Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006752.1 Hibiscus syriacus cultivar Beakdansim tig00017003_pilon, whole genome shotgun sequence
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: 59897
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:6891 original size:21 final size:22
Alignment explanation
Indices: 6853--6895 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
6843 TTGAATGCTT
* *
6853 TTGGATTGTTTTACTTTGTTTG
1 TTGGATTGTTTGAATTTGTTTG
6875 TTGGA-TGTTTGAATTTGTTTG
1 TTGGATTGTTTGAATTTGTTTG
6896 GATTTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.12, C:0.02, G:0.26, T:0.60
Consensus pattern (22 bp):
TTGGATTGTTTGAATTTGTTTG
Found at i:7689 original size:64 final size:65
Alignment explanation
Indices: 7574--7698 Score: 164
Period size: 64 Copynumber: 1.9 Consensus size: 65
7564 AATGCATTTT
* * * ** *
7574 ATGTATCGATGCACTCAAGTTTTTATGAAAAACATTGAATGCGTTTTATGCATCGATGCACAAGA
1 ATGTATCGATGCACTCAACTATTTATG-AAAACATCGAATGCACTTCATGCATCGATGCACAAGA
7639 C
65 C
7640 ATGTATCGATGCACTCAGACTATTT-TG-AAACATCGAATGCACTTCATGCATCGATGCAC
1 ATGTATCGATGCACTCA-ACTATTTATGAAAACATCGAATGCACTTCATGCATCGATGCAC
7699 TCTTAGTGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
64 28 0.54
66 19 0.37
67 5 0.10
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (65 bp):
ATGTATCGATGCACTCAACTATTTATGAAAACATCGAATGCACTTCATGCATCGATGCACAAGAC
Found at i:10091 original size:36 final size:36
Alignment explanation
Indices: 10051--10123 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
10041 ATATGGTTAT
* *
10051 GGAATAATGGCAAGTGTATTGGTAAAATAAGCTTAC
1 GGAATAATGGCAAATATATTGGTAAAATAAGCTTAC
*
10087 GGAATAATGGTAAATATATTGGTAAAATAAGCTTAC
1 GGAATAATGGCAAATATATTGGTAAAATAAGCTTAC
10123 G
1 G
10124 AGCTTATGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (36 bp):
GGAATAATGGCAAATATATTGGTAAAATAAGCTTAC
Found at i:10145 original size:46 final size:45
Alignment explanation
Indices: 10079--10191 Score: 165
Period size: 46 Copynumber: 2.5 Consensus size: 45
10069 TTGGTAAAAT
* *
10079 AAGCTTACGGAAT-AATGGTAAATATATTGGTAAAATAAGCTTAC
1 AAGCTTATGGGATAAATGGTAAATATATTGGTAAAATAAGCTTAC
* * *
10123 GAGCTTATGGTATTAAATGGTAAGTATATTGGTAAAATAAGCTTAC
1 AAGCTTATGGGA-TAAATGGTAAATATATTGGTAAAATAAGCTTAC
10169 AAGCTTATGGGATAAATGGTAAA
1 AAGCTTATGGGATAAATGGTAAA
10192 AGATTTTATA
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
44 9 0.15
45 11 0.18
46 40 0.67
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (45 bp):
AAGCTTATGGGATAAATGGTAAATATATTGGTAAAATAAGCTTAC
Found at i:15200 original size:17 final size:17
Alignment explanation
Indices: 15180--15218 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
15170 ATTTCAAAGT
15180 TATAATTATATAAAAAA
1 TATAATTATATAAAAAA
* *
15197 TATATTTATATATAAAA
1 TATAATTATATAAAAAA
15214 TATAA
1 TATAA
15219 ATAAAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAATTATATAAAAAA
Found at i:15527 original size:3 final size:3
Alignment explanation
Indices: 15519--15548 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
15509 TTTATGACTA
*
15519 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
15549 TAAGAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17040 original size:3 final size:3
Alignment explanation
Indices: 17032--17080 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
17022 TTATTTTATT
* *
17032 TAA TAA TAA TAA CAA TAA TAA TATT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
17078 TAA
1 TAA
17081 AAGTAAACTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 39 0.95
4 2 0.05
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17057 original size:25 final size:25
Alignment explanation
Indices: 17028--17079 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
17018 ATATTTATTT
17028 TATTTAATAATAATAACAATAATAA
1 TATTTAATAATAATAACAATAATAA
*
17053 TATTTAATAATAATAATAATAATAA
1 TATTTAATAATAATAACAATAATAA
17078 TA
1 TA
17080 AAAGTAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
TATTTAATAATAATAACAATAATAA
Found at i:17060 original size:22 final size:22
Alignment explanation
Indices: 17035--17076 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
17025 TTTTATTTAA
17035 TAATAATAACAATAATAATATT
1 TAATAATAACAATAATAATATT
*
17057 TAATAATAATAATAATAATA
1 TAATAATAACAATAATAATA
17077 ATAAAAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
TAATAATAACAATAATAATATT
Found at i:17361 original size:76 final size:76
Alignment explanation
Indices: 17233--17393 Score: 270
Period size: 76 Copynumber: 2.1 Consensus size: 76
17223 AGAGGTCTTA
*
17233 AAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACC
1 AAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
17298 CTG-AGGGTTTG
66 C-GAAGGGTTTG
*
17309 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
1 AAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
* *
17374 CGAATGTTTTG
66 CGAAGGGTTTG
17385 AAAACATCA
1 AAAACATCA
17394 TGCACTGAAG
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
75 1 0.01
76 79 0.99
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (76 bp):
AAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
CGAAGGGTTTG
Found at i:17391 original size:45 final size:45
Alignment explanation
Indices: 17325--17438 Score: 174
Period size: 45 Copynumber: 2.5 Consensus size: 45
17315 TCAAAAAGCT
*
17325 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
17372 CCCGAATGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
17417 CCCGAAGGCTTTGAAAACATCA
1 CCCGAAGGTTTTGAAAACATCA
17439 AAAAGCTCCC
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
45 55 0.89
47 7 0.11
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:17460 original size:76 final size:76
Alignment explanation
Indices: 17380--17590 Score: 395
Period size: 76 Copynumber: 2.8 Consensus size: 76
17370 GACCCGAATG
*
17380 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
1 TTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
17445 TCCCGAAGGCT
66 TCCCGAAGGCT
*
17456 TTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
1 TTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
17521 TCCCGAAGGCT
66 TCCCGAAGGCT
*
17532 TTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
1 TTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCA
17591 TGCACTGAAG
Statistics
Matches: 131, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 131 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
TCCCGAAGGCT
Found at i:17473 original size:121 final size:121
Alignment explanation
Indices: 17259--17514 Score: 442
Period size: 121 Copynumber: 2.1 Consensus size: 121
17249 CCCAAAGGCT
* * *
17259 TTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGC
*
17324 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAATG
66 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
*
17380 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC-GAAGGCTTTGAAAACATCAAAAAG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTG-AGGCTTTGAAAACATCAAAAAG
17444 CTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
65 CTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
*
17501 CTTTGAAAACATCA
1 TTTTGAAAACATCA
17515 AAAAGCTCCC
Statistics
Matches: 128, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
120 1 0.01
121 127 0.99
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (121 bp):
TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGC
TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
Found at i:17568 original size:197 final size:196
Alignment explanation
Indices: 17233--17984 Score: 1061
Period size: 197 Copynumber: 3.8 Consensus size: 196
17223 AGAGGTCTTA
* * *
17233 AAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACC
1 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACC
* *
17298 CTG-AGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGAC
66 C-GAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGAC
*
17362 TTACAGATGACCCGAATGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCT
130 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAA-GCT
17427 TTG
194 TTG
*
17430 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
1 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACC
* * *
17495 CGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCT
66 CGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACT
17560 TACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGCTTT
131 TACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGC-TT
17625 TG
195 TG
* *
17627 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCAGTGAAGGGCTTACAGATGACC
1 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACC
17692 CGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACT
66 CGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACT
* * * *** * *
17757 TACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCTCGAA-GGCTTTTTGGA-AACATC-A
131 TACAGATGACCCGAAGGTTTTGAAAACATC---ATGCACT-GAAGGGC-TTACAGATGAC-CCGA
* **
17819 TGCACTG
190 AGCTTTG
** * * * * *
17826 AAGGGC-TTACAGATG-ACCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 AA-AACATCA-AAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
17887 CCCGAAGGTTTTGAAAACATCAAAAAGCTCTCGAAGGCTTTTTGAAAACATCATGCACTGAAGGG
64 CCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGA
17952 CTTACAGATGACCCGAAGGTTTTGAAAACATCA
129 CTTACAGATGACCCGAAGGTTTTGAAAACATCA
17985 AAAAGCTCCC
Statistics
Matches: 513, Mismatches: 32, Indels: 23
0.90 0.06 0.04
Matches are distributed among these distances:
194 1 0.00
196 3 0.01
197 470 0.92
199 14 0.03
200 17 0.03
201 8 0.02
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (196 bp):
AAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACC
CGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACT
TACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGCTTT
G
Found at i:17581 original size:121 final size:121
Alignment explanation
Indices: 17446--17711 Score: 462
Period size: 121 Copynumber: 2.2 Consensus size: 121
17436 TCAAAAAGCT
*
17446 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAA-GCTTTTGAAAA
*
17510 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
63 CATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
17569 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGCTTTTGAAAACAT
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGCTTTTGAAAACAT
*
17634 CAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCAGTGAAGGGCTTACAGATGA
66 CAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
17690 CCCGAAGGTTTTGAAAACATCA
1 CCCGAAGGTTTTGAAAACATCA
17712 AAAAGCTCCC
Statistics
Matches: 138, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
120 2 0.01
121 128 0.93
123 8 0.06
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.22
Consensus pattern (121 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGCTTTTGAAAACAT
CAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:17588 original size:45 final size:45
Alignment explanation
Indices: 17522--17635 Score: 192
Period size: 45 Copynumber: 2.5 Consensus size: 45
17512 TCAAAAAGCT
*
17522 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
17569 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
17614 CCCGAAGCTTTTGAAAACATCA
1 CCCGAAGGTTTTGAAAACATCA
17636 AAAAGCTCCC
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
45 57 0.88
47 8 0.12
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:17657 original size:76 final size:76
Alignment explanation
Indices: 17569--17863 Score: 506
Period size: 76 Copynumber: 3.9 Consensus size: 76
17559 TTACAGATGA
17569 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGCTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGCTTTTGAAAAC
17632 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
17643 CCCGAAGGCTTTTTGAAAACATCATGCAGTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGCTTTTGAAAAC
17708 ATCAAAAAGCT
66 ATCAAAAAGCT
*
17719 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAA
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAA-GCTTTTGAAAA
17783 CATCAAAAAGCT
65 CATCAAAAAGCT
* * *
17795 CTCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGCTTTTGAAAAC
17860 ATCA
66 ATCA
17864 TGCACTGAAG
Statistics
Matches: 208, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
74 8 0.04
75 1 0.00
76 198 0.95
77 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGCTTTTGAAAAC
ATCAAAAAGCT
Found at i:17720 original size:273 final size:273
Alignment explanation
Indices: 17380--18091 Score: 1352
Period size: 273 Copynumber: 2.6 Consensus size: 273
17370 GACCCGAATG
*
17380 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGC
*
17445 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
66 TCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
17510 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAA
131 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAA
17575 GGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGCTTTTGAAAACATCAAAAA
196 GGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGCTTTTGAAAACATCAAAAA
17640 GCTCCCGAAGGCT
261 GCTCCCGAAGGCT
*
17653 TTTTGAAAACATCATGCAGTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGC
17718 TCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
66 TCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
*
17783 CATCAAAAAGCTCTCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAA
131 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAA
*
17848 GGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAA
196 GGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGCTTTTGAAAACATCAAAAA
*
17913 GCTCTCGAAGGCT
261 GCTCCCGAAGGCT
17926 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGC
*
17991 TCCCGAAGGCTTTTTGAAAACATCATGCACTAAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
66 TCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
*
18056 CATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCA
131 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
18092 AAAAGCTCCC
Statistics
Matches: 429, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
273 429 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (273 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGC
TCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAA
GGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGCTTTTGAAAACATCAAAAA
GCTCCCGAAGGCT
Found at i:17859 original size:121 final size:121
Alignment explanation
Indices: 17719--17984 Score: 487
Period size: 121 Copynumber: 2.2 Consensus size: 121
17709 TCAAAAAGCT
17719 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
*
17784 ATCAAAAAGCTCTCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
64 ATCAAAAAGCTCTCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* *
17842 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACAT
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACAT
17907 CAAAAAGCTCTCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
66 CAAAAAGCTCTCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
17963 CCCGAAGGTTTTGAAAACATCA
1 CCCGAAGGTTTTGAAAACATCA
17985 AAAAGCTCCC
Statistics
Matches: 140, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
121 132 0.94
123 8 0.06
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.23
Consensus pattern (121 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACAT
CAAAAAGCTCTCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:17863 original size:45 final size:45
Alignment explanation
Indices: 17805--17908 Score: 199
Period size: 45 Copynumber: 2.3 Consensus size: 45
17795 CTCGAAGGCT
*
17805 TTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
17850 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
17895 TTTTGAAAACATCA
1 TTTTGAAAACATCA
17909 AAAAGCTCTC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
Found at i:17930 original size:76 final size:76
Alignment explanation
Indices: 17842--18091 Score: 450
Period size: 76 Copynumber: 3.3 Consensus size: 76
17832 TTACAGATGA
17842 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
17905 ATCAAAAAGCT
66 ATCAAAAAGCT
*
17916 CTCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
17981 ATCAAAAAGCT
66 ATCAAAAAGCT
* * *
17992 CCCGAAGGCTTTTTGAAAACATCATGCACTAAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
18057 ATCAAAAAGCT
66 ATCAAAAAGCT
18068 CCCGAAGGCTTTTTGAAAACATCA
1 CCCGAAGGCTTTTTGAAAACATCA
18092 AAAAGCTCCC
Statistics
Matches: 169, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
74 7 0.04
76 162 0.96
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
ATCAAAAAGCT
Found at i:17931 original size:152 final size:154
Alignment explanation
Indices: 17766--18144 Score: 406
Period size: 152 Copynumber: 2.5 Consensus size: 154
17756 TTACAGATGA
17766 CCCGAAGGC--TTTGAAAACATCAAAAAGCTCTCGAAGGCTTTTTGGAAACATCATGCACTGAAG
1 CCCGAAGGCTTTTTGAAAACATCAAAAAGCTCTCGAAGGCTTTTTGGAAACATCATGCACTGAAG
* * *
17829 GGCTTACAGATG-ACCCGAAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGA
66 GACTTACAGATGCACCCGAAGGCTTTTGAAAACATCATGCACTAAAGGACTTACAGATGACCCGA
*
17892 AGGTTTTGAAAACATCAAAAAGCT
131 AGGCTTTGAAAACATCAAAAAGCT
* * * *** * * * ***
17916 CTCGAAGGCTTTTTGAAAACATC---ATGCACT-GAAGGGC-TTACAGATGAC-CCGAAGGTTTT
1 CCCGAAGGCTTTTTGAAAACATCAAAAAGCTCTCGAA-GGCTTTTTGGA-AACATC--ATGCACT
* * * * *
17975 GAA-AACAT-CAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTAAAGGACTTACAGATG
62 GAAGGACTTAC-AGATGCACCCGAAGGC-TTTTGAAAACATCATGCACTAAAGGACTTACAGATG
18038 ACCCGAAGGCTTTGAAAACATCAAAAAGCT
125 ACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
18068 CCCGAAGGCTTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACT-ACA
1 CCCGAAGGCTTTTTGAAAACATCAAAAAGCTCTCGAAGGCTTTTTGGAAACATCATGCACTGA-A
18132 GGACTTACAGATG
65 GGACTTACAGATG
18145 TGGGAAATAG
Statistics
Matches: 172, Mismatches: 38, Indels: 33
0.71 0.16 0.14
Matches are distributed among these distances:
148 9 0.05
149 15 0.09
150 22 0.13
152 97 0.56
153 1 0.01
154 4 0.02
155 15 0.09
156 9 0.05
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (154 bp):
CCCGAAGGCTTTTTGAAAACATCAAAAAGCTCTCGAAGGCTTTTTGGAAACATCATGCACTGAAG
GACTTACAGATGCACCCGAAGGCTTTTGAAAACATCATGCACTAAAGGACTTACAGATGACCCGA
AGGCTTTGAAAACATCAAAAAGCT
Found at i:18086 original size:31 final size:31
Alignment explanation
Indices: 18039--18122 Score: 145
Period size: 31 Copynumber: 2.8 Consensus size: 31
18029 TTACAGATGA
18039 CCCGAAGGC--TTTGAAAACATCAAAAAGCT
1 CCCGAAGGCTTTTTGAAAACATCAAAAAGCT
18068 CCCGAAGGCTTTTTGAAAACATCAAAAAGCT
1 CCCGAAGGCTTTTTGAAAACATCAAAAAGCT
*
18099 CCCGAAGGCTTTTTGGAAACATCA
1 CCCGAAGGCTTTTTGAAAACATCA
18123 TGCACTACAG
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 9 0.17
31 43 0.83
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (31 bp):
CCCGAAGGCTTTTTGAAAACATCAAAAAGCT
Found at i:18901 original size:22 final size:22
Alignment explanation
Indices: 18821--18898 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
18811 GATAAAGCTT
* *
18821 TCATCTTTGAAAAGAAAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
18843 TCATCTTTTAAAAAGAGAATCTA
1 TCATC-TTTGAAAAGAGAATCTA
*
18866 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
18888 TCATCTTTGAA
1 TCATCTTTGAA
18899 GAGTGTAGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
22 31 0.62
23 19 0.38
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:21639 original size:115 final size:115
Alignment explanation
Indices: 21438--21775 Score: 561
Period size: 115 Copynumber: 2.9 Consensus size: 115
21428 ACGATCATGC
* * * * *
21438 AATTCATCTTTTAATTCTAATGATTGG-TTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAA
1 AATTCATCTTTTAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAA
* * * *
21502 AGAACACTTCTAGAAGATGCTATTGGGCCTCCTTATTTCTACTATGAGCA
66 AGAACACTTCCAGAAAATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
*
21552 AATTCATCTTTTAAATCCAATGATTGGTTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAA
1 AATTCATCTTTTAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAA
21617 AGAACACTTCCAGAAAATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
66 AGAACACTTCCAGAAAATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
* *
21667 AATTCTTCTTTTAAATCCAATGATTAGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAA
1 AATTCATCTTTTAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAA
21732 AGAACACTTCCAGAAAATGCTATTGGGTCTTCTTATTTCTACTA
66 AGAACACTTCCAGAAAATGCTATTGGGTCTTCTTATTTCTACTA
21776 CGAGAACGTA
Statistics
Matches: 210, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
114 25 0.12
115 185 0.88
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (115 bp):
AATTCATCTTTTAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAA
AGAACACTTCCAGAAAATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
Found at i:25981 original size:13 final size:14
Alignment explanation
Indices: 25952--25983 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
25942 AAAAGTATGC
25952 ATGCAAAATGAAAA
1 ATGCAAAATGAAAA
25966 ATGCAAAATG-AAA
1 ATGCAAAATGAAAA
25979 ATGCA
1 ATGCA
25984 TGTATGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.59, C:0.09, G:0.16, T:0.16
Consensus pattern (14 bp):
ATGCAAAATGAAAA
Found at i:28002 original size:17 final size:18
Alignment explanation
Indices: 27982--28024 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
27972 TAATATCTGA
*
27982 ATAAAAAAAAT-ATTAAT
1 ATAAAAAAAATAAGTAAT
*
27999 ATAAAAATAATAAGTAAT
1 ATAAAAAAAATAAGTAAT
28017 A-AAAAAAA
1 ATAAAAAAA
28025 TTGAAAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (18 bp):
ATAAAAAAAATAAGTAAT
Found at i:28059 original size:20 final size:21
Alignment explanation
Indices: 28020--28060 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
28010 AAGTAATAAA
28020 AAAAATTGAAAGAAAAGAATT
1 AAAAATTGAAAGAAAAGAATT
* *
28041 AAAAATT-AAATAAATGAATT
1 AAAAATTGAAAGAAAAGAATT
28061 TTTTAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (21 bp):
AAAAATTGAAAGAAAAGAATT
Found at i:28518 original size:17 final size:17
Alignment explanation
Indices: 28498--28536 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
28488 ATTTCAAAGT
28498 TATAATTATATAAAAAA
1 TATAATTATATAAAAAA
* *
28515 TATATTTATATATAAAA
1 TATAATTATATAAAAAA
28532 TATAA
1 TATAA
28537 ATAAAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAATTATATAAAAAA
Found at i:28717 original size:114 final size:108
Alignment explanation
Indices: 28535--28757 Score: 250
Period size: 114 Copynumber: 2.0 Consensus size: 108
28525 TATAAAATAT
* * * *
28535 AAATAAAATATTTATGTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCCTTAAGACAGCTCTT
1 AAATAAAATATTTATGTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCTTAAGACAGCTCCT
* *
28600 TTCTTCGATATAAAAAAATATAATTAAAATAATTAATATATGATTTAAA
66 TTCTT-AATATAAAAAAATA-AA-T-AAAT-ATTAAAATATGA-TTAAA
* * * ** *
28649 AAATAAAATATTTATTTATTTAAAAATATCATAAAATGGACATCCAGTTGTTTTAAGACTGC-CC
1 AAATAAAATATTTATGTATTTAAAAATATCAGAAAA-GGACATCCAGGTGCCTTAAGACAGCTCC
**
28713 TTTCTTAATATTGAAAAATAAATAAATATTAAAATATGATTAAA
65 TTTCTTAATATAAAAAAATAAATAAATATTAAAATATGATTAAA
28757 A
1 A
28758 TAGGTTAAAA
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
108 6 0.06
109 11 0.12
110 4 0.04
111 1 0.01
112 2 0.02
113 11 0.12
114 40 0.43
115 19 0.20
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (108 bp):
AAATAAAATATTTATGTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCTTAAGACAGCTCCT
TTCTTAATATAAAAAAATAAATAAATATTAAAATATGATTAAA
Found at i:30364 original size:3 final size:3
Alignment explanation
Indices: 30356--30396 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
30346 TTATTTTATT
* *
30356 TAA TAA TAA TAA CAA TAA TAA T-A TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
30397 AAGTAAACTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:37577 original size:43 final size:44
Alignment explanation
Indices: 37529--37654 Score: 127
Period size: 43 Copynumber: 3.0 Consensus size: 44
37519 CACAAGTGCG
*
37529 ACGTTTATTCTAAAAAAAC-CA-CTAAATGACCTAACATTTTGCA
1 ACGTTT-TTCTAAAAAAACACAGCTAAAAGACCTAACATTTTGCA
* * *
37572 GCGTTTGT-TACAAAAACACAGCTAAAAGACCTAACATTTTGCA
1 ACGTTTTTCTAAAAAAACACAGCTAAAAGACCTAACATTTTGCA
* ** * *
37615 ACGTTTGT-TACTAAAATAC-GCTAAAAGACGTAACATTTTG
1 ACGTTTTTCTAAAAAAACACAGCTAAAAGACCTAACATTTTG
37655 TGGCGTTTGT
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
41 8 0.11
42 23 0.32
43 42 0.58
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (44 bp):
ACGTTTTTCTAAAAAAACACAGCTAAAAGACCTAACATTTTGCA
Found at i:37587 original size:42 final size:42
Alignment explanation
Indices: 37541--37737 Score: 170
Period size: 42 Copynumber: 4.7 Consensus size: 42
37531 GTTTATTCTA
*
37541 AAAAAACCACTAAATGACCTAACATTTTGCAGCGTTTGTTAC
1 AAAAAACCACTAAAAGACCTAACATTTTGCAGCGTTTGTTAC
*
37583 -AAAAACACAGCTAAAAGACCTAACATTTTGCAACGTTTGTTAC
1 AAAAAAC-CA-CTAAAAGACCTAACATTTTGCAGCGTTTGTTAC
* * * ** *
37626 TAAAATA-CGCTAAAAGACGTAACATTTTGTGGCGTTTGTTTC
1 -AAAAAACCACTAAAAGACCTAACATTTTGCAGCGTTTGTTAC
***** *
37668 AAATCGTTACT-AAA-ACCTTAACATTTTGCGGCGTTTGTTA-
1 AAAAAACCACTAAAAGACC-TAACATTTTGCAGCGTTTGTTAC
* *
37708 AAAAAAGCCGCTAAAAGACCTAACCTTTTG
1 AAAAAA-CCACTAAAAGACCTAACATTTTG
37738 AAAAAAAACT
Statistics
Matches: 122, Mismatches: 24, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
40 5 0.04
41 34 0.28
42 44 0.36
43 35 0.29
45 4 0.03
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (42 bp):
AAAAAACCACTAAAAGACCTAACATTTTGCAGCGTTTGTTAC
Found at i:37752 original size:31 final size:31
Alignment explanation
Indices: 37707--37768 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
37697 GGCGTTTGTT
*
37707 AAAAAAAGCCGCTAAAAGACCTAACCTTTTG
1 AAAAAAAACCGCTAAAAGACCTAACCTTTTG
* *
37738 AAAAAAAACTGCTAAAAGATCTAACCTTTTG
1 AAAAAAAACCGCTAAAAGACCTAACCTTTTG
37769 CGACATTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.23
Consensus pattern (31 bp):
AAAAAAAACCGCTAAAAGACCTAACCTTTTG
Found at i:41199 original size:13 final size:13
Alignment explanation
Indices: 41181--41207 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41171 AGCAATTTAA
41181 AATGAATCTATTG
1 AATGAATCTATTG
41194 AATGAATCTATTG
1 AATGAATCTATTG
41207 A
1 A
41208 CTGTTATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
AATGAATCTATTG
Found at i:42450 original size:2 final size:2
Alignment explanation
Indices: 42443--42470 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42433 TGCATGTAAA
42443 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
42471 CCTATTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42945 original size:43 final size:43
Alignment explanation
Indices: 42888--42978 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 43
42878 TTTGTTCTAA
* * *
42888 AAAAACACAACTAAATGACCTAATAGTTTGCAACTTTTGTTAC
1 AAAAACACAACTAAAAGACCTAACAGTTTGCAACGTTTGTTAC
* * *
42931 AAAAACACAGCTAAAAGACCTAACATTTTGCAGCGTTTGTTAC
1 AAAAACACAACTAAAAGACCTAACAGTTTGCAACGTTTGTTAC
*
42974 TAAAA
1 AAAAA
42979 TGCGCTAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.27
Consensus pattern (43 bp):
AAAAACACAACTAAAAGACCTAACAGTTTGCAACGTTTGTTAC
Found at i:43028 original size:42 final size:42
Alignment explanation
Indices: 42940--43085 Score: 124
Period size: 42 Copynumber: 3.5 Consensus size: 42
42930 CAAAAACACA
*
42940 GCTAAAAGACCTAACATTTTGCAGCGTTTGTTACTAAAATGC
1 GCTAAAAGACCTAACATTTTGCGGCGTTTGTTACTAAAATGC
* * * *
42982 GCTAAAAGACGTAACATTTTGTGGCGTTTGTT-C-CAAATCGTT
1 GCTAAAAGACCTAACATTTTGCGGCGTTTGTTACTAAAAT-G-C
* **
43024 GCT-AAA-ACCTTAACATTTTGCGGTGTTTGTT--TAAAAACACC
1 GCTAAAAGACC-TAACATTTTGCGGCGTTTGTTACT-AAAA-TGC
*
43065 GCTAAAAGACCCAACATTTTG
1 GCTAAAAGACCTAACATTTTG
43086 AAAAACACTG
Statistics
Matches: 83, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
40 6 0.07
41 27 0.33
42 47 0.57
43 3 0.04
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (42 bp):
GCTAAAAGACCTAACATTTTGCGGCGTTTGTTACTAAAATGC
Found at i:43090 original size:30 final size:30
Alignment explanation
Indices: 43056--43115 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
43046 GTGTTTGTTT
*
43056 AAAAACACCGCTAAAAGACCCAACATTTTG
1 AAAAACACCGATAAAAGACCCAACATTTTG
* * *
43086 AAAAACACTGATAAAAGACCTAACCTTTTG
1 AAAAACACCGATAAAAGACCCAACATTTTG
43116 CGGCATTTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.47, C:0.23, G:0.10, T:0.20
Consensus pattern (30 bp):
AAAAACACCGATAAAAGACCCAACATTTTG
Found at i:49347 original size:11 final size:11
Alignment explanation
Indices: 49331--49358 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
49321 GAGAGTTTAA
49331 ATTGATGCATG
1 ATTGATGCATG
49342 ATTGATGCATG
1 ATTGATGCATG
49353 ATTGAT
1 ATTGAT
49359 ACAATATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.07, G:0.25, T:0.39
Consensus pattern (11 bp):
ATTGATGCATG
Found at i:50996 original size:11 final size:11
Alignment explanation
Indices: 50980--51022 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
50970 TGCAATCTCT
50980 TTGTCAAGTTA
1 TTGTCAAGTTA
50991 TTGTCAAGTTA
1 TTGTCAAGTTA
*
51002 TTGTTAAGTTA
1 TTGTCAAGTTA
*
51013 TTGTAAAGTT
1 TTGTCAAGTT
51023 GATATGGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.28, C:0.05, G:0.19, T:0.49
Consensus pattern (11 bp):
TTGTCAAGTTA
Found at i:57663 original size:390 final size:388
Alignment explanation
Indices: 56916--57705 Score: 1219
Period size: 390 Copynumber: 2.0 Consensus size: 388
56906 TTCCATCTTT
*
56916 TCACCATGAAATCACATTTTGTTGTTGATCTATAGTCCTGGCATAATAGCTGGTAATAGATTCCC
1 TCACCATTAAATCACATTTTGTTGTTGATCTATAGTCCTGGCATAATAGCTGGTAATAGATTCCC
56981 CATCCTTCATTTGTAGAGTCATAAAATCTCTTCTCAAAGCTTGAAGTTGTGCACACTTACTCTAG
66 CATCCTTCATTTGTAGAGTCATAAAATCTCTTCTCAAAGCTTGAAGTTGTGCACACTTACTCTAG
* * *
57046 CAGAGCCTTGATATTTTGTCTTCAGGCAATTAATCGTCCCATCTTGGAAATTATTCTTAACAAAG
131 CAGAGCCTTGATATTTTGTCTTCAGGCAATAAATCAT-CCATCTTGGAAAGTATTCTTAACAAAG
* * *
57111 AAACTTCCAAAGATATTTGGGATTCCATGAAGACAAAATATCAAGGCTCTGCTAGAGTAAAGTGT
195 AAAATTCCAAAGATAATT-GAATTCCATGAAGACAAAATATCAAGGCTCTGCTAGAGTAAAGTGT
57176 GCACAACTTCAAGCTTTGAGAAGAGATTTTATGACTCTACAAATGAAGGATGGGGAATCTATTAC
259 GCACAACTTCAAGCTTTGAGAAGAGATTTTATGACTCTACAAATGAAGGATGGGGAATCTATTAC
57241 CAGCTATATGCCAGGACTATAGAGATCAACAACAAAATGTGATTTCA-GTGAAAAGA-GAAGATG
324 CAGCTATATGCCAGGACTATAGAGATCAACAACAAAATGTGATTTCAGGTGAAAAGAGGAAGATG
57304 TCACCATTAAATCACATTTTGTTGTTGATCTCTATAGTCCTGGCATAATAGCTGGTAATAGATTC
1 TCACCATTAAATCACATTTTGTTGTTGA--TCTATAGTCCTGGCATAATAGCTGGTAATAGATTC
57369 CCCATCCTTCATTTGTAGAGTCATAAAATCTCTTCTCAAAGCTTGAAGTTGTGCACACTTTACTC
64 CCCATCCTTCATTTGTAGAGTCATAAAATCTCTTCTCAAAGCTTGAAGTTGTGCACAC-TTACTC
*
57434 TAGCAGAGCCTTGATATTTTGTCTTCATGG-AATCCCAAAT-AT-C-T-TTGG-AAGT-TTCTTT
128 TAGCAGAGCCTTGATATTTTGTCTTCA-GGCAAT---AAATCATCCATCTTGGAAAGTATTCTTA
***
57492 GTTAAGAATAATTCC-AAGATGGGACGATT-AATTGCC-TGAAGACAAAATATCAAGGCTCTGCT
189 ACAAAGAA-AATTCCAAAGAT---A--ATTGAATT-CCATGAAGACAAAATATCAAGGCTCTGCT
57554 AGAGT-AAGTGTGCACAACTTCAAGCTTTGAGAAGAGATTTTATGACTCTACAAATGAAGGATGG
247 AGAGTAAAGTGTGCACAACTTCAAGCTTTGAGAAGAGATTTTATGACTCTACAAATGAAGGATGG
57618 GGAATCTATTACCAGCTATTATGCCAGGACTATAGAGATCAACAACAAAATGTGATTTCATGGTG
312 GGAATCTATTACCAGCTA-TATGCCAGGACTATAGAGATCAACAACAAAATGTGATTTCA-GGTG
57683 AAAAGATGGAAGATG
375 AAAAGA-GGAAGATG
57698 TCACCATT
1 TCACCATT
57706 GTGGAGAGAA
Statistics
Matches: 372, Mismatches: 11, Indels: 32
0.90 0.03 0.08
Matches are distributed among these distances:
387 15 0.04
388 35 0.09
389 81 0.22
390 170 0.46
391 39 0.10
392 13 0.03
393 1 0.00
394 18 0.05
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (388 bp):
TCACCATTAAATCACATTTTGTTGTTGATCTATAGTCCTGGCATAATAGCTGGTAATAGATTCCC
CATCCTTCATTTGTAGAGTCATAAAATCTCTTCTCAAAGCTTGAAGTTGTGCACACTTACTCTAG
CAGAGCCTTGATATTTTGTCTTCAGGCAATAAATCATCCATCTTGGAAAGTATTCTTAACAAAGA
AAATTCCAAAGATAATTGAATTCCATGAAGACAAAATATCAAGGCTCTGCTAGAGTAAAGTGTGC
ACAACTTCAAGCTTTGAGAAGAGATTTTATGACTCTACAAATGAAGGATGGGGAATCTATTACCA
GCTATATGCCAGGACTATAGAGATCAACAACAAAATGTGATTTCAGGTGAAAAGAGGAAGATG
Found at i:58215 original size:955 final size:953
Alignment explanation
Indices: 56351--58269 Score: 3536
Period size: 955 Copynumber: 2.0 Consensus size: 953
56341 CTTCCATCTT
*
56351 TCACCATGAAATCACATTTGTTGTTGATCTCTATAGTCCTGGCATAATAGCTGGTAATAGATTCC
1 TCACCATTAAATCACATTTGTTGTTGATCTCTATAGTCCTGGCATAATAGCTGGTAATAGATTCC
56416 CCATCCTTCATTGTAGAGTCATAAATCTCTTCTCAAAGCTTGAAGTTGTGCACACTTTACTCTAG
66 CCATCCTTCATTGTAGAGTCATAAATCTCTTCTCAAAGCTTGAAGTTGTGCACACTTTACTCTAG
56481 CAGAGCCTTGATATTTTGTCTTCATGGAATCCCAAATATCTTTGGAAGTTTCTTTGTTAAGAATA
131 CAGAGCCTTGATATTTTGTCTTCATGGAATCCCAAATATCTTTGGAAGTTTCTTTGTTAAGAATA
56546 ATTTCCAAGATGGGACGATTAATTGCCTGAAGACAAAATATCAAGGCTCTGCTAGAGTAAGTGTG
196 ATTTCCAAGATGGGACGATTAATTGCCTGAAGACAAAATATCAAGGCTCTGCTAGAGTAAGTGTG
56611 CACAACTTCAAGCTTTGAGAAGAGATTTTATGACTCTACAAATGAAGGATGGGGAATCTATTACC
261 CACAACTTCAAGCTTTGAGAAGAGATTTTATGACTCTACAAATGAAGGATGGGGAATCTATTACC
56676 AGCTATTATGCCAGGACTATAGAGATCAACAACAAAATGTGATTTCATGGTGAAAAGATGGAAGA
326 AGCTATTATGCCAGGACTATAGAGATCAACAACAAAATGTGATTTCATGGTGAAAAGATGGAAGA
56741 TGTCACCATTGTGGAGAGAATATTGCATTCCCTGACACCAACTTTTAATTATGTTGTATGTTCAA
391 TGTCACCATTGTGGAGAGAATATTGCATTCCCTGACACCAACTTTTAATTATGTTGTATGTTCAA
** **
56806 TTGAATAATCGAAAGGCATAGATGAATTTTCTTTTGAACATACAACATAATTAAAAGTTGGTGTC
456 AAGAATAATCGAAAGGCATA-ATGAATTTTCTAATGAACATACAACATAATTAAAAGTTGGTGTC
56871 AGGGAATGCAATATTCTCTCCACAATGGTGACATCTTCCATCTTTTCACCATGAAATCACATTTT
520 AGGGAATGCAATATTCTCTCCACAATGGTGACATCTTCCATCTTTTCACCATGAAATCACATTTT
56936 GTTGTTGATCTATAGTCCTGGCATAATAGCTGGTAATAGATTCCCCATCCTTCATTTGTAGAGTC
585 GTTGTTGATCTATAGTCCTGGCATAATAGCTGGTAATAGATTCCCCATCCTTCATTTGTAGAGTC
57001 ATAAAATCTCTTCTCAAAGCTTGAAGTTGTGCACACTTACTCTAGCAGAGCCTTGATATTTTGTC
650 ATAAAATCTCTTCTCAAAGCTTGAAGTTGTGCACACTTACTCTAGCAGAGCCTTGATATTTTGTC
57066 TTCAGGCAATTAATCGTCCCATCTTGGAAATTATTCTTAACAAAGAAACTTCCAAAGATATTTGG
715 TTCAGGCAATTAATCGTCCCATCTTGGAAATTATTCTTAACAAAGAAACTTCCAAAGATATTTGG
57131 GATTCCATGAAGACAAAATATCAAGGCTCTGCTAGAGTAAAGTGTGCACAACTTCAAGCTTTGAG
780 GATTCCATGAAGACAAAATATCAAGGCTCTGCTAGAGTAAAGTGTGCACAACTTCAAGCTTTGAG
57196 AAGAGATTTTATGACTCTACAAATGAAGGATGGGGAATCTATTACCAGCTATATGCCAGGACTAT
845 AAGAGATTTTATGACTCTACAAATGAAGGATGGGGAATCTATTACCAGCTATATGCCAGGACTAT
57261 AGAGATCAACAACAAAATGTGATTTCA-GTGAAA-AGAGAAGATG
910 AGAGATCAACAACAAAATGTGATTTCAGGTGAAAGAG-GAAGATG
57304 TCACCATTAAATCACATTTTGTTGTTGATCTCTATAGTCCTGGCATAATAGCTGGTAATAGATTC
1 TCACCATTAAATCACA-TTTGTTGTTGATCTCTATAGTCCTGGCATAATAGCTGGTAATAGATTC
57369 CCCATCCTTCATTTGTAGAGTCATAAAATCTCTTCTCAAAGCTTGAAGTTGTGCACACTTTACTC
65 CCCATCCTTCA-TTGTAGAGTCAT-AAATCTCTTCTCAAAGCTTGAAGTTGTGCACACTTTACTC
57434 TAGCAGAGCCTTGATATTTTGTCTTCATGGAATCCCAAATATCTTTGGAAGTTTCTTTGTTAAGA
128 TAGCAGAGCCTTGATATTTTGTCTTCATGGAATCCCAAATATCTTTGGAAGTTTCTTTGTTAAGA
57499 ATAA-TTCCAAGATGGGACGATTAATTGCCTGAAGACAAAATATCAAGGCTCTGCTAGAGTAAGT
193 ATAATTTCCAAGATGGGACGATTAATTGCCTGAAGACAAAATATCAAGGCTCTGCTAGAGTAAGT
57563 GTGCACAACTTCAAGCTTTGAGAAGAGATTTTATGACTCTACAAATGAAGGATGGGGAATCTATT
258 GTGCACAACTTCAAGCTTTGAGAAGAGATTTTATGACTCTACAAATGAAGGATGGGGAATCTATT
57628 ACCAGCTATTATGCCAGGACTATAGAGATCAACAACAAAATGTGATTTCATGGTGAAAAGATGGA
323 ACCAGCTATTATGCCAGGACTATAGAGATCAACAACAAAATGTGATTTCATGGTGAAAAGATGGA
57693 AGATGTCACCATTGTGGAGAGAATATTGCATTCCCTGACACCAACTTTTAATTATGTTGTATGTT
388 AGATGTCACCATTGTGGAGAGAATATTGCATTCCCTGACACCAACTTTTAATTATGTTGTATGTT
* * * *
57758 CAAAAGAA-AATTC-ATCTATGCCT-TTCG-ATTATTC-AATGAACATACAACATAATTAAAAGT
453 CAAAAGAATAA-TCGA--AAGGCATAAT-GAATT-TTCTAATGAACATACAACATAATTAAAAGT
57818 TGGTGTCAGGGAATGCAATATTCTCTCCACAATGGTGACATCTTCCATC-TTTCACCATGAAATC
513 TGGTGTCAGGGAATGCAATATTCTCTCCACAATGGTGACATCTTCCATCTTTTCACCATGAAATC
57882 ACATTTTGTTGTTGATCTCTATAGTCCTGGCATAATAGCTGGTAATAGATTCCCCATCCTTCATT
578 ACATTTTGTTGTTGA--TCTATAGTCCTGGCATAATAGCTGGTAATAGATTCCCCATCCTTCATT
57947 TGTAGAGTCATAAAATCTCTTCTCAAAGC-TGAAGTTGTGCACACTTACTCTAGCAGAGCCTTGA
641 TGTAGAGTCATAAAATCTCTTCTCAAAGCTTGAAGTTGTGCACACTTACTCTAGCAGAGCCTTGA
58011 TATTTTGTCTTCAGGCAATTAATCGTCCCATCTTGGAAATTATTCTTAACAAAGAAAACTTCCAA
706 TATTTTGTCTTCAGGCAATTAATCGTCCCATCTTGGAAATTATTCTTAACAAAG-AAACTTCCAA
58076 AGATATTTGGGATTCCATGAAGACAAAATATCAAGGCTCTGCTAGAGTAAAGTGTGCACAACTTC
770 AGATATTTGGGATTCCATGAAGACAAAATATCAAGGCTCTGCTAGAGTAAAGTGTGCACAACTTC
58141 AAGCTTTGAGAAGAGA-TTTATGACTCTACAAATGAAGGATGGGGAATCTATTACCAGCTATTAT
835 AAGCTTTGAGAAGAGATTTTATGACTCTACAAATGAAGGATGGGGAATCTATTACCAGCTA-TAT
58205 GCCAGGACTATAGAGATCAACAACAAAATGTGATTTCATGGTGAAAGATGGAAGATG
899 GCCAGGACTATAGAGATCAACAACAAAATGTGATTTCA-GGTGAAAGA-GGAAGATG
58262 TCACCATT
1 TCACCATT
58270 GTGGAGAGAA
Statistics
Matches: 941, Mismatches: 9, Indels: 27
0.96 0.01 0.03
Matches are distributed among these distances:
953 45 0.05
954 272 0.29
955 488 0.52
956 113 0.12
957 6 0.01
958 16 0.02
959 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (953 bp):
TCACCATTAAATCACATTTGTTGTTGATCTCTATAGTCCTGGCATAATAGCTGGTAATAGATTCC
CCATCCTTCATTGTAGAGTCATAAATCTCTTCTCAAAGCTTGAAGTTGTGCACACTTTACTCTAG
CAGAGCCTTGATATTTTGTCTTCATGGAATCCCAAATATCTTTGGAAGTTTCTTTGTTAAGAATA
ATTTCCAAGATGGGACGATTAATTGCCTGAAGACAAAATATCAAGGCTCTGCTAGAGTAAGTGTG
CACAACTTCAAGCTTTGAGAAGAGATTTTATGACTCTACAAATGAAGGATGGGGAATCTATTACC
AGCTATTATGCCAGGACTATAGAGATCAACAACAAAATGTGATTTCATGGTGAAAAGATGGAAGA
TGTCACCATTGTGGAGAGAATATTGCATTCCCTGACACCAACTTTTAATTATGTTGTATGTTCAA
AAGAATAATCGAAAGGCATAATGAATTTTCTAATGAACATACAACATAATTAAAAGTTGGTGTCA
GGGAATGCAATATTCTCTCCACAATGGTGACATCTTCCATCTTTTCACCATGAAATCACATTTTG
TTGTTGATCTATAGTCCTGGCATAATAGCTGGTAATAGATTCCCCATCCTTCATTTGTAGAGTCA
TAAAATCTCTTCTCAAAGCTTGAAGTTGTGCACACTTACTCTAGCAGAGCCTTGATATTTTGTCT
TCAGGCAATTAATCGTCCCATCTTGGAAATTATTCTTAACAAAGAAACTTCCAAAGATATTTGGG
ATTCCATGAAGACAAAATATCAAGGCTCTGCTAGAGTAAAGTGTGCACAACTTCAAGCTTTGAGA
AGAGATTTTATGACTCTACAAATGAAGGATGGGGAATCTATTACCAGCTATATGCCAGGACTATA
GAGATCAACAACAAAATGTGATTTCAGGTGAAAGAGGAAGATG
Done.