GTGTAACAACTAAA-TTTTCAACATGACGTGTAACAACTAAATTTTTCAACATGA-T
* * *
17880770 GTGT---AACTAAATCTTCAACATGACGTGTAATAACTAAA-TTTTCAACAAGAT
1 GTGTAACAACTAAATTTTCAACATGACGTGTAACAACTAAATTTTTCAACATGAT
* ** * *
17880821 GTGTAACAACTACATTTTTCAACATGGGGTGTAACAATTAAATTTTTTAACATGAT
1 GTGTAACAACTA-AATTTTCAACATGACGTGTAACAACTAAATTTTTCAACATGAT
* *
17880877 GTGTAATAACTACATTTTCA
1 GTGTAACAACTAAATTTTCA
17880897 GCGCTTGAAA
Statistics
Matches: 315, Mismatches: 64, Indels: 39
0.75 0.15 0.09
Matches are distributed among these distances:
50 2 0.01
51 68 0.22
52 13 0.04
53 3 0.01
54 15 0.05
55 155 0.49
56 59 0.19
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (55 bp):
GTGTAACAACTAAATTTTCAACATGACGTGTAACAACTAAATTTTTCAACATGAT
Found at i:17880693 original size:161 final size:159
Alignment explanation
Indices: 17880478--17880873 Score: 388
Period size: 161 Copynumber: 2.5 Consensus size: 159
17880468 CACGTGTAAC
* *
17880478 AACTAAATTTTTCAACATGATGTGTAGC-ATCT-AATTCTTCAACAAAACGTGTAACAACTACAT
1 AACTAAA-TTTTCAACATGATGTGTAACAAT-TAAATT-TTCAACAAGACGTGTAACAACTACAT
* *
17880541 TTTTTAACATCACATGTAACAACTAAA-TTTCCAATATGATGTGTAACAGCTACATTTTTCAACA
63 TTTTTAACATCACATGTAACAACTAAATTTTCCAACATGATGTGTAACAACTACA-TTTTCAACA
* * *
17880605 TGGAGTATAATAACTAAATTTTTAACAT-AGCGTG-T
127 T--AGCAT-ATAACTAAATCTTCAACATGA-CGTGAT
* * *
17880640 AACTAAATCTTCAACATGATGTGTAATAATTAAATTTTCAACAAGATGTGTAACAACTACATTTT
1 AACTAAATTTTCAACATGATGTGTAACAATTAAATTTTCAACAAGACGTGTAACAACTACATTTT
* **** * ** * *
17880705 TCAACATGGGGTGTAACAATTAAATTTTTTAGCATGATGTGTAATAACTACATTTTCAACATAGC
66 TTAACATCACATGTAACAACTAAATTTTCCAACATGATGTGTAACAACTACATTTTCAACATAGC
* *
17880770 GTGTAACTAAATCTTCAACATGACGTGTAAT
131 ATATAACTAAATCTTCAACATGACGTG--AT
* * * * ** * *
17880801 AACTAAATTTTCAACAAGATGTGTAACAACTACATTTTTCAACATGGGGTGTAACAATTAAATTT
1 AACTAAATTTTCAACATGATGTGTAACAATTA-AATTTTCAACAAGACGTGTAACAACTACATTT
17880866 TTTAACAT
65 TTTAACAT
17880874 GATGTGTAAT
Statistics
Matches: 193, Mismatches: 33, Indels: 16
0.80 0.14 0.07
Matches are distributed among these distances:
158 20 0.10
159 4 0.02
161 102 0.53
162 67 0.35
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (159 bp):
AACTAAATTTTCAACATGATGTGTAACAATTAAATTTTCAACAAGACGTGTAACAACTACATTTT
TTAACATCACATGTAACAACTAAATTTTCCAACATGATGTGTAACAACTACATTTTCAACATAGC
ATATAACTAAATCTTCAACATGACGTGAT
Found at i:17880732 original size:134 final size:134
Alignment explanation
Indices: 17880443--17880896 Score: 527
Period size: 134 Copynumber: 3.4 Consensus size: 134
17880433 ACAACAAAAC
* * * * * * * *
17880443 GTGTAACAACTACATATTTTAACATCACGTGTAACAACTAAATTTTTCAACAT-GATGTGTAGCA
1 GTGTAACAATTAAATTTTTTAACATGATGTGTAATAACTACA-TTTTCAACATAG-CGTGTA--A
* ** * * * ** ** *
17880507 TCTAATTCTTCAACAAAACGTGTAACAACTACATTTTTTAACATCACATGTAACAACTA-AATTT
62 -CTAAATCTTCAACATGACGTGTAATAACTA-AATTTTCAACAAGATGTGTAACAACTACATTTT
* * **
17880571 CCAATATGAT
125 TCAACATGGG
** * * * * *
17880581 GTGTAACAGCTACATTTTTCAACATGGA-GTATAATAACTAAATTTTTAACATAGCGTGTAACTA
1 GTGTAACAATTAAATTTTTTAACAT-GATGTGTAATAACTACATTTTCAACATAGCGTGTAACTA
* *
17880645 AATCTTCAACATGATGTGTAATAATTAAATTTTCAACAAGATGTGTAACAACTACATTTTTCAAC
65 AATCTTCAACATGACGTGTAATAACTAAATTTTCAACAAGATGTGTAACAACTACATTTTTCAAC
17880710 ATGGG
130 ATGGG
*
17880715 GTGTAACAATTAAATTTTTTAGCATGATGTGTAATAACTACATTTTCAACATAGCGTGTAACTAA
1 GTGTAACAATTAAATTTTTTAACATGATGTGTAATAACTACATTTTCAACATAGCGTGTAACTAA
17880780 ATCTTCAACATGACGTGTAATAACTAAATTTTCAACAAGATGTGTAACAACTACATTTTTCAACA
66 ATCTTCAACATGACGTGTAATAACTAAATTTTCAACAAGATGTGTAACAACTACATTTTTCAACA
17880845 TGGG
131 TGGG
17880849 GTGTAACAATTAAATTTTTTAACATGATGTGTAATAACTACATTTTCA
1 GTGTAACAATTAAATTTTTTAACATGATGTGTAATAACTACATTTTCA
17880897 GCGCTTGAAA
Statistics
Matches: 276, Mismatches: 36, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
133 23 0.08
134 202 0.73
135 1 0.00
137 14 0.05
138 35 0.13
139 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (134 bp):
GTGTAACAATTAAATTTTTTAACATGATGTGTAATAACTACATTTTCAACATAGCGTGTAACTAA
ATCTTCAACATGACGTGTAATAACTAAATTTTCAACAAGATGTGTAACAACTACATTTTTCAACA
TGGG
Found at i:17887893 original size:183 final size:183
Alignment explanation
Indices: 17887586--17887953 Score: 589
Period size: 183 Copynumber: 2.0 Consensus size: 183
17887576 GAAAGGCATT
*
17887586 CTCGCTGCAGCAAAATTTGGGCTCAAATTCTCAGCTGGCCGAGGGTTCTCACTAAAAGCCCTCAT
1 CTCGCTGCAGCAAAATTTGGGCTCAAATTCTCAGCTGGCCGAGGGTTCTCACTAAAACCCCTCAT
** *
17887651 TTCAAACTTAATTAATTAATTCCTTGATGTTGGAAGTCCATGGTCAACTATGATGTTAAAGAATT
66 TTCAAACTTAATTAATTAATTCCTTGATGTTGGAAGTCCATGACCAACTATGATGTTAAAGAAGT
17887716 GGAAAATATGGCAGAAACCAAACAAGGTAGCAAGCAAGACAGAA-GTCTCTCG
131 GGAAAATATGGCAGAAACCAAACAAGGTAGCAAGCAAGACAGAAGGTCTCTCG
* * *
17887768 CTCGCTGCAGCGAAATTTGGGCTTAAA-TCATCAGTTGGCCGAGGGTT-TCACATTAAAACCCCT
1 CTCGCTGCAGCAAAATTTGGGCTCAAATTC-TCAGCTGGCCGAGGGTTCTCAC--TAAAACCCCT
*
17887831 CATTTCAAACTTAATTAATTAATTCTTTGATGTTGGAAGTCCATGACCAACTATGATGTTAAAGA
63 CATTTCAAACTTAATTAATTAATTCCTTGATGTTGGAAGTCCATGACCAACTATGATGTTAAAGA
* * *
17887896 AGTGGAAAATATGGTAGAAACCAAACAAGGTAGCAAGCACGACAGAAGGTTTCTCG
128 AGTGGAAAATATGGCAGAAACCAAACAAGGTAGCAAGCAAGACAGAAGGTCTCTCG
17887952 CT
1 CT
17887954 GCAGCGAAAC
Statistics
Matches: 171, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
181 6 0.04
182 41 0.24
183 115 0.67
184 9 0.05
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (183 bp):
CTCGCTGCAGCAAAATTTGGGCTCAAATTCTCAGCTGGCCGAGGGTTCTCACTAAAACCCCTCAT
TTCAAACTTAATTAATTAATTCCTTGATGTTGGAAGTCCATGACCAACTATGATGTTAAAGAAGT
GGAAAATATGGCAGAAACCAAACAAGGTAGCAAGCAAGACAGAAGGTCTCTCG
Found at i:17888463 original size:2 final size:2
Alignment explanation
Indices: 17888456--17888504 Score: 80
Period size: 2 Copynumber: 24.0 Consensus size: 2
17888446 ATTACTATCA
*
17888456 AT AT AT AT CAT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17888499 AT AT AT
1 AT AT AT
17888505 CAACATAACA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:17889263 original size:20 final size:20
Alignment explanation
Indices: 17889231--17889279 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
17889221 GATGGGAGGA
17889231 AGAAAAA-GAAGAAGCTACT
1 AGAAAAATGAAGAAGCTACT
* *
17889250 AGAGAAATGAAGAAGCTGCT
1 AGAAAAATGAAGAAGCTACT
17889270 AGAAAAATGA
1 AGAAAAATGA
17889280 TATTTAGAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.55, C:0.08, G:0.24, T:0.12
Consensus pattern (20 bp):
AGAAAAATGAAGAAGCTACT
Found at i:17905445 original size:22 final size:23
Alignment explanation
Indices: 17905418--17905464 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
17905408 AAATTAATTA
*
17905418 AACAA-TTTAATTAATTAAGCCC
1 AACAATTTTAATCAATTAAGCCC
*
17905440 AACAATTTTAATCAATTAGGCCC
1 AACAATTTTAATCAATTAAGCCC
17905463 AA
1 AA
17905465 TGACTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (23 bp):
AACAATTTTAATCAATTAAGCCC
Found at i:17905521 original size:71 final size:71
Alignment explanation
Indices: 17905440--17905628 Score: 233
Period size: 70 Copynumber: 2.7 Consensus size: 71
17905430 AATTAAGCCC
* *
17905440 AACAATTTTAATCAATTAGGCCCAATGACTTAATTAAACAAATTTAATCAATTAGGCCTAATAAC
1 AACAA-TTTAATTAATTAGGCCCAATGACTTAATTAAACAAATTTAATCAATTAGGCCCAATAAC
*
17905505 TTAATTG
65 TTAATTA
*** * ***
17905512 TTTAATTTAATTAATTAGGCCCAATGACTTAATTAAAC-AATTTAATTAATTAGGCCCAATGGTT
1 AACAATTTAATTAATTAGGCCCAATGACTTAATTAAACAAATTTAATCAATTAGGCCCAATAACT
17905576 TAATTA
66 TAATTA
* *
17905582 AACAATTTAATTAATTAGGCAC-A--ACTTAATTAAACAATTTTAATCAA
1 AACAATTTAATTAATTAGGCCCAATGACTTAATTAAACAAATTTAATCAA
17905629 GTGCTTGAGA
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
67 12 0.12
68 9 0.09
69 1 0.01
70 44 0.44
71 32 0.32
72 2 0.02
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (71 bp):
AACAATTTAATTAATTAGGCCCAATGACTTAATTAAACAAATTTAATCAATTAGGCCCAATAACT
TAATTA
Found at i:17905528 original size:35 final size:35
Alignment explanation
Indices: 17905440--17905621 Score: 208
Period size: 35 Copynumber: 5.2 Consensus size: 35
17905430 AATTAAGCCC
* *
17905440 AACAATTTTAATCAATTAGGCCCAATGACTTAATTA
1 AACAA-TTTAATTAATTAGGCCCAATAACTTAATTA
* * *
17905476 AACAAATTTAATCAATTAGGCCTAATAACTTAATTG
1 AAC-AATTTAATTAATTAGGCCCAATAACTTAATTA
*** *
17905512 TTTAATTTAATTAATTAGGCCCAATGACTTAATTA
1 AACAATTTAATTAATTAGGCCCAATAACTTAATTA
***
17905547 AACAATTTAATTAATTAGGCCCAATGGTTTAATTA
1 AACAATTTAATTAATTAGGCCCAATAACTTAATTA
*
17905582 AACAATTTAATTAATTAGG--C-ACAACTTAATTA
1 AACAATTTAATTAATTAGGCCCAATAACTTAATTA
17905614 AACAATTT
1 AACAATTT
17905622 TAATCAAGTG
Statistics
Matches: 126, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
32 16 0.13
33 1 0.01
35 77 0.61
36 30 0.24
37 2 0.02
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.36
Consensus pattern (35 bp):
AACAATTTAATTAATTAGGCCCAATAACTTAATTA
Found at i:17911159 original size:180 final size:180
Alignment explanation
Indices: 17910818--17911166 Score: 452
Period size: 180 Copynumber: 1.9 Consensus size: 180
17910808 GCCATGAAAA
17910818 TTTCCAAAAGTAATCCTCATTGAACAATTTAATAAAGATAATTTTTATAGAATTTTTCAGAATTA
1 TTTCCAAAAGTAATCCTCATTGAACAATTTAATAAAGATAATTTTTATAGAATTTTTCAGAATTA
* * * * *
17910883 ATTTTCAAGAGTTTCTTGTCAATTAAAACTGAAATTTATGCCAAAACAGTGAGTTGGACCAATTT
66 ATTTCCAAAACTTTCTTGTCAATTAAAACTGAAATTCATGCCAAAACAGTGAGGTGGACCAATTT
*
17910948 ATATTTGCACCAATTTTTTTGCTTGAAATCAGCATATTTGACCGTGATAT
131 ATATTTGCACCAATTTTCTTGCTTGAAATCAGCATATTTGACCGTGATAT
* * * * *
17910998 TTTCCAGAAA-TAATCCTTATTGAACATTTTAATAAATATAATTTTTTTGGAATTTTTCAGAATT
1 TTTCCA-AAAGTAATCCTCATTGAACAATTTAATAAAGATAATTTTTATAGAATTTTTCAGAATT
* * **** * *
17911062 AATTTCCAAAACTTTCTTGTTAATTAAAACTGAAATTCATGTCATGTTAGTGAGGTGGACTACTT
65 AATTTCCAAAACTTTCTTGTCAATTAAAACTGAAATTCATGCCAAAACAGTGAGGTGGACCAATT
* * *
17911127 TCACTTTTTGCTCCAA-TTTCTTGCTT-AAATCAGCCTATTT
130 T-A-TATTTGCACCAATTTTCTTGCTTGAAATCAGCATATTT
17911167 ATTCATGAAC
Statistics
Matches: 144, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
180 121 0.84
181 13 0.09
182 10 0.07
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.41
Consensus pattern (180 bp):
TTTCCAAAAGTAATCCTCATTGAACAATTTAATAAAGATAATTTTTATAGAATTTTTCAGAATTA
ATTTCCAAAACTTTCTTGTCAATTAAAACTGAAATTCATGCCAAAACAGTGAGGTGGACCAATTT
ATATTTGCACCAATTTTCTTGCTTGAAATCAGCATATTTGACCGTGATAT
Found at i:17912290 original size:35 final size:35
Alignment explanation
Indices: 17912242--17912511 Score: 269
Period size: 35 Copynumber: 7.7 Consensus size: 35
17912232 CCTTAAAAAA
*** *
17912242 GCCCAATTAACTTAATTGTTTAATTTAATCAATTAG
1 GCCCAA-TAACTTAATTAAATAATTTAATTAATTAG
* *
17912278 GCCCAATAACTTAATTAAACAATTTAATTAATTAA
1 GCCCAATAACTTAATTAAATAATTTAATTAATTAG
* * * *
17912313 GCCCAACAATTTAATTCAAA-AATTTTAGTCAATTAG
1 GCCCAATAACTTAATT-AAATAA-TTTAATTAATTAG
* * * *
17912349 GCCTAATGACTTAATTAAAAAAATTTAATCAATTAG
1 GCCCAATAACTTAATT-AAATAATTTAATTAATTAG
***
17912385 GCCCAATAACTTAATTGTTTAATTTAATTAATTAG
1 GCCCAATAACTTAATTAAATAATTTAATTAATTAG
* *
17912420 CCCCAATGACTTAATTAAATAATTTAATTAATTAG
1 GCCCAATAACTTAATTAAATAATTTAATTAATTAG
* * *
17912455 ACCCAATGATTTAATTAAATAATTTAATTAATTAG
1 GCCCAATAACTTAATTAAATAATTTAATTAATTAG
*
17912490 G--C-ATAACTTAATTAAACAATTT
1 GCCCAATAACTTAATTAAATAATTT
17912512 TAATCAAGTG
Statistics
Matches: 196, Mismatches: 35, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
32 17 0.09
33 1 0.01
35 116 0.59
36 60 0.31
37 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (35 bp):
GCCCAATAACTTAATTAAATAATTTAATTAATTAG
Found at i:17912386 original size:107 final size:105
Alignment explanation
Indices: 17912263--17912511 Score: 301
Period size: 107 Copynumber: 2.4 Consensus size: 105
17912253 TTAATTGTTT
*
17912263 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAG-CCCAACAATTTAA
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATT-AGCCCCAACAACTTAA
* * *
17912327 TTCAAA-AATTTTAGTCAATTAGGCCTAATGACTTAATTAAAAA
65 TT-AAATAA-TTTAATCAATTAGACCCAATGACTTAATT-AAAA
**** **
17912370 AATTTAATCAATTAGGCCCAATAACTTAATTGTTTAATTTAATTAATTAGCCCCAATGACTTAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAGCCCCAACAACTTAAT
* * *
17912435 TAAATAATTTAATTAATTAGACCCAATGATTTAATTAAAT
66 TAAATAATTTAATCAATTAGACCCAATGACTTAATTAAAA
*
17912475 AATTTAATTAATTAGG--C-ATAACTTAATTAAACAATTT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTT
17912512 TAATCAAGTG
Statistics
Matches: 122, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
102 16 0.13
103 1 0.01
105 18 0.15
106 29 0.24
107 58 0.48
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.37
Consensus pattern (105 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAGCCCCAACAACTTAAT
TAAATAATTTAATCAATTAGACCCAATGACTTAATTAAAA
Found at i:17912397 original size:142 final size:139
Alignment explanation
Indices: 17912242--17912518 Score: 380
Period size: 142 Copynumber: 2.0 Consensus size: 139
17912232 CCTTAAAAAA
*
17912242 GCCCAATTAACTTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATT
1 GCCCAATTAACTTAATTGTTTAATTTAATCAATTAGCCCCAATAACTTAATTAAACAATTTAATT
* *
17912307 AATTA-AGCCCAACAATTTAATTCAAA-AATTTTAGTCAATTAGGCCTAATGACTTAATTAAAAA
66 AATTAGA-CCCAACAATTTAATT-AAATAA-TTTAATCAATTAGG-C--ATAACTTAATTAAAAA
17912370 AATTTAATCAATTAG
125 AATTTAATCAATTAG
* * *
17912385 GCCCAA-TAACTTAATTGTTTAATTTAATTAATTAGCCCCAATGACTTAATTAAATAATTTAATT
1 GCCCAATTAACTTAATTGTTTAATTTAATCAATTAGCCCCAATAACTTAATTAAACAATTTAATT
** * * *
17912449 AATTAGACCCAATGATTTAATTAAATAATTTAATTAATTAGGCATAACTTAATTAAACAATTTTA
66 AATTAGACCCAACAATTTAATTAAATAATTTAATCAATTAGGCATAACTTAATTAAAAAAATTTA
17912514 ATCAA
131 ATCAA
17912519 GTGCTTGAGA
Statistics
Matches: 121, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
138 24 0.20
140 1 0.01
141 15 0.12
142 74 0.61
143 7 0.06
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.37
Consensus pattern (139 bp):
GCCCAATTAACTTAATTGTTTAATTTAATCAATTAGCCCCAATAACTTAATTAAACAATTTAATT
AATTAGACCCAACAATTTAATTAAATAATTTAATCAATTAGGCATAACTTAATTAAAAAAATTTA
ATCAATTAG
Found at i:17913960 original size:13 final size:13
Alignment explanation
Indices: 17913942--17913966 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17913932 NNNNAATGGG
17913942 ATTTTATAAAATA
1 ATTTTATAAAATA
17913955 ATTTTATAAAAT
1 ATTTTATAAAAT
17913967 TTTTGCAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Done.