Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 131 of 290
Found at i:41230731 original size:40 final size:40
Alignment explanation
Indices: 41230615--41230826 Score: 239
Period size: 40 Copynumber: 5.3 Consensus size: 40
41230605 TCTTCGAAAT
* * *
41230615 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
** * * *
41230654 TTAGCCCGGATTTAGTAACTACGCACAAATGCCTTCGGATC
1 TTAGCCCGGATAAAATCACTA-GCACAAATGCCTTCGGGTC
* *
41230695 TTAGTCCGGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* * * * *
41230735 TTAACCCGGGT-ATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTC
* *
41230775 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGAC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
41230815 TTAGCCCGGATA
1 TTAGCCCGGATA
41230827 TCATTCAAAT
Statistics
Matches: 142, Mismatches: 27, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
39 7 0.05
40 98 0.69
41 37 0.26
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
Found at i:41230787 original size:80 final size:80
Alignment explanation
Indices: 41230615--41230827 Score: 311
Period size: 80 Copynumber: 2.6 Consensus size: 80
41230605 TCTTCGAAAT
* * * * * *
41230615 TTAGCCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAGTAACTACGCAC
1 TTAGCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTACGCAC
41230680 AAATGCCTTCGGATC
66 AAATGCCTTCGGATC
* *
41230695 TTAGTCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACT-CGCA
1 TTAG-CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTACGCA
*
41230759 CAAATGCCTTCGGGTC
65 CAAATGCCTTCGGATC
*
41230775 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCCGGATAT
1 TTAG-CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATAT
41230828 CATTCAAATG
Statistics
Matches: 119, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
80 72 0.61
81 47 0.39
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
TTAGCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTACGCAC
AAATGCCTTCGGATC
Found at i:41236116 original size:41 final size:40
Alignment explanation
Indices: 41236037--41236116 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 40
41236027 TTCATCTCCA
* * **
41236037 AAATTAAAAAATTCAATTTAATCATTTTTAAAGTTTAATT
1 AAATAAAAAAATTCAATTTAATCATTTTAAAAAATTAATT
41236077 AAATAAAAAAATAT-AATTTTAATCATTTTAAAAAATTAAT
1 AAATAAAAAAAT-TCAA-TTTAATCATTTTAAAAAATTAAT
41236117 AATTTAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 13 0.38
41 21 0.62
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (40 bp):
AAATAAAAAAATTCAATTTAATCATTTTAAAAAATTAATT
Found at i:41237697 original size:24 final size:24
Alignment explanation
Indices: 41237669--41237720 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
41237659 CATCATGTCC
*
41237669 TTTAGAAACCTTAATCTATGACCT
1 TTTAGAAACCTTAATCTAAGACCT
*
41237693 TTTAGAAACCTTAATTTAAGACCT
1 TTTAGAAACCTTAATCTAAGACCT
41237717 TTTA
1 TTTA
41237721 ATAAACTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (24 bp):
TTTAGAAACCTTAATCTAAGACCT
Found at i:41237729 original size:24 final size:24
Alignment explanation
Indices: 41237669--41237729 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
41237659 CATCATGTCC
* *
41237669 TTTAGAAACCTTAATCTATGACCT
1 TTTAGAAAACTTAATCTAAGACCT
* *
41237693 TTTAGAAACCTTAATTTAAGACCT
1 TTTAGAAAACTTAATCTAAGACCT
41237717 TTTA-ATAAACTTA
1 TTTAGA-AAACTTA
41237730 TTTTTGGACA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 1 0.03
24 32 0.97
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (24 bp):
TTTAGAAAACTTAATCTAAGACCT
Found at i:41242755 original size:22 final size:22
Alignment explanation
Indices: 41242729--41242773 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
41242719 ATTATATGTA
41242729 TTAATTCATAATATAA-TTAATT
1 TTAATTCAT-ATATAAGTTAATT
* *
41242751 TTAATTTATATCTAAGTTAATT
1 TTAATTCATATATAAGTTAATT
41242773 T
1 T
41242774 GGGTTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
TTAATTCATATATAAGTTAATT
Found at i:41260169 original size:19 final size:17
Alignment explanation
Indices: 41260135--41260176 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
41260125 GTAAGACCGT
41260135 ATTTTTTCTTAAATTTTA
1 ATTTTTTCTTAAA-TTTA
41260153 ATTTTATTC-TAATATTTA
1 ATTTT-TTCTTAA-ATTTA
41260171 ATTTTT
1 ATTTTT
41260177 CAATTTATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 17 0.77
19 4 0.18
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTTTCTTAAATTTA
Found at i:41265558 original size:20 final size:18
Alignment explanation
Indices: 41265515--41265549 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41265505 TTCTTGTCAA
**
41265515 AAAATAATTAATTTGCAT
1 AAAATAATTAAAGTGCAT
41265533 AAAATAATTAAAGTGCA
1 AAAATAATTAAAGTGCA
41265550 CTTAAAATAT
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:0.06, G:0.09, T:0.31
Consensus pattern (18 bp):
AAAATAATTAAAGTGCAT
Found at i:41269015 original size:16 final size:16
Alignment explanation
Indices: 41268994--41269025 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41268984 ATGAAATAGC
*
41268994 ATAAATAAACAATTAA
1 ATAAATAAAAAATTAA
41269010 ATAAATAAAAAATTAA
1 ATAAATAAAAAATTAA
41269026 GTTAAATTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (16 bp):
ATAAATAAAAAATTAA
Found at i:41270608 original size:49 final size:49
Alignment explanation
Indices: 41270551--41270644 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
41270541 TGCTATGCAA
*
41270551 TGCTAAACTTGGTCTTCCACTTTCTAGACTCTTATCACTATTTATACAT
1 TGCTAAACTTGGTCTTCCACTGTCTAGACTCTTATCACTATTTATACAT
*
41270600 TGCTAAACTTGGTCTTCCACTGTCTATACTCTTATCACTATTTAT
1 TGCTAAACTTGGTCTTCCACTGTCTAGACTCTTATCACTATTTAT
41270645 TTCCTCTTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.44
Consensus pattern (49 bp):
TGCTAAACTTGGTCTTCCACTGTCTAGACTCTTATCACTATTTATACAT
Found at i:41273911 original size:21 final size:21
Alignment explanation
Indices: 41273885--41273925 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41273875 TGGGCTAAGT
* * *
41273885 ATGATGTTTTAAGCATGATAA
1 ATGATGGTATAAGAATGATAA
41273906 ATGATGGTATAAGAATGATA
1 ATGATGGTATAAGAATGATA
41273926 TTTTACTATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.34
Consensus pattern (21 bp):
ATGATGGTATAAGAATGATAA
Found at i:41275226 original size:43 final size:43
Alignment explanation
Indices: 41275146--41275232 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
41275136 TCATATTTCA
**
41275146 TTTCTCATCTCATATTCATTTCTCATATTTGTTATTTCAATAT
1 TTTCTCATCTCATATTCATTTCTCATATTTGCCATTTCAATAT
* * * *
41275189 TTTCTCATCTCATATTCATTTTTCGTCTTTGCCATTTCCATAT
1 TTTCTCATCTCATATTCATTTCTCATATTTGCCATTTCAATAT
41275232 T
1 T
41275233 AAACACATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.20, C:0.22, G:0.03, T:0.55
Consensus pattern (43 bp):
TTTCTCATCTCATATTCATTTCTCATATTTGCCATTTCAATAT
Found at i:41287551 original size:6 final size:6
Alignment explanation
Indices: 41287507--41287557 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
41287497 AAAGTCTAAG
* *
41287507 AAAATA ACAATA AACATA AAAATA GAAAA-A AAAACTA AAAAT- AAAATA
1 AAAATA AAAATA AAAATA AAAATA -AAAATA AAAA-TA AAAATA AAAATA
41287555 AAA
1 AAA
41287558 TGAATAGACT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 9 0.24
6 19 0.51
7 9 0.24
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:41289012 original size:23 final size:28
Alignment explanation
Indices: 41288957--41289015 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
41288947 AGTAATAATG
*
41288957 AGCAATAATAATCATAAAGAAGTAGACT
1 AGCAAGAATAATCATAAAGAAGTAGACT
41288985 AGCAAGAATAAT-ATAAA-AA-TAG-C-
1 AGCAAGAATAATCATAAAGAAGTAGACT
41289008 AGCAAGAA
1 AGCAAGAA
41289016 ACAAGTAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 8 0.27
24 1 0.03
25 3 0.10
26 2 0.07
27 5 0.17
28 11 0.37
ACGTcount: A:0.58, C:0.10, G:0.15, T:0.17
Consensus pattern (28 bp):
AGCAAGAATAATCATAAAGAAGTAGACT
Found at i:41289459 original size:12 final size:13
Alignment explanation
Indices: 41289436--41289464 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
41289426 GCGCGGGAAA
41289436 GAAAAAGAAAAGG
1 GAAAAAGAAAAGG
41289449 GAAAAAG-AAAGG
1 GAAAAAGAAAAGG
41289461 GAAA
1 GAAA
41289465 GGTCTGGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
GAAAAAGAAAAGG
Found at i:41302930 original size:22 final size:22
Alignment explanation
Indices: 41302903--41302947 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
41302893 GAGTTAAAGG
41302903 TAAATCATTAGAAAGAAGAAAA
1 TAAATCATTAGAAAGAAGAAAA
41302925 TAAATCATTAGAAAGAAGAAAA
1 TAAATCATTAGAAAGAAGAAAA
41302947 T
1 T
41302948 GACTTCACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.62, C:0.04, G:0.13, T:0.20
Consensus pattern (22 bp):
TAAATCATTAGAAAGAAGAAAA
Found at i:41305934 original size:34 final size:34
Alignment explanation
Indices: 41305890--41305971 Score: 105
Period size: 34 Copynumber: 2.4 Consensus size: 34
41305880 TTAGCCCCTT
*
41305890 TTTCAATAACAGTATCAGTCTGGGCCTGAGCCCA
1 TTTCAGTAACAGTATCAGTCTGGGCCTGAGCCCA
* *
41305924 TTTCAGTAACAG-AGGCAGTCTGGGCCTTAGCCCA
1 TTTCAGTAACAGTA-TCAGTCTGGGCCTGAGCCCA
*
41305958 TTTTAGT-ACAGTAT
1 TTTCAGTAACAGTAT
41305972 GCAAACAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
33 5 0.12
34 36 0.88
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (34 bp):
TTTCAGTAACAGTATCAGTCTGGGCCTGAGCCCA
Found at i:41309200 original size:28 final size:28
Alignment explanation
Indices: 41309156--41309210 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
41309146 CCCAAAAACT
41309156 CATCCTCTAACTATTTACTCTTAATCTA
1 CATCCTCTAACTATTTACTCTTAATCTA
* *
41309184 CATCCTCTAATTGTTTACTCTTAATCT
1 CATCCTCTAACTATTTACTCTTAATCT
41309211 GCTCAATCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.25, C:0.27, G:0.02, T:0.45
Consensus pattern (28 bp):
CATCCTCTAACTATTTACTCTTAATCTA
Found at i:41313313 original size:34 final size:34
Alignment explanation
Indices: 41313275--41313347 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
41313265 TTAGCCCCTT
*
41313275 TTTCAACAACAGTA-TCAGTCTGGACCTGAGCCCA
1 TTTCAACAACAG-AGGCAGTCTGGACCTGAGCCCA
** * *
41313309 TTTCAGTAACAGAGGCAGTCTGGGCCTTAGCCCA
1 TTTCAACAACAGAGGCAGTCTGGACCTGAGCCCA
41313343 TTTCA
1 TTTCA
41313348 GTACAGTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
33 1 0.03
34 32 0.97
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (34 bp):
TTTCAACAACAGAGGCAGTCTGGACCTGAGCCCA
Found at i:41315796 original size:46 final size:44
Alignment explanation
Indices: 41315651--41315821 Score: 168
Period size: 46 Copynumber: 3.7 Consensus size: 44
41315641 TGTGTGAGCT
* * *
41315651 AGTGTAAGACATGTTTGGGATATGCGTCGGCCACATT-ATGA-GAGCC
1 AGTGTAAGACATGTTTGGGACATGCATCGG---CATTGA-GATAAGCC
*
41315697 AGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGATGAGCAC
1 AGTGTAAGA-CATGTTTGGGACAT-GCATCGGCATTGAGATAAGC-C
* *
41315744 TAGTGTAAGACATGTCTGGGACATGCATCGGTC-TTGATACGTAAGCC
1 -AGTGTAAGACATGTTTGGGACATGCATCGG-CATTGAGA--TAAGCC
41315791 AGTGTAAGACATGTTTGGGACATGCATCGGC
1 AGTGTAAGACATGTTTGGGACATGCATCGGC
41315822 TACAAGATGT
Statistics
Matches: 110, Mismatches: 6, Indels: 19
0.81 0.04 0.14
Matches are distributed among these distances:
45 7 0.06
46 55 0.50
47 29 0.26
48 19 0.17
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (44 bp):
AGTGTAAGACATGTTTGGGACATGCATCGGCATTGAGATAAGCC
Found at i:41315864 original size:46 final size:44
Alignment explanation
Indices: 41315651--41315864 Score: 146
Period size: 46 Copynumber: 4.6 Consensus size: 44
41315641 TGTGTGAGCT
* * * * ** *
41315651 AGTGTAAGACATGTTTGGGATATGCGTCGGCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACAAGATGTGA--C
* ** *
41315697 AGTGTAAGACCATGTTTGGGACATGGCATCGGC-ATTGAGATGAGCAC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTA-CAAGATGTG-AC
** *
41315744 TAGTGTAAGACATGTCTGGGACATGCATCGG-T-CTTGATACGTAAGCC
1 -AGTGTAAGACATGTCTGGGACATGCATCGGCTACAAGAT--GT--GAC
* *
41315791 AGTGTAAGACATGTTTGGGACATGCATCGGCTACAAGATGTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACAAGATGTGAC
41315835 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATC
41315865 AGCACAGATA
Statistics
Matches: 137, Mismatches: 17, Indels: 28
0.75 0.09 0.15
Matches are distributed among these distances:
44 14 0.10
45 13 0.09
46 53 0.39
47 30 0.22
48 26 0.19
49 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.26
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTACAAGATGTGAC
Found at i:41315894 original size:50 final size:50
Alignment explanation
Indices: 41315836--41315968 Score: 221
Period size: 50 Copynumber: 2.7 Consensus size: 50
41315826 AGATGTGTCA
*
41315836 GTGTAAGACCATGTCTGGGACATGGCATCAGCACAGATATACTAGATATT
1 GTGTAAGACCATGTCTGGGACATGGCATCAGCACAGATATACTAGAGATT
* * *
41315886 GTGTAAGACCATGTTTGGGACATGGCATCAGCACATATATACTAGAGCTT
1 GTGTAAGACCATGTCTGGGACATGGCATCAGCACAGATATACTAGAGATT
*
41315936 GTGTAAGACCATGTCTGGGATATGGCATCAGCA
1 GTGTAAGACCATGTCTGGGACATGGCATCAGCA
41315969 TCTGACCCAT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 77 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (50 bp):
GTGTAAGACCATGTCTGGGACATGGCATCAGCACAGATATACTAGAGATT
Found at i:41320120 original size:21 final size:21
Alignment explanation
Indices: 41320092--41320143 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
41320082 ATTTTCCTAA
41320092 GATG-TAAATTGGATTGAA-TT
1 GATGTTAAATTGGATT-AACTT
* *
41320112 GATTTTAAATTGTATTAACTT
1 GATGTTAAATTGGATTAACTT
41320133 GATGTTAAATT
1 GATGTTAAATT
41320144 TACTCGTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (21 bp):
GATGTTAAATTGGATTAACTT
Found at i:41321211 original size:26 final size:26
Alignment explanation
Indices: 41321172--41321222 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
41321162 ATTATGAAAA
*
41321172 TATACTTGTAATATAAATATATGATT
1 TATACATGTAATATAAATATATGATT
* * *
41321198 TATACATGTTATATGAATATGTGAT
1 TATACATGTAATATAAATATATGAT
41321223 ACGAAATGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (26 bp):
TATACATGTAATATAAATATATGATT
Found at i:41330633 original size:61 final size:59
Alignment explanation
Indices: 41330554--41330721 Score: 189
Period size: 60 Copynumber: 2.8 Consensus size: 59
41330544 CCTTAGAAAA
* * * * * *
41330554 ATTTTAATATGATAATTATTGAATATACTTTAATAAAAAATAATAAAAATAATTTAATCAT
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAAATAAT--AAATAATTTAATAAC
**
41330615 ATTTTAATATAATTATTATTAAATATAATTTAAT-AAAAATAATATTTAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAAATAATAAATAATTTAATAAC
* *
41330673 ATTCTCAATATAATTATTATTAAAATATAAATTAAT-AAAAATAA-AAATA
1 ATT-TTAATATAATTATTATT-AAATATAATTTAATAAAAAATAATAAATA
41330722 TATAATATAT
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
58 14 0.15
59 19 0.20
60 30 0.32
61 30 0.32
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (59 bp):
ATTTTAATATAATTATTATTAAATATAATTTAATAAAAAATAATAAATAATTTAATAAC
Found at i:41330646 original size:26 final size:26
Alignment explanation
Indices: 41330617--41330709 Score: 71
Period size: 29 Copynumber: 3.3 Consensus size: 26
41330607 TTAATCATAT
41330617 TTTAATATAATTATTATTAAATATAA
1 TTTAATATAATTATTATTAAATATAA
* *
41330643 TTTAATAAAAATAATATTTAATTTAATA-ACA
1 TTTAAT-ATAAT--TA-TT-ATTAAATATA-A
41330674 TTCTCAATATAATTATTATTAAAATATAA
1 TT-T-AATATAATTATTATT-AAATATAA
*
41330703 ATTAATA
1 TTTAATA
41330710 AAAATAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 19
0.68 0.07 0.25
Matches are distributed among these distances:
26 6 0.12
27 8 0.15
28 4 0.08
29 10 0.19
30 6 0.12
31 10 0.19
32 5 0.10
33 3 0.06
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (26 bp):
TTTAATATAATTATTATTAAATATAA
Found at i:41339534 original size:65 final size:65
Alignment explanation
Indices: 41339430--41339552 Score: 201
Period size: 65 Copynumber: 1.9 Consensus size: 65
41339420 GGCAAAGCAC
*
41339430 GGGAAACAAGTTGAACAAAGCTAAAACACAAATGGAAAGGACTCAAACCTTTCGGTTACTAATAT
1 GGGAAACAAGATGAACAAAGCTAAAACACAAATGGAAAGGACTCAAACCTTTCGGTTACTAATAT
** **
41339495 GGGAAACAAGATGAACAAAGCTAAAACATGAATGGAAAGGACTTGAACCTTTCGGTTA
1 GGGAAACAAGATGAACAAAGCTAAAACACAAATGGAAAGGACTCAAACCTTTCGGTTA
41339553 TTAGCATGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 53 1.00
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.20
Consensus pattern (65 bp):
GGGAAACAAGATGAACAAAGCTAAAACACAAATGGAAAGGACTCAAACCTTTCGGTTACTAATAT
Found at i:41347339 original size:41 final size:41
Alignment explanation
Indices: 41347286--41347475 Score: 328
Period size: 41 Copynumber: 4.7 Consensus size: 41
41347276 CGTTTTACCA
41347286 AAAACGCC-CTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
* *
41347326 AAAACGCCGCTAAAAACCAGAGCATTAGCGGTGCTTCTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
41347367 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
* *
41347408 AAAACGCCGCTAAAAACCAGAGCATTAGCGGTGCTTTTTGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
*
41347449 AAAACGCCGCTAAAAACCATAGCATTA
1 AAAACGCCGCTAAAAACCAGAGCATTA
41347476 TTTATATTAA
Statistics
Matches: 142, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
40 8 0.06
41 134 0.94
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
Found at i:41347745 original size:22 final size:23
Alignment explanation
Indices: 41347720--41347767 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 23
41347710 TAGGGATTAT
*
41347720 GGTTTATGATTTATGGTTC-AAG
1 GGTTTAGGATTTATGGTTCAAAG
* *
41347742 GG-TTGGGGTTTATGGTTCAAAG
1 GGTTTAGGATTTATGGTTCAAAG
41347764 GGTT
1 GGTT
41347768 AGGGGTTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
21 13 0.62
22 7 0.33
23 1 0.05
ACGTcount: A:0.19, C:0.04, G:0.35, T:0.42
Consensus pattern (23 bp):
GGTTTAGGATTTATGGTTCAAAG
Found at i:41347753 original size:21 final size:23
Alignment explanation
Indices: 41347729--41347776 Score: 82
Period size: 21 Copynumber: 2.2 Consensus size: 23
41347719 TGGTTTATGA
41347729 TTTATGGTTC-AAGGGTT-GGGG
1 TTTATGGTTCAAAGGGTTAGGGG
41347750 TTTATGGTTCAAAGGGTTAGGGG
1 TTTATGGTTCAAAGGGTTAGGGG
41347773 TTTA
1 TTTA
41347777 GGCCTAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 10 0.40
22 7 0.28
23 8 0.32
ACGTcount: A:0.19, C:0.04, G:0.38, T:0.40
Consensus pattern (23 bp):
TTTATGGTTCAAAGGGTTAGGGG
Found at i:41348855 original size:14 final size:14
Alignment explanation
Indices: 41348836--41348865 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
41348826 ATTTCTTGCT
41348836 TCTCTAAATCTCCA
1 TCTCTAAATCTCCA
41348850 TCTCTAAATCTCCA
1 TCTCTAAATCTCCA
41348864 TC
1 TC
41348866 CCTTTGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.37, G:0.00, T:0.37
Consensus pattern (14 bp):
TCTCTAAATCTCCA
Found at i:41352044 original size:22 final size:23
Alignment explanation
Indices: 41351993--41352045 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
41351983 AGAAAACCAT
41351993 TTTAT-GTGTTAAATGCTGAAAA
1 TTTATGGTGTTAAATGCTGAAAA
*
41352015 TTTA-GGTGTTAAATGCTG-CAA
1 TTTATGGTGTTAAATGCTGAAAA
41352036 TTTATGGTGT
1 TTTATGGTGT
41352046 CTGAAAGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.28, C:0.06, G:0.23, T:0.43
Consensus pattern (23 bp):
TTTATGGTGTTAAATGCTGAAAA
Found at i:41352893 original size:43 final size:43
Alignment explanation
Indices: 41352820--41353004 Score: 214
Period size: 43 Copynumber: 4.3 Consensus size: 43
41352810 TTTTATGACC
*
41352820 TTTAGCGGCGTTTGTG-GAAAAAGCGCCGCTAAAGGTCCCAG-CT
1 TTTAGTGGCGTTTGTGAG-AAAAGCGCCGCTAAAGGT-CCAGACT
* * * * *
41352863 TTTAATGGCGTTTGTGAGAGAAGTGTCGCTAAAGGT-CATGATT
1 TTTAGTGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCCA-GACT
* * *
41352906 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAAGACT
1 TTTAGTGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCCAGACT
* *
41352949 TTTAGTGGCGTTTGTGAGAAAAGCGCCGTTAAAGGTCAAGACT
1 TTTAGTGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCCAGACT
*
41352992 TTTAGCGGCGTTT
1 TTTAGTGGCGTTT
41353005 TTTAAAATAA
Statistics
Matches: 120, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 115 0.96
44 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (43 bp):
TTTAGTGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCCAGACT
Found at i:41352965 original size:86 final size:86
Alignment explanation
Indices: 41352820--41353004 Score: 273
Period size: 86 Copynumber: 2.2 Consensus size: 86
41352810 TTTTATGACC
* *
41352820 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCCAGCTTTTAATGGCGTTTGTGAGAGAA
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCAAGCTTTTAATGGCGTTTGTGAGAAAA
* * * *
41352885 GTGTCGCTAAAGGTCATGATT
66 GCGCCGCTAAAGGTCAAGACT
* *
41352906 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-CAAGACTTTTAGTGGCGTTTGTGAGAAA
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCAAG-CTTTTAATGGCGTTTGTGAGAAA
*
41352970 AGCGCCGTTAAAGGTCAAGACT
65 AGCGCCGCTAAAGGTCAAGACT
41352992 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
41353005 TTTAAAATAA
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
85 3 0.03
86 86 0.97
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCAAGCTTTTAATGGCGTTTGTGAGAAAA
GCGCCGCTAAAGGTCAAGACT
Found at i:41353181 original size:10 final size:10
Alignment explanation
Indices: 41353166--41353195 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
41353156 ATTTGATTGT
41353166 TTTTTTTAAA
1 TTTTTTTAAA
41353176 TTTTTTTAAA
1 TTTTTTTAAA
*
41353186 TTTATTTAAA
1 TTTTTTTAAA
41353196 AAAATAAAAT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:41355184 original size:23 final size:22
Alignment explanation
Indices: 41355148--41355190 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
41355138 TTATAAAATA
41355148 TTAAAATATTAAAATCAATATTT
1 TTAAAATATTAAAAT-AATATTT
41355171 TTAAAA-ATTAAAAATAATAT
1 TTAAAATATT-AAAATAATAT
41355191 AGGCGGGCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAAATATTAAAATAATATTT
Found at i:41358154 original size:48 final size:46
Alignment explanation
Indices: 41358096--41358220 Score: 148
Period size: 48 Copynumber: 2.7 Consensus size: 46
41358086 CATATTCATA
*
41358096 CCGATGCCATGTCCCAGACATGGTCTTACACTGACACATTTATACGT-G
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAACACA--TAT-CGTAG
* * * *
41358144 CTGATGCCATGTCCCAGATATGGTTTTACACTAACACATCTCGTAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAACACATATCGTAG
*
41358190 CCGATG-CATGTCCCAGACAT-GTCCTACACTA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTA
41358221 GCTCTCGACT
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
44 9 0.13
45 16 0.24
46 8 0.12
48 34 0.51
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (46 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAACACATATCGTAG
Found at i:41358255 original size:47 final size:45
Alignment explanation
Indices: 41358193--41358316 Score: 135
Period size: 47 Copynumber: 2.7 Consensus size: 45
41358183 CTCGTAGCCG
* *
41358193 ATGCATGTCCCAGACATGTCCTACACTAGCTCTCGACTCAA-T-GCCA
1 ATGCATGTCCTAGACATGTCTTACACTAGCTCTC-A-T-AAGTGGCCA
* * *
41358239 ATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGTCG
1 ATG-CATGTCCTAGACAT-GTCTTACACTAGCTCTCATAA-GTGGCCA
41358287 ATGCATGTCCTAGACATGTCTTACACTAGC
1 ATGCATGTCCTAGACATGTCTTACACTAGC
41358317 ACACAAATAA
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
45 2 0.03
46 16 0.24
47 29 0.43
48 20 0.30
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (45 bp):
ATGCATGTCCTAGACATGTCTTACACTAGCTCTCATAAGTGGCCA
Found at i:41359475 original size:11 final size:10
Alignment explanation
Indices: 41359447--41359480 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
41359437 AGCCTGTAAG
41359447 TATTCTGAAT
1 TATTCTGAAT
*
41359457 TTTTCTGAAT
1 TATTCTGAAT
41359467 ATATTCTGAAT
1 -TATTCTGAAT
41359478 TAT
1 TAT
41359481 CTGTCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:41364678 original size:24 final size:24
Alignment explanation
Indices: 41364651--41364697 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
41364641 TTGTCAGGAG
**
41364651 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGCAGATAAGGGAT
41364675 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGCAGATAAGGGA
41364698 GGAAATCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.38, T:0.23
Consensus pattern (24 bp):
AGGATTTAGGAGCAGATAAGGGAT
Found at i:41366153 original size:27 final size:27
Alignment explanation
Indices: 41366113--41366220 Score: 102
Period size: 27 Copynumber: 4.1 Consensus size: 27
41366103 AGGAAGCGTC
*
41366113 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
41366140 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
41366167 C-GGTGG-TCTGCCACGATTA-CTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
41366192 CTGGTGACTCTG--TCAATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
41366217 CTGG
1 CTGG
41366221 CAGCCATGCT
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
24 3 0.04
25 22 0.32
26 16 0.24
27 27 0.40
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:41368821 original size:19 final size:20
Alignment explanation
Indices: 41368797--41368834 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
41368787 GGTACCACCA
41368797 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
41368816 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
41368835 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:41375194 original size:19 final size:20
Alignment explanation
Indices: 41375170--41375207 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
41375160 GGTACCACCA
41375170 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
41375189 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
41375208 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:41375556 original size:46 final size:46
Alignment explanation
Indices: 41375432--41375557 Score: 189
Period size: 46 Copynumber: 2.7 Consensus size: 46
41375422 AACCCGCCCC
* * *
41375432 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
41375478 TAAATGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
41375524 TAAGTGAACTCAGACTCAACTCAACGAATTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
41375558 TGCTCAACCA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:41377462 original size:12 final size:12
Alignment explanation
Indices: 41377447--41377477 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
41377437 CATGTCCTAG
*
41377447 CCCGTGTCTTTA
1 CCCGTGTCCTTA
41377459 CCCGTGTCCTTA
1 CCCGTGTCCTTA
41377471 CCCGTGT
1 CCCGTGT
41377478 AACACCCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.39, G:0.19, T:0.35
Consensus pattern (12 bp):
CCCGTGTCCTTA
Found at i:41386096 original size:16 final size:17
Alignment explanation
Indices: 41386075--41386106 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
41386065 TCAAGTAGTT
41386075 GAATCAGT-TGAACCGG
1 GAATCAGTATGAACCGG
41386091 GAATCAGTATGAACCG
1 GAATCAGTATGAACCG
41386107 ATTGAATTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (17 bp):
GAATCAGTATGAACCGG
Found at i:41387109 original size:43 final size:43
Alignment explanation
Indices: 41387029--41387305 Score: 245
Period size: 43 Copynumber: 6.6 Consensus size: 43
41387019 TTATGTAAAG
* * * *
41387029 AAACGCCGTTAAAAAACATGACCTTTAGCGGCTCTTTTCCCAC
1 AAACTCCGCTAAAGAACATGACCTTTAGCGGCACTTTTCCCAC
* * **
41387072 AAACTCCGCTAAAGAACATGACCTTTAGTGGCGCTTTTATCAC
1 AAACTCCGCTAAAGAACATGACCTTTAGCGGCACTTTTCCCAC
* * *
41387115 AAACGCCGTTAAAGAACATGACCTTTAACGGCACTTTTCCCAC
1 AAACTCCGCTAAAGAACATGACCTTTAGCGGCACTTTTCCCAC
* * *
41387158 AAGCTCCACTAAAGAACATGTCCTTT------ACTTTTCCCAC
1 AAACTCCGCTAAAGAACATGACCTTTAGCGGCACTTTTCCCAC
** * *
41387195 AAA-TGTTGCTAAAGAACATGACCTTTAGCGACGC-TTTCCCAC
1 AAACT-CCGCTAAAGAACATGACCTTTAGCGGCACTTTTCCCAC
* * *
41387237 AAA-TGCCACTATA-AA-ATAGACCTTTAGCGGCACTTTTCTCAC
1 AAACT-CCGCTAAAGAACAT-GACCTTTAGCGGCACTTTTCCCAC
41387279 AAACGT-CGCTAAAGAACATGACCTTTA
1 AAAC-TCCGCTAAAGAACATGACCTTTA
41387306 AAAATATATA
Statistics
Matches: 187, Mismatches: 34, Indels: 26
0.76 0.14 0.11
Matches are distributed among these distances:
36 1 0.01
37 30 0.16
40 2 0.01
41 15 0.08
42 32 0.17
43 104 0.56
44 3 0.02
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (43 bp):
AAACTCCGCTAAAGAACATGACCTTTAGCGGCACTTTTCCCAC
Found at i:41387174 original size:86 final size:83
Alignment explanation
Indices: 41387029--41387306 Score: 273
Period size: 86 Copynumber: 3.3 Consensus size: 83
41387019 TTATGTAAAG
* * * * *
41387029 AAACGCCGTTAAAAAACATGACCTTTAGCGGCTCTTTTCCCACAAACTCCGCTAAAGAACATGAC
1 AAACGCCGCTAAAGAACATGACCTTTAACGGCACTTTTCCCAC-AACTCCACTAAAGAACATGAC
*
41387094 CTTTAGTGGCGCTTTTATCAC
65 CTTTAG-GGC-CTTTTCTCAC
* *
41387115 AAACGCCGTTAAAGAACATGACCTTTAACGGCACTTTTCCCACAAGCTCCACTAAAGAACATGTC
1 AAACGCCGCTAAAGAACATGACCTTTAACGGCACTTTTCCCACAA-CTCCACTAAAGAACATGAC
*
41387180 CTTTA----CTTTTCCCAC
65 CTTTAGGGCCTTTTCTCAC
* ** * * * * *
41387195 AAATGTTGCTAAAGAACATGACCTTTAGCGACGC-TTTCCCACAAATGCCACTATA-AA-ATAGA
1 AAACGCCGCTAAAGAACATGACCTTTAACGGCACTTTTCCCACAACT-CCACTAAAGAACAT-GA
41387257 CCTTTAGCGGCACTTTTCTCAC
64 CCTTTAG-GGC-CTTTTCTCAC
*
41387279 AAACGTCGCTAAAGAACATGACCTTTAA
1 AAACGCCGCTAAAGAACATGACCTTTAA
41387307 AAATATATAT
Statistics
Matches: 162, Mismatches: 21, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
77 2 0.01
78 10 0.06
79 17 0.10
80 35 0.22
84 34 0.21
85 2 0.01
86 62 0.38
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (83 bp):
AAACGCCGCTAAAGAACATGACCTTTAACGGCACTTTTCCCACAACTCCACTAAAGAACATGACC
TTTAGGGCCTTTTCTCAC
Found at i:41389515 original size:14 final size:14
Alignment explanation
Indices: 41389496--41389527 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
41389486 ATAAGTCGAG
41389496 ATTATGTATATGAT
1 ATTATGTATATGAT
41389510 ATTATGTATATGAT
1 ATTATGTATATGAT
41389524 ATTA
1 ATTA
41389528 ATACCATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (14 bp):
ATTATGTATATGAT
Found at i:41391285 original size:9 final size:8
Alignment explanation
Indices: 41391219--41391292 Score: 60
Period size: 8 Copynumber: 8.9 Consensus size: 8
41391209 ATATTAAATA
41391219 TTAAATTT
1 TTAAATTT
*
41391227 TTAAGTTT
1 TTAAATTT
41391235 TT-AATTT
1 TTAAATTT
**
41391242 TTTTATTT
1 TTAAATTT
41391250 TTAAATTT
1 TTAAATTT
**
41391258 CAAAATTTT
1 TTAAA-TTT
41391267 TTGAAGATTT
1 TT-AA-ATTT
41391277 TTATAATTT
1 TTA-AATTT
41391286 TTAAATT
1 TTAAATT
41391293 AACGTATAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
7 6 0.12
8 26 0.50
9 11 0.21
10 8 0.15
11 1 0.02
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (8 bp):
TTAAATTT
Found at i:41391951 original size:21 final size:21
Alignment explanation
Indices: 41391927--41391973 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
41391917 CCCAAATATC
* *
41391927 AAACCCCAAATCCTAGTCCAT
1 AAACCCCAAATCATAGACCAT
*
41391948 AAACCCTAAATCATAGACCAT
1 AAACCCCAAATCATAGACCAT
41391969 AAACC
1 AAACC
41391974 TACACCCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.34, G:0.04, T:0.17
Consensus pattern (21 bp):
AAACCCCAAATCATAGACCAT
Found at i:41392033 original size:4 final size:4
Alignment explanation
Indices: 41392024--41392048 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
41392014 AATCTGTTAC
41392024 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
41392049 CAATTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:41392379 original size:22 final size:22
Alignment explanation
Indices: 41392327--41392381 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
41392317 ACTAATTAAT
*
41392327 ATAAACCCTAAACCCCTATCCTC
1 ATAAACCCT-AACCCCTATCCCC
**
41392350 -TATCCCCTAACCCCTATCCCC
1 ATAAACCCTAACCCCTATCCCC
41392371 ATAAACCCTAA
1 ATAAACCCTAA
41392382 ATCATAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.22
Consensus pattern (22 bp):
ATAAACCCTAACCCCTATCCCC
Found at i:41392387 original size:14 final size:14
Alignment explanation
Indices: 41392369--41392480 Score: 77
Period size: 14 Copynumber: 7.9 Consensus size: 14
41392359 ACCCCTATCC
41392369 CCATAAACCCTAAA
1 CCATAAACCCTAAA
* ***
41392383 TCATAAAATATAAA
1 CCATAAACCCTAAA
41392397 CCATAAACCC-ATAA
1 CCATAAACCCTA-AA
*
41392411 CCATTAATCCCT-AA
1 CCA-TAAACCCTAAA
* *
41392425 CTCCTAAACCTTAAA
1 C-CATAAACCCTAAA
**
41392440 CC-CCAACCCTTAAA
1 CCATAAACCC-TAAA
*
41392454 CCATAAACCATAAA
1 CCATAAACCCTAAA
41392468 CCATAAACCCTAA
1 CCATAAACCCTAA
41392481 TGATAATTAA
Statistics
Matches: 72, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
13 5 0.07
14 53 0.74
15 14 0.19
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (14 bp):
CCATAAACCCTAAA
Found at i:41392408 original size:8 final size:7
Alignment explanation
Indices: 41392369--41392476 Score: 67
Period size: 7 Copynumber: 15.3 Consensus size: 7
41392359 ACCCCTATCC
41392369 CCATAAA
1 CCATAAA
*
41392376 CCCTAAA
1 CCATAAA
*
41392383 TCATAAA
1 CCATAAA
**
41392390 ATATAAA
1 CCATAAA
41392397 CCATAAA
1 CCATAAA
41392404 CCCAT-AA
1 -CCATAAA
*
41392411 CCATTAAT
1 CCA-TAAA
*
41392419 CCCT-AA
1 CCATAAA
*
41392425 CTCCTAAA
1 C-CATAAA
*
41392433 CCTTAAA
1 CCATAAA
** *
41392440 CCCCAAC
1 CCATAAA
*
41392447 CCTTAAA
1 CCATAAA
41392454 CCATAAA
1 CCATAAA
41392461 CCATAAA
1 CCATAAA
41392468 CCATAAA
1 CCATAAA
41392475 CC
1 CC
41392477 CTAATGATAA
Statistics
Matches: 78, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
6 5 0.06
7 63 0.81
8 10 0.13
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.19
Consensus pattern (7 bp):
CCATAAA
Found at i:41392474 original size:21 final size:21
Alignment explanation
Indices: 41392369--41392476 Score: 76
Period size: 21 Copynumber: 5.1 Consensus size: 21
41392359 ACCCCTATCC
*
41392369 CCATAAACCCTAAATCATAAA
1 CCATAAACCCTAAACCATAAA
** *
41392390 ATATAAACCATAAACCCAT-AA
1 CCATAAACCCTAAA-CCATAAA
* *
41392411 CCATTAATCCCT-AACTCCTAAA
1 CCA-TAAACCCTAAAC-CATAAA
* * * *
41392433 CCTTAAACCCCAACCCTTAAA
1 CCATAAACCCTAAACCATAAA
*
41392454 CCATAAACCATAAACCATAAA
1 CCATAAACCCTAAACCATAAA
41392475 CC
1 CC
41392477 CTAATGATAA
Statistics
Matches: 63, Mismatches: 19, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
20 1 0.02
21 47 0.75
22 15 0.24
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.19
Consensus pattern (21 bp):
CCATAAACCCTAAACCATAAA
Found at i:41392831 original size:40 final size:40
Alignment explanation
Indices: 41392787--41392970 Score: 208
Period size: 40 Copynumber: 4.6 Consensus size: 40
41392777 TTTTGCGGCG
* * *
41392787 TTTTCATAAAGCGCCGCTAAAGCTCGATCTATAGCGGCAT
1 TTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCAT
* * *
41392827 TTTTCAAAAAGCGCCGCTAATGGTCGACCTATAGTGGCGT
1 TTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCAT
* * *
41392867 TTTTCAAAAACCGTCC-CTAATGGTCGACCTATAACGGCATT
1 TTTTCAAAAAGCG-CCGCTAATGCTCGACCTATAGCGGCA-T
* * * * * *
41392908 TTTTTAAAAACCGCCGCTAATGCTCAATCTATAGCAGCGT
1 TTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCAT
41392948 TTTTCAAAAAGCGCCGCTAATGC
1 TTTTCAAAAAGCGCCGCTAATGC
41392971 CTCTAAAGCT
Statistics
Matches: 122, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
40 90 0.74
41 32 0.26
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (40 bp):
TTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCAT
Found at i:41392968 original size:81 final size:80
Alignment explanation
Indices: 41392787--41392970 Score: 226
Period size: 81 Copynumber: 2.3 Consensus size: 80
41392777 TTTTGCGGCG
* * * * * *
41392787 TTTTCATAAAGCGCCGCTAAAGCTCGATCTATAGCGGCATTTTTCAAAAAGCGCCGCTAATGGTC
1 TTTTCAAAAAGCGCCGCTAATGCTCGACCTATAACGGCATTTTTCAAAAACCGCCGCTAATGCTC
* **
41392852 GACCTATAGTGGCGT
66 AACCTATAGCAGCGT
* * *
41392867 TTTTCAAAAACCGTCC-CTAATGGTCGACCTATAACGGCATTTTTTTAAAAACCGCCGCTAATGC
1 TTTTCAAAAAGCG-CCGCTAATGCTCGACCTATAACGGCA-TTTTTCAAAAACCGCCGCTAATGC
*
41392931 TCAATCTATAGCAGCGT
64 TCAACCTATAGCAGCGT
41392948 TTTTCAAAAAGCGCCGCTAATGC
1 TTTTCAAAAAGCGCCGCTAATGC
41392971 CTCTAAAGCT
Statistics
Matches: 86, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
80 32 0.37
81 54 0.63
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (80 bp):
TTTTCAAAAAGCGCCGCTAATGCTCGACCTATAACGGCATTTTTCAAAAACCGCCGCTAATGCTC
AACCTATAGCAGCGT
Found at i:41393035 original size:75 final size:75
Alignment explanation
Indices: 41392941--41393119 Score: 259
Period size: 75 Copynumber: 2.4 Consensus size: 75
41392931 TCAATCTATA
* * *
41392941 GCAGCGTTTTTCAAAAAGCGCCGCTAATGCCTCTAAAGCTCAACACAAAACAATAGCGTTGTGCT
1 GCAGCGTTTTTCAAAAAGCGCCGCTAATGCCACTAAAACTCAACACAAAACAACAGCGTTGTGCT
41393006 AAATTTTTTT
66 AAATTTTTTT
* *
41393016 GCAGCGTTTTTCAAAAAGCGCCACTAATGCCACTAAAACTCAACACAAAACAACGGCGTTGTGCT
1 GCAGCGTTTTTCAAAAAGCGCCGCTAATGCCACTAAAACTCAACACAAAACAACAGCGTTGTGCT
*
41393081 TAATTTTTTT
66 AAATTTTTTT
** * * *
41393091 GTGGCATTTTTCAAAAAGTGCCGCGAATG
1 GCAGCGTTTTTCAAAAAGCGCCGCTAATG
41393120 GTCGACCTAT
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 92 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (75 bp):
GCAGCGTTTTTCAAAAAGCGCCGCTAATGCCACTAAAACTCAACACAAAACAACAGCGTTGTGCT
AAATTTTTTT
Found at i:41393176 original size:18 final size:18
Alignment explanation
Indices: 41393153--41393190 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
41393143 AGAAGGCGCC
41393153 GCTAATGCTCGATCTATA
1 GCTAATGCTCGATCTATA
41393171 GCTAATGCTCGATCTATA
1 GCTAATGCTCGATCTATA
41393189 GC
1 GC
41393191 GGCGTTTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (18 bp):
GCTAATGCTCGATCTATA
Found at i:41393472 original size:28 final size:28
Alignment explanation
Indices: 41393440--41393495 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
41393430 CATTTCCAGA
*
41393440 GATTCTTGTCAAGTTCCCTTGTTTGATT
1 GATTCTTGTCAAGTTCCCTTGTTCGATT
*
41393468 GATTCTTGTTAAGTTCCCTTGTTCGATT
1 GATTCTTGTCAAGTTCCCTTGTTCGATT
41393496 ACTCTACACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.50
Consensus pattern (28 bp):
GATTCTTGTCAAGTTCCCTTGTTCGATT
Found at i:41397221 original size:19 final size:19
Alignment explanation
Indices: 41397197--41397238 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
41397187 TAAGAAAAAT
41397197 CAATAGCATACAACTTTTA
1 CAATAGCATACAACTTTTA
*
41397216 CAATAGCCTACAACTTTTA
1 CAATAGCATACAACTTTTA
41397235 CAAT
1 CAAT
41397239 TTTTACGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.31
Consensus pattern (19 bp):
CAATAGCATACAACTTTTA
Found at i:41403235 original size:40 final size:40
Alignment explanation
Indices: 41403189--41403373 Score: 237
Period size: 40 Copynumber: 4.6 Consensus size: 40
41403179 CTTGCGCAAG
* * *
41403189 GCCTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
41403229 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
41403269 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * *
41403309 GCCTTCGGATCTTAGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
*
41403350 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
41403374 CATTCGAATA
Statistics
Matches: 123, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 93 0.76
41 29 0.24
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:41407785 original size:39 final size:39
Alignment explanation
Indices: 41407742--41407955 Score: 207
Period size: 39 Copynumber: 5.7 Consensus size: 39
41407732 TCCTCGTTCA
* * **
41407742 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACATAACCCGGATTTAACAACTCACAC
* *
41407781 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCAC
1 AATGCCTTCGGGACATAACCCGGATTTAACAACTCACAC
* *
41407820 AATGCCTTC-GGAC-T--TCCGGATTTAACAACTCGCAC
1 AATGCCTTCGGGACATAACCCGGATTTAACAACTCACAC
* * *
41407855 ---G--ATCGGGACTTAACCCGGATTTAA-AACTCGCAC
1 AATGCCTTCGGGACATAACCCGGATTTAACAACTCACAC
* *
41407888 GAATGCCTTCGGGACTTAACCCGGATTTAA-AACTCGCAC
1 -AATGCCTTCGGGACATAACCCGGATTTAACAACTCACAC
*
41407927 GAATGCCTTCGGGACTTAACCCGGATTTA
1 -AATGCCTTCGGGACATAACCCGGATTTA
41407956 GTATCTCGCA
Statistics
Matches: 155, Mismatches: 10, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
30 2 0.01
31 4 0.03
32 2 0.01
33 9 0.06
34 10 0.06
35 20 0.13
37 2 0.01
38 4 0.03
39 102 0.66
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACATAACCCGGATTTAACAACTCACAC
Found at i:41408040 original size:41 final size:41
Alignment explanation
Indices: 41407963--41408040 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
41407953 TTAGTATCTC
* * *
41407963 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41408004 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
41408041 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:41415757 original size:40 final size:40
Alignment explanation
Indices: 41415712--41415896 Score: 210
Period size: 40 Copynumber: 4.6 Consensus size: 40
41415702 CTTGCGCAAG
* * *
41415712 GCCTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
41415752 GCCTTCGGGACTTAGCTCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
41415792 GCCTTCGAGTCTTAGCCCGGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * *
41415832 GCCTTCGGATCTTAGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
* *
41415873 GCCTTCGGGACTTAGCCCAGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
41415897 CATTCGAATA
Statistics
Matches: 118, Mismatches: 24, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 89 0.75
41 28 0.24
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:41420410 original size:15 final size:16
Alignment explanation
Indices: 41420390--41420419 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41420380 CAATTTTGTC
41420390 CCCTTTTA-CCTTTTA
1 CCCTTTTACCCTTTTA
41420405 CCCTTTTACCCTTTT
1 CCCTTTTACCCTTTT
41420420 CTTTATCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.37, G:0.00, T:0.53
Consensus pattern (16 bp):
CCCTTTTACCCTTTTA
Found at i:41420411 original size:8 final size:8
Alignment explanation
Indices: 41420390--41420419 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
41420380 CAATTTTGTC
41420390 CCCTTTTA
1 CCCTTTTA
41420398 -CCTTTTA
1 CCCTTTTA
41420405 CCCTTTTA
1 CCCTTTTA
41420413 CCCTTTT
1 CCCTTTT
41420420 CTTTATCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.10, C:0.37, G:0.00, T:0.53
Consensus pattern (8 bp):
CCCTTTTA
Found at i:41422124 original size:20 final size:19
Alignment explanation
Indices: 41422099--41422170 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
41422089 CATTGAGTCC
*
41422099 ATTTATTTTTATTTTATTTT
1 ATTTATTTTTATTTT-TTCT
**
41422119 ATTTATTTTTATTTTTAGT
1 ATTTATTTTTATTTTTTCT
*
41422138 AATTATTTTTA-TTTTTCT
1 ATTTATTTTTATTTTTTCT
*
41422156 GTTTATTTTTATTTT
1 ATTTATTTTTATTTT
41422171 CTTGGACTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 14 0.32
19 15 0.34
20 15 0.34
ACGTcount: A:0.19, C:0.01, G:0.03, T:0.76
Consensus pattern (19 bp):
ATTTATTTTTATTTTTTCT
Found at i:41422170 original size:5 final size:6
Alignment explanation
Indices: 41422100--41422170 Score: 70
Period size: 6 Copynumber: 11.3 Consensus size: 6
41422090 ATTGAGTCCA
* * *
41422100 TTTATT TTTATT TTATTTT ATTTATT TTTATT TTTAGTA ATTATT TTTATT
1 TTTATT TTTATT TT-TATT -TTTATT TTTATT TTTA-TT TTTATT TTTATT
* *
41422151 TTTCTG TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TT
41422171 CTTGGACTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
6 40 0.77
7 10 0.19
8 2 0.04
ACGTcount: A:0.18, C:0.01, G:0.03, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:41425221 original size:24 final size:23
Alignment explanation
Indices: 41425161--41425224 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 23
41425151 TAAAGGCTCG
*
41425161 CTTAAAATATGAAAGGGATTCGGTAA
1 CTTAAAATAT--AA-GGATTCAGTAA
*
41425187 CTTTAAATATAAGGATTCAGTAA
1 CTTAAAATATAAGGATTCAGTAA
41425210 CTTAAAATTATAAGG
1 CTTAAAA-TATAAGG
41425225 TTAAATTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 16 0.47
24 9 0.26
26 9 0.26
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (23 bp):
CTTAAAATATAAGGATTCAGTAA
Found at i:41427991 original size:18 final size:17
Alignment explanation
Indices: 41427951--41427991 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
41427941 CACTTTTTCA
*
41427951 ATCATCCCTCATCCTTC
1 ATCATCCCTCATCATTC
41427968 ATTCATCCCTCACTCATTC
1 A-TCATCCCTCA-TCATTC
41427987 ATCAT
1 ATCAT
41427992 TCTCTTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 14 0.67
19 6 0.29
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.37
Consensus pattern (17 bp):
ATCATCCCTCATCATTC
Found at i:41436627 original size:40 final size:41
Alignment explanation
Indices: 41436546--41436631 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
41436536 CGAGCATTAG
*
41436546 ATTAGTGCCGCTTTTTCTAAAAACGTCGCTATAGGTAGAGT
1 ATTAGTGCCGCTTTTTCTAAAAACGCCGCTATAGGTAGAGT
* * *
41436587 ATTAGTGGCG-TTTTTTTGAAAAACGCCGCTATATGT-GAGT
1 ATTAGTGCCGCTTTTTCT-AAAAACGCCGCTATAGGTAGAGT
41436627 ATTAG
1 ATTAG
41436632 CGACGCTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
40 15 0.38
41 25 0.62
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (41 bp):
ATTAGTGCCGCTTTTTCTAAAAACGCCGCTATAGGTAGAGT
Found at i:41437012 original size:15 final size:15
Alignment explanation
Indices: 41436991--41437029 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
41436981 AATATTTTAA
41436991 GGTTTAGGGATTATG
1 GGTTTAGGGATTATG
*
41437006 TGTTTAGGGATTATG
1 GGTTTAGGGATTATG
41437021 GGTTTAGGG
1 GGTTTAGGG
41437030 GTTGTGGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.41, T:0.41
Consensus pattern (15 bp):
GGTTTAGGGATTATG
Found at i:41437092 original size:15 final size:15
Alignment explanation
Indices: 41437064--41437147 Score: 66
Period size: 15 Copynumber: 5.6 Consensus size: 15
41437054 AATGGGTAAA
*
41437064 GGTTAAGCGTTTTAAG
1 GGTTAAG-GGTTTAAG
*
41437080 GGTTATGGGTTTAAG
1 GGTTAAGGGTTTAAG
*
41437095 GGTTAAGGG-TTATG
1 GGTTAAGGGTTTAAG
*
41437109 GGTTTAATGG-TTAAGG
1 GG-TTAAGGGTTTAA-G
* *
41437125 GGATAAGGG-TTAGG
1 GGTTAAGGGTTTAAG
41437139 GGTTAAGGG
1 GGTTAAGGG
41437148 GTTTTATGGT
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
14 15 0.27
15 32 0.57
16 9 0.16
ACGTcount: A:0.24, C:0.01, G:0.42, T:0.33
Consensus pattern (15 bp):
GGTTAAGGGTTTAAG
Found at i:41437100 original size:7 final size:7
Alignment explanation
Indices: 41437075--41437147 Score: 74
Period size: 7 Copynumber: 10.0 Consensus size: 7
41437065 GTTAAGCGTT
41437075 TTAAGGG
1 TTAAGGG
*
41437082 TTATGGG
1 TTAAGGG
41437089 TTTAAGGG
1 -TTAAGGG
41437097 TTAAGGG
1 TTAAGGG
*
41437104 TTATGGG
1 TTAAGGG
*
41437111 TTTAATGG
1 -TTAAGGG
41437119 TTAAGGGG
1 TTAA-GGG
*
41437127 ATAAGGG
1 TTAAGGG
*
41437134 TTAGGGG
1 TTAAGGG
41437141 TTAAGGG
1 TTAAGGG
41437148 GTTTTATGGT
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
7 37 0.70
8 16 0.30
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.33
Consensus pattern (7 bp):
TTAAGGG
Found at i:41437100 original size:22 final size:22
Alignment explanation
Indices: 41437075--41437147 Score: 94
Period size: 22 Copynumber: 3.3 Consensus size: 22
41437065 GTTAAGCGTT
41437075 TTAAGGGTTATGGGTTTAAGGG
1 TTAAGGGTTATGGGTTTAAGGG
*
41437097 TTAAGGGTTATGGGTTTAATGG
1 TTAAGGGTTATGGGTTTAAGGG
* * *
41437119 TTAAGGGGATAAGGG-TTAGGGG
1 TTAA-GGGTTATGGGTTTAAGGG
41437141 TTAAGGG
1 TTAAGGG
41437148 GTTTTATGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
21 3 0.07
22 34 0.76
23 8 0.18
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.33
Consensus pattern (22 bp):
TTAAGGGTTATGGGTTTAAGGG
Found at i:41437323 original size:14 final size:14
Alignment explanation
Indices: 41437306--41437345 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
41437296 TGAGGGTATA
*
41437306 GGGTTAGGGGTTAT
1 GGGTTATGGGTTAT
41437320 GGGTTATGGGTTAT
1 GGGTTATGGGTTAT
41437334 GGGTTATGGGTT
1 GGGTTATGGGTT
41437346 TAGGGTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.47, T:0.40
Consensus pattern (14 bp):
GGGTTATGGGTTAT
Found at i:41437351 original size:14 final size:15
Alignment explanation
Indices: 41437306--41437352 Score: 64
Period size: 14 Copynumber: 3.3 Consensus size: 15
41437296 TGAGGGTATA
*
41437306 GGGTTA-GGGGTTAT
1 GGGTTATGGGTTTAT
41437320 GGGTTATGGG-TTAT
1 GGGTTATGGGTTTAT
41437334 GGGTTATGGGTTTA-
1 GGGTTATGGGTTTAT
41437348 GGGTT
1 GGGTT
41437353 TAAGGTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
14 25 0.81
15 6 0.19
ACGTcount: A:0.13, C:0.00, G:0.47, T:0.40
Consensus pattern (15 bp):
GGGTTATGGGTTTAT
Found at i:41437351 original size:21 final size:21
Alignment explanation
Indices: 41437299--41437352 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
41437289 TAGTGGATGA
*
41437299 GGGTATAGGGTTAGGGGTTAT
1 GGGTTTAGGGTTAGGGGTTAT
*
41437320 GGG-TTATGGGTTATGGGTTAT
1 GGGTTTA-GGGTTAGGGGTTAT
41437341 GGGTTTAGGGTT
1 GGGTTTAGGGTT
41437353 TAAGGTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 2 0.07
21 24 0.83
22 3 0.10
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.39
Consensus pattern (21 bp):
GGGTTTAGGGTTAGGGGTTAT
Found at i:41437558 original size:26 final size:26
Alignment explanation
Indices: 41437468--41437556 Score: 135
Period size: 26 Copynumber: 3.4 Consensus size: 26
41437458 AGAATTAAAG
*
41437468 ATTTCAAATTTAGAATAATTTTCAAG
1 ATTTCAAATTTAGAATAATTTTCAAT
* *
41437494 AATTCAAATTTAGAATAAGTTTCAAT
1 ATTTCAAATTTAGAATAATTTTCAAT
41437520 ATTTCAAATTTTA-AATAATTTTCAAT
1 ATTTCAAA-TTTAGAATAATTTTCAAT
41437546 ATTTCAAATTT
1 ATTTCAAATTT
41437557 TATCTAATTC
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
25 3 0.05
26 50 0.88
27 4 0.07
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (26 bp):
ATTTCAAATTTAGAATAATTTTCAAT
Found at i:41439174 original size:25 final size:25
Alignment explanation
Indices: 41439146--41439196 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
41439136 GTTAGTAGGT
41439146 TAAAATATGCTACAATTCCTTAGAA
1 TAAAATATGCTACAATTCCTTAGAA
41439171 TAAAATATGCTACAATTCCTTAGAA
1 TAAAATATGCTACAATTCCTTAGAA
41439196 T
1 T
41439197 TCAATCTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (25 bp):
TAAAATATGCTACAATTCCTTAGAA
Found at i:41440574 original size:44 final size:44
Alignment explanation
Indices: 41440511--41440599 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
41440501 AGTGATGATC
41440511 AATCTTTCAATTTATAATGGCAAACCACAAAGACAACTAAGATT
1 AATCTTTCAATTTATAATGGCAAACCACAAAGACAACTAAGATT
*
41440555 AATCTTTCAATTTATAATGGCAAACCACATAGACAACTAAGATT
1 AATCTTTCAATTTATAATGGCAAACCACAAAGACAACTAAGATT
41440599 A
1 A
41440600 GCCATTGGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.28
Consensus pattern (44 bp):
AATCTTTCAATTTATAATGGCAAACCACAAAGACAACTAAGATT
Found at i:41441529 original size:28 final size:28
Alignment explanation
Indices: 41441494--41441554 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
41441484 TCAATCTTAT
*
41441494 TTTAATTAATATAATTCGTATTAATTTA
1 TTTAATTAATATAATTCGGATTAATTTA
*
41441522 TTTAATTAATATAATTTGGATTAATTTA
1 TTTAATTAATATAATTCGGATTAATTTA
41441550 TTTAA
1 TTTAA
41441555 ATATTATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (28 bp):
TTTAATTAATATAATTCGGATTAATTTA
Found at i:41441548 original size:24 final size:24
Alignment explanation
Indices: 41441516--41441576 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
41441506 AATTCGTATT
*
41441516 AATTTATTTAATTAATATAATTTG
1 AATTAATTTAATTAATATAATTTG
* * *
41441540 GATTAATTTATTTAAATATTATTT-
1 AATTAATTTAATT-AATATAATTTG
*
41441564 AATTAATATAATT
1 AATTAATTTAATT
41441577 TTTATAAGTA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
24 20 0.69
25 9 0.31
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (24 bp):
AATTAATTTAATTAATATAATTTG
Found at i:41441563 original size:15 final size:15
Alignment explanation
Indices: 41441543--41441603 Score: 58
Period size: 15 Copynumber: 4.2 Consensus size: 15
41441533 TAATTTGGAT
*
41441543 TAATTTATTTAAATA
1 TAATTTAATTAAATA
*
41441558 TTATTTAATT-AATA
1 TAATTTAATTAAATA
41441572 TAATTT--TTATAAGTA
1 TAATTTAATTA-AA-TA
41441587 TAATTTAATTAAA-A
1 TAATTTAATTAAATA
41441601 TAA
1 TAA
41441604 ATTTTTTTCC
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
12 2 0.05
14 15 0.39
15 16 0.42
16 2 0.05
17 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TAATTTAATTAAATA
Found at i:41441581 original size:20 final size:20
Alignment explanation
Indices: 41441518--41441581 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
41441508 TTCGTATTAA
41441518 TTTATTTAATTAATATAATT
1 TTTATTTAATTAATATAATT
** * * *
41441538 TGGA-TTAATTTATTTAAAT
1 TTTATTTAATTAATATAATT
*
41441557 ATTATTTAATTAATATAATT
1 TTTATTTAATTAATATAATT
41441577 TTTAT
1 TTTAT
41441582 AAGTATAATT
Statistics
Matches: 31, Mismatches: 12, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
TTTATTTAATTAATATAATT
Found at i:41441592 original size:29 final size:28
Alignment explanation
Indices: 41441543--41441610 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
41441533 TAATTTGGAT
* *
41441543 TAATTTATTTAAATATTATTTAATTAATA
1 TAATTT-TTTAAATATAATTTAATTAAAA
*
41441572 TAATTTTTATAAGTATAATTTAATTAAAA
1 TAATTTTT-TAAATATAATTTAATTAAAA
41441601 TAAATTTTTT
1 T-AATTTTTT
41441611 TCCATGTGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.06
29 25 0.74
30 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (28 bp):
TAATTTTTTAAATATAATTTAATTAAAA
Found at i:41441892 original size:9 final size:9
Alignment explanation
Indices: 41441878--41441946 Score: 102
Period size: 9 Copynumber: 7.7 Consensus size: 9
41441868 TATATACTTG
41441878 AACTTACAT
1 AACTTACAT
*
41441887 AACTTAAAT
1 AACTTACAT
41441896 AACTTACAT
1 AACTTACAT
*
41441905 GACTTACAT
1 AACTTACAT
*
41441914 AACTCACAT
1 AACTTACAT
*
41441923 AACTTACAG
1 AACTTACAT
41441932 AACTTACAT
1 AACTTACAT
41441941 AACTTA
1 AACTTA
41441947 ATTATACTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 52 1.00
ACGTcount: A:0.45, C:0.22, G:0.03, T:0.30
Consensus pattern (9 bp):
AACTTACAT
Found at i:41446863 original size:13 final size:14
Alignment explanation
Indices: 41446847--41446875 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41446837 TTATAAATAT
41446847 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
41446860 TTATAATGGTTTAA
1 TTATAATGGTTTAA
41446874 TT
1 TT
41446876 CATCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:41447621 original size:31 final size:31
Alignment explanation
Indices: 41447585--41447650 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
41447575 TGTATTTTTT
*
41447585 ATGCTACATTTGCTGTTTTTGGTTGGATTTC
1 ATGCTACATTTGCTGTTTTTGGTTGGATTTA
*
41447616 ATGCTATATTTGCTGTTTTTGGTTGGATTTA
1 ATGCTACATTTGCTGTTTTTGGTTGGATTTA
41447647 ATGC
1 ATGC
41447651 AAGAAGGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.15, C:0.11, G:0.23, T:0.52
Consensus pattern (31 bp):
ATGCTACATTTGCTGTTTTTGGTTGGATTTA
Found at i:41447823 original size:25 final size:25
Alignment explanation
Indices: 41447783--41447830 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
41447773 AAAAGTAAGG
* * *
41447783 CTTTTAGCGTCTCTTTTCTCACATA
1 CTTTTAGCGGCACTTTTCCCACATA
41447808 CTTTTAGCGGCACTTTTCCCACA
1 CTTTTAGCGGCACTTTTCCCACA
41447831 AATATCGCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.17, C:0.31, G:0.10, T:0.42
Consensus pattern (25 bp):
CTTTTAGCGGCACTTTTCCCACATA
Found at i:41463334 original size:9 final size:9
Alignment explanation
Indices: 41463309--41463337 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
41463299 GATTTTTCAG
41463309 ACATCATTT
1 ACATCATTT
41463318 AC-TCATTT
1 ACATCATTT
41463326 ACATCATTT
1 ACATCATTT
41463335 ACA
1 ACA
41463338 CTTTTTCGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.41
Consensus pattern (9 bp):
ACATCATTT
Found at i:41466570 original size:33 final size:33
Alignment explanation
Indices: 41466533--41466596 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
41466523 TCCTCAAATG
41466533 AGTAGCATG-ACTAGTGGCTGGAGAAGACAAGGT
1 AGTAGCATGAAC-AGTGGCTGGAGAAGACAAGGT
*
41466566 AGTAGTATGAACAGTGGCTGGAGAAGACAAG
1 AGTAGCATGAACAGTGGCTGGAGAAGACAAG
41466597 ACAGTGCTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.36, C:0.11, G:0.36, T:0.17
Consensus pattern (33 bp):
AGTAGCATGAACAGTGGCTGGAGAAGACAAGGT
Found at i:41471013 original size:46 final size:46
Alignment explanation
Indices: 41470963--41471135 Score: 226
Period size: 46 Copynumber: 3.7 Consensus size: 46
41470953 TGGTTGAGCA
*
41470963 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * *
41471009 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
41471054 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* *
41471102 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
41471136 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 11, Indels: 14
0.81 0.08 0.10
Matches are distributed among these distances:
43 5 0.05
45 4 0.04
46 61 0.56
47 29 0.27
48 4 0.04
50 6 0.06
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:41471119 original size:93 final size:93
Alignment explanation
Indices: 41470960--41471130 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
41470950 GGATGGTTGA
* *
41470960 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAGT
41471025 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
41471053 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAGT
41471118 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
41471131 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:41476363 original size:46 final size:46
Alignment explanation
Indices: 41476211--41476421 Score: 160
Period size: 46 Copynumber: 4.5 Consensus size: 46
41476201 TGTGTGAGCT
* * * * * * *
41476211 AGTGTAAGACATGTATGGGGCATCCATCAGCCAC-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCTACGA-GACGATAGCC
* * * * ** *
41476257 AATGTAAGACCATGTCTGGGACATGGCATCAAC-ATTGAGACAAGGGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCTA-CGAGACGATAGCC
* * *
41476305 AGTGTAAGACATGTTTGGGACATGCATCGGCCT-CGAGATG-TAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAG-CTACGAGACGAT-AGCC
* *
41476351 AGTGCAAGACATGTCTGGGACATGCATCAGCTACGAGACGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCTACGAGACGATAGCC
41476397 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
41476422 GAATCAACTT
Statistics
Matches: 128, Mismatches: 27, Indels: 19
0.74 0.16 0.11
Matches are distributed among these distances:
45 2 0.02
46 63 0.49
47 43 0.34
48 19 0.15
49 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCTACGAGACGATAGCC
Found at i:41476452 original size:47 final size:47
Alignment explanation
Indices: 41476252--41476472 Score: 191
Period size: 47 Copynumber: 4.7 Consensus size: 47
41476242 CACATTATGA
* * * *
41476252 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCAACATTGAGACAA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAAC-TCGAGATAT
* * * ** *
41476300 GGGCTAGTGTAAGA-CATGTTTGGGACAT-GCATCGGCCTCGAGATGT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-AACTCGAGATAT
* * * *
41476346 AAGCCAGTGCAAGA-CATGTCTGGGACAT-GCATCAGCTACGAGACGAT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACT-CGAGA-TAT
* * *
41476393 -AGTCAGTGTAAGACCATGTCTGGGACATGGAATCAACTTGAGATAT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACTCGAGATAT
* * *
41476439 GAGCCAGTATAAGACCATGCCTAGGACATGGCAT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCAT
41476473 TGGCACCTTA
Statistics
Matches: 137, Mismatches: 30, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
45 2 0.01
46 56 0.41
47 61 0.45
48 18 0.13
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (47 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACTCGAGATAT
Found at i:41482059 original size:17 final size:17
Alignment explanation
Indices: 41482037--41482072 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
41482027 AAATTTGGGG
41482037 TTCTCCATAGCTAGGGC
1 TTCTCCATAGCTAGGGC
41482054 TTCTCCATAGCTAGGGC
1 TTCTCCATAGCTAGGGC
41482071 TT
1 TT
41482073 TCAAGCTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (17 bp):
TTCTCCATAGCTAGGGC
Found at i:41487100 original size:45 final size:46
Alignment explanation
Indices: 41486942--41487156 Score: 217
Period size: 47 Copynumber: 4.6 Consensus size: 46
41486932 ATTCGTGTGT
* * * * *
41486942 GAGCTAGTGTAAGA-CATGTCTGGGGCATGCATCGGCCAC-ATTATGA
1 GAGC-AGTGTAAGACCATGTCTAGGACATGCATCGGCCTCGA-GACGA
* *
41486988 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGACGA
1 GAG-CAGTGTAAGACCATGTCTAGGACAT-GCATCGGCCTCGAGACGA
* *
41487036 GGGCTAGTGTAAGA-CATGTCTAGGACATGCAACGGCCTCGAGACGTA
1 GAGC-AGTGTAAGACCATGTCTAGGACATGCATCGGCCTCGAGACG-A
*
41487083 -AGCAGTGTAAGA-CATGTCTGGGACATGCATCGG-CTACGAGACGA
1 GAGCAGTGTAAGACCATGTCTAGGACATGCATCGGCCT-CGAGACGA
*
41487127 TAGTCAGTGTAAGACCATGTCTAGGACATG
1 GAG-CAGTGTAAGACCATGTCTAGGACATG
41487157 ACATTGACTT
Statistics
Matches: 144, Mismatches: 15, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
44 3 0.02
45 37 0.26
46 38 0.26
47 43 0.30
48 22 0.15
49 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.31, T:0.21
Consensus pattern (46 bp):
GAGCAGTGTAAGACCATGTCTAGGACATGCATCGGCCTCGAGACGA
Found at i:41487198 original size:139 final size:139
Alignment explanation
Indices: 41486947--41487199 Score: 323
Period size: 139 Copynumber: 1.8 Consensus size: 139
41486937 TGTGTGAGCT
* * *
41486947 AGTGTAAGACATGTCTGGGGCATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTAG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATGACGAGAGCCAGTGTAAGACCATGTCTAG
* * * * * *
41487012 GACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACATGTCTAGGACATGCAACGGCCTCGA
66 GACATGACATCGACATTCAGACGAGAGCTAGTATAAGACATGCCTAGGACATGCAACGGCCTCGA
41487077 GACGTAAGC
131 GACGTAAGC
* * *
41487086 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GACGATAGTCAGTGTAAGACCATGTCTA
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATGACGAGAGCCAGTGTAAGACCATGTCTA
* * *
41487150 GGACATGACATTGAC-TTCAGA-TATGAGCTAGTATAAGACCGTGCCTAGGA
65 GGACATGACATCGACATTCAGACGA-GAGCTAGTATAAGA-CATGCCTAGGA
41487200 TATGGAATCG
Statistics
Matches: 96, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
137 1 0.01
138 17 0.18
139 77 0.80
140 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (139 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATGACGAGAGCCAGTGTAAGACCATGTCTAG
GACATGACATCGACATTCAGACGAGAGCTAGTATAAGACATGCCTAGGACATGCAACGGCCTCGA
GACGTAAGC
Found at i:41493316 original size:55 final size:54
Alignment explanation
Indices: 41493249--41493392 Score: 171
Period size: 55 Copynumber: 2.6 Consensus size: 54
41493239 TATGTAGGCC
* * * **
41493249 CACGCCCTTGTTAATTTAACAGGTTCACCCACGGTTGCTTGGCACGGGCGTGTCG
1 CACGCCCATGTTAATTTGACAGGTTCGCCCACGGTT-CAAGGCACGGGCGTGTCG
* *
41493304 CACGCCCGTGTTAATTTGACAGGTTCGGCCACGGGTTCAAGGCACGGGCGTGTCG
1 CACGCCCATGTTAATTTGACAGGTTCGCCCAC-GGTTCAAGGCACGGGCGTGTCG
* * * *
41493359 AACGCCCATGCTATTTTGGCAGGTTCGCCCACGG
1 CACGCCCATGTTAATTTGACAGGTTCGCCCACGG
41493393 CCATGTCTCA
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
54 2 0.03
55 70 0.92
56 4 0.05
ACGTcount: A:0.17, C:0.29, G:0.30, T:0.24
Consensus pattern (54 bp):
CACGCCCATGTTAATTTGACAGGTTCGCCCACGGTTCAAGGCACGGGCGTGTCG
Found at i:41507497 original size:30 final size:30
Alignment explanation
Indices: 41507463--41507522 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
41507453 CTTTAATATG
*
41507463 AACTTTGGAAAAATTACATTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
41507493 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
41507523 GGCTCGAGAA
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:0.30, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:41509565 original size:95 final size:96
Alignment explanation
Indices: 41509444--41509661 Score: 246
Period size: 95 Copynumber: 2.3 Consensus size: 96
41509434 GATCCGACCT
* * * *
41509444 ACTGTAACTTCAGAGG-TATAGGATTTGT-GACTTGTAG-TCATAATTTATTTCACTACAACTTC
1 ACTGTAACTTCAG-GGAAATAAGATTTGTAG-CTTGTAGCT-ATAATCTATTCCACTACAACTTC
*
41509506 AGGGAAATAAGATTTGTTATC-TCAATCTGCTCC
63 AGGGAAATAAGATTTGCTATCTTCAATCTGCTCC
* * * ** *
41509539 ACTGTAACTTCAGGGAGATAAGATTTGTAGCTTGTAGCTTTAATCTGTTCCACTGTAACTTTAGG
1 ACTGTAACTTCAGGGAAATAAGATTTGTAGCTTGTAGCTATAATCTATTCCACTACAACTTCAGG
* *
41509604 GAAATAAGATTTGCTATCTTCAGTCTGTTCC
66 GAAATAAGATTTGCTATCTTCAATCTGCTCC
**
41509635 ACTACAACTTCAGGGAAATAAGATTTG
1 ACTGTAACTTCAGGGAAATAAGATTTG
41509662 CTATCTTCAA
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
94 2 0.02
95 66 0.63
96 36 0.35
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (96 bp):
ACTGTAACTTCAGGGAAATAAGATTTGTAGCTTGTAGCTATAATCTATTCCACTACAACTTCAGG
GAAATAAGATTTGCTATCTTCAATCTGCTCC
Found at i:41509650 original size:45 final size:45
Alignment explanation
Indices: 41509494--41509844 Score: 283
Period size: 45 Copynumber: 7.6 Consensus size: 45
41509484 TAATTTATTT
* *
41509494 CACTACAACTTCAGGGAAATAAGATTTGTTATC-TCAATCTGCTC
1 CACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTGCTC
* * * * *
41509538 CACTGTAACTTCAGGGAGATAAGATTTGTAGCTTGTAGCTTTAATCTGTTC
1 CACTGCAACTTCAGGGAAATAAGA-TT-T-GC---TATCTTCAATCTGCTC
* * * *
41509589 CACTGTAACTTTAGGGAAATAAGATTTGCTATCTTCAGTCTGTTC
1 CACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTGCTC
*
41509634 CACTACAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTGCTC
1 CACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTGCTC
* * * * **
41509679 CACTGTAACTTCAGGGAGATAAGATTTGTAGCTTGTAGCTTTAATCTATTC
1 CACTGCAACTTCAGGGAAATAAGA-TT-T-GC---TATCTTCAATCTGCTC
* * * * * *
41509730 CACTCCAACGTCTGGGAAATAAGATTTTCTGTCTTCAGTCTGCTC
1 CACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTGCTC
** * * * **
41509775 TGCTGCAACTTCAAGGAGATAAGAATTG-TGGCTTCAATCTGCTC
1 CACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTGCTC
* *
41509819 CACTACAACTTCAGGGAGATAAGATT
1 CACTGCAACTTCAGGGAAATAAGATT
41509845 CACCATGATG
Statistics
Matches: 242, Mismatches: 52, Indels: 26
0.76 0.16 0.08
Matches are distributed among these distances:
44 56 0.23
45 105 0.43
46 3 0.01
47 2 0.01
48 5 0.02
49 2 0.01
50 7 0.03
51 62 0.26
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (45 bp):
CACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTGCTC
Found at i:41509703 original size:141 final size:140
Alignment explanation
Indices: 41509494--41509844 Score: 508
Period size: 141 Copynumber: 2.5 Consensus size: 140
41509484 TAATTTATTT
41509494 CACTACAACTTCAGGGAAATAAGATTTGTTATC-TCAATCTGCTCCACTGTAACTTCAGGGAGAT
1 CACTACAACTTCAGGGAAATAAGATTTG-TATCTTCAATCTGCTCCACTGTAACTTCAGGGAGAT
* ** *
41509558 AAGATTTGTAGCTTGTAGCTTTAATCTGTTCCACTGTAAC-TTTAGGGAAATAAGATTTGCTATC
65 AAGATTTGTAGCTTGTAGCTTTAATCTATTCCACTCCAACGTCT-GGGAAATAAGATTTGCTATC
*
41509622 TTCAGTCTGTTC
129 TTCAGTCTGCTC
41509634 CACTACAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTGCTCCACTGTAACTTCAGGGAGAT
1 CACTACAACTTCAGGGAAATAAGATTTG-TATCTTCAATCTGCTCCACTGTAACTTCAGGGAGAT
* *
41509699 AAGATTTGTAGCTTGTAGCTTTAATCTATTCCACTCCAACGTCTGGGAAATAAGATTTTCTGTCT
65 AAGATTTGTAGCTTGTAGCTTTAATCTATTCCACTCCAACGTCTGGGAAATAAGATTTGCTATCT
41509764 TCAGTCTGCTC
130 TCAGTCTGCTC
** * * * * ** **
41509775 TGCTGCAACTTCAAGGAGATAAGAATTGTGGCTTCAATCTGCTCCACTACAACTTCAGGGAGATA
1 CACTACAACTTCAGGGAAATAAGATTTGTATCTTCAATCTGCTCCACTGTAACTTCAGGGAGATA
41509840 AGATT
66 AGATT
41509845 CACCATGATG
Statistics
Matches: 191, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
140 70 0.37
141 119 0.62
142 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (140 bp):
CACTACAACTTCAGGGAAATAAGATTTGTATCTTCAATCTGCTCCACTGTAACTTCAGGGAGATA
AGATTTGTAGCTTGTAGCTTTAATCTATTCCACTCCAACGTCTGGGAAATAAGATTTGCTATCTT
CAGTCTGCTC
Found at i:41509772 original size:96 final size:96
Alignment explanation
Indices: 41509631--41509808 Score: 248
Period size: 96 Copynumber: 1.9 Consensus size: 96
41509621 CTTCAGTCTG
* * *
41509631 TTCCACTACAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTGCTCCACTGTAACTTCAGGGA
1 TTCCACTACAACGTCAGGGAAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAAGGA
*
41509696 GATAAGATTTGTAGCTTGTAGCTTTAATCTA
66 GATAAGAATTGTAGCTTGTAGCTTTAATCTA
* * * * * **
41509727 TTCCACTCCAACGTCTGGGAAATAAGATTTTCTGTCTTCAGTCTGCTCTGCTGCAACTTCAAGGA
1 TTCCACTACAACGTCAGGGAAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAAGGA
*
41509792 GATAAGAATTGTGGCTT
66 GATAAGAATTGTAGCTT
41509809 CAATCTGCTC
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
96 70 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.34
Consensus pattern (96 bp):
TTCCACTACAACGTCAGGGAAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAAGGA
GATAAGAATTGTAGCTTGTAGCTTTAATCTA
Found at i:41514365 original size:46 final size:46
Alignment explanation
Indices: 41514315--41514484 Score: 184
Period size: 46 Copynumber: 3.7 Consensus size: 46
41514305 TTGAGCATCT
* * *
41514315 GAACTCATTGATTTGAGTCCGAGTTCACTTATGGATGCAAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
* * * *
41514361 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CGTCC
* * *
41514408 GAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
*
41514454 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
41514485 GGGGCGGGTT
Statistics
Matches: 102, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 56 0.55
47 29 0.28
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
Found at i:41514468 original size:93 final size:93
Alignment explanation
Indices: 41514309--41514479 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
41514299 GGATGGTTGA
* * * *
41514309 GCATCTGAACTCATTGATTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
41514374 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
41514402 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
41514467 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
41514480 ACTTAGGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:41514746 original size:19 final size:20
Alignment explanation
Indices: 41514709--41514746 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
41514699 ATAAGGTGGT
41514709 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
41514729 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
41514747 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:41517057 original size:20 final size:20
Alignment explanation
Indices: 41517032--41517069 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
41517022 ATAGAGATAA
41517032 AAGAATAATCATCTGCATCT
1 AAGAATAATCATCTGCATCT
41517052 AAGAATAATCATCTGCAT
1 AAGAATAATCATCTGCAT
41517070 GGTATGATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (20 bp):
AAGAATAATCATCTGCATCT
Found at i:41520396 original size:22 final size:22
Alignment explanation
Indices: 41520368--41520489 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
41520358 TTCCACATCC
41520368 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
41520390 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
41520414 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
41520437 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
41520461 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
41520484 ATCACA
1 ATCACA
41520490 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:41520666 original size:49 final size:47
Alignment explanation
Indices: 41520340--41520828 Score: 689
Period size: 47 Copynumber: 10.3 Consensus size: 47
41520330 CCCTTCGGGA
* * * *
41520340 CTTATCACATTTATGCACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
41520387 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
41520434 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
41520481 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
41520528 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
41520575 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
41520622 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
41520671 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
41520718 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
41520767 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
41520816 CTTATCACATATA
1 CTTATCACATATA
41520829 ATGGCCTTAT
Statistics
Matches: 413, Mismatches: 23, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
46 1 0.00
47 275 0.67
49 136 0.33
50 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:41520844 original size:116 final size:116
Alignment explanation
Indices: 41520715--41520944 Score: 451
Period size: 116 Copynumber: 2.0 Consensus size: 116
41520705 TCGGCCATTA
41520715 GGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
1 GGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
41520780 TATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATAAT
66 TATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATAAT
*
41520831 GGCCTTATCACATATATATACACTTTCACATTCATTACATCGGCCATTAGGCCTTATCACATATA
1 GGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
41520896 TATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATA
66 TATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATA
41520945 TACACTTTCA
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 113 1.00
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.34
Consensus pattern (116 bp):
GGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
TATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATAAT
Found at i:41520846 original size:67 final size:67
Alignment explanation
Indices: 41520764--41520895 Score: 246
Period size: 67 Copynumber: 2.0 Consensus size: 67
41520754 TCGGCCATTA
*
41520764 GGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATA
1 GGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
41520829 AT
66 AT
*
41520831 GGCCTTATCACATATATATACACTTTCACATTCATTACATCGGCCATTAGGCCTTATCACATATA
1 GGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
41520896 TATACACTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (67 bp):
GGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
AT
Found at i:41520887 original size:49 final size:49
Alignment explanation
Indices: 41520831--41520958 Score: 224
Period size: 49 Copynumber: 2.7 Consensus size: 49
41520821 CACATATAAT
*
41520831 GGCCTTATCACATATATATACACTTTCACATTCATTACATCGGCCATTA
1 GGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTA
*
41520880 GGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTA
1 GGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTA
41520929 GGCCTTATCAC--ATATATACACTTTCACATT
1 GGCCTTATCACATATATATACACTTTCACATT
41520959 TATTCAAATA
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
47 19 0.25
49 58 0.75
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.35
Consensus pattern (49 bp):
GGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTA
Found at i:41533528 original size:48 final size:48
Alignment explanation
Indices: 41533453--41533680 Score: 216
Period size: 48 Copynumber: 4.9 Consensus size: 48
41533443 CACATGGTAG
* * *
41533453 GATGCCAATGTCATATCCCAGATATGGTCTTACATGGGATCACATATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
* * ** ** *
41533501 GATGCCAATGCCATGTACGAGACATGGTCTTACATGGGATCGTAGGTT
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
* *
41533549 GATGCCAATGCCATGTCCCAGGCATGGTCTTAGATGGGATCACATATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
* ** ** *
41533597 GATGCCGAT---A-G-CCCA-ACTATTATCTTACATGAAATTACATATC
1 GATGCCAATGCCATGTCCCAGAC-ATGGTCTTACATGGGATCACATATC
* * *
41533640 GATGCCAAAGCCATGTCCCAAACATGGTCTTATATGGGATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATC
41533681 GTACATAACC
Statistics
Matches: 138, Mismatches: 35, Indels: 14
0.74 0.19 0.07
Matches are distributed among these distances:
42 1 0.01
43 30 0.22
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 101 0.73
49 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (48 bp):
GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
Found at i:41547978 original size:31 final size:30
Alignment explanation
Indices: 41547937--41548000 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
41547927 CCTTTTCATA
*
41547937 TTTCATATTTCATAACACTAGGCCGAAGACT
1 TTTCAAATTTCATAACACTAGGCCGAAG-CT
** *
41547968 TTTCAAATTTCATATTACTGGGCCGAAGCT
1 TTTCAAATTTCATAACACTAGGCCGAAGCT
41547998 TTT
1 TTT
41548001 ACAGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (30 bp):
TTTCAAATTTCATAACACTAGGCCGAAGCT
Found at i:41548269 original size:23 final size:23
Alignment explanation
Indices: 41548215--41548425 Score: 343
Period size: 23 Copynumber: 9.1 Consensus size: 23
41548205 CCTAGCCTCT
*
41548215 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
41548238 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
41548262 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
**
41548285 TTTAATAACAAGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
41548308 CTTAATAACTGGGGCATAAG-CC
1 TTTAATAACTGGGGCATAAGCCC
*
41548330 TTTCAATAACTGGGGCACAAGCCC
1 TTT-AATAACTGGGGCATAAGCCC
41548354 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
41548377 TTTAATAACTGGGGCACAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
41548400 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
41548423 TTT
1 TTT
41548426 TTCACTTCCT
Statistics
Matches: 174, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
22 4 0.02
23 143 0.82
24 27 0.16
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:41548504 original size:20 final size:20
Alignment explanation
Indices: 41548476--41548542 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
41548466 TTATGATTAC
*
41548476 ATCACGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
41548496 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
41548516 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
41548536 ACCATGT
1 ATCATGT
41548543 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Done.