Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 85 of 313
Found at i:28464352 original size:152 final size:148
Alignment explanation
Indices: 28464076--28464429 Score: 408
Period size: 152 Copynumber: 2.4 Consensus size: 148
28464066 AAGGCAGAAA
* * * ***
28464076 TTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACATGAGGCTCAACTCGCCTCTCACAATAC
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGT--CTTGAGGCTCAACTCATTTCTCACAATAC
**** * * * *
28464141 GAGTTGATTTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCT
64 GAGTTGATTTTTAAAAAAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTAACCT
*
28464206 CTCGCAATATGAGTTGATTTTT
129 CTCGCAATATGAGTTGA--ATT
* * *
28464228 TTGAAAAACAGAAATTAAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCACAATACGA
*
28464293 GTTGATTTTTAAAAAAAAAACAGAAATTGAAAATACCTCAGCATGT-CT-ATTGGCTCAACTAAT
66 GTTGATTTTT--AAAAAAAACAGAAATTGAAAATACCTCAGCATGTCCTGA--GGCTCAACTAAC
*
28464356 TTCTCGCAATATGAGTTGAATT
127 CTCTCGCAATATGAGTTGAATT
* * *
28464378 TTG-AAAATAGAAATTGAAATTACCTCAGCGGGTCTTGAGGCTCAACTCATTT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTT
28464430 TGAACAGAAA
Statistics
Matches: 173, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
149 44 0.25
150 42 0.24
151 2 0.01
152 85 0.49
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (148 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCACAATACGA
GTTGATTTTTAAAAAAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTAACCTCT
CGCAATATGAGTTGAATT
Found at i:28464512 original size:72 final size:72
Alignment explanation
Indices: 28464432--28464656 Score: 283
Period size: 72 Copynumber: 3.0 Consensus size: 72
28464422 ACTCATTTTG
*
28464432 AACAGAAATTGAAATTACCTCAACGTGTCTTAAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
28464497 TTTTGAA
66 TTTTGAA
28464504 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
28464569 TTTTTTTTTGAA
66 -----TTTTGAA
* * * * ** *
28464581 AGACAGAAATTGAAAATACCTCAGCATGTGAAC-CGAGGCTCAACTCACCTCTCGCAATATGAGC
1 A-ACAGAAATTGAAATTACCTCA--ACGTG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
28464645 TG-ATTTTGAA
62 TGAATTTTGAA
28464655 AA
1 AA
28464657 AGTAGAAATT
Statistics
Matches: 136, Mismatches: 8, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
72 64 0.47
73 1 0.01
74 8 0.06
77 8 0.06
78 20 0.15
79 1 0.01
80 33 0.24
81 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (72 bp):
AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
TTTTGAA
Found at i:28464525 original size:121 final size:121
Alignment explanation
Indices: 28464311--28464550 Score: 392
Period size: 121 Copynumber: 2.0 Consensus size: 121
28464301 TTAAAAAAAA
* *
28464311 AACAGAAATTGAAAATACCTCAGCATGTCTATTGGCTCAACTAATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAAATACCTCAACATGTCTATAGGCTCAACTAATTTCTCGCAATATGAGTTGAA
* *
28464376 TTTTGAAAATAGAAATTGAAATTACCTCAGCGGGTCTTGAGGCTCAACTCATTTTG
66 TTTTGAAAACAGAAATTGAAATTACCTCAACGGGTCTTGAGGCTCAACTCATTTTG
* * *
28464432 AACAGAAATTGAAATTACCTCAACGTGTCT-TAAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 AACAGAAATTGAAAATACCTCAACATGTCTAT-AGGCTCAACTAATTTCTCGCAATATGAGTTGA
*
28464496 ATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
65 ATTTTGAAAACAGAAATTGAAATTACCTCAACGGGTCTTGAGGCTCAACTCATTT
28464551 CTCGCAATAT
Statistics
Matches: 110, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
120 1 0.01
121 109 0.99
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (121 bp):
AACAGAAATTGAAAATACCTCAACATGTCTATAGGCTCAACTAATTTCTCGCAATATGAGTTGAA
TTTTGAAAACAGAAATTGAAATTACCTCAACGGGTCTTGAGGCTCAACTCATTTTG
Found at i:28464720 original size:54 final size:55
Alignment explanation
Indices: 28464620--28464725 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 55
28464610 GAACCGAGGC
* *
28464620 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
* * *
28464674 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAA-CATAAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAAAAAGCAGAAATTGAAAA
28464726 CAGAAATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
54 34 0.76
55 11 0.24
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (55 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
Found at i:28464732 original size:13 final size:13
Alignment explanation
Indices: 28464705--28464738 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
28464695 GAGTTGATTC
*
28464705 TTGAACAACATAAA
1 TTGAA-AACAGAAA
28464719 TTGAAAACAGAAA
1 TTGAAAACAGAAA
28464732 TTGAAAA
1 TTGAAAA
28464739 TACCTCAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
TTGAAAACAGAAA
Found at i:28464786 original size:140 final size:140
Alignment explanation
Indices: 28464576--28465203 Score: 1114
Period size: 140 Copynumber: 4.5 Consensus size: 140
28464566 GAATTTTTTT
28464576 TTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAA-ACAGAAATTGAAAATACCTCAGC--GTG-ACCTGAGGCTCAACTCACCTCTCGCAATA
28464640 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTC
62 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTC
*
28464705 TTGAACAACATAAA
127 TTGAACAACGTAAA
* *
28464719 TTGAAAACAGAAATTGAAAATACCTCAGTGTGACCTGAAGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
*
28464784 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTTGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
28464849 ACAACGTAAA
131 ACAACGTAAA
* * *
28464859 TTGAAAACAGAAATTGAAAATACCTTAGCGTGACCTGAGCCTCAACTCACCTCTTGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
*
28464924 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTTGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
28464989 ACAACGTAAA
131 ACAACGTAAA
* * *
28464999 TTGAAAATAGAAATTGAAAATACCTCAACGTGACCTGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
28465064 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
28465129 ACAACGTAAA
131 ACAACGTAAA
28465139 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
28465204 TTGAAATTAA
Statistics
Matches: 465, Mismatches: 19, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
139 3 0.01
140 434 0.93
142 22 0.05
143 6 0.01
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (140 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
ACAACGTAAA
Found at i:28464860 original size:54 final size:54
Alignment explanation
Indices: 28464760--28464865 Score: 135
Period size: 54 Copynumber: 1.9 Consensus size: 54
28464750 GACCTGAAGC
*
28464760 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* * *
28464814 TCAACCCACCTCTTGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
28464866 CAGAAATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
54 32 0.71
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:28465000 original size:54 final size:54
Alignment explanation
Indices: 28464900--28465005 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 54
28464890 GACCTGAGCC
*
28464900 TCAACTCACCTCTTGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTTGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* *
28464954 TCAACCCACCTCTTGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTTGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
28465006 TAGAAATTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 33 0.72
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (54 bp):
TCAACCCACCTCTTGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:28465014 original size:13 final size:13
Alignment explanation
Indices: 28464996--28465020 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28464986 TGAACAACGT
28464996 AAATTGAAAATAG
1 AAATTGAAAATAG
28465009 AAATTGAAAATA
1 AAATTGAAAATA
28465021 CCTCAACGTG
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:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (13 bp):
AAATTGAAAATAG
Found at i:28465140 original size:54 final size:54
Alignment explanation
Indices: 28465040--28465145 Score: 135
Period size: 54 Copynumber: 1.9 Consensus size: 54
28465030 GACCTGAGGC
* *
28465040 TCAACTCATCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* *
28465094 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
28465146 CAGAAATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
54 32 0.71
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:28465270 original size:72 final size:71
Alignment explanation
Indices: 28465136--28465297 Score: 243
Period size: 72 Copynumber: 2.3 Consensus size: 71
28465126 TGAACAACGT
* * * *
28465136 AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
28465201 GAGTTG
66 GAGTTG
*
28465207 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
1 AAATTAAAA-ACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATA
28465272 TGAGTTG
65 TGAGTTG
**
28465279 ATTTTGAAAAACAAAAATT
1 AAATT-AAAAACAAAAATT
28465298 AAAGGCTTAA
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
71 8 0.10
72 70 0.85
73 4 0.05
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (71 bp):
AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
GAGTTG
Found at i:28465326 original size:52 final size:52
Alignment explanation
Indices: 28465248--28465349 Score: 152
Period size: 52 Copynumber: 2.0 Consensus size: 52
28465238 GCGTGCCCCG
**
28465248 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAA-ACAAAAATTAA
1 AGGCTCAACTCACCTCTAGCAATATGAGTTGAAATT-AAAACACAAAAATTAA
* *
28465300 AGGCTTAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATT
1 AGGCTCAACTCACCTCTAGCAATATGAGTTGAAATTAAAACACAAAAATT
28465350 GAAAATACCT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 4 0.09
52 41 0.91
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (52 bp):
AGGCTCAACTCACCTCTAGCAATATGAGTTGAAATTAAAACACAAAAATTAA
Found at i:28465329 original size:124 final size:124
Alignment explanation
Indices: 28465176--28465421 Score: 422
Period size: 124 Copynumber: 2.0 Consensus size: 124
28465166 GCGTGACCTG
28465176 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
* **
28465241 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAA-ACAAAAATTAA
66 TGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGAAATT-AAAACACAAAAATTAA
*
28465300 AGGCTTAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
* *
28465365 TGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATT
66 TGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGAAATTAAAACACAAAAATT
28465422 GAAAATACCT
Statistics
Matches: 115, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
123 4 0.03
124 111 0.97
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (124 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
TGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGAAATTAAAACACAAAAATTAA
Found at i:28465393 original size:72 final size:72
Alignment explanation
Indices: 28465300--28465475 Score: 343
Period size: 72 Copynumber: 2.4 Consensus size: 72
28465290 CAAAAATTAA
*
28465300 AGGCTTAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
28465365 TGACCTG
66 TGACCTG
28465372 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
28465437 TGACCTG
66 TGACCTG
28465444 AGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA
28465476 TTTCCCTTGA
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 103 1.00
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (72 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
TGACCTG
Found at i:28473776 original size:12 final size:12
Alignment explanation
Indices: 28473759--28473789 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
28473749 TATGCAATGT
28473759 ATGAATGAATAC
1 ATGAATGAATAC
*
28473771 ATGAATGAATGC
1 ATGAATGAATAC
28473783 ATGAATG
1 ATGAATG
28473790 TCAAATGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (12 bp):
ATGAATGAATAC
Found at i:28475918 original size:40 final size:40
Alignment explanation
Indices: 28475863--28475940 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
28475853 AAGGGGGGCC
* * *
28475863 GGTCATCGGTCGATCGTCAGTCGCCGCCCGTCGTCGGAGG
1 GGTCACCGGTCGATCGTCAGCCGCCGCCCGTCGCCGGAGG
*
28475903 GGTCACCGGTCGATCGTCGGCCGCCGCCCGTCGCCGGA
1 GGTCACCGGTCGATCGTCAGCCGCCGCCCGTCGCCGGA
28475941 CACCGCCCAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.09, C:0.37, G:0.37, T:0.17
Consensus pattern (40 bp):
GGTCACCGGTCGATCGTCAGCCGCCGCCCGTCGCCGGAGG
Found at i:28478144 original size:27 final size:27
Alignment explanation
Indices: 28478101--28478155 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
28478091 TTCTGAAATT
*
28478101 ATTATGTCTTGAATTTGTTAGATATTG
1 ATTATGTCTTCAATTTGTTAGATATTG
28478128 ATTATGT-TTCAAGTTTGTTAGATATTG
1 ATTATGTCTTCAA-TTTGTTAGATATTG
28478155 A
1 A
28478156 ATTTATTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51
Consensus pattern (27 bp):
ATTATGTCTTCAATTTGTTAGATATTG
Found at i:28478167 original size:32 final size:31
Alignment explanation
Indices: 28478080--28478188 Score: 88
Period size: 32 Copynumber: 3.6 Consensus size: 31
28478070 TTGAAATTTT
* *
28478080 AGTTTGTTCGAT-TCTGAAATTATTATGTCTTGA
1 AGTTTGTTAGATAT-TG-AATTATTATGT-TTCA
28478113 A-TTTGTTAGATATTG----ATTATGTTTCA
1 AGTTTGTTAGATATTGAATTATTATGTTTCA
*
28478139 AGTTTGTTAGATATTGAATTTATTATGTTTTA
1 AGTTTGTTAGATATTGAA-TTATTATGTTTCA
*
28478171 AGCTTT-TTGGATATTGAA
1 AG-TTTGTTAGATATTGAA
28478189 ATGATTGACA
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
26 4 0.06
27 21 0.33
32 34 0.53
33 5 0.08
ACGTcount: A:0.27, C:0.05, G:0.17, T:0.51
Consensus pattern (31 bp):
AGTTTGTTAGATATTGAATTATTATGTTTCA
Found at i:28479208 original size:46 final size:46
Alignment explanation
Indices: 28479141--28479262 Score: 217
Period size: 46 Copynumber: 2.7 Consensus size: 46
28479131 AATACTTTTA
28479141 ATGTGGTGTAATATTAGTTATGCACTTGGACAATGTTGTTGTTATC
1 ATGTGGTGTAATATTAGTTATGCACTTGGACAATGTTGTTGTTATC
28479187 ATGTGGTGTAATATTAGTTATGCACTTGGACAATGTTGTTGTTATC
1 ATGTGGTGTAATATTAGTTATGCACTTGGACAATGTTGTTGTTATC
* * *
28479233 ATGTGGTGTACTACTAGTTATGCATTTGGA
1 ATGTGGTGTAATATTAGTTATGCACTTGGA
28479263 TAATATTATT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.43
Consensus pattern (46 bp):
ATGTGGTGTAATATTAGTTATGCACTTGGACAATGTTGTTGTTATC
Found at i:28479670 original size:14 final size:15
Alignment explanation
Indices: 28479637--28479676 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
28479627 ACACCAGAAA
28479637 AGAAAATCATTTTCC
1 AGAAAATCATTTTCC
*
28479652 A-AAAATCATTTT-T
1 AGAAAATCATTTTCC
28479665 AGAAAAT-ATTTT
1 AGAAAATCATTTT
28479677 ACTGACAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 6 0.26
14 16 0.70
15 1 0.04
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (15 bp):
AGAAAATCATTTTCC
Found at i:28480919 original size:11 final size:11
Alignment explanation
Indices: 28480903--28480933 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
28480893 AAGTATGGGT
28480903 AGGTATGGGAA
1 AGGTATGGGAA
*
28480914 AGGTATGGGCA
1 AGGTATGGGAA
28480925 AGGTATGGG
1 AGGTATGGG
28480934 GTATGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:28485544 original size:30 final size:30
Alignment explanation
Indices: 28485498--28485591 Score: 152
Period size: 30 Copynumber: 3.1 Consensus size: 30
28485488 TTTTATTATG
*
28485498 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
28485529 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
28485559 CCATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
28485589 CCA
1 CCA
28485592 TAAATATGGA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
30 53 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:28485553 original size:15 final size:15
Alignment explanation
Indices: 28485508--28485585 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
28485498 CCAATATCTC
28485508 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
28485523 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
28485538 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
28485553 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
28485568 GATACCCATATCTTT
1 GATACCCATATCTTT
28485583 GAT
1 GAT
28485586 TTTCCATAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.19
15 29 0.62
16 9 0.19
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:28489669 original size:28 final size:28
Alignment explanation
Indices: 28489629--28489685 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
28489619 ACTTTAAAAA
28489629 GTAGTCAACAATTTGGTGCAGTAAGCGT
1 GTAGTCAACAATTTGGTGCAGTAAGCGT
28489657 GTAGTCAACAATTTGGTGCAGTAAGCGT
1 GTAGTCAACAATTTGGTGCAGTAAGCGT
28489685 G
1 G
28489686 AACAAACTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (28 bp):
GTAGTCAACAATTTGGTGCAGTAAGCGT
Found at i:28491179 original size:18 final size:17
Alignment explanation
Indices: 28491151--28491184 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
28491141 TTAATCACTT
28491151 TAATATTAAATTTAATC
1 TAATATTAAATTTAATC
28491168 TAATATTTAAATTTAAT
1 TAATA-TTAAATTTAAT
28491185 ATTAAATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATATTAAATTTAATC
Found at i:28491253 original size:29 final size:30
Alignment explanation
Indices: 28491221--28491278 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 30
28491211 ATTTATCCAC
28491221 AAGATAAACAC-TAA-ATTAAATTTAATATT
1 AAGATAAACACTTAATATTAAA-TTAATATT
*
28491250 AAGATAATCACTTTAATATTAAATTAATA
1 AAGATAAACAC-TTAATATTAAATTAATA
28491279 AAATATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 10 0.40
31 9 0.36
32 6 0.24
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.36
Consensus pattern (30 bp):
AAGATAAACACTTAATATTAAATTAATATT
Found at i:28501798 original size:11 final size:11
Alignment explanation
Indices: 28501784--28501821 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
28501774 TTTTGTTGCC
28501784 ATTTTGCTATT
1 ATTTTGCTATT
*
28501795 ATTTTTCTATT
1 ATTTTGCTATT
*
28501806 ATATTGCTATT
1 ATTTTGCTATT
28501817 ATTTT
1 ATTTT
28501822 ATTGTTATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.66
Consensus pattern (11 bp):
ATTTTGCTATT
Found at i:28502501 original size:42 final size:42
Alignment explanation
Indices: 28502444--28502524 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
28502434 TATGAACAAT
*
28502444 CAACTATTTTGCATGTAAAGATGCAAGTTTTGGAAAGAGAAA
1 CAACTATTTTACATGTAAAGATGCAAGTTTTGGAAAGAGAAA
*
28502486 CAACTATTTTACATGTAAAGATGCAAGTTTTGGAGAGAG
1 CAACTATTTTACATGTAAAGATGCAAGTTTTGGAAAGAG
28502525 TGTTGCGTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (42 bp):
CAACTATTTTACATGTAAAGATGCAAGTTTTGGAAAGAGAAA
Found at i:28505454 original size:16 final size:17
Alignment explanation
Indices: 28505433--28505465 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28505423 CACATTGAAG
28505433 TGTTTT-TTGAAAACCT
1 TGTTTTATTGAAAACCT
28505449 TGTTTTCATTGAAAACC
1 TGTTTT-ATTGAAAACC
28505466 CTTCTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.45
Consensus pattern (17 bp):
TGTTTTATTGAAAACCT
Found at i:28506804 original size:28 final size:29
Alignment explanation
Indices: 28506772--28506843 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
28506762 ACATACATAT
*
28506772 ATATGGCCCACTGGGCCC-AATCTCATTC
1 ATATGGCCCACTGGGCCCAAATCACATTC
* *
28506800 ATATGGCCCATTAGGCCCAAATCACATTC
1 ATATGGCCCACTGGGCCCAAATCACATTC
28506829 ATATGGCCCATCTGG
1 ATATGGCCCA-CTGG
28506844 CCTGAATCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 16 0.43
29 19 0.51
30 2 0.05
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (29 bp):
ATATGGCCCACTGGGCCCAAATCACATTC
Found at i:28507098 original size:16 final size:16
Alignment explanation
Indices: 28507073--28507110 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
28507063 GTAGCCAAAC
* *
28507073 TTTCGGCTTTTCGGCA
1 TTTCGACTTTTCAGCA
28507089 TTTCGACTTTTCAGCA
1 TTTCGACTTTTCAGCA
28507105 TTTCGA
1 TTTCGA
28507111 GATTTGCCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (16 bp):
TTTCGACTTTTCAGCA
Found at i:28512916 original size:18 final size:18
Alignment explanation
Indices: 28512893--28512981 Score: 56
Period size: 18 Copynumber: 4.8 Consensus size: 18
28512883 AACAAGTGAG
28512893 GAAAAAGAAAAAGAGAAT
1 GAAAAAGAAAAAGAGAAT
*
28512911 GAAAAAGAGCAAAAAGAGATT
1 G-AAAA-AG-AAAAAGAGAAT
* **
28512932 GAGAGTGAAAAAGA-AATT
1 GAAAAAGAAAAAGAGAA-T
* *
28512950 GAAGAAAG-AAGAGAAAAT
1 GAA-AAAGAAAAAGAGAAT
*
28512968 GAAATAGAAAAAGA
1 GAAAAAGAAAAAGA
28512982 AACAAAAGAA
Statistics
Matches: 53, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
17 4 0.08
18 25 0.47
19 9 0.17
20 4 0.08
21 11 0.21
ACGTcount: A:0.65, C:0.01, G:0.25, T:0.09
Consensus pattern (18 bp):
GAAAAAGAAAAAGAGAAT
Found at i:28512971 original size:24 final size:23
Alignment explanation
Indices: 28512938--28512982 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
28512928 GATTGAGAGT
*
28512938 GAAAAAGAAATTGAAGAAAGAAGA
1 GAAAAAGAAATAGAA-AAAGAAGA
*
28512962 GAAAATGAAATAGAAAAAGAA
1 GAAAAAGAAATAGAAAAAGAA
28512983 ACAAAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.09
Consensus pattern (23 bp):
GAAAAAGAAATAGAAAAAGAAGA
Found at i:28526401 original size:16 final size:17
Alignment explanation
Indices: 28526363--28526401 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
28526353 TAAGTAAATA
28526363 ATATT-ATATTATAATT
1 ATATTAATATTATAATT
28526379 ATATTAATATTATAA-T
1 ATATTAATATTATAATT
28526395 ATATTAA
1 ATATTAA
28526402 GTGAATAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTAATATTATAATT
Found at i:28527714 original size:20 final size:19
Alignment explanation
Indices: 28527687--28527732 Score: 74
Period size: 21 Copynumber: 2.3 Consensus size: 19
28527677 AAGTGAGTAA
28527687 TTATTTTTTTATTGGTTATAT
1 TTATTTTTTTATT-GTTAT-T
28527708 TTATTTTTTTATTGTTATT
1 TTATTTTTTTATTGTTATT
28527727 TTATTT
1 TTATTT
28527733 CATTCTGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 7 0.28
20 5 0.20
21 13 0.52
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (19 bp):
TTATTTTTTTATTGTTATT
Found at i:28527940 original size:64 final size:64
Alignment explanation
Indices: 28527827--28527956 Score: 174
Period size: 64 Copynumber: 2.0 Consensus size: 64
28527817 ATAATACTCA
* * * *
28527827 AGTTTTAGTTTGACTTGTTGGCTTTGGGAATTCTGCTCCTCTATCGTCTTCTCCGATCGCAAAT
1 AGTTTTAGCTTGACTTGTTGGCTTCGAGAATTCTGCTCATCTATCGTCTTCTCCGATCGCAAAT
* *
28527891 AGTTTTGGCTTGACTTGTTGGCTTCGAGAA-TCTCGCTCATC-AGTTGTCTTCTCCGATCGCAAA
1 AGTTTTAGCTTGACTTGTTGGCTTCGAGAATTCT-GCTCATCTA-TCGTCTTCTCCGATCGCAAA
28527954 T
64 T
28527955 AG
1 AG
28527957 GTGTGGGATT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
63 4 0.07
64 54 0.93
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (64 bp):
AGTTTTAGCTTGACTTGTTGGCTTCGAGAATTCTGCTCATCTATCGTCTTCTCCGATCGCAAAT
Found at i:28534547 original size:26 final size:28
Alignment explanation
Indices: 28534508--28534561 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
28534498 ATTTACTATT
*
28534508 TTTTCCTCCTCTCTACTT-CCCTTTTCC
1 TTTTCCTCCCCTCTACTTCCCCTTTTCC
**
28534535 TTTT-CTCCCCTCTTTTTCCCCTTTTCC
1 TTTTCCTCCCCTCTACTTCCCCTTTTCC
28534562 ACTTTCCCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTTCCTCCCCTCTACTTCCCCTTTTCC
Found at i:28540203 original size:16 final size:16
Alignment explanation
Indices: 28540182--28540212 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28540172 ATTGGGTTAA
*
28540182 GAAAACTATTTAATTG
1 GAAAACTAATTAATTG
28540198 GAAAACTAATTAATT
1 GAAAACTAATTAATT
28540213 AAAATTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.35
Consensus pattern (16 bp):
GAAAACTAATTAATTG
Found at i:28551458 original size:17 final size:17
Alignment explanation
Indices: 28551436--28551469 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28551426 TAAAATTATC
28551436 TTATAAAATTTTCAAAA
1 TTATAAAATTTTCAAAA
*
28551453 TTATAAAATTTTTAAAA
1 TTATAAAATTTTCAAAA
28551470 ATTAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTATAAAATTTTCAAAA
Found at i:28551470 original size:18 final size:17
Alignment explanation
Indices: 28551436--28551473 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
28551426 TAAAATTATC
*
28551436 TTATAAAATTTTCAAAA
1 TTATAAAATTTTAAAAA
28551453 TTATAAAATTTTTAAAAA
1 TTATAAAA-TTTTAAAAA
28551471 TTA
1 TTA
28551474 AATTAAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TTATAAAATTTTAAAAA
Found at i:28552832 original size:19 final size:19
Alignment explanation
Indices: 28552771--28552832 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
28552761 TATTATATAA
28552771 ATATTTAATTATTTTATATGTTT
1 ATATTT-ATT-TTTTA-AT-TTT
* * * *
28552794 TTATATATTTTTTGAGTTT
1 ATATTTATTTTTTAATTTT
28552813 ATATTTATTTTTTAATTTT
1 ATATTTATTTTTTAATTTT
28552832 A
1 A
28552833 ATAAACATGT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
19 19 0.61
20 1 0.03
21 4 0.13
22 3 0.10
23 4 0.13
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
ATATTTATTTTTTAATTTT
Found at i:28554046 original size:24 final size:24
Alignment explanation
Indices: 28554014--28554059 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
28554004 CAGATGTATT
* *
28554014 TTCAGATTTAGATACATATGCATA
1 TTCAAATTTAGATACAAATGCATA
28554038 TTCAAATTTAGATACAAATGCA
1 TTCAAATTTAGATACAAATGCA
28554060 GACGCAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (24 bp):
TTCAAATTTAGATACAAATGCATA
Found at i:28563382 original size:18 final size:18
Alignment explanation
Indices: 28563359--28563445 Score: 129
Period size: 18 Copynumber: 4.8 Consensus size: 18
28563349 CGTTTATGGT
*
28563359 ACTATTCACGTATACGAC
1 ACTATTCACGTATACGGC
*
28563377 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGGC
*
28563395 ACTATTCACATATACGGC
1 ACTATTCACGTATACGGC
*
28563413 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGGC
*
28563431 ACTGTTCACGTATAC
1 ACTATTCACGTATAC
28563446 AGTAGTTGGG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (18 bp):
ACTATTCACGTATACGGC
Found at i:28563403 original size:36 final size:36
Alignment explanation
Indices: 28563356--28563445 Score: 153
Period size: 36 Copynumber: 2.5 Consensus size: 36
28563346 GACCGTTTAT
28563356 GGTACTATTCACGTATACGACACTATTCACGTATAC
1 GGTACTATTCACGTATACGACACTATTCACGTATAC
* *
28563392 GGTACTATTCACATATACGGCACTATTCACGTATAC
1 GGTACTATTCACGTATACGACACTATTCACGTATAC
*
28563428 GGTACTGTTCACGTATAC
1 GGTACTATTCACGTATAC
28563446 AGTAGTTGGG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (36 bp):
GGTACTATTCACGTATACGACACTATTCACGTATAC
Found at i:28566756 original size:96 final size:96
Alignment explanation
Indices: 28566592--28566776 Score: 352
Period size: 96 Copynumber: 1.9 Consensus size: 96
28566582 TTTGAAGAAA
28566592 GTACTACAGCAGTTTGGCATGAACGAGCAGACCAAACCTGTAAGTACCCCGTTGGCTTCTCATTT
1 GTACTACAGCAGTTTGGCATGAACGAGCAGACCAAACCTGTAAGTACCCCGTTGGCTTCTCATTT
*
28566657 CAAGCTTTGTGCACAACTATCTCCGAAAAAG
66 CAAGCTTTCTGCACAACTATCTCCGAAAAAG
28566688 GTACTACAGCAGTTTGGCATGAACGAGCAGACCAAACCTGTAAGTACCCCGTTGGCTTCTCATTT
1 GTACTACAGCAGTTTGGCATGAACGAGCAGACCAAACCTGTAAGTACCCCGTTGGCTTCTCATTT
*
28566753 CAAGCTTTCTGCATAACTATCTCC
66 CAAGCTTTCTGCACAACTATCTCC
28566777 TTCGACGAAT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 87 1.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (96 bp):
GTACTACAGCAGTTTGGCATGAACGAGCAGACCAAACCTGTAAGTACCCCGTTGGCTTCTCATTT
CAAGCTTTCTGCACAACTATCTCCGAAAAAG
Found at i:28568550 original size:20 final size:20
Alignment explanation
Indices: 28568525--28568588 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
28568515 CTATCATTTT
28568525 ATTTTTAAATTCGACTCTAA
1 ATTTTTAAATTCGACTCTAA
**
28568545 ATTTTTAAA--C-A-T-TTT
1 ATTTTTAAATTCGACTCTAA
28568560 ATTTTTAAATTCGACTCTAA
1 ATTTTTAAATTCGACTCTAA
28568580 ATTTTTAAA
1 ATTTTTAAA
28568589 CATATTGCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
15 10 0.29
16 1 0.03
17 2 0.06
18 2 0.06
19 1 0.03
20 19 0.54
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.50
Consensus pattern (20 bp):
ATTTTTAAATTCGACTCTAA
Found at i:28568558 original size:35 final size:35
Alignment explanation
Indices: 28568519--28568591 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
28568509 CTTAAACTAT
28568519 CATTTTATTTTTAAATTCGACTCTAAATTTTTAAA
1 CATTTTATTTTTAAATTCGACTCTAAATTTTTAAA
28568554 CATTTTATTTTTAAATTCGACTCTAAATTTTTAAA
1 CATTTTATTTTTAAATTCGACTCTAAATTTTTAAA
28568589 CAT
1 CAT
28568592 ATTGCAAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.51
Consensus pattern (35 bp):
CATTTTATTTTTAAATTCGACTCTAAATTTTTAAA
Found at i:28569087 original size:14 final size:14
Alignment explanation
Indices: 28569068--28569094 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28569058 TTGTATAGCT
28569068 GTAAAAGCTTTTCC
1 GTAAAAGCTTTTCC
28569082 GTAAAAGCTTTTC
1 GTAAAAGCTTTTC
28569095 AGCATTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (14 bp):
GTAAAAGCTTTTCC
Found at i:28569273 original size:6 final size:6
Alignment explanation
Indices: 28569262--28569299 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
28569252 TTGAAACGCT
* *
28569262 TTCTCC TTCTCC TTCTCC TTCCCC TTCCCC TTC-CC TTC
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTC
28569300 ATTGCGTCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (6 bp):
TTCTCC
Found at i:28573102 original size:19 final size:19
Alignment explanation
Indices: 28573078--28573116 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
28573068 ATCCAAACAC
28573078 CAGAAAAGTAAATCATTTT
1 CAGAAAAGTAAATCATTTT
28573097 CAGAAAAGTAAATCATTTT
1 CAGAAAAGTAAATCATTTT
28573116 C
1 C
28573117 CGTAAATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (19 bp):
CAGAAAAGTAAATCATTTT
Found at i:28573123 original size:14 final size:14
Alignment explanation
Indices: 28573104--28573143 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
28573094 TTTCAGAAAA
28573104 GTAAATCATTTTCC
1 GTAAATCATTTTCC
28573118 GTAAATCATTTTCC
1 GTAAATCATTTTCC
* *
28573132 GGAAAACATTTT
1 GTAAATCATTTT
28573144 ACTGGCAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (14 bp):
GTAAATCATTTTCC
Found at i:28588536 original size:75 final size:75
Alignment explanation
Indices: 28588444--28588587 Score: 288
Period size: 75 Copynumber: 1.9 Consensus size: 75
28588434 ATATAGGCTG
28588444 CTATAAAGTTGTATTAAATTTGGCTAGGCTTGGGTTTGGCCAAAATTGAATGAATTTCATTTTAC
1 CTATAAAGTTGTATTAAATTTGGCTAGGCTTGGGTTTGGCCAAAATTGAATGAATTTCATTTTAC
28588509 GAGCGGGCAA
66 GAGCGGGCAA
28588519 CTATAAAGTTGTATTAAATTTGGCTAGGCTTGGGTTTGGCCAAAATTGAATGAATTTCATTTTAC
1 CTATAAAGTTGTATTAAATTTGGCTAGGCTTGGGTTTGGCCAAAATTGAATGAATTTCATTTTAC
28588584 GAGC
66 GAGC
28588588 TTAGGGACTA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (75 bp):
CTATAAAGTTGTATTAAATTTGGCTAGGCTTGGGTTTGGCCAAAATTGAATGAATTTCATTTTAC
GAGCGGGCAA
Found at i:28589298 original size:23 final size:23
Alignment explanation
Indices: 28589209--28589309 Score: 82
Period size: 23 Copynumber: 4.3 Consensus size: 23
28589199 CAACTTGTAT
28589209 GAGCTTACCGATATATCAGCTCG-TAA
1 GAGCTTACCG-T-T-TCAGCTCGAT-A
** *
28589235 GAGCTTACTATTTTAGCTCGTATA
1 GAGCTTACCGTTTCAGCTCG-ATA
* *
28589259 -AACTTACTG-TTCAGCTCGATA
1 GAGCTTACCGTTTCAGCTCGATA
*
28589280 GAGCTTACCGTTTCAGCTCAATA
1 GAGCTTACCGTTTCAGCTCGATA
28589303 GAGCTTA
1 GAGCTTA
28589310 ATGTTCATCA
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
21 3 0.05
22 15 0.24
23 32 0.52
24 2 0.03
25 2 0.03
26 8 0.13
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (23 bp):
GAGCTTACCGTTTCAGCTCGATA
Found at i:28589555 original size:20 final size:20
Alignment explanation
Indices: 28589482--28589591 Score: 87
Period size: 20 Copynumber: 5.5 Consensus size: 20
28589472 ATAAGATATG
* *
28589482 TGTTTATATGGATGAATTAC
1 TGTTTATACGGATGAACTAC
* * *
28589502 TATTGATACGGATGAATTAC
1 TGTTTATACGGATGAACTAC
**
28589522 TG-TTATTATTGATGAACTAC
1 TGTTTA-TACGGATGAACTAC
*
28589542 TGTTTATACAGATGAACTAC
1 TGTTTATACGGATGAACTAC
* * * *
28589562 TGGTTATATGAATGAATTAC
1 TGTTTATACGGATGAACTAC
*
28589582 AGTTTATACG
1 TGTTTATACG
28589592 AATAGAAATG
Statistics
Matches: 70, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
19 2 0.03
20 65 0.93
21 3 0.04
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (20 bp):
TGTTTATACGGATGAACTAC
Found at i:28589587 original size:40 final size:38
Alignment explanation
Indices: 28589485--28589590 Score: 106
Period size: 40 Copynumber: 2.7 Consensus size: 38
28589475 AGATATGTGT
* * *
28589485 TTATATGGATGAATTACTA-TTGATACGGATGAATTACTG
1 TTATAT-GATGAATTAC-AGTTTATACAGATGAACTACTG
* *
28589524 TTATTATTGATGAACTACTGTTTATACAGATGAACTACTGG
1 TTA-TA-TGATGAATTACAGTTTATACAGATGAACTACT-G
28589565 TTATATGAATGAATTACAGTTTATAC
1 TTATATG-ATGAATTACAGTTTATAC
28589591 GAATAGAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
39 5 0.09
40 45 0.82
41 5 0.09
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (38 bp):
TTATATGATGAATTACAGTTTATACAGATGAACTACTG
Found at i:28590629 original size:23 final size:23
Alignment explanation
Indices: 28590599--28590645 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
28590589 ATAAGTTAGT
28590599 GAGTTACACGGCTTAGACACACG
1 GAGTTACACGGCTTAGACACACG
28590622 GAGTTACACGGCTTAGACACACG
1 GAGTTACACGGCTTAGACACACG
28590645 G
1 G
28590646 GCGTGTCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.26, G:0.28, T:0.17
Consensus pattern (23 bp):
GAGTTACACGGCTTAGACACACG
Found at i:28600656 original size:42 final size:43
Alignment explanation
Indices: 28600596--28600716 Score: 138
Period size: 43 Copynumber: 2.8 Consensus size: 43
28600586 ACAGGCCTCG
* *
28600596 ATTGAGATTACGTATAAGACCATGTTTGGGACATCGACATC-AT
1 ATTGA-ATTACATGTAAGACCATGTTTGGGACATCGACATCGAT
* * ** *
28600639 ATCTG-ATTTCATGTAAGACCTTGTTTGGGACAGAGGCATCGAT
1 AT-TGAATTACATGTAAGACCATGTTTGGGACATCGACATCGAT
*
28600682 ATTGAATTACATGTAAGACCACGTTTGGGACATCG
1 ATTGAATTACATGTAAGACCATGTTTGGGACATCG
28600717 GCATTGTACT
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
42 30 0.48
43 31 0.49
44 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Consensus pattern (43 bp):
ATTGAATTACATGTAAGACCATGTTTGGGACATCGACATCGAT
Found at i:28600720 original size:43 final size:42
Alignment explanation
Indices: 28600566--28600720 Score: 145
Period size: 42 Copynumber: 3.7 Consensus size: 42
28600556 TGAGACATCG
* * * * *
28600566 TGTAAGACCGTGTCTGGGACA-CAGGCCTC-GATTGAGATTACG
1 TGTAAGACCATGTTTGGGACATC-GGCATCATATTGA-ATTACA
* * *
28600608 TATAAGACCATGTTTGGGACATCGACATCATATCTG-ATTTCA
1 TGTAAGACCATGTTTGGGACATCGGCATCATAT-TGAATTACA
* **
28600650 TGTAAGACCTTGTTTGGGACAGAGGCATCGATATTGAATTACA
1 TGTAAGACCATGTTTGGGACATCGGCATC-ATATTGAATTACA
*
28600693 TGTAAGACCACGTTTGGGACATCGGCAT
1 TGTAAGACCATGTTTGGGACATCGGCAT
28600721 TGTACTTGTT
Statistics
Matches: 90, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
42 52 0.58
43 36 0.40
44 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (42 bp):
TGTAAGACCATGTTTGGGACATCGGCATCATATTGAATTACA
Found at i:28604668 original size:8 final size:8
Alignment explanation
Indices: 28604657--28604681 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28604647 TGAATGCTTG
28604657 AGTGTTTA
1 AGTGTTTA
28604665 AGTGTTTA
1 AGTGTTTA
28604673 AGTGTTTA
1 AGTGTTTA
28604681 A
1 A
28604682 TGATAGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (8 bp):
AGTGTTTA
Found at i:28605558 original size:23 final size:26
Alignment explanation
Indices: 28605507--28605563 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 26
28605497 TAGCTTGTAT
28605507 GAGCTTACTGATATATTAGCTCATAA
1 GAGCTTACTGATATATTAGCTCATAA
* *
28605533 GAGCTTACTG-T-TTTTAG-TCATTA
1 GAGCTTACTGATATATTAGCTCATAA
28605556 GAGCTTAC
1 GAGCTTAC
28605564 CATTTCAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 13 0.45
24 5 0.17
25 1 0.03
26 10 0.34
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.39
Consensus pattern (26 bp):
GAGCTTACTGATATATTAGCTCATAA
Found at i:28605595 original size:22 final size:23
Alignment explanation
Indices: 28605556--28605619 Score: 87
Period size: 22 Copynumber: 2.8 Consensus size: 23
28605546 TTAGTCATTA
*
28605556 GAGCTTACCATTTCAGCTCGTAT-
1 GAGCTTACCGTTTCAGCTCG-ATG
*
28605579 GAGCTTACTG-TTCAGCTCGATG
1 GAGCTTACCGTTTCAGCTCGATG
28605601 GAGCTTACCGTTTCAGCTC
1 GAGCTTACCGTTTCAGCTC
28605620 AATAGCGCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 2 0.06
22 18 0.50
23 16 0.44
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.33
Consensus pattern (23 bp):
GAGCTTACCGTTTCAGCTCGATG
Found at i:28605629 original size:23 final size:22
Alignment explanation
Indices: 28605524--28605630 Score: 83
Period size: 23 Copynumber: 4.7 Consensus size: 22
28605514 CTGATATATT
* *
28605524 AGCTCATAAGAGCTTACTGTTTTT
1 AGCTCAT-AGAGCTTACCG-TTTC
*
28605548 AG-TCATTAGAGCTTACCATTTC
1 AGCTCA-TAGAGCTTACCGTTTC
* *
28605570 AGCTCGTATGAGCTTACTG-TTC
1 AGCTCATA-GAGCTTACCGTTTC
*
28605592 AGCTCGATGGAGCTTACCGTTTC
1 AGCTC-ATAGAGCTTACCGTTTC
*
28605615 AGCTCAATAGCGCTTA
1 AGCTC-ATAGAGCTTA
28605631 TTATTCATCA
Statistics
Matches: 66, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
22 24 0.36
23 39 0.59
24 3 0.05
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (22 bp):
AGCTCATAGAGCTTACCGTTTC
Found at i:28605888 original size:20 final size:20
Alignment explanation
Indices: 28605832--28605888 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
28605822 CGTTGATACG
*
28605832 GATGAATTACTGTTATTACT
1 GATGAACTACTGTTATTACT
* * *
28605852 GATAAACTACTATTTATT-TT
1 GATGAACTACT-GTTATTACT
28605872 GATGAACTACTGGTTAT
1 GATGAACTACT-GTTAT
28605889 ATGAATGAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.44
Consensus pattern (20 bp):
GATGAACTACTGTTATTACT
Found at i:28608790 original size:6 final size:6
Alignment explanation
Indices: 28608761--28608858 Score: 112
Period size: 6 Copynumber: 16.8 Consensus size: 6
28608751 CAACCCAATT
* * * *
28608761 TATTT- TATTT- TATTT- TATTTA TAATTA TAATTA TAATTA TAATTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
* * *
28608806 CATTTA TATTTA TATTTA TATTTA TATTTA TATTTG TATTTG TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
28608854 TATTT
1 TATTT
28608859 TCTTTATTTT
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
5 15 0.17
6 71 0.83
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (6 bp):
TATTTA
Found at i:28612214 original size:75 final size:75
Alignment explanation
Indices: 28612121--28612262 Score: 187
Period size: 75 Copynumber: 1.9 Consensus size: 75
28612111 CCAATAAATG
* * * * *
28612121 TGAGCCCAGATCTGGTTGGATAGACCAACAATATTTGTACCCAGTGCTAGT-AGGATTTACCGAC
1 TGAGCCCAGATCTAGTTGGATAAACCAACAATATTTGCACCCAGCGCTAGTCA-GATTAACCGAC
28612185 GATAATTATTA
65 GATAATTATTA
* ** *
28612196 TGAGCCCAGCTCTAGTTGGATAAACCAACGGTGTTTGCACCCAGCGCTAGTCAGATTAACCGACG
1 TGAGCCCAGATCTAGTTGGATAAACCAACAATATTTGCACCCAGCGCTAGTCAGATTAACCGACG
28612261 AT
66 AT
28612263 TATGTGCCCA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
75 56 0.98
76 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (75 bp):
TGAGCCCAGATCTAGTTGGATAAACCAACAATATTTGCACCCAGCGCTAGTCAGATTAACCGACG
ATAATTATTA
Found at i:28614316 original size:29 final size:29
Alignment explanation
Indices: 28614274--28614331 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
28614264 TGATTGTATT
**
28614274 AGAACAATTGTAACTTTTAAAAAAACATC
1 AGAACAATTGTAACTTAAAAAAAAACATC
28614303 AGAACAATTGTAACTTAAAAAAAAACATC
1 AGAACAATTGTAACTTAAAAAAAAACATC
28614332 GTGGGCAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.24
Consensus pattern (29 bp):
AGAACAATTGTAACTTAAAAAAAAACATC
Found at i:28615578 original size:16 final size:16
Alignment explanation
Indices: 28615530--28615579 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
28615520 ATATGATTTG
**
28615530 ATGATAAATTATTTTT
1 ATGATAAATTATTTAA
*
28615546 AT-AGAAATTATTTTAA
1 ATGATAAATTA-TTTAA
28615562 ATGATAAATTATTTAA
1 ATGATAAATTATTTAA
28615578 AT
1 AT
28615580 ATTTTATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 7 0.25
16 14 0.50
17 7 0.25
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
ATGATAAATTATTTAA
Found at i:28618502 original size:21 final size:21
Alignment explanation
Indices: 28618476--28618516 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
28618466 TTAGCAATAG
28618476 TCATTCACAAAAACATAAGCT
1 TCATTCACAAAAACATAAGCT
28618497 TCATTCACAAAAACATAAGC
1 TCATTCACAAAAACATAAGC
28618517 CTTAGTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.24, G:0.05, T:0.22
Consensus pattern (21 bp):
TCATTCACAAAAACATAAGCT
Found at i:28621185 original size:16 final size:18
Alignment explanation
Indices: 28621149--28621187 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
28621139 AATCCTTATT
*
28621149 AAATAAAATACAACGGTA
1 AAATAAAATACAACAGTA
28621167 AAATAAAATA-AA-AGTA
1 AAATAAAATACAACAGTA
28621183 AAATA
1 AAATA
28621188 CATATAGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.69, C:0.05, G:0.08, T:0.18
Consensus pattern (18 bp):
AAATAAAATACAACAGTA
Found at i:28623761 original size:12 final size:13
Alignment explanation
Indices: 28623743--28623810 Score: 57
Period size: 14 Copynumber: 5.2 Consensus size: 13
28623733 TAAAAATATG
28623743 ATATTTAATAATA
1 ATATTTAATAATA
*
28623756 AT-TTTAAAAATA
1 ATATTTAATAATA
* *
28623768 GTATTTAATATTTA
1 ATATTTAATA-ATA
*
28623782 ATATATAATATATA
1 ATATTTAATA-ATA
**
28623796 ATAAATAATAATA
1 ATATTTAATAATA
28623809 AT
1 AT
28623811 TATATATAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
12 10 0.22
13 13 0.29
14 22 0.49
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (13 bp):
ATATTTAATAATA
Found at i:28623781 original size:7 final size:7
Alignment explanation
Indices: 28623773--28623831 Score: 58
Period size: 7 Copynumber: 9.3 Consensus size: 7
28623763 AAATAGTATT
*
28623773 TAATATT
1 TAATATA
28623780 TAATATA
1 TAATATA
28623787 TAATATA
1 TAATATA
*
28623794 TAATAAA
1 TAATATA
28623801 TAATA-A
1 TAATATA
28623807 TAAT-TA
1 TAATATA
28623813 T-ATATA
1 TAATATA
28623819 -AA-A-A
1 TAATATA
28623823 TAATATA
1 TAATATA
28623830 TA
1 TA
28623832 TTAGTTAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 1 0.02
5 5 0.11
6 11 0.25
7 27 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TAATATA
Found at i:28623826 original size:22 final size:23
Alignment explanation
Indices: 28623780--28623853 Score: 84
Period size: 22 Copynumber: 3.3 Consensus size: 23
28623770 ATTTAATATT
*
28623780 TAATATATAATATATAATAAATAA
1 TAATATATTATATATAA-AAATAA
28623804 TAATA-ATTATATATAAAAATAA
1 TAATATATTATATATAAAAATAA
*
28623826 T-ATATATTAGT-TAAAAAAATAA
1 TAATATATTA-TATATAAAAATAA
28623848 T-ATATA
1 TAATATA
28623854 AAATAAAAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
21 3 0.07
22 27 0.59
23 11 0.24
24 5 0.11
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (23 bp):
TAATATATTATATATAAAAATAA
Found at i:28623861 original size:19 final size:19
Alignment explanation
Indices: 28623786--28623862 Score: 52
Period size: 22 Copynumber: 4.0 Consensus size: 19
28623776 TATTTAATAT
*
28623786 ATAATATAT--AATAAATA
1 ATAATATATAAAATAAAAA
* *
28623803 ATAATA-ATTATATATAAAA
1 ATAATATATAAAATA-AAAA
**
28623822 ATAATATATATTAGTTAAAAAA
1 ATAATATATA--AAAT-AAAAA
28623844 ATAATATATAAAATAAAAA
1 ATAATATATAAAATAAAAA
28623863 GTATGTAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
16 2 0.04
17 6 0.13
18 3 0.07
19 14 0.30
20 4 0.09
22 16 0.35
23 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (19 bp):
ATAATATATAAAATAAAAA
Found at i:28624115 original size:10 final size:10
Alignment explanation
Indices: 28624081--28624143 Score: 56
Period size: 10 Copynumber: 5.8 Consensus size: 10
28624071 TACATAACAT
28624081 ATATAA-AAA
1 ATATAATAAA
*
28624090 ATAATAAGTAAT
1 AT-ATAA-TAAA
28624102 ATATAATAAA
1 ATATAATAAA
28624112 ATATAATAAA
1 ATATAATAAA
28624122 TGTTATATAATAAA
1 ----ATATAATAAA
28624136 ATATAATA
1 ATATAATA
28624144 TATAGGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
9 2 0.04
10 25 0.56
11 4 0.09
12 4 0.09
14 10 0.22
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (10 bp):
ATATAATAAA
Found at i:28624117 original size:24 final size:24
Alignment explanation
Indices: 28624042--28624143 Score: 89
Period size: 24 Copynumber: 4.1 Consensus size: 24
28624032 AATATAAAAC
* *
28624042 ATAAATAATATAATAGATAATATACGA
1 ATAAATAATAT-ATA-ATAAAATA-TA
* * *
28624069 TATACATAACATAT-ATAAAAAATA
1 -ATAAATAATATATAATAAAATATA
*
28624093 ATAAGTAATATATAATAAAATATA
1 ATAAATAATATATAATAAAATATA
**
28624117 ATAAATGTTATATAATAAAATATA
1 ATAAATAATATATAATAAAATATA
28624141 ATA
1 ATA
28624144 TATAGGAAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
23 10 0.16
24 34 0.56
25 6 0.10
27 2 0.03
28 9 0.15
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (24 bp):
ATAAATAATATATAATAAAATATA
Found at i:28624200 original size:26 final size:25
Alignment explanation
Indices: 28624153--28624242 Score: 78
Period size: 26 Copynumber: 3.6 Consensus size: 25
28624143 ATATAGGAAA
* *
28624153 ATAATATATGATAAATA-AATTTTTT
1 ATAAAATAT-ATAAATAGTATTTTTT
*
28624178 ATATAAATATATAAATAGTATTTTTA
1 ATA-AAATATATAAATAGTATTTTTT
**
28624204 ATAATAATATATGTATAGT-TTTTTT
1 ATAA-AATATATAAATAGTATTTTTT
*
28624229 -TAAAATAAATAAAT
1 ATAAAATATATAAAT
28624243 GATATATCTA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
23 8 0.15
24 3 0.06
25 16 0.30
26 26 0.49
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (25 bp):
ATAAAATATATAAATAGTATTTTTT
Found at i:28626352 original size:205 final size:205
Alignment explanation
Indices: 28625838--28626624 Score: 1256
Period size: 205 Copynumber: 3.8 Consensus size: 205
28625828 AATCTACTTT
* *
28625838 TTCGATTTGTTCTCTGACAATACAAAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACG
1 TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACACG
* *
28625903 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGAATGTCAAATCATCTTG
66 TGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTG
* ** * *
28625968 GATCTACTTCAGTGA-AATTATCTGAAGGTGAGATCTGCTATGTGTTTGCTCTCCGTCGAATATG
131 GATCTGCTTCAGT-ATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCCGTCGAA-ATG
** *
28626032 GAGATGCTAGAC
194 GAGACACCAGAC
* * * * *
28626044 TTCAATTTATTCTCTAACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCATG
1 TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACACG
*
28626109 TGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAATACAAGAATGCCAAATCATCTTG
66 TGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTG
* *
28626174 GATCTGTTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGA
131 GATCTGCTTCAGTATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGA
28626239 GACACCAGAC
196 GACACCAGAC
*
28626249 TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAAT-ATAAACAC
1 TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTC-ATCGTAAACAC
* *
28626313 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGGTCCTTGTAAACACAAGAATGTCAAATCATCTT
65 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTT
* * *
28626378 GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTACTCTCCGTTGAAATGG
130 GGATCTGCTTCAGTATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCCGTCGAAATGG
28626443 AGACACCAGAC
195 AGACACCAGAC
* * *
28626454 TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTAGCTTCAACGTAAACACA
1 TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACACG
28626519 TGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTG
66 TGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTG
*
28626584 GATCT-ATTCAGTATAAACATCTGAAGGTGAGATCTGCTATG
131 GATCTGCTTCAGTATAAACATCTGAAGGTGAGATCTGCTATG
28626625 CTGCGGCCTA
Statistics
Matches: 540, Mismatches: 38, Indels: 8
0.92 0.06 0.01
Matches are distributed among these distances:
204 35 0.06
205 330 0.61
206 175 0.32
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (205 bp):
TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACACG
TGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTG
GATCTGCTTCAGTATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGA
GACACCAGAC
Found at i:28633196 original size:22 final size:22
Alignment explanation
Indices: 28633171--28633214 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
28633161 TGCAGTTTTC
28633171 AATCGAATACCCC-AGCATTCCT
1 AATCGAATACCCCGA-CATTCCT
*
28633193 AATCGAATGCCCCGACATTCCT
1 AATCGAATACCCCGACATTCCT
28633215 GCGTGATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.30, C:0.36, G:0.11, T:0.23
Consensus pattern (22 bp):
AATCGAATACCCCGACATTCCT
Found at i:28634757 original size:15 final size:15
Alignment explanation
Indices: 28634727--28634758 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
28634717 ATTCTGATTC
28634727 AATTTCATTTAGAAA
1 AATTTCATTTAGAAA
28634742 AATTT-ATTTAGAAA
1 AATTTCATTTAGAAA
28634756 AAT
1 AAT
28634759 AATATCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (15 bp):
AATTTCATTTAGAAA
Found at i:28638530 original size:7 final size:7
Alignment explanation
Indices: 28638518--28638565 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
28638508 AAATAGTATT
28638518 TAATATA
1 TAATATA
28638525 TAATATA
1 TAATATA
28638532 TAATATA
1 TAATATA
28638539 TAATA-A
1 TAATATA
28638545 -AATA-A
1 TAATATA
28638550 TAATA-A
1 TAATATA
*
28638556 TTATATA
1 TAATATA
28638563 TAA
1 TAA
28638566 AAATAAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 5 0.14
6 10 0.27
7 22 0.59
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAATATA
Found at i:28638535 original size:14 final size:13
Alignment explanation
Indices: 28638518--28638577 Score: 70
Period size: 13 Copynumber: 4.7 Consensus size: 13
28638508 AAATAGTATT
28638518 TAATATATAATATA
1 TAATATATAATA-A
28638532 TAATATATAATAA
1 TAATATATAATAA
28638545 -AATA-ATAATAA
1 TAATATATAATAA
* *
28638556 TTATATATAAAAA
1 TAATATATAATAA
*
28638569 TAAAATATA
1 TAATATATA
28638578 TTGGTTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
11 7 0.17
12 7 0.17
13 14 0.35
14 12 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TAATATATAATAA
Found at i:28638550 original size:22 final size:21
Alignment explanation
Indices: 28638524--28638601 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 21
28638514 TATTTAATAT
28638524 ATAATATATAATATATAATAAA
1 ATAATATATAAT-TATAATAAA
28638546 ATAATA-ATAATTATATATAAAA
1 ATAATATATAATTATA-AT-AAA
* * * *
28638568 ATAAAATATATTGGTTTAAAAAA
1 ATAATATATAAT--TATAATAAA
28638591 ATAATATATAA
1 ATAATATATAA
28638602 AATAAAAAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.09
21 7 0.16
22 14 0.31
23 16 0.36
24 1 0.02
25 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (21 bp):
ATAATATATAATTATAATAAA
Found at i:28638575 original size:24 final size:25
Alignment explanation
Indices: 28638524--28638575 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
28638514 TATTTAATAT
*
28638524 ATAATATATAATATATAATAAAATA
1 ATAATATATAATATATAATAAAAAA
*
28638549 ATAATA-ATTATATATAA-AAATAAA
1 ATAATATATAATATATAATAAA-AAA
28638573 ATA
1 ATA
28638576 TATTGGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 3 0.12
24 15 0.62
25 6 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
ATAATATATAATATATAATAAAAAA
Found at i:28638735 original size:13 final size:13
Alignment explanation
Indices: 28638717--28638746 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28638707 ATGTGTATAT
28638717 AATATGAGTTAAA
1 AATATGAGTTAAA
*
28638730 AATATGATTTAAA
1 AATATGAGTTAAA
28638743 AATA
1 AATA
28638747 ATTTACAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (13 bp):
AATATGAGTTAAA
Found at i:28638856 original size:24 final size:24
Alignment explanation
Indices: 28638800--28638908 Score: 87
Period size: 24 Copynumber: 4.6 Consensus size: 24
28638790 AAACATAAAT
* **
28638800 AATATAATAGATAATATACGAT-A
1 AATATAATAAATAATATATAATAA
* * *
28638823 TACATAATAAGTAATATATAATAA
1 AATATAATAAATAATATATAATAA
**
28638847 AATATAATAAATGTTATATAATAA
1 AATATAATAAATAATATATAATAA
* * *
28638871 AATATAATATAT-ATAGGAAAATAA
1 AATATAATAAATAATA-TATAATAA
*
28638895 AATATGATAAATAA
1 AATATAATAAATAA
28638909 AATTTTTATA
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
23 18 0.27
24 47 0.71
25 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (24 bp):
AATATAATAAATAATATATAATAA
Found at i:28638883 original size:19 final size:19
Alignment explanation
Indices: 28638836--28638911 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 19
28638826 ATAATAAGTA
28638836 ATATATAATAAAATATAAT
1 ATATATAATAAAATATAAT
28638855 AAATGTTATATAATAAAATATAAT
1 --A---TATATAATAAAATATAAT
** *
28638879 ATATATAGGAAAATAAAAT
1 ATATATAATAAAATATAAT
28638898 ATGATA-AATAAAAT
1 AT-ATATAATAAAAT
28638912 TTTTATATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
19 23 0.50
20 3 0.07
21 1 0.02
22 1 0.02
24 18 0.39
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
ATATATAATAAAATATAAT
Found at i:28638938 original size:25 final size:25
Alignment explanation
Indices: 28638894--28638980 Score: 72
Period size: 25 Copynumber: 3.5 Consensus size: 25
28638884 TAGGAAAATA
**
28638894 AAATATGATAAATAAAATTTTTATAT
1 AAATAT-ATAAATAGTATTTTTATAT
28638920 AAATATATAAATAGTATTTTTA-AT
1 AAATATATAAATAGTATTTTTATAT
** *
28638944 AATAATATATGTATAGT-TTTTTTTA-
1 -A-AATATATAAATAGTATTTTTATAT
*
28638969 AAATAAATAAAT
1 AAATATATAAAT
28638981 GATATATCTA
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
23 8 0.16
24 3 0.06
25 20 0.40
26 19 0.38
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.45
Consensus pattern (25 bp):
AAATATATAAATAGTATTTTTATAT
Found at i:28638940 original size:26 final size:25
Alignment explanation
Indices: 28638891--28638980 Score: 78
Period size: 26 Copynumber: 3.6 Consensus size: 25
28638881 ATATAGGAAA
* *
28638891 ATAAAATATGATAAATA-AAATTTTT
1 ATAAAATAT-ATAAATAGTATTTTTT
*
28638916 ATATAAATATATAAATAGTATTTTTA
1 ATA-AAATATATAAATAGTATTTTTT
**
28638942 ATAATAATATATGTATAGT-TTTTTT
1 ATAA-AATATATAAATAGTATTTTTT
*
28638967 -TAAAATAAATAAAT
1 ATAAAATATATAAAT
28638981 GATATATCTA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
23 8 0.15
24 3 0.06
25 16 0.30
26 26 0.49
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (25 bp):
ATAAAATATATAAATAGTATTTTTT
Found at i:28645137 original size:3 final size:3
Alignment explanation
Indices: 28645129--28645154 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28645119 CTTCCCTCAA
28645129 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
28645155 GCATGCGCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28647425 original size:23 final size:22
Alignment explanation
Indices: 28647378--28647424 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
28647368 GACTTCAATA
*
28647378 TTTAATTTGATACTTGAATTTT
1 TTTAAATTGATACTTGAATTTT
28647400 TTTAAATTGATACTTGAATTTT
1 TTTAAATTGATACTTGAATTTT
28647422 TTT
1 TTT
28647425 TGTCCCATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.60
Consensus pattern (22 bp):
TTTAAATTGATACTTGAATTTT
Found at i:28650987 original size:39 final size:39
Alignment explanation
Indices: 28650933--28651842 Score: 1698
Period size: 39 Copynumber: 23.3 Consensus size: 39
28650923 TAATGGAGAA
* * *
28650933 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28650972 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651011 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651050 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651089 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651128 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651167 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651206 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651245 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651284 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651323 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651362 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651401 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651440 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651479 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651518 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651557 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651596 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651635 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651674 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
28651713 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
* *
28651752 TTATATCCGGGCTAAGCCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
* * * *
28651791 TTATATCCGAGCTAAAGTCCC-ATAGGC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGCCCCGA-AGGCATTTGTCCTGGTG
*
28651830 TTATATTCGGGCT
1 TTATATCCGGGCT
28651843 TAAAGTCCCG
Statistics
Matches: 858, Mismatches: 11, Indels: 4
0.98 0.01 0.00
Matches are distributed among these distances:
39 848 0.99
40 10 0.01
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.29
Consensus pattern (39 bp):
TTATATCCGGGCTAAGCCCCGAAGGCATTTGTCCTGGTG
Found at i:28656481 original size:17 final size:20
Alignment explanation
Indices: 28656443--28656481 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
28656433 TAAAATTAGT
28656443 ATAATTTAAAAGTAATAACA
1 ATAATTTAAAAGTAATAACA
28656463 ATAA-TTAAAAG-AA-AACA
1 ATAATTTAAAAGTAATAACA
28656480 AT
1 AT
28656482 TAGTTAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 2 0.11
19 7 0.37
20 4 0.21
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (20 bp):
ATAATTTAAAAGTAATAACA
Found at i:28661493 original size:39 final size:40
Alignment explanation
Indices: 28661315--28661549 Score: 214
Period size: 39 Copynumber: 6.0 Consensus size: 40
28661305 ATTTGATGTG
*
28661315 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA
1 TATCCGGGCTTAAAGTCCCGCAGGCTATATGCTGGAATTA
* *
28661355 TATCCGGGCTTAAAGACCCGTAGGCTATATGCTGGAATTA
1 TATCCGGGCTTAAAGTCCCGCAGGCTATATGCTGGAATTA
* * * *
28661395 TACCCGGACTTAAGGT-CCGCAGGCTATGTGCTGGAATTA
1 TATCCGGGCTTAAAGTCCCGCAGGCTATATGCTGGAATTA
* * * ** *
28661434 TAACCGGACTTAAGGT-CCGCAGGCTATGCGCTGGAAATA
1 TATCCGGGCTTAAAGTCCCGCAGGCTATATGCTGGAATTA
* * *
28661473 TGTCCGGGC-AAAAGTCCCGCAGGCT-TCGA-GCTGGTATTA
1 TATCCGGGCTTAAAGTCCCGCAGGCTAT--ATGCTGGAATTA
* * * *
28661512 TA-CCGGGTTTAAATTCTCGCAGGCT-TGTGCTGGTAATT
1 TATCCGGGCTTAAAGTCCCGCAGGCTATATGCTGG-AATT
28661550 GGTTTCAAGT
Statistics
Matches: 164, Mismatches: 25, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
38 15 0.09
39 98 0.60
40 51 0.31
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TATCCGGGCTTAAAGTCCCGCAGGCTATATGCTGGAATTA
Found at i:28668453 original size:16 final size:16
Alignment explanation
Indices: 28668434--28668477 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
28668424 ATAATGACAT
*
28668434 TTTAGGAATAACTATG
1 TTTAGGAACAACTATG
*
28668450 TTTA-GAACAACCATG
1 TTTAGGAACAACTATG
*
28668465 TTTTGGAACAACT
1 TTTAGGAACAACT
28668478 TGTATTTAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (16 bp):
TTTAGGAACAACTATG
Found at i:28668602 original size:15 final size:15
Alignment explanation
Indices: 28668579--28668611 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28668569 AGAACAATCT
28668579 CTATATTGAGAACAA
1 CTATATTGAGAACAA
*
28668594 CTATGTTGAGAACAA
1 CTATATTGAGAACAA
28668609 CTA
1 CTA
28668612 ACATTTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (15 bp):
CTATATTGAGAACAA
Found at i:28670392 original size:18 final size:18
Alignment explanation
Indices: 28670371--28670406 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
28670361 ATTTTTAAAA
28670371 TTTTA-AAATATATATAAT
1 TTTTACAAATA-ATATAAT
28670389 TTTTACAAATAATATAAT
1 TTTTACAAATAATATAAT
28670407 AAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTTACAAATAATATAAT
Found at i:28677531 original size:17 final size:19
Alignment explanation
Indices: 28677510--28677550 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
28677500 AATTTTTTGA
*
28677510 ATTTTATGAA-CTTTTTAT
1 ATTTTATGAATATTTTTAT
28677528 -TTTT-TGAATATTTTTAT
1 ATTTTATGAATATTTTTAT
28677545 ATTTTA
1 ATTTTA
28677551 AATTACTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 5
0.76 0.04 0.20
Matches are distributed among these distances:
16 4 0.21
17 11 0.58
18 4 0.21
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (19 bp):
ATTTTATGAATATTTTTAT
Found at i:28679443 original size:4 final size:4
Alignment explanation
Indices: 28679434--28679590 Score: 314
Period size: 4 Copynumber: 39.2 Consensus size: 4
28679424 TCTTTAAACT
28679434 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
28679482 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
28679530 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
28679578 CATA CATA CATA C
1 CATA CATA CATA C
28679591 GAGGTTAGAT
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 153 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:28679921 original size:11 final size:10
Alignment explanation
Indices: 28679905--28679974 Score: 59
Period size: 10 Copynumber: 6.7 Consensus size: 10
28679895 ATAATAAAAC
28679905 AAATTATCAAA
1 AAATTAT-AAA
28679916 AAATTATTAAA
1 AAATTA-TAAA
*
28679927 AAACTATAAA
1 AAATTATAAA
* * *
28679937 AAGTCATAGA
1 AAATTATAAA
*
28679947 AAATTATATTA
1 AAATTATA-AA
*
28679958 AAATGATAAA
1 AAATTATAAA
28679968 AAATTAT
1 AAATTAT
28679975 TTAAAATTTA
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
10 23 0.50
11 22 0.48
12 1 0.02
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.30
Consensus pattern (10 bp):
AAATTATAAA
Found at i:28679980 original size:10 final size:11
Alignment explanation
Indices: 28679946--28679991 Score: 53
Period size: 10 Copynumber: 4.5 Consensus size: 11
28679936 AAAGTCATAG
28679946 AAAATTATATT
1 AAAATTATATT
* *
28679957 AAAATGATA-A
1 AAAATTATATT
28679967 AAAATTAT-TT
1 AAAATTATATT
28679977 AAAATT-TATT
1 AAAATTATATT
28679987 AAAAT
1 AAAAT
28679992 CATAATAGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
9 1 0.03
10 20 0.69
11 8 0.28
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
AAAATTATATT
Found at i:28680108 original size:19 final size:17
Alignment explanation
Indices: 28680073--28680140 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 17
28680063 ATAACTTTCT
*
28680073 ATTTTTATTATTTTTAAA
1 ATTTTTAATA-TTTTAAA
*
28680091 ATTTTCATAATATTTTAAT
1 ATTTT--TAATATTTTAAA
28680110 A-TTTTAATATTTTAATA
1 ATTTTTAATATTTTAA-A
*
28680127 ATTTTTAAAATTTT
1 ATTTTTAATATTTT
28680141 TTAACAGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
16 11 0.26
17 1 0.02
18 19 0.45
19 7 0.17
20 4 0.10
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTTAATATTTTAAA
Found at i:28680119 original size:16 final size:17
Alignment explanation
Indices: 28680098--28680131 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
28680088 AAAATTTTCA
28680098 TAATATTTTAAT-ATTT
1 TAATATTTTAATAATTT
28680114 TAATATTTTAATAATTT
1 TAATATTTTAATAATTT
28680131 T
1 T
28680132 TAAAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TAATATTTTAATAATTT
Found at i:28680122 original size:27 final size:26
Alignment explanation
Indices: 28680073--28680140 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 26
28680063 ATAACTTTCT
* *
28680073 ATTTTTATTATTTTTAAAATTTTCATA
1 ATTTTTAATA-TTTTAAAATTTTAATA
*
28680100 ATATTTTAATATTTTAATATTTTAATA
1 AT-TTTTAATATTTTAAAATTTTAATA
*
28680127 ATTTTTAAAATTTT
1 ATTTTTAATATTTT
28680141 TTAACAGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 11 0.31
27 18 0.50
28 7 0.19
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (26 bp):
ATTTTTAATATTTTAAAATTTTAATA
Found at i:28680143 original size:36 final size:36
Alignment explanation
Indices: 28680032--28680144 Score: 97
Period size: 36 Copynumber: 3.1 Consensus size: 36
28680022 AAAAACATTA
* *
28680032 AATATTTTATATATTTTATATAAAATTTTCTATAACTTTCT
1 AATATTTTA-ATATTTTA-AT--AATTTT-TATAATTTTTT
* * *
28680073 -AT-TTTTATTATTTTTAA-AATTTTCATAATATTTT
1 AATATTTTAATA-TTTTAATAATTTTTATAATTTTTT
*
28680107 AATATTTTAATATTTTAATAATTTTTAAAATTTTTT
1 AATATTTTAATATTTTAATAATTTTTATAATTTTTT
28680143 AA
1 AA
28680145 CAGAAAATTA
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
34 7 0.12
35 14 0.24
36 23 0.39
38 3 0.05
39 10 0.17
40 2 0.03
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (36 bp):
AATATTTTAATATTTTAATAATTTTTATAATTTTTT
Found at i:28680144 original size:10 final size:10
Alignment explanation
Indices: 28680073--28680141 Score: 55
Period size: 8 Copynumber: 7.6 Consensus size: 10
28680063 ATAACTTTCT
*
28680073 ATTTTT-ATT
1 ATTTTTAATA
28680082 ATTTTTAA-A
1 ATTTTTAATA
*
28680091 A-TTTTCATA
1 ATTTTTAATA
28680100 ATATTTTAAT-
1 AT-TTTTAATA
28680110 A-TTTTAAT-
1 ATTTTTAATA
28680118 A-TTTTAATA
1 ATTTTTAATA
28680127 ATTTTTAA-A
1 ATTTTTAATA
28680136 ATTTTT
1 ATTTTT
28680142 TAACAGAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
8 20 0.39
9 17 0.33
10 8 0.16
11 6 0.12
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:28680559 original size:11 final size:10
Alignment explanation
Indices: 28680498--28680594 Score: 80
Period size: 11 Copynumber: 9.8 Consensus size: 10
28680488 TAATTCTAGT
28680498 TTTTATAATA
1 TTTTATAATA
*
28680508 TTTCATAATA
1 TTTTATAATA
*
28680518 TATTAATAAT-
1 T-TTTATAATA
28680528 TTTTAT-AT-
1 TTTTATAATA
28680536 TTTTAGTAA-A
1 TTTTA-TAATA
28680546 TTTGTATAATA
1 TTT-TATAATA
28680557 TTTTTATAAT-
1 -TTTTATAATA
*
28680567 TTGTATAATTA
1 TTTTATAA-TA
28680578 TTTTATAAT-
1 TTTTATAATA
28680587 TTTTATAA
1 TTTTATAA
28680595 GTTTCTACTT
Statistics
Matches: 73, Mismatches: 5, Indels: 19
0.75 0.05 0.20
Matches are distributed among these distances:
8 7 0.10
9 20 0.27
10 20 0.27
11 23 0.32
12 3 0.04
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (10 bp):
TTTTATAATA
Found at i:28680569 original size:20 final size:19
Alignment explanation
Indices: 28680497--28680616 Score: 88
Period size: 20 Copynumber: 6.2 Consensus size: 19
28680487 ATAATTCTAG
28680497 TTTTTATAATATTTCATAATA
1 TTTTTATAAT-TTT-ATAATA
* *
28680518 TATTAATAATTTT-T-ATA
1 TTTTTATAATTTTATAATA
28680535 TTTTTAGTAAATTTGTATAATA
1 TTTTTA-T-AATTT-TATAATA
28680557 TTTTTATAATTTGTATAAT-
1 TTTTTATAATTT-TATAATA
28680576 TATTTTATAATTTT-T-ATA
1 T-TTTTATAATTTTATAATA
** * *
28680594 AGTTTCTACTTTTATAATA
1 TTTTTATAATTTTATAATA
28680613 TTTT
1 TTTT
28680617 AATAGGCTTA
Statistics
Matches: 80, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
17 18 0.22
18 4 0.05
19 12 0.15
20 27 0.34
21 10 0.12
22 9 0.11
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (19 bp):
TTTTTATAATTTTATAATA
Found at i:28685653 original size:23 final size:24
Alignment explanation
Indices: 28685602--28685653 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
28685592 ATAGGTTTGT
*
28685602 ATGTAACAATCATGAGAGGTTCGC
1 ATGTAACAATCAAGAGAGGTTCGC
*
28685626 TTGTAACAA-CAAGA-AGGGTTCGC
1 ATGTAACAATCAAGAGA-GGTTCGC
28685649 ATGTA
1 ATGTA
28685654 CATACATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 15 0.62
24 8 0.33
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (24 bp):
ATGTAACAATCAAGAGAGGTTCGC
Found at i:28685862 original size:28 final size:27
Alignment explanation
Indices: 28685812--28685937 Score: 101
Period size: 28 Copynumber: 4.4 Consensus size: 27
28685802 GCAACTAGGT
28685812 GTTCGCCTATAGGGGGTTACATACAAGG
1 GTTCGCCTATA-GGGGTTACATACAAGG
*
28685840 GCTT-GCCTATAGGGGTTCGCATACAAGG
1 G-TTCGCCTATAGGGGTT-ACATACAAGG
* *
28685868 GTTCGCCTATAGGGTTTCACATGCAAAAGGG
1 GTTCGCCTATAGGGGTT-ACAT--ACAA-GG
* ** *
28685899 GATCATCTATAGGGGTTTGCATACAAGG
1 GTTCGCCTATAGGGG-TTACATACAAGG
*
28685927 GTTAGCCTATA
1 GTTCGCCTATA
28685938 TGGTTCACAT
Statistics
Matches: 77, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
27 8 0.10
28 43 0.56
29 5 0.06
30 3 0.04
31 16 0.21
32 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.27
Consensus pattern (27 bp):
GTTCGCCTATAGGGGTTACATACAAGG
Found at i:28685973 original size:58 final size:59
Alignment explanation
Indices: 28685846--28685987 Score: 189
Period size: 58 Copynumber: 2.4 Consensus size: 59
28685836 AAGGGCTTGC
* *
28685846 CTATAGGGGTTCGCATACAAGGGTTCGCCTATAGGGTTTCACATGCAAAAGGGGATCAT
1 CTATAGGGGTTAGCATACAAGGGTTAGCCTATAGGGTTTCACATGCAAAAGGGGATCAT
* * * *
28685905 CTATAGGGGTTTGCATACAAGGGTTAGCCTATATGG-TTCACATGCAAATGGGGATC-G
1 CTATAGGGGTTAGCATACAAGGGTTAGCCTATAGGGTTTCACATGCAAAAGGGGATCAT
* *
28685962 CTTATAGGGGTTAGCACACAAAGGTT
1 C-TATAGGGGTTAGCATACAAGGGTT
28685988 TACCTAAGGG
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
57 1 0.01
58 40 0.54
59 33 0.45
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (59 bp):
CTATAGGGGTTAGCATACAAGGGTTAGCCTATAGGGTTTCACATGCAAAAGGGGATCAT
Found at i:28687045 original size:26 final size:26
Alignment explanation
Indices: 28687016--28687065 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
28687006 GTCACGTTGA
* *
28687016 TAAAAGTTTA-AAATATAATTAATTAC
1 TAAAAATTTAGAAAAATAA-TAATTAC
28687042 TAAAAATTTAGAAAAATAATAATT
1 TAAAAATTTAGAAAAATAATAATT
28687066 TAATTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (26 bp):
TAAAAATTTAGAAAAATAATAATTAC
Found at i:28705400 original size:21 final size:22
Alignment explanation
Indices: 28705376--28705432 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 22
28705366 ATGGCCATGC
28705376 CTCTCAATCACACGGGCGTGT-
1 CTCTCAATCACACGGGCGTGTG
* *
28705397 CTCTCAGTCACACAGGCGTGTG
1 CTCTCAATCACACGGGCGTGTG
28705419 C-CTCAATCACACGG
1 CTCTCAATCACACGG
28705433 CCATGTACCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.21, C:0.35, G:0.23, T:0.21
Consensus pattern (22 bp):
CTCTCAATCACACGGGCGTGTG
Found at i:28705443 original size:21 final size:19
Alignment explanation
Indices: 28705378--28705453 Score: 71
Period size: 21 Copynumber: 3.7 Consensus size: 19
28705368 GGCCATGCCT
28705378 CTCAATCACACGGGCGTGTC
1 CTCAATCACAC-GGCGTGTC
*
28705398 TCTCAGTCACACAGGCGTGTGC
1 -CTCAATCACAC-GGCGTGT-C
*
28705420 CTCAATCACACGGCCATGTAC
1 CTCAATCACACGG-CGTGT-C
*
28705441 CTCTATCACACGG
1 CTCAATCACACGG
28705454 TCTGGACCTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.94
22 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.21, T:0.21
Consensus pattern (19 bp):
CTCAATCACACGGCGTGTC
Found at i:28707191 original size:12 final size:12
Alignment explanation
Indices: 28707170--28707201 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
28707160 ACACTGCATG
28707170 TTTAAACATCTA
1 TTTAAACATCTA
*
28707182 TTTAAGCATCTA
1 TTTAAACATCTA
28707194 TTTAAACA
1 TTTAAACA
28707202 ACCTATGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.41
Consensus pattern (12 bp):
TTTAAACATCTA
Found at i:28707776 original size:11 final size:12
Alignment explanation
Indices: 28707754--28707782 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
28707744 TCATGTCTCA
28707754 CTTTTTTCTTTT
1 CTTTTTTCTTTT
28707766 CTTTTTT-TTTT
1 CTTTTTTCTTTT
28707777 CTTTTT
1 CTTTTT
28707783 GGGTTGGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
CTTTTTTCTTTT
Found at i:28708836 original size:40 final size:41
Alignment explanation
Indices: 28708787--28708869 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
28708777 TATTTGCTAC
*
28708787 TTGTTATTAT-AGTTTGCTTTTTTGGATGGTGAGGATTGCA
1 TTGTAATTATAAGTTTGCTTTTTTGGATGGTGAGGATTGCA
*
28708827 TTGTAATTATAAGTTTGCTTTTTTGGATGGTGAGTATTGCA
1 TTGTAATTATAAGTTTGCTTTTTTGGATGGTGAGGATTGCA
28708868 TT
1 TT
28708870 TTGTAGGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 9 0.22
41 31 0.77
ACGTcount: A:0.19, C:0.05, G:0.25, T:0.51
Consensus pattern (41 bp):
TTGTAATTATAAGTTTGCTTTTTTGGATGGTGAGGATTGCA
Found at i:28710351 original size:21 final size:22
Alignment explanation
Indices: 28710316--28710356 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28710306 AATTTATTAA
28710316 AAAATTAATAATTTT-TTTTAC
1 AAAATTAATAATTTTATTTTAC
**
28710337 AAAATTAATTTTTTTATTTT
1 AAAATTAATAATTTTATTTT
28710357 TTGCTGATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
AAAATTAATAATTTTATTTTAC
Found at i:28716062 original size:2 final size:2
Alignment explanation
Indices: 28716055--28716906 Score: 1704
Period size: 2 Copynumber: 426.0 Consensus size: 2
28716045 CCTATCAGAG
28716055 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716097 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716139 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716181 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716223 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716265 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716307 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716349 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716391 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716433 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716475 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716517 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716559 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716601 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716643 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716685 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716727 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716769 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716811 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716853 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28716895 CA CA CA CA CA CA
1 CA CA CA CA CA CA
28716907 TATATATATC
Statistics
Matches: 850, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 850 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:28723547 original size:53 final size:53
Alignment explanation
Indices: 28723466--28723574 Score: 155
Period size: 53 Copynumber: 2.1 Consensus size: 53
28723456 CCATGTCATT
* * * *
28723466 AAAGAAGATCATATCGTGTAAGATCGTAACTAGTGGGTTAGGACATCATATGG
1 AAAGAAGACCATATCATGTAAAACCGTAACTAGTGGGTTAGGACATCATATGG
* * *
28723519 AAAGAAGACCATATCATGTAAAACCGTAACTGGTGGGTTATGACATCATATTG
1 AAAGAAGACCATATCATGTAAAACCGTAACTAGTGGGTTAGGACATCATATGG
28723572 AAA
1 AAA
28723575 TGACTAAAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.26
Consensus pattern (53 bp):
AAAGAAGACCATATCATGTAAAACCGTAACTAGTGGGTTAGGACATCATATGG
Found at i:28723791 original size:57 final size:55
Alignment explanation
Indices: 28723686--28723804 Score: 130
Period size: 57 Copynumber: 2.1 Consensus size: 55
28723676 AAAACACCAG
* * * ** * *
28723686 TAAAGGACGCCTTTGTGGCAAAAATTTGAAAAGTAAGCCTTTGTGGCGAACTTGT
1 TAAAGGACACCTTTATGGCAAAAATTTGAAAAGCAAGCCTTCATGGCGAACCTCT
* **
28723741 TAAAGGACAACCTTTATGGCAAAACTTTGGAACGGCAAGCCTTCATGGCGAACCTCT
1 TAAAGGAC-ACCTTTATGGCAAAAATTT-GAAAAGCAAGCCTTCATGGCGAACCTCT
28723798 TAAAGGA
1 TAAAGGA
28723805 TGCCTTTGTG
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
55 8 0.15
56 16 0.31
57 28 0.54
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (55 bp):
TAAAGGACACCTTTATGGCAAAAATTTGAAAAGCAAGCCTTCATGGCGAACCTCT
Done.