Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 1 of 141
Found at i:697 original size:44 final size:44
Alignment explanation
Indices: 631--803 Score: 204
Period size: 44 Copynumber: 3.9 Consensus size: 44
621 GGCTGTTACA
* *
631 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC
1 ACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT
* * * * *
675 ACAAACCTTATCTCCCTAAAGTTGCAATGGAGCAGGTTGAAGAT
1 ACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT
* * * ** *
719 ACCAATCTTGTCTCTTTGAAGTTGCAGTGGAGCAGATTGAAGCT
1 ACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT
*
763 ACTAATCC-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
1 AC-AAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
804 ACAATGAATC
Statistics
Matches: 105, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
44 103 0.98
45 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (44 bp):
ACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT
Found at i:2637 original size:11 final size:11
Alignment explanation
Indices: 2621--2645 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2611 TCCCTTTTTT
2621 AAAAAAAAATC
1 AAAAAAAAATC
2632 AAAAAAAAATC
1 AAAAAAAAATC
2643 AAA
1 AAA
2646 TGCCTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAAAAATC
Found at i:2767 original size:14 final size:13
Alignment explanation
Indices: 2750--2783 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2740 TGCTCTTATT
2750 TTTATTATATCACC
1 TTTATTA-ATCACC
*
2764 TTTATTACTCACC
1 TTTATTAATCACC
2777 TTTATTA
1 TTTATTA
2784 CTCTCAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTATTAATCACC
Found at i:2777 original size:13 final size:13
Alignment explanation
Indices: 2759--2786 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2749 TTTTATTATA
2759 TCACCTTTATTAC
1 TCACCTTTATTAC
2772 TCACCTTTATTAC
1 TCACCTTTATTAC
2785 TC
1 TC
2787 TCAAGTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.32, G:0.00, T:0.46
Consensus pattern (13 bp):
TCACCTTTATTAC
Found at i:2942 original size:16 final size:17
Alignment explanation
Indices: 2906--2943 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2896 TTATTTGGTG
2906 TTATTATTATAATCACA
1 TTATTATTATAATCACA
* *
2923 TTATTATTGT-ATCCCA
1 TTATTATTATAATCACA
2939 TTATT
1 TTATT
2944 TACCTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.53
Consensus pattern (17 bp):
TTATTATTATAATCACA
Found at i:8085 original size:4 final size:4
Alignment explanation
Indices: 8076--8105 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
8066 AAAAATGAGT
*
8076 AATA AATA AATA AATG AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
8106 AACAATTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:19695 original size:24 final size:24
Alignment explanation
Indices: 19661--19718 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
19651 ATGTCCCAAA
*
19661 ATTACATTGGACTGAACCTTGAAG
1 ATTACAGTGGACTGAACCTTGAAG
* *
19685 ATTACAGTGGATTGAGCCTTGAAG
1 ATTACAGTGGACTGAACCTTGAAG
*
19709 ATTAGAGTGG
1 ATTACAGTGG
19719 GGGGCAATCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.29
Consensus pattern (24 bp):
ATTACAGTGGACTGAACCTTGAAG
Found at i:20181 original size:88 final size:88
Alignment explanation
Indices: 20032--20371 Score: 547
Period size: 88 Copynumber: 3.9 Consensus size: 88
20022 AAGAATATTA
* *
20032 TAGATCTTGTCTTCCTGTACTAGCAGTAAAGCAGATAAAAAACACTAGCCTTATCTCCCTGAGCA
1 TAGATCTTGTCTTCCTGTACTGGCAGTAAAGCAGATAAAAAACACCAGCCTTATCTCCCTGAGCA
*
20097 ACAGTGGAGTAGGTTGAAGATTG
66 GCAGTGGAGTAGGTTGAAGATTG
* *
20120 TAGATCTTGTCTTCCTGTACTGGCAATAAAGCAGATAAAAAACACCAGTCTTATCTCCCTGAGCA
1 TAGATCTTGTCTTCCTGTACTGGCAGTAAAGCAGATAAAAAACACCAGCCTTATCTCCCTGAGCA
20185 GCAGTGGAGTAGGTTGAAGATTG
66 GCAGTGGAGTAGGTTGAAGATTG
* *
20208 TAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATCGAAAAA-ACCAGCCTTATCTCCCTGAGC
1 TAGATCTTGTCTTCCTGTACTGGCAGTAAAGCAGAT-AAAAAACACCAGCCTTATCTCCCTGAGC
* *
20272 AGTAGTGAAGTAGGTTGAAGATTG
65 AGCAGTGGAGTAGGTTGAAGATTG
* * *
20296 TAGATCTTGTCTTCCTGTATTGGCAGTGAAGCAGATCAAAAACACCAGCCTTATCTCCCTGAGCA
1 TAGATCTTGTCTTCCTGTACTGGCAGTAAAGCAGATAAAAAACACCAGCCTTATCTCCCTGAGCA
*
20361 GTAGTGGAGTA
66 GCAGTGGAGTA
20372 TGTAACACCC
Statistics
Matches: 236, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
87 5 0.02
88 226 0.96
89 5 0.02
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (88 bp):
TAGATCTTGTCTTCCTGTACTGGCAGTAAAGCAGATAAAAAACACCAGCCTTATCTCCCTGAGCA
GCAGTGGAGTAGGTTGAAGATTG
Found at i:25580 original size:21 final size:21
Alignment explanation
Indices: 25556--25597 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25546 CTTTTTGTTC
*
25556 AATTAATTATCGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
**
25577 AATTTCTTAACGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
25598 TACTAACTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
AATTAATTAACGAAACTTTAA
Found at i:26070 original size:88 final size:88
Alignment explanation
Indices: 25921--26213 Score: 390
Period size: 88 Copynumber: 3.3 Consensus size: 88
25911 GGCTGTTACA
*
25921 GAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGTAAAGCAGATTGAAAACACCAG
1 GAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATTGAAAACACCAG
**
25986 CCTTATCTCCCTGAATTGTAGTG
66 CCTTATCTCCCTGAACAGTAGTG
* * * * *
26009 GAGTAGGTTGAAGATTGTATATCTTATCTTCCTGTACTGGCAGTGAGGCAGATCGAAAACACTAG
1 GAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATTGAAAACACCAG
*
26074 CCTTATCTCCCTGAGCAGTAGTG
66 CCTTATCTCCCTGAACAGTAGTG
* * * * *
26097 GAGTAGGTTGAAGATTGTAGATCTTGTCTTCTTGTACTAGTAGTGAAGCAGATTGAAAATACTAG
1 GAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATTGAAAACACCAG
* * *
26162 TCC-TGTCTCCCTGAGCAGCAGTG
66 -CCTTATCTCCCTGAACAGTAGTG
* * *
26185 GAGTGGGTCGAAGATTGTAGATCCTGTCT
1 GAGTAGGTTGAAGATTGTAGATCTTGTCT
26214 CCCTAAACAG
Statistics
Matches: 182, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
88 180 0.99
89 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (88 bp):
GAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATTGAAAACACCAG
CCTTATCTCCCTGAACAGTAGTG
Found at i:26261 original size:88 final size:88
Alignment explanation
Indices: 25921--26262 Score: 231
Period size: 88 Copynumber: 3.9 Consensus size: 88
25911 GGCTGTTACA
* * * ** * * * * * *
25921 GAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGTAAAGCAGATTGAAAACACCAG
1 GAGTAGGTCGAAGATTGTAGATCCTGTCTCCCTAAACTAGTAGTGAAGCAGATTCAAAACACAAA
* *** *
25986 CCTTATCTCCCTGAATTGTAGTG
66 TCTTATCTCCCTGAGCAGCAGTG
* * * * * ** * * * *
26009 GAGTAGGTTGAAGATTGTATATCTTATCTTCCTGTACTGGCAGTGAGGCAGA-TCGAAAACACTA
1 GAGTAGGTCGAAGATTGTAGATCCTGTCTCCCTAAACTAGTAGTGAAGCAGATTC-AAAACACAA
** *
26073 GCCTTATCTCCCTGAGCAGTAGTG
65 ATCTTATCTCCCTGAGCAGCAGTG
* * * * ** * * * *
26097 GAGTAGGTTGAAGATTGTAGATCTTGTCTTCTTGTACTAGTAGTGAAGCAGATTGAAAATACTAG
1 GAGTAGGTCGAAGATTGTAGATCCTGTCTCCCTAAACTAGTAGTGAAGCAGATTCAAAACACAAA
* *
26162 TCCTGTCTCCCTGAGCAGCAGTG
66 TCTTATCTCCCTGAGCAGCAGTG
* *
26185 GAGTGGGTCGAAGATTGTAGATCCTGTCTCCCTAAAC-AGTAGTGGAGCAGA-TCAAAGACAGCA
1 GAGTAGGTCGAAGATTGTAGATCCTGTCTCCCTAAACTAGTAGTGAAGCAGATTCAAA-ACA-CA
*
26248 AATCTTATTTCCCTG
64 AATCTTATCTCCCTG
26263 GTTTTGCAGT
Statistics
Matches: 214, Mismatches: 36, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
86 4 0.02
87 16 0.07
88 193 0.90
89 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (88 bp):
GAGTAGGTCGAAGATTGTAGATCCTGTCTCCCTAAACTAGTAGTGAAGCAGATTCAAAACACAAA
TCTTATCTCCCTGAGCAGCAGTG
Found at i:26515 original size:36 final size:36
Alignment explanation
Indices: 26455--26523 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
26445 GCGGAGCAGA
* *
26455 TTAAAGTTGAAGGAAGCGAATCTTATCTCCCTGGTG
1 TTAAAGTTGAAGAAAGCGAATCTTATCCCCCTGGTG
*
26491 TTAAAGTTGAAGAAAG-TAAGTCTTATCCCCCTG
1 TTAAAGTTGAAGAAAGCGAA-TCTTATCCCCCTG
26524 AAGGCAGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 2 0.07
36 27 0.93
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (36 bp):
TTAAAGTTGAAGAAAGCGAATCTTATCCCCCTGGTG
Found at i:26652 original size:90 final size:88
Alignment explanation
Indices: 26553--26759 Score: 236
Period size: 90 Copynumber: 2.3 Consensus size: 88
26543 AAGATGGCAT
* *
26553 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAACAAGTCTTATCTTCCTGAAGTTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAACAAGTCCTATCTCCCTGAAGTTA
26618 CAGAGGAACAGACTGACTA-AAACCA
65 CAGAGGAACAGACTGA--AGAAACCA
* * ** * *
26643 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAGTCCTATCTCCCTGAAGTTGC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAACAAGTCCTATCTCCCTGAAGTTAC
* * * ** *
26708 AGTGGAGCAGATTGAAGTTACTA
66 AGAGGAACAGACTGAAGAAACCA
* *
26731 GTCCTATCTCCCTGAAGTTGCAGTGGAGC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGC
26760 GGCATAAAAT
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
87 1 0.01
88 29 0.29
89 33 0.33
90 36 0.36
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (88 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAACAAGTCCTATCTCCCTGAAGTTAC
AGAGGAACAGACTGAAGAAACCA
Found at i:26702 original size:44 final size:44
Alignment explanation
Indices: 26557--26759 Score: 228
Period size: 44 Copynumber: 4.6 Consensus size: 44
26547 TGGCATATCT
* * * *
26557 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAACAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-TAACTAGTCC
* * * * * * * * *
26602 TATCTTCCTGAAGTTACAGAGGAACAGACTGACTA-AAACCAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGA--AGTAACTAGTCC
* *
26647 TATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAGTCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAACTAGTCC
*
26691 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAGTCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAACTAGTCC
26735 TATCTCCCTGAAGTTGCAGTGGAGC
1 TATCTCCCTGAAGTTGCAGTGGAGC
26760 GGCATAAAAT
Statistics
Matches: 134, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
43 1 0.01
44 73 0.54
45 59 0.44
47 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAACTAGTCC
Found at i:26783 original size:44 final size:44
Alignment explanation
Indices: 26647--26807 Score: 155
Period size: 44 Copynumber: 3.7 Consensus size: 44
26637 AAACCAATCT
* * * * *
26647 TATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAGTCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGACTAGACC
* * * *
26691 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAGTCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGACTAGACC
* *
26735 TATCTCCCTGAAGTTGCAGTGGAGCGGCA-TAAAATGA-TGGACC
1 TATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAATGACTAGACC
** * *
26778 TTATCTCTTTGAAGTTGTAGTAGAGCAGAT
1 -TATCTCCCTGAAGTTGCAGTGGAGCAGAT
26808 CGCATCAGAC
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
43 5 0.05
44 96 0.94
45 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGACTAGACC
Found at i:26913 original size:45 final size:44
Alignment explanation
Indices: 26849--27102 Score: 190
Period size: 44 Copynumber: 5.7 Consensus size: 44
26839 AAGCTACAAG
* * * * *
26849 TCTTATCTCACTGATGTTGCAGTAGAGTAGACTGAAGATAGCAGA
1 TCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGAAGATACCA-A
* * * *
26894 TCTTATCTCTCTAAAGTTGCAGTAGAGCAGA-TCACACCATAACAA
1 TCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGA-A-GATACCAA
* * *
26939 GTATTATCTCCCTAAAATTGCAGTGGAGCAGACTGAAGATAACCAA
1 -TCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGAAGAT-ACCAA
* * * ** *
26985 CCTTATCTCTCTAAA-TTGCAGTGGAGCAGGTTGAAGAAACCAA
1 TCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGAAGATACCAA
* * * * **
27028 TCTTATCTCCCTGAAGTTGTAGT-GAAGCAGATTGAAGCTATTAA
1 TCTTATCTCCCTAAAGTTGCAGTAG-AGCAGACTGAAGATACCAA
* * *
27072 TCCTATCTCCTTAAAGTTGCAGTGGAGCAGA
1 TCTTATCTCCCTAAAGTTGCAGTAGAGCAGA
27103 TTAAAACGAT
Statistics
Matches: 168, Mismatches: 33, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
43 18 0.11
44 67 0.40
45 44 0.26
46 37 0.22
47 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGAAGATACCAA
Found at i:27118 original size:44 final size:44
Alignment explanation
Indices: 27026--27362 Score: 123
Period size: 44 Copynumber: 7.5 Consensus size: 44
27016 TGAAGAAACC
* * * * * * *
27026 AATCTTATCTCCCTGAAGTTGTAGTGAAGCAGATTGAAGCTATT
1 AATCCTATCTCCTTGAAGTTGCAGTGAAGCAGATTAAAACGATG
* *
27070 AATCCTATCTCCTTAAAGTTGCAGTGGAGCAGATTAAAACGATG
1 AATCCTATCTCCTTGAAGTTGCAGTGAAGCAGATTAAAACGATG
* * * * *
27114 AATCCTAT-ACCTCTGAAGTTGCAGT-AGGTCGGATTAAATCTACCATAAA
1 AATCCTATCTCCT-TGAAGTTGCAGTGAAG-CAGATTAAA---ACGAT--G
* * * * * * *
27163 AAGTCTTATCTCCCTGACGTTGCAGTGGAGCAGACTAAAACCA-C
1 AA-TCCTATCTCCTTGAAGTTGCAGTGAAGCAGATTAAAACGATG
* * * * * *
27207 AAACCTTATCTCCCTGAAGTTGTAGTGAAACA-AGTTGAAGATACTA-A
1 AATCC-TATCTCCTTGAAGTTGCAGTGAAGCAGA-TT-AA-A-ACGATG
* * * * * * * *
27254 AAT--TTTCTCCCTGAAGTTGCAATGGAGCAGATTGAAGCTATT
1 AATCCTATCTCCTTGAAGTTGCAGTGAAGCAGATTAAAACGATG
* * * * *
27296 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGACTAAAACAATG
1 AATCCTATCTCCTTGAAGTTGCAGTGAAGCAGATTAAAACGATG
*
27340 AATCCTAT-ACCTCTGAAGTTGCA
1 AATCCTATCTCCT-TGAAGTTGCA
27363 CCAGGTCGGA
Statistics
Matches: 220, Mismatches: 53, Indels: 40
0.70 0.17 0.13
Matches are distributed among these distances:
41 3 0.01
42 4 0.02
43 9 0.04
44 159 0.72
45 3 0.01
46 1 0.00
47 13 0.06
49 2 0.01
50 23 0.10
51 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (44 bp):
AATCCTATCTCCTTGAAGTTGCAGTGAAGCAGATTAAAACGATG
Found at i:27246 original size:226 final size:226
Alignment explanation
Indices: 26929--27425 Score: 672
Period size: 226 Copynumber: 2.2 Consensus size: 226
26919 AGCAGATCAC
* * * * *
26929 ACCATAACAAGTATTATCTCCCTAAAATTGCAGTGGAGCAGACTGAAGATAACCAACCTTATCTC
1 ACCATAACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAAACAACAAACCTTATCTC
* * * * ** * *
26994 TCTAAATTGCAGTGGAGCAGGTTGAAGAAACCAATCTTATCTCCCTGAAGTTGTAGTGAAGCAGA
66 CCTAAATTGCAGTGAAACAAGTTGAAGAAACCAAAATTATCTCCCTGAAGTTGCAATGAAGCAGA
* * *
27059 TTGAAGCTATTAATCCTATCTCCTTAAAGTTGCAGTGGAGCAGATTAAAACGATGAATCCTATAC
131 TTGAAGCTATTAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAACAATGAATCCTATAC
**
27124 CTCTGAAGTTGCAGTAGGTCGGATTAAATCT
196 CTCTGAAGTTGCACCAGGTCGGATTAAATCT
* * * *
27155 ACCATAAAAAGTCTTATCTCCCTGACGTTGCAGTGGAGCAGACT-AAAACCACAAACCTTATCTC
1 ACCATAACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAAACAACAAACCTTATCTC
* * * * * *
27219 CCTGAAGTTGTAGTGAAACAAGTTGAAGATACTAAAATTTTCTCCCTGAAGTTGCAATGGAGCAG
66 CCT-AAATTGCAGTGAAACAAGTTGAAGAAACCAAAATTATCTCCCTGAAGTTGCAATGAAGCAG
* *
27284 ATTGAAGCTATTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGACTAAAACAATGAATCCTATA
130 ATTGAAGCTATTAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAACAATGAATCCTATA
*
27349 CCTCTGAAGTTGCACCAGGTCGGATTAAGTCT
195 CCTCTGAAGTTGCACCAGGTCGGATTAAATCT
* * *
27381 ATCATAACAAGTCTTATCTCCCTAAAGTTGTAGTGGAGTAGACTG
1 ACCATAACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTG
27426 TAGATAGCAG
Statistics
Matches: 232, Mismatches: 37, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
225 18 0.08
226 214 0.92
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (226 bp):
ACCATAACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAAACAACAAACCTTATCTC
CCTAAATTGCAGTGAAACAAGTTGAAGAAACCAAAATTATCTCCCTGAAGTTGCAATGAAGCAGA
TTGAAGCTATTAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAACAATGAATCCTATAC
CTCTGAAGTTGCACCAGGTCGGATTAAATCT
Found at i:27989 original size:3 final size:3
Alignment explanation
Indices: 27981--28033 Score: 58
Period size: 3 Copynumber: 17.7 Consensus size: 3
27971 CAAAATTTGT
27981 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TT- TCTA TT- TATA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA T-TA -TTA
28026 TTA TTA TT
1 TTA TTA TT
28034 TGTTTTAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
2 4 0.09
3 36 0.82
4 3 0.07
5 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28070 original size:28 final size:27
Alignment explanation
Indices: 27996--28079 Score: 80
Period size: 27 Copynumber: 3.0 Consensus size: 27
27986 ATTATTATTA
**
27996 TTATTATTATTATATT-TCTATTTATAT
1 TTATTATTATT-TATTGTAAATTTATAT
* * *
28023 TTATTATTATTTGTTTTAAATTTTTAT
1 TTATTATTATTTATTGTAAATTTATAT
28050 TTATTTATTATTTATTGTAAACTATTATAT
1 TTA-TTATTATTTATTGTAAA-T-TTATAT
28080 ATATATATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
26 3 0.07
27 22 0.48
28 15 0.33
29 1 0.02
30 5 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (27 bp):
TTATTATTATTTATTGTAAATTTATAT
Found at i:37270 original size:13 final size:13
Alignment explanation
Indices: 37261--37311 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
37251 AAATAAATGG
37261 AAATAATAAAAGA
1 AAATAATAAAAGA
*
37274 ACAATAA-ACAAACA
1 A-AATAATA-AAAGA
*
37288 AAATAATAAAAGG
1 AAATAATAAAAGA
37301 AAATAATAAAA
1 AAATAATAAAA
37312 ACAAGTCAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 21 0.66
14 11 0.34
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.14
Consensus pattern (13 bp):
AAATAATAAAAGA
Found at i:37313 original size:27 final size:27
Alignment explanation
Indices: 37261--37315 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
37251 AAATAAATGG
*
37261 AAATAATAAAAGAACAATAAACAAACA
1 AAATAATAAAAGAACAATAAAAAAACA
*
37288 AAATAATAAAAGGA-AATAATAAAAACA
1 AAATAATAAAAGAACAATAA-AAAAACA
37315 A
1 A
37316 GTCAGGGACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.13
Consensus pattern (27 bp):
AAATAATAAAAGAACAATAAAAAAACA
Found at i:37953 original size:15 final size:15
Alignment explanation
Indices: 37918--37956 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
37908 TTTTTGTGTT
*
37918 AAAAAACAAAACATA
1 AAAAAACAAAAAATA
* *
37933 ATAAAATAAAAAATA
1 AAAAAACAAAAAATA
37948 AAAAAACAA
1 AAAAAACAA
37957 TCGAGTCTGT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.82, C:0.08, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAACAAAAAATA
Found at i:55801 original size:26 final size:26
Alignment explanation
Indices: 55762--55819 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
55752 ATTATTACTA
*
55762 TTATTATTTAGTCACATGGTTGATGT
1 TTATTATTTAGTCAAATGGTTGATGT
* * *
55788 TTATTTTTTTGTCAAATTGTTGATG-
1 TTATTATTTAGTCAAATGGTTGATGT
55813 TTATTAT
1 TTATTAT
55820 ATTCATTCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.22, C:0.05, G:0.16, T:0.57
Consensus pattern (26 bp):
TTATTATTTAGTCAAATGGTTGATGT
Found at i:57784 original size:40 final size:40
Alignment explanation
Indices: 57740--57820 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
57730 AGTCCTATAC
57740 TCGAAATCCATTACTATGTTTTAGCTTGTTAATAATTGTA
1 TCGAAATCCATTACTATGTTTTAGCTTGTTAATAATTGTA
57780 TCGAAATCCATTACTATGTTTTAGCTTGTTAATAATTGTA
1 TCGAAATCCATTACTATGTTTTAGCTTGTTAATAATTGTA
57820 T
1 T
57821 AATTGTAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (40 bp):
TCGAAATCCATTACTATGTTTTAGCTTGTTAATAATTGTA
Found at i:58574 original size:26 final size:26
Alignment explanation
Indices: 58545--58600 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
58535 CTACGCCAAA
58545 TATTGAATCTTTTATTTGT-TTTT-TTT
1 TATT-AATCTTTTATTT-TATTTTATTT
**
58571 TATTTCTCTTTTATTTTATTTTATTT
1 TATTAATCTTTTATTTTATTTTATTT
58597 TATT
1 TATT
58601 TTATTTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 1 0.04
25 14 0.54
26 11 0.42
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.75
Consensus pattern (26 bp):
TATTAATCTTTTATTTTATTTTATTT
Found at i:58580 original size:25 final size:26
Alignment explanation
Indices: 58552--58601 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
58542 AAATATTGAA
58552 TCTTTTATTTGT-TTTT-TTTTATTTC
1 TCTTTTATTT-TATTTTATTTTATTTC
58577 TCTTTTATTTTATTTTATTTTATTT
1 TCTTTTATTTTATTTTATTTTATTT
58602 TATTTTTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 1 0.04
25 14 0.61
26 8 0.35
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.80
Consensus pattern (26 bp):
TCTTTTATTTTATTTTATTTTATTTC
Found at i:58587 original size:5 final size:5
Alignment explanation
Indices: 58554--58607 Score: 67
Period size: 5 Copynumber: 10.8 Consensus size: 5
58544 ATATTGAATC
*
58554 TTTTA TTTGT- TTTT- TTTTA TTTCTC TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTT-TA TTTTA TTTTA TTT-TA TTTTA TTTTA TTTTA TTTTA TTTTA
58604 TTTT
1 TTTT
58608 TGAGTATTAG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
4 5 0.11
5 34 0.77
6 5 0.11
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:59690 original size:64 final size:64
Alignment explanation
Indices: 59577--59710 Score: 214
Period size: 64 Copynumber: 2.1 Consensus size: 64
59567 AGATCTACTC
* * * *
59577 TTAAACAGGGTCTATTCAAACTTTGATTTAAGCACATCATACATAGATCAATACTCTAGAAATA
1 TTAAACAAGGTCTATTCAAACTTGGATTTAAGCAAATCAAACATAGATCAATACTCTAGAAATA
* *
59641 TTAAACAAGGTCTATTCAACCTTGGATTTAAGCAAATCAAACATGGATCAATACTCTAGAAATA
1 TTAAACAAGGTCTATTCAAACTTGGATTTAAGCAAATCAAACATAGATCAATACTCTAGAAATA
59705 TTAAAC
1 TTAAAC
59711 CAAGAATTAA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (64 bp):
TTAAACAAGGTCTATTCAAACTTGGATTTAAGCAAATCAAACATAGATCAATACTCTAGAAATA
Found at i:63010 original size:15 final size:15
Alignment explanation
Indices: 62990--63020 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
62980 TTATTTTTCG
62990 TTTTTGCTCATATTA
1 TTTTTGCTCATATTA
*
63005 TTTTTGTTCATATTA
1 TTTTTGCTCATATTA
63020 T
1 T
63021 CATGTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (15 bp):
TTTTTGCTCATATTA
Found at i:63257 original size:23 final size:23
Alignment explanation
Indices: 63227--63274 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
63217 AAGTATCGTA
63227 TCCTAATGTGCTGGATGTGATAT
1 TCCTAATGTGCTGGATGTGATAT
*
63250 TCCTAATGTGTTGGATGTGATAT
1 TCCTAATGTGCTGGATGTGATAT
63273 TC
1 TC
63275 TTTTTGAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.42
Consensus pattern (23 bp):
TCCTAATGTGCTGGATGTGATAT
Found at i:74319 original size:44 final size:44
Alignment explanation
Indices: 74255--74709 Score: 135
Period size: 44 Copynumber: 10.6 Consensus size: 44
74245 TAACAAGTCC
* * *
74255 TATCTCTCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCT
1 TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGATTGTAGATCT
* * * **
74299 TATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-CGGCGAATCT
1 TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGATTGTAG-ATCT
* * * ***** *
74343 TATCTTTCC-GAG-A-TAGTAGGAAGCAGATTTAAGCCACCAGTTC-
1 TATC-TCCCTGAGCAGTAGT-GG-AGTAGATTGAAGATTGTAGATCT
** * * *
74386 TATCTCCCTGAGCAACAATGGAGTAGGTTGAATATTGTAGATCT
1 TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGATTGTAGATCT
* ** *
74430 TATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGA-CG-ACGAATCT
1 TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGATTGTA-G-ATCT
* ***** *
74474 TATCTTCCC---G-AG-A-T--A--AGATTTAAGCCACCA-ATCC
1 TATC-TCCCTGAGCAGTAGTGGAGTAGATTGAAGATTGTAGATCT
* * * * *
74508 TATCTCCCTAAGCAATAGTGGAGTAGGTTAAAGATTGCAGATCT
1 TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGATTGTAGATCT
* * * **
74552 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGT-GAATCT
1 TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGATTGTAG-ATCT
* * * * * ***** *
74596 TATCTTCCTGAG-ATGTAG-GAAGCAAATTTAAGCCACCAG-TCC
1 TATCTCCCTGAGCA-GTAGTGGAGTAGATTGAAGATTGTAGATCT
* * *
74638 TATCTCCCTGAACAGTAGTGGAGTAGGTTAAAGATTGTAGATCT
1 TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGATTGTAGATCT
* * *
74682 TATCACCCTAAGCAGTAGTGGAGCAGAT
1 TATCTCCCTGAGCAGTAGTGGAGTAGAT
74710 CGCATCCAGT
Statistics
Matches: 290, Mismatches: 90, Indels: 62
0.66 0.20 0.14
Matches are distributed among these distances:
33 4 0.01
34 7 0.02
35 7 0.02
36 1 0.00
37 3 0.01
38 1 0.00
39 2 0.01
40 1 0.00
41 3 0.01
42 25 0.09
43 60 0.21
44 166 0.57
45 10 0.03
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGAGCAGTAGTGGAGTAGATTGAAGATTGTAGATCT
Found at i:74488 original size:131 final size:131
Alignment explanation
Indices: 74250--74711 Score: 647
Period size: 122 Copynumber: 3.6 Consensus size: 131
74240 CATCATAACA
* * *
74250 AGTCCTATCTCTCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
1 AGTCCTATCTCCCTGAGCAACAGTGGAGTAGGTTAAAGATTGTAGATCTTATCTCCCTAAGCAGT
* *
74315 AGTGGAGCAGATTGAAGACGGCGAATCTTATCTTTCCGAGATAGTAGGAAGCAGATTTAAGCCAC
66 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAGCCAC
74380 C
131 C
* * * *
74381 AGTTCTATCTCCCTGAGCAACAATGGAGTAGGTTGAATATTGTAGATCTTATCTCCCTAAGCAGT
1 AGTCCTATCTCCCTGAGCAACAGTGGAGTAGGTTAAAGATTGTAGATCTTATCTCCCTAAGCAGT
* * *
74446 AGTGGAGTAGATCAAAGACGACGAATCTTATCTTCCCGAG--A-T----A--AGATTTAAGCCAC
66 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAGCCAC
74502 C
131 C
* * * *
74503 AATCCTATCTCCCTAAGCAATAGTGGAGTAGGTTAAAGATTGCAGATCTTATCTCCCTAAGCAGT
1 AGTCCTATCTCCCTGAGCAACAGTGGAGTAGGTTAAAGATTGTAGATCTTATCTCCCTAAGCAGT
* * *
74568 AGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCTGAGAT-GTAGGAAGCAAATTTAAGCCAC
66 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAGCCAC
74632 C
131 C
* ** *
74633 AGTCCTATCTCCCTGAACAGTAGTGGAGTAGGTTAAAGATTGTAGATCTTATCACCCTAAGCAGT
1 AGTCCTATCTCCCTGAGCAACAGTGGAGTAGGTTAAAGATTGTAGATCTTATCTCCCTAAGCAGT
74698 AGTGGAGCAGATCG
66 AGTGGAGCAGATCG
74712 CATCCAGTCT
Statistics
Matches: 292, Mismatches: 30, Indels: 19
0.86 0.09 0.06
Matches are distributed among these distances:
122 106 0.36
124 2 0.01
128 2 0.01
129 1 0.00
130 86 0.29
131 95 0.33
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (131 bp):
AGTCCTATCTCCCTGAGCAACAGTGGAGTAGGTTAAAGATTGTAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAGCCAC
C
Found at i:74748 original size:41 final size:41
Alignment explanation
Indices: 74698--74874 Score: 142
Period size: 44 Copynumber: 4.2 Consensus size: 41
74688 CCTAAGCAGT
* * *
74698 AGTGGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGC
1 AGTGGAGCAGATCGAATCCAATCTTATCTCCCTAAAGTTGC
* * *
74739 AGTGGAGCAGA-CGAAAGAAACCAAT-TCTATCTCCCTAAAATTGT
1 AGTGGAGCAGATC----GAATCCAATCT-TATCTCCCTAAAGTTGC
* ** * *
74783 AGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGC
1 AGTGGAGCAGA-TCGAATC-CA-ATCTTATCTCCCTAAAGTTGC
* * *
74827 AGTAGAGCAGATCGCATCCAATCTTATCTTCCTAAAGTTGC
1 AGTGGAGCAGATCGAATCCAATCTTATCTCCCTAAAGTTGC
74868 AGTGGAG
1 AGTGGAG
74875 TAGACTAAAA
Statistics
Matches: 103, Mismatches: 23, Indels: 20
0.71 0.16 0.14
Matches are distributed among these distances:
40 1 0.01
41 35 0.34
42 5 0.05
43 7 0.07
44 54 0.52
45 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (41 bp):
AGTGGAGCAGATCGAATCCAATCTTATCTCCCTAAAGTTGC
Found at i:76774 original size:21 final size:21
Alignment explanation
Indices: 76749--76790 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
76739 CATATTATTT
*
76749 TTATTCACATTAT-CATGTTAA
1 TTATTC-CATTATGCATATTAA
76770 TTATTCCATTATGCATATTAA
1 TTATTCCATTATGCATATTAA
76791 CACCATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (21 bp):
TTATTCCATTATGCATATTAA
Found at i:82811 original size:44 final size:45
Alignment explanation
Indices: 82757--82892 Score: 166
Period size: 44 Copynumber: 3.0 Consensus size: 45
82747 ATAAAGATAG
*
82757 CAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATTGAAGACAC
1 CAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATTGAAGACAC
* * * * * * *
82802 CAG-TCTTGCCTCCCTGTACTGACGGCGGAGCAGACTGAAAATAG
1 CAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATTGAAGACAC
* * *
82846 CAGATCTTGTCTTCTTGTACTGACGGTGAAGCAGATCGAAGACAC
1 CAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATTGAAGACAC
82891 CA
1 CA
82893 TAGTTTGCAA
Statistics
Matches: 72, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
44 36 0.50
45 36 0.50
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (45 bp):
CAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATTGAAGACAC
Found at i:83070 original size:100 final size:100
Alignment explanation
Indices: 82897--83403 Score: 777
Period size: 100 Copynumber: 5.1 Consensus size: 100
82887 ACACCATAGT
* * * *
82897 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCTGG-CGATGCAATGGAACA
1 TTGCAATT-ATAAGATTGAGGCCACAACGGCGAATCTTACTTTCCCTGGTAG-TGCAGTGGAACA
*
82960 GATTGAAGCTACAATGGCGAATCTCGCTTCCCCGACA
64 GATTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
*
82997 TTGCAATTATAAGATTGAGGCCACAACGGTGAATCTTACTTTCCCTGGTAGTGCAGTGGAACAGA
1 TTGCAATTATAAGATTGAGGCCACAACGGCGAATCTTACTTTCCCTGGTAGTGCAGTGGAACAGA
* *
83062 TTGAAGCTACAACGGCGAATCTCGCTTCGCTGACA
66 TTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
* *
83097 TTGCAATTATAAGATTGAGGCCACAACGGTGAATCTTACTTTCCCTGGTAGTGCAGTGGAACAAA
1 TTGCAATTATAAGATTGAGGCCACAACGGCGAATCTTACTTTCCCTGGTAGTGCAGTGGAACAGA
*
83162 TTGAAGCTACAACGGCTAATCTCGCTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
83197 TTGCAATTATAAGATTGAGGCCACAACGGCGAATCTTACTTTCCCTGGTAGTGCAGTGGAACAGA
1 TTGCAATTATAAGATTGAGGCCACAACGGCGAATCTTACTTTCCCTGGTAGTGCAGTGGAACAGA
* *
83262 TTGAAGCTACAACAGCGAATCTCGCTTCCTCGACA
66 TTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
* * * * *
83297 TTGCAATTAAAAGATTGAGGCTACAACGGCGAATCTTACTTTCCCAGG-CGATGCAGTGGAATAG
1 TTGCAATTATAAGATTGAGGCCACAACGGCGAATCTTACTTTCCCTGGTAG-TGCAGTGGAACAG
* * *
83361 ATTGAAGCTACAACGACGAATCTCCCTTCCCTGACA
65 ATTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
83397 TTGCAAT
1 TTGCAAT
83404 CTCATTTCCC
Statistics
Matches: 377, Mismatches: 27, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
99 29 0.08
100 347 0.92
101 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (100 bp):
TTGCAATTATAAGATTGAGGCCACAACGGCGAATCTTACTTTCCCTGGTAGTGCAGTGGAACAGA
TTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
Found at i:85132 original size:3 final size:3
Alignment explanation
Indices: 85124--85176 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
85114 AATTAATACC
* * * * * *
85124 TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA ATA CTA TTT TTG CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
85172 TTA TT
1 TTA TT
85177 GTTTATGTTT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:85402 original size:17 final size:17
Alignment explanation
Indices: 85365--85407 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
85355 TTTATTTACG
*
85365 TTTTATTGTTATTATTA
1 TTTTATTATTATTATTA
85382 TTTTATTATTATTAGTT-
1 TTTTATTATTATTA-TTA
85399 TTTT-TTATT
1 TTTTATTATT
85408 CTTTTAGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 5 0.21
17 17 0.71
18 2 0.08
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (17 bp):
TTTTATTATTATTATTA
Found at i:93186 original size:12 final size:12
Alignment explanation
Indices: 93171--93212 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
93161 GTGGTTATTG
93171 TTTTATTTTTAC
1 TTTTATTTTTAC
93183 TTTTATTTTTA-
1 TTTTATTTTTAC
93194 TTTTATTATTT-C
1 TTTTATT-TTTAC
93206 TTTTATT
1 TTTTATT
93213 ATACTCTCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.25
12 21 0.75
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTTTAC
Found at i:100286 original size:32 final size:33
Alignment explanation
Indices: 100244--100309 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 33
100234 TAAGTTAATG
* * *
100244 AAATTCAATGATTTTATAA-AAATAGTTATAAAA
1 AAATTCAATGATATTAAAATAAATA-ATATAAAA
100277 AAATT-AATGATATTAAAATAAATAATATAAAA
1 AAATTCAATGATATTAAAATAAATAATATAAAA
100309 A
1 A
100310 TGCAATATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (33 bp):
AAATTCAATGATATTAAAATAAATAATATAAAA
Found at i:100387 original size:27 final size:27
Alignment explanation
Indices: 100333--100389 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
100323 TCATTTTATC
* *
100333 TATAAAAATATTTTAAAGACTATAAAA
1 TATAAAAATATATTAAAGACTAAAAAA
*
100360 TATAAAAATATATTAAA-ATTAAATAAA
1 TATAAAAATATATTAAAGACTAAA-AAA
100387 TAT
1 TAT
100390 TATATTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (27 bp):
TATAAAAATATATTAAAGACTAAAAAA
Found at i:100389 original size:17 final size:18
Alignment explanation
Indices: 100355--100391 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
100345 TTAAAGACTA
100355 TAAAATATAAAAATATAT
1 TAAAATATAAAAATATAT
100373 TAAAAT-TAAATAA-ATAT
1 TAAAATATAAA-AATATAT
100390 TA
1 TA
100392 TATTTTAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAATATAAAAATATAT
Found at i:100527 original size:21 final size:21
Alignment explanation
Indices: 100489--100528 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
100479 TTTGAGTTAC
* * *
100489 TTAAAACTTTTGTTATTTTTT
1 TTAAAACCTTTATGATTTTTT
100510 TTAAAACCTTTATGATTTT
1 TTAAAACCTTTATGATTTT
100529 CTATTGTGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (21 bp):
TTAAAACCTTTATGATTTTTT
Found at i:107597 original size:12 final size:12
Alignment explanation
Indices: 107580--107604 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
107570 TATCAACTTT
107580 TAATATTATTGA
1 TAATATTATTGA
107592 TAATATTATTGA
1 TAATATTATTGA
107604 T
1 T
107605 TGAGTTTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TAATATTATTGA
Found at i:110938 original size:22 final size:22
Alignment explanation
Indices: 110895--110939 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
110885 TCGTGGACCA
* *
110895 AAATCGTTGTTTTAATAAAACC
1 AAATCGTTGTATTAAAAAAACC
110917 AAATCGTT-TATTAAAAATAACC
1 AAATCGTTGTATTAAAAA-AACC
110939 A
1 A
110940 CTTTTCGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (22 bp):
AAATCGTTGTATTAAAAAAACC
Found at i:115409 original size:18 final size:19
Alignment explanation
Indices: 115381--115421 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
115371 TTCCATCTTC
*
115381 CTTTCTTCCTTTTCTTTTT
1 CTTTCTTCCTTTACTTTTT
*
115400 CTTT-TTCCTTTAGTTTTT
1 CTTTCTTCCTTTACTTTTT
115418 CTTT
1 CTTT
115422 ATAGTCAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.73
Consensus pattern (19 bp):
CTTTCTTCCTTTACTTTTT
Found at i:123751 original size:27 final size:27
Alignment explanation
Indices: 123721--123780 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
123711 CTCAATTCTA
*
123721 TGTAATCTGAGGTTTTATACTTGTAAC
1 TGTAAACTGAGGTTTTATACTTGTAAC
*
123748 TGTAAAGTGAGGTTTTATACTTGTAAC
1 TGTAAACTGAGGTTTTATACTTGTAAC
123775 TGTAAA
1 TGTAAA
123781 GAGCATTGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (27 bp):
TGTAAACTGAGGTTTTATACTTGTAAC
Found at i:123781 original size:27 final size:27
Alignment explanation
Indices: 123728--123781 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
123718 CTATGTAATC
123728 TGAGGTTTTATACTTGTAACTGTAAAG
1 TGAGGTTTTATACTTGTAACTGTAAAG
123755 TGAGGTTTTATACTTGTAACTGTAAAG
1 TGAGGTTTTATACTTGTAACTGTAAAG
123782 AGCATTGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (27 bp):
TGAGGTTTTATACTTGTAACTGTAAAG
Found at i:128871 original size:18 final size:19
Alignment explanation
Indices: 128833--128872 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
128823 CAAAAAAAAT
* *
128833 ATTCAAAATAATTTTTTAA
1 ATTCAAAATAATTTATAAA
128852 ATTCAAAAT-ATTTATAAA
1 ATTCAAAATAATTTATAAA
128870 ATT
1 ATT
128873 TTTAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTCAAAATAATTTATAAA
Found at i:134746 original size:9 final size:9
Alignment explanation
Indices: 134732--134766 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
134722 ACTAGTTTCA
134732 CAACCTTCT
1 CAACCTTCT
134741 CAACCTTCT
1 CAACCTTCT
134750 CAACCTTCT
1 CAACCTTCT
134759 CAACCTTC
1 CAACCTTC
134767 AACATCTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.23, C:0.46, G:0.00, T:0.31
Consensus pattern (9 bp):
CAACCTTCT
Found at i:142071 original size:19 final size:19
Alignment explanation
Indices: 142049--142086 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
142039 AATTTAATTT
*
142049 ATTAGTAATAAATTACTAA
1 ATTACTAATAAATTACTAA
*
142068 ATTACTAATAAGTTACTAA
1 ATTACTAATAAATTACTAA
142087 TAAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTACTAATAAATTACTAA
Found at i:142237 original size:22 final size:22
Alignment explanation
Indices: 142182--142268 Score: 129
Period size: 22 Copynumber: 3.7 Consensus size: 22
142172 ATATACCGAC
142182 ATTACAATATTCATACAAAATTATAA
1 ATTACAATATTCATAC-AAA--A-AA
142208 TATTACAATATTCATACAAAAAA
1 -ATTACAATATTCATACAAAAAA
142231 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
142253 ATTACAATATTCATAC
1 ATTACAATATTCATAC
142269 TAAATATAGA
Statistics
Matches: 60, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
22 38 0.63
23 2 0.03
24 1 0.02
26 3 0.05
27 16 0.27
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (22 bp):
ATTACAATATTCATACAAAAAA
Found at i:142348 original size:27 final size:27
Alignment explanation
Indices: 142316--142387 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
142306 AAAATATTGC
* * *
142316 AATTTTATATGAATATTGTAATTTTGT
1 AATTTTGTATGAATATTGTAATATTAT
142343 AATTTTGTATGAATATTGTAATATTAT
1 AATTTTGTATGAATATTGTAATATTAT
142370 AATTTTGTATGAATATTG
1 AATTTTGTATGAATATTG
142388 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (27 bp):
AATTTTGTATGAATATTGTAATATTAT
Found at i:142838 original size:18 final size:18
Alignment explanation
Indices: 142814--142849 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
142804 AAAAAAATAT
142814 AAAAAAAAATATTTTATTC
1 AAAAAAAAA-ATTTTATTC
142833 AAAAAAAAAATTTTATT
1 AAAAAAAAAATTTTATT
142850 ATTATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAAAAAAAATTTTATTC
Found at i:150792 original size:40 final size:40
Alignment explanation
Indices: 150748--150888 Score: 119
Period size: 40 Copynumber: 3.6 Consensus size: 40
150738 AAAACACACC
*
150748 AATTTGGCACCCAGTGCCTCATCGGATAATACGAAGTAAT
1 AATTTGACACCCAGTGCCTCATCGGATAATACGAAGTAAT
* * * *
150788 AATTTGAAACCCAGTGTCTCATCAGCTAA-ACCGAAGT-A-
1 AATTTGACACCCAGTGCCTCATCGGATAATA-CGAAGTAAT
* * * * *
150826 AA-TTGGCACCTAGTGCCTCATCGAATTAATCCGAAGTAGT
1 AATTTGACACCCAGTGCCTCATCGGA-TAATACGAAGTAAT
* * *
150866 AAATTGACACCTAGTGTCTCATC
1 AATTTGACACCCAGTGCCTCATC
150889 AACTCAAAGT
Statistics
Matches: 79, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
37 16 0.20
38 11 0.14
39 2 0.03
40 32 0.41
41 18 0.23
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (40 bp):
AATTTGACACCCAGTGCCTCATCGGATAATACGAAGTAAT
Found at i:178683 original size:33 final size:35
Alignment explanation
Indices: 178627--178692 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 35
178617 TATCTATTTC
*
178627 TAAATAATTATAAGTAATTTTGATTTTAATAATTAA
1 TAAATAATTATAAGTAATATTGA-TTTAATAATTAA
178663 TAAA-AATTA-AA-TAATATTGATTTAATAATT
1 TAAATAATTATAAGTAATATTGATTTAATAATT
178693 TTTAATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 10 0.34
33 8 0.28
34 2 0.07
35 5 0.17
36 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (35 bp):
TAAATAATTATAAGTAATATTGATTTAATAATTAA
Found at i:183538 original size:45 final size:45
Alignment explanation
Indices: 183466--183786 Score: 380
Period size: 45 Copynumber: 7.4 Consensus size: 45
183456 ATGTGCCGAC
* * *
183466 TACTATTACTGTTACTGGTTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGT
* *
183511 TACCGTTACTGTTACTGATTCGACACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGT
183556 TACTGTTACTGTTACTGATTC-AGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACTGATTCGA-CACTTTGTGTGTCGAATACTGT
183601 TACTGTTACTGTTACTGATTC-AGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACTGATTCGA-CACTTTGTGTGTCGAATACTGT
* *
183646 TATTGTTACTGTTACCGATTCGACAC--TGTGTGTC-AA-AC---
1 TACTGTTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGT
* * * * *
183684 --C-GTTACTATTACCGATTCGGCACTTTGTGTGTCAAATACAGT
1 TACTGTTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGT
* * * *
183726 TACTGTTACTGTTACAGATTC-AGTACTTTGTGTGTTGAACACTGT
1 TACTGTTACTGTTACTGATTCGA-CACTTTGTGTGTCGAATACTGT
183771 TACTGTTACTGTTACT
1 TACTGTTACTGTTACT
183787 ACTACCGTTA
Statistics
Matches: 242, Mismatches: 21, Indels: 26
0.84 0.07 0.09
Matches are distributed among these distances:
35 20 0.08
37 8 0.03
38 2 0.01
39 2 0.01
41 2 0.01
42 2 0.01
43 8 0.03
44 2 0.01
45 195 0.81
46 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (45 bp):
TACTGTTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGT
Found at i:183696 original size:35 final size:36
Alignment explanation
Indices: 183650--183719 Score: 106
Period size: 35 Copynumber: 1.9 Consensus size: 36
183640 TACTGTTATT
*
183650 GTTACTGTTACCGATTCGACAC-TGTGTGTCAAACC
1 GTTACTATTACCGATTCGACACTTGTGTGTCAAACC
*
183685 GTTACTATTACCGATTCGGCACTTTGTGTGTCAAA
1 GTTACTATTACCGATTCGACAC-TTGTGTGTCAAA
183720 TACAGTTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 20 0.65
37 11 0.35
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (36 bp):
GTTACTATTACCGATTCGACACTTGTGTGTCAAACC
Found at i:186737 original size:25 final size:25
Alignment explanation
Indices: 186651--186765 Score: 81
Period size: 25 Copynumber: 4.6 Consensus size: 25
186641 GTACATGTAT
* *
186651 GCTCATACGAGCTGTA-AACGGTAA
1 GCTCATACGAGCTGAATAACAGTAA
* * *
186675 GCTCTTCCTAGCTGAATAACAGTAA
1 GCTCATACGAGCTGAATAACAGTAA
* * * *
186700 ACTTC-TCCAAGCTAAATAACAGTAA
1 GC-TCATACGAGCTGAATAACAGTAA
* * *
186725 GCTCATACGAGCTGAGTATCGGTAA
1 GCTCATACGAGCTGAATAACAGTAA
* *
186750 GCTCATAAGAGTTGAA
1 GCTCATACGAGCTGAA
186766 ATCGGTAACT
Statistics
Matches: 70, Mismatches: 18, Indels: 5
0.75 0.19 0.05
Matches are distributed among these distances:
24 14 0.20
25 54 0.77
26 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACAGTAA
Found at i:191031 original size:18 final size:20
Alignment explanation
Indices: 191005--191048 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 20
190995 ATGAATGTGA
*
191005 ATTTTTTATATA-TATTT-T
1 ATTTCTTATATACTATTTAT
191023 ATTTCTTATATACGTATTTAT
1 ATTTCTTATATAC-TATTTAT
191044 ATTTC
1 ATTTC
191049 AATGTTACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
20 5 0.23
21 6 0.27
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTTCTTATATACTATTTAT
Found at i:191681 original size:10 final size:10
Alignment explanation
Indices: 191666--191695 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
191656 TCTAATTATA
*
191666 TTTTTTTGCC
1 TTTTTTGGCC
191676 TTTTTTGGCC
1 TTTTTTGGCC
191686 TTTTTTGGCC
1 TTTTTTGGCC
191696 ACCAGCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.17, T:0.63
Consensus pattern (10 bp):
TTTTTTGGCC
Found at i:198414 original size:22 final size:22
Alignment explanation
Indices: 198384--198446 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
198374 AGATCAAATT
* *
198384 TTAATAAAATTATATTTAGTGC
1 TTAAAAAAATTATATTTAATGC
* *
198406 TTAAAAAAATGATCATTTAATGT
1 TTAAAAAAATTAT-ATTTAATGC
*
198429 TTAACAAAATTAATATTT
1 TTAAAAAAATT-ATATTT
198447 TTATTGCTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 11 0.33
23 20 0.61
24 2 0.06
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (22 bp):
TTAAAAAAATTATATTTAATGC
Found at i:199763 original size:20 final size:20
Alignment explanation
Indices: 199738--199777 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
199728 AATATTTTCC
*
199738 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
199758 AGTAAAACATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
199778 TCATTTTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:199779 original size:34 final size:35
Alignment explanation
Indices: 199726--199792 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
199716 CAAACACCAG
* *
199726 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTACAGTAAATCATTTTACAGAAAAGT
*
199761 AAAACATTTTACAG-AAATCATTTTACGGAAAA
1 AAAACATTTTACAGTAAATCATTTTACAGAAAA
199793 ATATTTTACT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTACAGTAAATCATTTTACAGAAAAGT
Found at i:201546 original size:14 final size:14
Alignment explanation
Indices: 201523--201566 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
201513 TAATTAAGCT
201523 TAAGGTTAATAATA
1 TAAGGTTAATAATA
* *
201537 TAAGGGTAATAACA
1 TAAGGTTAATAATA
*
201551 TAA-TTTAATAATA
1 TAAGGTTAATAATA
201564 TAA
1 TAA
201567 AAAAATATGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.34
Consensus pattern (14 bp):
TAAGGTTAATAATA
Found at i:203538 original size:127 final size:126
Alignment explanation
Indices: 203305--203557 Score: 479
Period size: 127 Copynumber: 2.0 Consensus size: 126
203295 ATTTTTGGGG
203305 GCGTATAGATACCTGGGCTCCGGGAGGGGAAAAATTACCAACTTGGCTCTTAGCCCAAGTGTTAT
1 GCGTATAGATACCTGGGCTCCGGGAGGGGAAAAATTACCAACTTGGCTCTTAGCCCAAGTGTTAT
* *
203370 ATTTGGTTATTTACTAAAATCGCCCTTTGGAGGCGAAGGGTGGATTGTTAGTGTGGACGAT
66 ATTTGGTTATTCACAAAAATCGCCCTTTGGAGGCGAAGGGTGGATTGTTAGTGTGGACGAT
203431 GCGTATACGATACCTGGGCTCCGGGAGGGGAAAAATTACCAACTTGGCTCTTAGCCCAAGTGTTA
1 GCGTATA-GATACCTGGGCTCCGGGAGGGGAAAAATTACCAACTTGGCTCTTAGCCCAAGTGTTA
203496 TATTTGGTTATTCACAAAAATCGCCCTTTGGAGGCGAAGGGTGGATTGTTAGTGTGGACGAT
65 TATTTGGTTATTCACAAAAATCGCCCTTTGGAGGCGAAGGGTGGATTGTTAGTGTGGACGAT
203558 TTGGAAGATA
Statistics
Matches: 124, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
126 7 0.06
127 117 0.94
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.28
Consensus pattern (126 bp):
GCGTATAGATACCTGGGCTCCGGGAGGGGAAAAATTACCAACTTGGCTCTTAGCCCAAGTGTTAT
ATTTGGTTATTCACAAAAATCGCCCTTTGGAGGCGAAGGGTGGATTGTTAGTGTGGACGAT
Found at i:214341 original size:18 final size:18
Alignment explanation
Indices: 214318--214352 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
214308 AAAATAAAAA
214318 AAAATTGTATAAAAATTG
1 AAAATTGTATAAAAATTG
* *
214336 AAAATTTTATTAAAATT
1 AAAATTGTATAAAAATT
214353 TTCAAAAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
AAAATTGTATAAAAATTG
Found at i:226150 original size:23 final size:23
Alignment explanation
Indices: 226099--226151 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
226089 AAAAAATAAC
*
226099 TCATAAAAATATAATTTAATGTT
1 TCATAAAAATATAATTTAATATT
*
226122 TACATAAAAA-ATATTTTAATAATT
1 T-CATAAAAATATAATTTAAT-ATT
226146 TCATAA
1 TCATAA
226152 TTGAATTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (23 bp):
TCATAAAAATATAATTTAATATT
Found at i:229722 original size:11 final size:10
Alignment explanation
Indices: 229684--229731 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
229674 CCGTTTATTA
229684 TATATATTTTT
1 TATA-ATTTTT
229695 TA-AA-TTTT
1 TATAATTTTT
229703 TATAATTTTT
1 TATAATTTTT
*
229713 TGTAACTTTTT
1 TATAA-TTTTT
229724 TATAATTT
1 TATAATTT
229732 AAGACTTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
8 6 0.19
9 3 0.09
10 12 0.38
11 11 0.34
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (10 bp):
TATAATTTTT
Found at i:233830 original size:17 final size:18
Alignment explanation
Indices: 233803--233836 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
233793 TAATTACATC
233803 TTTTTCATTTTTCGTTTT
1 TTTTTCATTTTTCGTTTT
*
233821 TTTTTC-TTTTTGGTTT
1 TTTTTCATTTTTCGTTT
233837 AGCCAAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.03, C:0.09, G:0.09, T:0.79
Consensus pattern (18 bp):
TTTTTCATTTTTCGTTTT
Found at i:235058 original size:97 final size:98
Alignment explanation
Indices: 234942--235147 Score: 389
Period size: 97 Copynumber: 2.1 Consensus size: 98
234932 TTGAAACTTT
234942 AATTTTGATTTAATTATACACATTTAAAAAAATAAATACATCAATTTATTTTAATATTGGATAAA
1 AATTTTGA-TTAATTATACACATTTAAAAAAATAAATACATCAATTTATTTTAATATTGGATAAA
235007 TATAATTATTTATGTATGAAACATATAAACAT-A
65 TATAATTATTTATGTATGAAACATATAAACATAA
235040 AATTTTGATTAATTATACACATTTAAAAAAATAAATACATCAATTTATTTTAATATTGGATAAAT
1 AATTTTGATTAATTATACACATTTAAAAAAATAAATACATCAATTTATTTTAATATTGGATAAAT
235105 ATAATTATTTATGTATGAAACATATAAACATAA
66 ATAATTATTTATGTATGAAACATATAAACATAA
235138 AATTTT-ATTA
1 AATTTTGATTA
235148 TATCAATAAT
Statistics
Matches: 107, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
97 92 0.86
98 15 0.14
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (98 bp):
AATTTTGATTAATTATACACATTTAAAAAAATAAATACATCAATTTATTTTAATATTGGATAAAT
ATAATTATTTATGTATGAAACATATAAACATAA
Found at i:235785 original size:69 final size:68
Alignment explanation
Indices: 235707--235912 Score: 277
Period size: 69 Copynumber: 3.0 Consensus size: 68
235697 AATGTATTTA
*
235707 TGTTTAAGAATCTAACGTCACTTGAGTTTTTAGATCTCTCTCACAATAAATTTTCTGGAGATATA
1 TGTTTAAGAATCTAACGTCACTCGAGTTTTTAGATCTCTCTC-CAATAAATTTTCTGGAGATATA
235772 TCTG
65 TCTG
* * * * * * * *
235776 TGTTCAAGAATCTAACCTCACTCAAGTATTTAGATCTCTTTTCCAATAATTTTTTTGGAAATATA
1 TGTTTAAGAATCTAACGTCACTCGAGTTTTTAGATCTC-TCTCCAATAAATTTTCTGGAGATATA
*
235841 TATG
65 TCTG
* *
235845 TGTTTAAGAATCTAAGGTCACTCGAGTTTTTAGATCTCTCGTCCAATAAGTTTTCTGGAGATATA
1 TGTTTAAGAATCTAACGTCACTCGAGTTTTTAGATCTCTC-TCCAATAAATTTTCTGGAGATATA
235910 TCT
65 TCT
235913 CATTTTAGAA
Statistics
Matches: 115, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
68 1 0.01
69 111 0.97
70 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (68 bp):
TGTTTAAGAATCTAACGTCACTCGAGTTTTTAGATCTCTCTCCAATAAATTTTCTGGAGATATAT
CTG
Found at i:238359 original size:47 final size:47
Alignment explanation
Indices: 238308--238429 Score: 181
Period size: 47 Copynumber: 2.6 Consensus size: 47
238298 TATAAATTCC
* * * *
238308 TCAAATATTTAAAACAAGTTATATATAACAATTCCAATAACATCGGT
1 TCAAATATATAAGACAATTTATATATAACAATTCCAATAACATCAGT
* * *
238355 TCAAATATATAAGACAATTTATATACAACAATTCTAATAATATCAGT
1 TCAAATATATAAGACAATTTATATATAACAATTCCAATAACATCAGT
238402 TCAAATATATAAGACAATTTATATATAA
1 TCAAATATATAAGACAATTTATATATAA
238430 GGTTCGAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 67 1.00
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (47 bp):
TCAAATATATAAGACAATTTATATATAACAATTCCAATAACATCAGT
Found at i:241218 original size:69 final size:68
Alignment explanation
Indices: 241018--241202 Score: 201
Period size: 68 Copynumber: 2.7 Consensus size: 68
241008 ACTCACATTC
* * * * * *
241018 CTCGAGCATTTAGATATTTCTTTTAATAGATTTTTTAGAAATATATCTGTGTTTAAAAATCTAAT
1 CTCGAGTATTTAGATATTTCTTCT-ATAAATTTTTTGGAAATATATCTATATTTAAAAATCTAAT
241083 AACA
65 AACA
* * * * * * *
241087 C-CCAGTATTTAGATTTTTCTTACAATAACTTTCTTGAAAATATATCTATATTTAATAATCTAAT
1 CTCGAGTATTTAGATATTTCTT-CTATAAATTTTTTGGAAATATATCTATATTTAAAAATCTAAT
*
241151 ATCA
65 AACA
*
241155 CTCGAGTATTTAGATATTTCTTCCTATAAATTTTTTGGAGATATATCT
1 CTCGAGTATTTAGATATTTCTT-CTATAAATTTTTTGGAAATATATCT
241203 CTTCTTAAGA
Statistics
Matches: 92, Mismatches: 22, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
68 53 0.58
69 39 0.42
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (68 bp):
CTCGAGTATTTAGATATTTCTTCTATAAATTTTTTGGAAATATATCTATATTTAAAAATCTAATA
ACA
Found at i:247908 original size:47 final size:47
Alignment explanation
Indices: 247811--247901 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
247801 ATTTAATATA
* *
247811 AATTCCAACAACATCAGTTCAAATATTTGAGACAATTTATATATAGC
1 AATTCCAACAACATCAGTTCAAATATATAAGACAATTTATATATAGC
*
247858 AATTCCAATAACATCAGTTCAAATATATAAGACAATTTATATAT
1 AATTCCAACAACATCAGTTCAAATATATAAGACAATTTATATAT
247902 TACAATTTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (47 bp):
AATTCCAACAACATCAGTTCAAATATATAAGACAATTTATATATAGC
Found at i:247995 original size:13 final size:13
Alignment explanation
Indices: 247977--248023 Score: 85
Period size: 13 Copynumber: 3.6 Consensus size: 13
247967 TTCTTCATTG
247977 CTTTTGAGAAGTA
1 CTTTTGAGAAGTA
*
247990 CTTTTGAGAAGTG
1 CTTTTGAGAAGTA
248003 CTTTTGAGAAGTA
1 CTTTTGAGAAGTA
248016 CTTTTGAG
1 CTTTTGAG
248024 TGTTTGACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.40
Consensus pattern (13 bp):
CTTTTGAGAAGTA
Found at i:248265 original size:20 final size:19
Alignment explanation
Indices: 248240--248286 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
248230 ATTAATTATT
248240 TATAAAATTTAATTAGAATA
1 TATAAAATTTAATTA-AATA
* * *
248260 TATAAACTATATTTAAATA
1 TATAAAATTTAATTAAATA
248279 TA-AAAATT
1 TATAAAATT
248287 AAATATTTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 12 0.55
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TATAAAATTTAATTAAATA
Found at i:249649 original size:58 final size:58
Alignment explanation
Indices: 249585--249859 Score: 541
Period size: 58 Copynumber: 4.7 Consensus size: 58
249575 TGCATCCAAA
249585 AGACATGCCAAGTTCATTGTCAAAATATAGCAGAATCCAGTAGTAATCTAAATTCAAC
1 AGACATGCCAAGTTCATTGTCAAAATATAGCAGAATCCAGTAGTAATCTAAATTCAAC
249643 AGACATGCCAAGTTCATTGTCAAAATATAGCAGAATCCAGTAGTAATCTAAATTCAAC
1 AGACATGCCAAGTTCATTGTCAAAATATAGCAGAATCCAGTAGTAATCTAAATTCAAC
249701 AGACATGCCAAGTTCATTGTCAAAATATAGCAGAATCCAGTAGTAATCTAAATTCAAC
1 AGACATGCCAAGTTCATTGTCAAAATATAGCAGAATCCAGTAGTAATCTAAATTCAAC
249759 AGACATGCCAAGTTCATTGTCAAAATATAGCAGAATCCAGTAGTAATCTAAATTCAAC
1 AGACATGCCAAGTTCATTGTCAAAATATAGCAGAATCCAGTAGTAATCTAAATTCAAC
*
249817 AGACATGCCAAGTTCATTGTCAAAATATAGCAGAATCTAGTAG
1 AGACATGCCAAGTTCATTGTCAAAATATAGCAGAATCCAGTAG
249860 CAAAACTTAA
Statistics
Matches: 216, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 216 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (58 bp):
AGACATGCCAAGTTCATTGTCAAAATATAGCAGAATCCAGTAGTAATCTAAATTCAAC
Found at i:258645 original size:23 final size:22
Alignment explanation
Indices: 258578--258663 Score: 97
Period size: 21 Copynumber: 4.0 Consensus size: 22
258568 CCTGATCAGT
*
258578 ATACGACACA-TAAGTGCCTGA
1 ATACGACACACGAAGTGCCTGA
258599 A-ACGACACACGAAGTGCCTG-
1 ATACGACACACGAAGTGCCTGA
* *
258619 ATACGGCACACGAGGTGCCTGA
1 ATACGACACACGAAGTGCCTGA
**
258641 TATACGACACATAAAGTGCCTGA
1 -ATACGACACACGAAGTGCCTGA
258664 TCGGCAAGGC
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
20 9 0.17
21 27 0.50
23 18 0.33
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (22 bp):
ATACGACACACGAAGTGCCTGA
Found at i:258984 original size:3 final size:3
Alignment explanation
Indices: 258976--259031 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
258966 TAATTCTCAC
258976 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
259024 TAA TAA TA
1 TAA TAA TA
259032 CTTACCTCAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:259701 original size:16 final size:17
Alignment explanation
Indices: 259674--259706 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
259664 TTGTTTATTA
259674 TTTAATAGATATAATAT
1 TTTAATAGATATAATAT
259691 TTTAATA-ATATAATAT
1 TTTAATAGATATAATAT
259707 AATAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATAGATATAATAT
Found at i:259712 original size:16 final size:17
Alignment explanation
Indices: 259676--259713 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
259666 GTTTATTATT
**
259676 TAATAGATATAATATTT
1 TAATAGATATAATATAA
259693 TAATA-ATATAATATAA
1 TAATAGATATAATATAA
259709 TAATA
1 TAATA
259714 TTTTATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TAATAGATATAATATAA
Found at i:259852 original size:15 final size:15
Alignment explanation
Indices: 259832--259869 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
259822 ATTTCACAAT
259832 ATAATAATAATATTA
1 ATAATAATAATATTA
* *
259847 ATAATATTATTATTA
1 ATAATAATAATATTA
259862 ATAATAAT
1 ATAATAAT
259870 TTAATAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATAATAATATTA
Found at i:259883 original size:12 final size:12
Alignment explanation
Indices: 259829--259882 Score: 60
Period size: 11 Copynumber: 4.5 Consensus size: 12
259819 TTTATTTCAC
259829 AATA-TAATAAT
1 AATATTAATAAT
259840 AATATTAATAAT
1 AATATTAATAAT
259852 ATTATTATTAATAAT
1 A--A-TATTAATAAT
259867 AAT-TTAATAAT
1 AATATTAATAAT
259878 -ATATT
1 AATATT
259883 TTTACACATA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
10 2 0.05
11 14 0.37
12 9 0.24
13 1 0.03
14 1 0.03
15 11 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AATATTAATAAT
Found at i:274062 original size:55 final size:54
Alignment explanation
Indices: 273978--274084 Score: 171
Period size: 55 Copynumber: 2.0 Consensus size: 54
273968 AAAGGTTGAA
* *
273978 GGCTAAATTTGTTATTATGCCTTATATATATAGAACACC-AAATAAGCAATTAAAG
1 GGCTAAACTTGTTATTATGCC-T-TATATATAGAACACCAAAATAAACAATTAAAG
274033 GGCTAAACTTGTTATTATGCCTTATATATAGAACACCAAAATAAACAATTAA
1 GGCTAAACTTGTTATTATGCCTTATATATAGAACACCAAAATAAACAATTAA
274085 CATTATTTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
53 15 0.31
54 14 0.29
55 20 0.41
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (54 bp):
GGCTAAACTTGTTATTATGCCTTATATATAGAACACCAAAATAAACAATTAAAG
Found at i:274454 original size:69 final size:69
Alignment explanation
Indices: 274347--274502 Score: 197
Period size: 69 Copynumber: 2.3 Consensus size: 69
274337 ATCCCTCAAG
* * * *
274347 TATTTAAATATCTCTTCCAATATTTTTTCTAAAAATATATCTATGTTTAAGAATTTAACATCACT
1 TATTTAGATATCTCTTCCAACATTTTTTCTAAAAATATATCTATGCTTAAAAATTTAACATCACT
*
274412 CGAC
66 AGAC
* * * *
274416 TATTTAGATATCTCTTTCAACAGTTTTTT-TGAAGATATATCTGTGCTTAAAAATTTAACATCAC
1 TATTTAGATATCTCTTCCAACA-TTTTTTCTAAAAATATATCTATGCTTAAAAATTTAACATCAC
*
274480 TAGAG
65 TAGAC
*
274485 TATTTAGATCTCTCTTCC
1 TATTTAGATATCTCTTCC
274503 GATAAGTTTT
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
69 68 0.92
70 6 0.08
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.44
Consensus pattern (69 bp):
TATTTAGATATCTCTTCCAACATTTTTTCTAAAAATATATCTATGCTTAAAAATTTAACATCACT
AGAC
Found at i:274523 original size:69 final size:68
Alignment explanation
Indices: 274345--274526 Score: 195
Period size: 69 Copynumber: 2.6 Consensus size: 68
274335 ACATCCCTCA
* ** * * *
274345 AGTATTTAAATATCTCTTCCAATATTTTTTCTAAAAATATATCTATGTTTAAGAATTTAACATCA
1 AGTATTTAGATATCTCTTCC-ATAAGTTTTCTAGAAATATATCTATGCTTAAAAATTTAACATCA
*
274410 CTCG
65 CTAG
* * * * *
274414 ACTATTTAGATATCTCTTTCA-ACAGTTTTTTTGAAGATATATCTGTGCTTAAAAATTTAACATC
1 AGTATTTAGATATCTCTTCCATA-AGTTTTCTAGAA-ATATATCTATGCTTAAAAATTTAACATC
274478 ACTAG
64 ACTAG
* *
274483 AGTATTTAGATCTCTCTTCCGATAAGTTTTCTGGAAATATATCT
1 AGTATTTAGATATCTCTTCC-ATAAGTTTTCTAGAAATATATCT
274527 CAAGAGTCTA
Statistics
Matches: 92, Mismatches: 17, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
67 1 0.01
68 8 0.09
69 71 0.77
70 11 0.12
71 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (68 bp):
AGTATTTAGATATCTCTTCCATAAGTTTTCTAGAAATATATCTATGCTTAAAAATTTAACATCAC
TAG
Found at i:277284 original size:51 final size:51
Alignment explanation
Indices: 277193--277314 Score: 145
Period size: 51 Copynumber: 2.4 Consensus size: 51
277183 TAATTAACTC
* * * * *
277193 AGATGACGTATAACTAGAAATAGAAGAACCCCTAAGTAACCCGGATGGAGT
1 AGATGACGTATGACCAGAAGTAGAAAAACCCCTAACTAACCCGGATGGAGT
***
277244 AGATGACGTATGACCAGAAGTAGAAAAACTTTTAACTAACCCGGATGGAGT
1 AGATGACGTATGACCAGAAGTAGAAAAACCCCTAACTAACCCGGATGGAGT
* **
277295 AGAGGATATATGACCAGAAG
1 AGATGACGTATGACCAGAAG
277315 AAATAGTACA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.19
Consensus pattern (51 bp):
AGATGACGTATGACCAGAAGTAGAAAAACCCCTAACTAACCCGGATGGAGT
Found at i:279823 original size:513 final size:513
Alignment explanation
Indices: 278856--279884 Score: 2013
Period size: 513 Copynumber: 2.0 Consensus size: 513
278846 AATTTTCATC
278856 AAACCTGTGATAACAGGTCTGAACCATATGTCTAATCTCTCTATATAACTGACATTGTAGTCTAG
1 AAACCTGTGATAACAGGTCTGAACCATATGTCTAATCTCTCTATATAACTGACATTGTAGTCTAG
278921 AATGTGACCAACTCCGACCATTCTCACGAGCTCTGCCACGAGACCAGCCACGACCTTACCCTCTG
66 AATGTGACCAACTCCGACCATTCTCACGAGCTCTGCCACGAGACCAGCCACGACCTTACCCTCTG
278986 TAGCCTTGTTTATGTTCTTGAGAATATCGATTTGACTCAGCAGATTGTTTCGAACTATTTCCAGT
131 TAGCCTTGTTTATGTTCTTGAGAATATCGATTTGACTCAGCAGATTGTTTCGAACTATTTCCAGT
279051 GTCTTGTTGATGAGAAGCCAAATTGGCTTGACAAGGAACTTCTGTCAATAGATCCAGTTGTCGTG
196 GTCTTGTTGATGAGAAGCCAAATTGGCTTGACAAGGAACTTCTGTCAATAGATCCAGTTGTCGTG
** *
279116 CTTCACAATCAAGCAACATTTCAGTCAACAAATCAAGAGATAAAGGAGTTGCATAGGCAAATATC
261 CTTCACAATCAAGCAACATTTCAGTCAACAAATCAAGAGATAAAAAAGGTGCATAGGCAAATATC
279181 CGAATAGACTCAAATTTGATCGAAAGACCAGCCAAGATAACACTTACTTGCTCTTGTTTAGAGAC
326 CGAATAGACTCAAATTTGATCGAAAGACCAGCCAAGATAACACTTACTTGCTCTTGTTTAGAGAC
279246 AAAACTACCAGCAGTAGTTAGGCTATCACTAAGATACTTTACCTTAGATTTATACTCATTGATTG
391 AAAACTACCAGCAGTAGTTAGGCTATCACTAAGATACTTTACCTTAGATTTATACTCATTGATTG
279311 TAAGATTTGCTTTCTTGAGCGAATATAGGGCATGACGCATACTTGAGATCTTGATATT
456 TAAGATTTGCTTTCTTGAGCGAATATAGGGCATGACGCATACTTGAGATCTTGATATT
279369 AAACCTGTGATAACAGGTCTGAACCATATGTCTAATCTCTCTATATAACTGACATTGTAGTCTAG
1 AAACCTGTGATAACAGGTCTGAACCATATGTCTAATCTCTCTATATAACTGACATTGTAGTCTAG
279434 AATGTGACCAACTCCGACCATTCTCACGAGCTCTGCCACGAGACCAGCCACGACCTTACCCTCTG
66 AATGTGACCAACTCCGACCATTCTCACGAGCTCTGCCACGAGACCAGCCACGACCTTACCCTCTG
279499 TAGCCTTGTTTATGTTCTTGAGAATATCGATTTGACTCAGCAGATTGTTTCGAACTATTTCCAGT
131 TAGCCTTGTTTATGTTCTTGAGAATATCGATTTGACTCAGCAGATTGTTTCGAACTATTTCCAGT
279564 GTCTTGTTGATGAGAAGCCAAATTGGCTTGACAAGGAACTTCTGTCAATAGATCCAGTTGTCGTG
196 GTCTTGTTGATGAGAAGCCAAATTGGCTTGACAAGGAACTTCTGTCAATAGATCCAGTTGTCGTG
*
279629 CTTCACAATCAAGCAACATTTCAGTCAACAAATCAAGAGATAAAAAAGGTGTATAGGCAAATATC
261 CTTCACAATCAAGCAACATTTCAGTCAACAAATCAAGAGATAAAAAAGGTGCATAGGCAAATATC
279694 CGAATAGACTCAAATTTGATCGAAAGACCAGCCAAGATAACACTTACTTGCTCTTGTTTAGAGAC
326 CGAATAGACTCAAATTTGATCGAAAGACCAGCCAAGATAACACTTACTTGCTCTTGTTTAGAGAC
279759 AAAACTACCAGCAGTAGTTAGGCTATCACTAAGATACTTTACCTTAGATTTATACTCATTGATTG
391 AAAACTACCAGCAGTAGTTAGGCTATCACTAAGATACTTTACCTTAGATTTATACTCATTGATTG
*
279824 TAAGATTTGCTTTCTTGAGCGAGTATAGGGCATGACGCATACTTGAGATCTTGATATT
456 TAAGATTTGCTTTCTTGAGCGAATATAGGGCATGACGCATACTTGAGATCTTGATATT
279882 AAA
1 AAA
279885 TTTGGCACTG
Statistics
Matches: 511, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
513 511 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (513 bp):
AAACCTGTGATAACAGGTCTGAACCATATGTCTAATCTCTCTATATAACTGACATTGTAGTCTAG
AATGTGACCAACTCCGACCATTCTCACGAGCTCTGCCACGAGACCAGCCACGACCTTACCCTCTG
TAGCCTTGTTTATGTTCTTGAGAATATCGATTTGACTCAGCAGATTGTTTCGAACTATTTCCAGT
GTCTTGTTGATGAGAAGCCAAATTGGCTTGACAAGGAACTTCTGTCAATAGATCCAGTTGTCGTG
CTTCACAATCAAGCAACATTTCAGTCAACAAATCAAGAGATAAAAAAGGTGCATAGGCAAATATC
CGAATAGACTCAAATTTGATCGAAAGACCAGCCAAGATAACACTTACTTGCTCTTGTTTAGAGAC
AAAACTACCAGCAGTAGTTAGGCTATCACTAAGATACTTTACCTTAGATTTATACTCATTGATTG
TAAGATTTGCTTTCTTGAGCGAATATAGGGCATGACGCATACTTGAGATCTTGATATT
Found at i:282242 original size:16 final size:17
Alignment explanation
Indices: 282223--282256 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
282213 TTGTTTTAAA
282223 TTATTTTTATTT-TATT
1 TTATTTTTATTTGTATT
282239 TTATTTTTATTTGTATT
1 TTATTTTTATTTGTATT
282256 T
1 T
282257 GTATATAAGA
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:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (17 bp):
TTATTTTTATTTGTATT
Found at i:282980 original size:22 final size:22
Alignment explanation
Indices: 282968--283010 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
282958 TCTCTCTATT
282968 TTGCTACCATTTTACTATTATG
1 TTGCTACCATTTTACTATTATG
* *
282990 TTGCTACTATTTTAATATTAT
1 TTGCTACCATTTTACTATTAT
283011 TGTTTGAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.14, G:0.07, T:0.53
Consensus pattern (22 bp):
TTGCTACCATTTTACTATTATG
Found at i:283051 original size:12 final size:11
Alignment explanation
Indices: 283032--283062 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
283022 TTTATAAAAC
283032 TTATTTTATTA
1 TTATTTTATTA
283043 TTAATTTTATTA
1 TT-ATTTTATTA
283055 TTATTTTA
1 TTATTTTA
283063 AAGACATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:286702 original size:16 final size:16
Alignment explanation
Indices: 286681--286714 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
286671 AATTTAATCT
286681 TTTTAAAAATTATAAA
1 TTTTAAAAATTATAAA
*
286697 TTTTAAAAATTTTAAA
1 TTTTAAAAATTATAAA
286713 TT
1 TT
286715 AAAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTAAAAATTATAAA
Found at i:286728 original size:89 final size:90
Alignment explanation
Indices: 286607--286781 Score: 246
Period size: 89 Copynumber: 2.0 Consensus size: 90
286597 CTTTTAAAAT
* *
286607 TTTTTAAAATTTTAAATTAATAAAAATAAAATTACATTCCGGTC-TCCTAAAATAATAAAAATTT
1 TTTTAAAAATTTTAAATTAATAAAAATAAAATTACATT-CGGACATCCTAAAATAATAAAAATTT
* *
286671 AATTTAATCTTTTTAAAAATTATAAA
65 AATTTAATCATTTAAAAAATTATAAA
** * * *
286697 TTTTAAAAATTTTAAATTAA-AAAAATAAAATTACATTTTGACATCTTAAAATGATAAAATTTTA
1 TTTTAAAAATTTTAAATTAATAAAAATAAAATTACATTCGGACATCCTAAAATAATAAAAATTTA
286761 ATTTAATCATTTAAAAAATTA
66 ATTTAATCATTTAAAAAATTA
286782 CATTTTCGAT
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
88 2 0.03
89 54 0.72
90 19 0.25
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.41
Consensus pattern (90 bp):
TTTTAAAAATTTTAAATTAATAAAAATAAAATTACATTCGGACATCCTAAAATAATAAAAATTTA
ATTTAATCATTTAAAAAATTATAAA
Found at i:287551 original size:69 final size:69
Alignment explanation
Indices: 287440--287621 Score: 224
Period size: 69 Copynumber: 2.6 Consensus size: 69
287430 ACATCCCTCA
* * * * * *
287440 AGTATTTAGATATCTCTTCCAATAATTTTTCTGGAAATATATCTGTGTTTAAGAATCTAACA-TT
1 AGTATTTAGATATCTCTTCCAATAATTTTTTTGGAGATATATCTATGCTTAAAAATCTAA-AGTC
287504 ACTCG
65 ACTCG
* * * *
287509 AGTATTTAGATATCTCTTCCAACAGTTTTTTTGGAGATATATCTATGCTTAAAAATTTAAAGTCG
1 AGTATTTAGATATCTCTTCCAATAATTTTTTTGGAGATATATCTATGCTTAAAAATCTAAAGTCA
287574 CTCG
66 CTCG
* *
287578 AGTATTTAGATCTC-CGTTCCAATAAATTTTTTGGAGATATATCT
1 AGTATTTAGATATCTC-TTCCAATAATTTTTTTGGAGATATATCT
287622 TATTTTATGA
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
68 2 0.02
69 95 0.98
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (69 bp):
AGTATTTAGATATCTCTTCCAATAATTTTTTTGGAGATATATCTATGCTTAAAAATCTAAAGTCA
CTCG
Found at i:300061 original size:14 final size:14
Alignment explanation
Indices: 300036--300071 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
300026 TTTCAACGTT
*
300036 CAAGCACCCTAAAC
1 CAAGCCCCCTAAAC
*
300050 CGAGCCCCCTAAAC
1 CAAGCCCCCTAAAC
300064 CAAGCCCC
1 CAAGCCCC
300072 GGATTGCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.33, C:0.50, G:0.11, T:0.06
Consensus pattern (14 bp):
CAAGCCCCCTAAAC
Found at i:304682 original size:10 final size:10
Alignment explanation
Indices: 304656--304710 Score: 60
Period size: 9 Copynumber: 5.5 Consensus size: 10
304646 GATCAAAATA
304656 TAAAACTTTATT
1 TAAAA-TTTA-T
304668 TAAAATTTAT
1 TAAAATTTAT
304678 TAAAA-TTAT
1 TAAAATTTAT
*
304687 TAAAATTTGT
1 TAAAATTTAT
*
304697 GAAAA-TTAT
1 TAAAATTTAT
304706 TAAAA
1 TAAAA
304711 AAATTGTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
9 16 0.42
10 13 0.34
11 4 0.11
12 5 0.13
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (10 bp):
TAAAATTTAT
Found at i:304689 original size:19 final size:19
Alignment explanation
Indices: 304667--304710 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
304657 AAAACTTTAT
*
304667 TTAAAATTTATTAAAATTA
1 TTAAAATTTATGAAAATTA
*
304686 TTAAAATTTGTGAAAATTA
1 TTAAAATTTATGAAAATTA
304705 TTAAAA
1 TTAAAA
304711 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
TTAAAATTTATGAAAATTA
Found at i:304717 original size:21 final size:19
Alignment explanation
Indices: 304679--304741 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 19
304669 AAAATTTATT
*
304679 AAAATTATTAAAATTTGTG
1 AAAATTATTAAAAATTGTG
*
304698 AAAATTATTAAAAAAATTGTA
1 AAAATTATT--AAAAATTGTG
*
304719 AAAATATATTTGAAAATTGTG
1 AAAAT-TA-TTAAAAATTGTG
304740 AA
1 AA
304742 CCGATGGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 9 0.25
21 23 0.64
22 2 0.06
23 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (19 bp):
AAAATTATTAAAAATTGTG
Found at i:305013 original size:21 final size:21
Alignment explanation
Indices: 304967--305049 Score: 59
Period size: 20 Copynumber: 4.0 Consensus size: 21
304957 TTATTTACAA
*
304967 TTTTTTA-AAAATTTAATTAA-
1 TTTTTTATAAATTTTAA-TAAT
* * *
304987 TATTTTATTATTTTTAATAAT
1 TTTTTTATAAATTTTAATAAT
*
305008 TTTTTTA-CAATTTTAA-AAT
1 TTTTTTATAAATTTTAATAAT
305027 ATTTTTTATAACA-TTTAATAAT
1 -TTTTTTATAA-ATTTTAATAAT
305049 T
1 T
305050 ATTCAATATT
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
19 3 0.06
20 23 0.47
21 19 0.39
22 4 0.08
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTTTATAAATTTTAATAAT
Found at i:305021 original size:20 final size:21
Alignment explanation
Indices: 304998--305049 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
304988 ATTTTATTAT
304998 TTTTAATAATTTTTTTACAA-
1 TTTTAATAATTTTTTTACAAC
*
305018 TTTTAA-AATATTTTTTATAAC
1 TTTTAATAAT-TTTTTTACAAC
*
305039 ATTTAATAATT
1 TTTTAATAATT
305050 ATTCAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 3 0.11
20 15 0.56
21 6 0.22
22 3 0.11
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTAATAATTTTTTTACAAC
Found at i:308431 original size:6 final size:6
Alignment explanation
Indices: 308422--308463 Score: 66
Period size: 6 Copynumber: 6.7 Consensus size: 6
308412 GCACATAAAC
308422 ATACAT ATACGCAT ATACAT ATACAT ATACAT ATACAT ATAC
1 ATACAT ATA--CAT ATACAT ATACAT ATACAT ATACAT ATAC
308464 TCAAGATAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 28 0.82
8 6 0.18
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (6 bp):
ATACAT
Found at i:308545 original size:11 final size:11
Alignment explanation
Indices: 308523--308551 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
308513 ACATATACAT
308523 ATACAC-TCAC
1 ATACACATCAC
308533 ATACACATCAC
1 ATACACATCAC
308544 ATACACAT
1 ATACACAT
308552 ACGTATATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (11 bp):
ATACACATCAC
Found at i:312669 original size:18 final size:17
Alignment explanation
Indices: 312646--312679 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
312636 TGGTCGGAGA
312646 TATTAATCAGATCTTTTG
1 TATTAATCAGAT-TTTTG
312664 TATTAATCAGATTTTT
1 TATTAATCAGATTTTT
312680 AGGTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (17 bp):
TATTAATCAGATTTTTG
Found at i:314432 original size:29 final size:30
Alignment explanation
Indices: 314390--314447 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
314380 TTTGGTCTAA
*
314390 TATGCAATTTTATATAT-AAATTTTGATTT
1 TATGCAATTTTATAAATGAAATTTTGATTT
* *
314419 TATGTAATTTTATAAATGTAATTTTGATT
1 TATGCAATTTTATAAATGAAATTTTGATT
314448 GGATTCAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (30 bp):
TATGCAATTTTATAAATGAAATTTTGATTT
Found at i:314480 original size:12 final size:12
Alignment explanation
Indices: 314463--314487 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
314453 CAATTCTTGT
314463 ATTATTAACATA
1 ATTATTAACATA
314475 ATTATTAACATA
1 ATTATTAACATA
314487 A
1 A
314488 CATCATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTATTAACATA
Found at i:314672 original size:27 final size:29
Alignment explanation
Indices: 314641--314697 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
314631 TAAAGTTTTG
314641 TATGTAT-AATTATAC-TAAATCAAAATT
1 TATGTATAAATTATACATAAATCAAAATT
*
314668 TATGTATAAATTATACATTGAATCAAAATT
1 TATGTATAAATTATACA-TAAATCAAAATT
314698 GCATAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 7 0.27
28 8 0.31
30 11 0.42
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (29 bp):
TATGTATAAATTATACATAAATCAAAATT
Found at i:318628 original size:94 final size:94
Alignment explanation
Indices: 318501--318779 Score: 344
Period size: 94 Copynumber: 2.9 Consensus size: 94
318491 CACTTTTTTT
* * * * * * *
318501 TTTTTGCCCTTTTAATTATACTGGTAAATTTTCATTTTTGATCCCTCTATTAAACTCAATTTTAA
1 TTTTTGCCATTTCAATTATAATGGTAAAATTTCAGTTTTGGTCCCTCTATTAAACTCAAATTTAA
318566 GATTTAATCTTTATATTTTTATGCCA-CTC
66 GATTTAATCTTTATATTTTTAT-CCAGCTC
* * *
318595 TTTTTGCCATTTCAATTATAATGGAAAAATTTCAGTTTTGGTCCCTTTGTTAAACTCAAATTTAA
1 TTTTTGCCATTTCAATTATAATGGTAAAATTTCAGTTTTGGTCCCTCTATTAAACTCAAATTTAA
* * *
318660 GATTTAATCTTTAAATTTTTACTTCAGCTT
66 GATTTAATCTTTATATTTTTA-TCCAGCTC
* * * **
318690 TTGTTTGCCATTTCAATTATAATGGTAAGATTACAGTTTTGGTCCCTCTACTAAACTCAAAACTA
1 TT-TTTGCCATTTCAATTATAATGGTAAAATTTCAGTTTTGGTCCCTCTATTAAACTCAAATTTA
318755 AGATTTAATCTTTTTATATTTTTAT
65 AGATTTAATC--TTTATATTTTTAT
318780 TTGACATGAT
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
94 77 0.49
95 5 0.03
96 64 0.41
97 1 0.01
98 11 0.07
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (94 bp):
TTTTTGCCATTTCAATTATAATGGTAAAATTTCAGTTTTGGTCCCTCTATTAAACTCAAATTTAA
GATTTAATCTTTATATTTTTATCCAGCTC
Found at i:319461 original size:17 final size:17
Alignment explanation
Indices: 319439--319476 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
319429 GTTTGTATTA
319439 TTAATTATTAAGTTCGG
1 TTAATTATTAAGTTCGG
319456 TTAATTATTAAGTTCGG
1 TTAATTATTAAGTTCGG
319473 TTAA
1 TTAA
319477 ATACCCGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (17 bp):
TTAATTATTAAGTTCGG
Found at i:324631 original size:13 final size:14
Alignment explanation
Indices: 324613--324641 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
324603 ATTATCATGG
324613 AATACAAG-CTTTA
1 AATACAAGTCTTTA
324626 AATACAAGTCTTTA
1 AATACAAGTCTTTA
324640 AA
1 AA
324642 ATATTGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (14 bp):
AATACAAGTCTTTA
Found at i:326809 original size:20 final size:20
Alignment explanation
Indices: 326786--326837 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
326776 TTTAAAAAAG
326786 TTTTTATTTTTTTCATAAAT
1 TTTTTATTTTTTTCATAAAT
**
326806 TTTTT-TGTTTTTTGTTAAAT
1 TTTTTAT-TTTTTTCATAAAT
*
326826 TATTATATTTTT
1 T-TTTTATTTTT
326838 AATTTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.04
20 17 0.65
21 7 0.27
22 1 0.04
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.73
Consensus pattern (20 bp):
TTTTTATTTTTTTCATAAAT
Found at i:327527 original size:15 final size:17
Alignment explanation
Indices: 327506--327546 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
327496 TAATTTTTTA
327506 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
327522 -AAATTATTAAAATGAT
1 AAAATTATAAAAATGAT
327538 AAAATTATA
1 AAAATTATA
327547 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:327574 original size:22 final size:22
Alignment explanation
Indices: 327512--327574 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 22
327502 TTTAAAAATT
*
327512 ATAAAAA-TATAAATTATTAAA
1 ATAAAAATTATAATTTATTAAA
* **
327533 ATGATAAAATTATATTTTTATTATC
1 AT-A-AAAATTATA-ATTTATTAAA
327558 ATAAAAATTATAATTTA
1 ATAAAAATTATAATTTA
327575 ATTTCGATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
21 2 0.06
22 5 0.15
23 13 0.39
24 5 0.15
25 8 0.24
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
ATAAAAATTATAATTTATTAAA
Found at i:328474 original size:27 final size:29
Alignment explanation
Indices: 328429--328496 Score: 106
Period size: 28 Copynumber: 2.4 Consensus size: 29
328419 ATAAAAAATA
*
328429 ACCAAAATGT-TATACA-TTTTTTTATTT
1 ACCAAAATATATATACATTTTTTTTATTT
328456 ACCAAAATATATATA-ATTTTTTTTATTT
1 ACCAAAATATATATACATTTTTTTTATTT
328484 ACCAAAATATATA
1 ACCAAAATATATA
328497 AAAAAACCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
27 10 0.26
28 28 0.74
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.47
Consensus pattern (29 bp):
ACCAAAATATATATACATTTTTTTTATTT
Found at i:328592 original size:27 final size:27
Alignment explanation
Indices: 328562--328629 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
328552 AAGGGAACAC
328562 TGTTGGCGGCACCAAACAAGGAAACCT
1 TGTTGGCGGCACCAAACAAGGAAACCT
**
328589 TGTTGGCGGCACCAAACAAGGATTCCT
1 TGTTGGCGGCACCAAACAAGGAAACCT
328616 TGTTGGCGGCACCA
1 TGTTGGCGGCACCA
328630 CCTTAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.19
Consensus pattern (27 bp):
TGTTGGCGGCACCAAACAAGGAAACCT
Found at i:328716 original size:28 final size:30
Alignment explanation
Indices: 328681--328758 Score: 106
Period size: 28 Copynumber: 2.6 Consensus size: 30
328671 AGAGGGGAAG
328681 AAGAAGAAAGAAAGGAA-GAAAGAAAGAAA
1 AAGAAGAAAGAAAGGAATGAAAGAAAGAAA
*
328710 AA-AAGAAAGAAAGGAGATGAAAGAAGGAAA
1 AAGAAGAAAGAAAGGA-ATGAAAGAAAGAAA
328740 AAGAAGGAAAGAAAAGGAA
1 AAGAA-GAAAG-AAAGGAA
328759 AGGGGAGGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
28 13 0.30
29 3 0.07
30 13 0.30
31 2 0.05
32 6 0.14
33 6 0.14
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.01
Consensus pattern (30 bp):
AAGAAGAAAGAAAGGAATGAAAGAAAGAAA
Found at i:328720 original size:38 final size:39
Alignment explanation
Indices: 328678--328805 Score: 129
Period size: 38 Copynumber: 3.3 Consensus size: 39
328668 AGGAGAGGGG
*
328678 AAGAAGAAGAAAGAAAGGAAGAAAGAAAGAAA-AAAA-GA
1 AAGAAGAAGAAAGAAAGGAA-AAAGAAGGAAAGAAAAGGA
328716 AAGAAAGGAGATGAAAG-AAGGAAAAAGAAGGAAAGAAAAGGA
1 AAG-AA-GA-A-GAAAGAAAGGAAAAAGAAGGAAAGAAAAGGA
** * *
328758 AAGGGGAGGAAAGAAA-GAAAAATAAGGAAAGAAAAGGA
1 AAGAAGAAGAAAGAAAGGAAAAAGAAGGAAAGAAAAGGA
*
328796 AAGGAGAAGA
1 AAGAAGAAGA
328806 GGAAAAAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 14
0.78 0.07 0.14
Matches are distributed among these distances:
38 37 0.49
39 4 0.05
40 14 0.18
41 11 0.14
42 10 0.13
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (39 bp):
AAGAAGAAGAAAGAAAGGAAAAAGAAGGAAAGAAAAGGA
Found at i:328759 original size:28 final size:27
Alignment explanation
Indices: 328678--328790 Score: 90
Period size: 28 Copynumber: 4.2 Consensus size: 27
328668 AGGAGAGGGG
*
328678 AAGAAGAAGAAAGAAAGGAAG-AAA-GA
1 AAGAAGAA-AAAGAAAGAAAGAAAAGGA
* * *
328704 AAGAA-AAAAAGAAAGAAAGGAGATGA
1 AAGAAGAAAAAGAAAGAAAGAAAAGGA
*
328730 AAGAAGGAAAAAGAAGGAAAGAAAAGGA
1 AAGAA-GAAAAAGAAAGAAAGAAAAGGA
** *
328758 AAGGGGAGGAAAGAAAGAAA-AATAAGGA
1 AAGAAGA-AAAAGAAAGAAAGAA-AAGGA
328786 AAGAA
1 AAGAA
328791 AAGGAAAGGA
Statistics
Matches: 69, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
24 11 0.16
25 4 0.06
26 12 0.17
27 4 0.06
28 38 0.55
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (27 bp):
AAGAAGAAAAAGAAAGAAAGAAAAGGA
Found at i:328777 original size:4 final size:4
Alignment explanation
Indices: 328684--328753 Score: 63
Period size: 4 Copynumber: 17.5 Consensus size: 4
328674 GGGGAAGAAG
* * *
328684 AAGA AAGA AAGG AAGA AAGA AAGA AAAA AAGA AAGA AAGGA GATGA AAG-
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA-GA -AAGA AAGA
* *
328733 AAGG AA-A AAGA AGGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AA
328754 AGGAAAGGGG
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
3 5 0.09
4 43 0.81
5 4 0.08
6 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (4 bp):
AAGA
Done.