Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 92 of 117
Found at i:16535350 original size:91 final size:91
Alignment explanation
Indices: 16535132--16535358 Score: 230
Period size: 91 Copynumber: 2.5 Consensus size: 91
16535122 GAACTTTTCA
** ** *
16535132 AATGAGAATCTTTGAAATTTTGGATGCAAAATCCTAAAA-TTTTTGAATGAGAATCTTTAAAGTT
1 AATGAGAATCTTTGAAATTTTGGATGTGAAATATTAAAATTTTTTAAATGAGAATCTTTAAAGTT
16535196 TTGAATATGAAGCCATAAAGTTTTTG
66 TTGAATATGAAGCCATAAAGTTTTTG
** * * * *
16535222 AAAAAGAACCTTTGAAACTTTGGATGTG-AATCTTTAAAATTTTTTAAATGTGAATCTTTGAAA-
1 AATGAGAATCTTTGAAATTTTGGATGTGAAAT-ATTAAAATTTTTTAAATGAGAATCTTT-AAAG
* * * *
16535285 TTTTGGATGTGAATCC-TAAAATTTTTTG
64 TTTTGAATATGAAGCCAT-AAAGTTTTTG
* *
16535313 AATGAGAATCTTT-ATAATTTTGGTTGTGAAATATTAAAGTTTTTTA
1 AATGAGAATCTTTGA-AATTTTGGATGTGAAATATTAAAATTTTTTA
16535359 GAAATTTCAA
Statistics
Matches: 110, Mismatches: 21, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
89 3 0.03
90 29 0.26
91 72 0.65
92 6 0.05
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (91 bp):
AATGAGAATCTTTGAAATTTTGGATGTGAAATATTAAAATTTTTTAAATGAGAATCTTTAAAGTT
TTGAATATGAAGCCATAAAGTTTTTG
Found at i:16535495 original size:21 final size:20
Alignment explanation
Indices: 16535457--16535494 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16535447 GAATTCTAGC
*
16535457 TGTGAACCTTGAAATTTTGA
1 TGTGAACCCTGAAATTTTGA
16535477 TGTGAATCCCTG-AATTTT
1 TGTGAA-CCCTGAAATTTT
16535495 TCAAATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.42
Consensus pattern (20 bp):
TGTGAACCCTGAAATTTTGA
Found at i:16535616 original size:35 final size:35
Alignment explanation
Indices: 16535564--16535643 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 35
16535554 ATCTTTAATA
* * *
16535564 TGAAAATATTAGGAATTTTCAA-TTCTCACGAATC
1 TGAAAATCTTATGAATTTTCAAGTACTCACGAATC
* * *
16535598 TGAAAACTCTTATGAATTTTTAAGTACTTATGAATC
1 TGAAAA-TCTTATGAATTTTCAAGTACTCACGAATC
16535634 TGAAAATCTT
1 TGAAAATCTT
16535644 GTAAAACTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 6 0.16
35 17 0.45
36 15 0.39
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (35 bp):
TGAAAATCTTATGAATTTTCAAGTACTCACGAATC
Found at i:16535823 original size:35 final size:35
Alignment explanation
Indices: 16535784--16535857 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
16535774 AAACCTTGAT
* * *
16535784 AAATTTGGAAACTTTACGAAACTTGAAATTTTTGG
1 AAATTTGGAAACTTTACGAAACTTAAAATCTTTGC
* **
16535819 AAATTTGGAACCTTTGTGAAACTTAAAATCTTTGC
1 AAATTTGGAAACTTTACGAAACTTAAAATCTTTGC
16535854 AAAT
1 AAAT
16535858 CTAGAATCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (35 bp):
AAATTTGGAAACTTTACGAAACTTAAAATCTTTGC
Found at i:16535869 original size:35 final size:35
Alignment explanation
Indices: 16535801--16535908 Score: 101
Period size: 35 Copynumber: 3.1 Consensus size: 35
16535791 GAAACTTTAC
* * * * *
16535801 GAAACTTGAAATTTTTGGAAATTTGGAACCTTTGT
1 GAAACTTGAAATCTTTGCAAATCTAGAATCTTTGT
* *
16535836 GAAACTTAAAATCTTTGCAAATCTAGAATCTTTGC
1 GAAACTTGAAATCTTTGCAAATCTAGAATCTTTGT
* * * *
16535871 G-AATTTGAAACCTTTGCAAAACTTGAAATCTTTGT
1 GAAACTTGAAATCTTTGCAAATCTAG-AATCTTTGT
16535906 GAA
1 GAA
16535909 TTTGGAACCC
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
34 19 0.33
35 38 0.66
36 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (35 bp):
GAAACTTGAAATCTTTGCAAATCTAGAATCTTTGT
Found at i:16535885 original size:17 final size:17
Alignment explanation
Indices: 16535865--16535917 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
16535855 AATCTAGAAT
16535865 CTTTGCGAATTTGAAAC
1 CTTTGCGAATTTGAAAC
* * *
16535882 CTTTGCAAAACTTGAAAT
1 CTTTGC-GAATTTGAAAC
* *
16535900 CTTTGTGAATTTGGAAC
1 CTTTGCGAATTTGAAAC
16535917 C
1 C
16535918 CCTGAGAGTC
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (17 bp):
CTTTGCGAATTTGAAAC
Found at i:16535910 original size:35 final size:34
Alignment explanation
Indices: 16535830--16535917 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 34
16535820 AATTTGGAAC
* * * *
16535830 CTTTGTGAAACTTAAAATCTTTGCAAATCTAGAAT
1 CTTTGTG-AATTTGAAACCTTTGCAAAACTAGAAT
* *
16535865 CTTTGCGAATTTGAAACCTTTGCAAAACTTGAAAT
1 CTTTGTGAATTTGAAACCTTTGCAAAACTAG-AAT
*
16535900 CTTTGTGAATTTGGAACC
1 CTTTGTGAATTTGAAACC
16535918 CCTGAGAGTC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
34 19 0.43
35 25 0.57
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (34 bp):
CTTTGTGAATTTGAAACCTTTGCAAAACTAGAAT
Found at i:16546162 original size:16 final size:16
Alignment explanation
Indices: 16546142--16546178 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
16546132 GTTTAAAATT
16546142 ATCATAAATCATCATC
1 ATCATAAATCATCATC
* *
16546158 GTCATAAATTATCATC
1 ATCATAAATCATCATC
16546174 ATCAT
1 ATCAT
16546179 TCATTTATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.35
Consensus pattern (16 bp):
ATCATAAATCATCATC
Found at i:16547522 original size:13 final size:13
Alignment explanation
Indices: 16547504--16547536 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
16547494 TGGTTTTGCT
16547504 CTTAAAACTTCAA
1 CTTAAAACTTCAA
16547517 CTTAAAACTTCAA
1 CTTAAAACTTCAA
16547530 CTCTAAA
1 CT-TAAA
16547537 TAATAGCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (13 bp):
CTTAAAACTTCAA
Found at i:16550684 original size:132 final size:131
Alignment explanation
Indices: 16550535--16550906 Score: 326
Period size: 132 Copynumber: 2.8 Consensus size: 131
16550525 CAATCTTGGT
* * * * *
16550535 CATTTATCTTTGATCTTAGTTCAGTCTAGATCATTTATTTTTCTAATCTATG-GTTCAATCATAG
1 CATTCATCTTTGGTCTTAGTTTAGTCCAGATCATTTATTTTTCTAAT-T-TGAGTTCAATCACAG
** * * * *
16550599 TCACTTATTTTTTACTTTGGCTT-GGTGC-AAGTTATTTTATTTTTTTTTACTTACAG-TTCAAT
64 TCACTTATTTTCGACTTTGG-TTCAGT-CTAAGTCATTTTATTTTTTCTAACTT-CAGATTCAAT
16550661 CTCAAC
126 CTCAAC
* * * *
16550667 CATTCATCTTTGGTCTTAGTTTAATCCAGATCATTTATTTTTCTGATTTGCATTTCAATCCCAGT
1 CATTCATCTTTGGTCTTAGTTTAGTCCAGATCATTTATTTTTCTAATTTG-AGTTCAATCACAGT
* * **
16550732 CACTTATTTTCGACTTTGGTTCAGTCTAGGTCATTTTATTTTTTCTAACTTCTGATTCAATCTTG
65 CACTTATTTTCGACTTTGGTTCAGTCTAAGTCATTTTATTTTTTCTAACTTCAGATTCAATCTCA
*
16550797 AT
130 AC
* * * * * *
16550799 CATTCATATTCGGTCTTGGTTTAGTCCAGATCATTTATTTTTTTGATTTGCAATTCAATTC-C-G
1 CATTCATCTTTGGTCTTAGTTTAGTCCAGATCATTTATTTTTCTAATTTG-AGTTCAA-TCACAG
* ** * *
16550862 ATCACTCATTTTTTACTTTGGCTT-GGTCTAGGTCATTTTATTTTT
64 -TCACTTATTTTCGACTTTGG-TTCAGTCTAAGTCATTTTATTTTT
16550907 CTAGCTTACT
Statistics
Matches: 202, Mismatches: 30, Indels: 16
0.81 0.12 0.06
Matches are distributed among these distances:
130 2 0.01
131 7 0.03
132 189 0.94
133 4 0.02
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.50
Consensus pattern (131 bp):
CATTCATCTTTGGTCTTAGTTTAGTCCAGATCATTTATTTTTCTAATTTGAGTTCAATCACAGTC
ACTTATTTTCGACTTTGGTTCAGTCTAAGTCATTTTATTTTTTCTAACTTCAGATTCAATCTCAA
C
Found at i:16550724 original size:65 final size:63
Alignment explanation
Indices: 16550655--16550857 Score: 167
Period size: 65 Copynumber: 3.1 Consensus size: 63
16550645 TTACTTACAG
* * *
16550655 TTCAATCTCAACCATTCATCTTTGGTCTTAGTTTAATCCAGATCATTTATTTTTCTGATTTGCA
1 TTCAATCTCAATCATTCAT-TTTGGTCTTGGTTTAGTCCAGATCATTTATTTTTCTGATTTGCA
* * * * * * * *
16550719 TTTCAATCCCAGTCACTT-ATTTTCGACTTTGGTTCAGTCTAGGTCATTTTATTTTTTCTAACTT
1 -TTCAATCTCAATCA-TTCATTTTGGTC-TTGGTTTAGTCCAGATCA-TTTA-TTTTTCTGA-TT
16550783 CTG-A
60 -TGCA
** * *
16550787 TTCAATCTTGATCATTCATATTCGGTCTTGGTTTAGTCCAGATCATTTATTTTTTTGATTTGCAA
1 TTCAATCTCAATCATTCAT-TTTGGTCTTGGTTTAGTCCAGATCATTTATTTTTCTGATTTGC-A
16550852 TTCAAT
1 TTCAAT
16550858 TCCGATCACT
Statistics
Matches: 105, Mismatches: 23, Indels: 20
0.71 0.16 0.14
Matches are distributed among these distances:
63 2 0.02
64 7 0.07
65 40 0.38
66 12 0.11
67 35 0.33
68 7 0.07
69 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.48
Consensus pattern (63 bp):
TTCAATCTCAATCATTCATTTTGGTCTTGGTTTAGTCCAGATCATTTATTTTTCTGATTTGCA
Found at i:16550971 original size:132 final size:132
Alignment explanation
Indices: 16550679--16551006 Score: 378
Period size: 132 Copynumber: 2.5 Consensus size: 132
16550669 TTCATCTTTG
* * * * *
16550679 GTCTTAGTTTAATCCAGATCATTTATTTTTCTGATTTGCATTTCAATCCCAGTCACTTATTTTCG
1 GTCTTAGTTCAGTCCAGATCATTTATTTTTTTGATTTGCAATTCAATCCCAGTCACTCATTTTCG
**
16550744 ACTTTGGTTCAGTCTAGGTCATTTTATTTTTTCTAACTTCTGATTCAATCTTGATCATTCATATT
66 ACTTTGGTTCAGTCTAGGTCATTTTATTTTTTCTAACTTCTGATTCAATCCCGATCATTCATATT
*
16550809 CG
131 CA
* * * *
16550811 GTCTTGGTTTAGTCCAGATCATTTATTTTTTTGATTTGCAATTCAATTCC-GATCACTCATTTTT
1 GTCTTAGTTCAGTCCAGATCATTTATTTTTTTGATTTGCAATTCAATCCCAG-TCACTCATTTTC
* * * *
16550875 TACTTTGGCTT-GGTCTAGGTCATTTTA-TTTTTCTAGCTTACT-ATTCAATCCCGGTCATTCAT
65 GACTTTGG-TTCAGTCTAGGTCATTTTATTTTTTCTAACTT-CTGATTCAATCCCGATCATTCAT
16550937 ATTCA
128 ATTCA
* * * * *
16550942 GTTTTAGTTCAGTTCAGATCATTTAATTTTTTGACTTTG-GACTCAATCCCAGTCATCTTCATTT
1 GTCTTAGTTCAGTCCAGATCATTTATTTTTTTGA-TTTGCAATTCAATCCCAGTCA-C-TCATTT
16551006 T
63 T
16551007 TTGATTTTGG
Statistics
Matches: 167, Mismatches: 22, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
131 73 0.44
132 85 0.51
133 9 0.05
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (132 bp):
GTCTTAGTTCAGTCCAGATCATTTATTTTTTTGATTTGCAATTCAATCCCAGTCACTCATTTTCG
ACTTTGGTTCAGTCTAGGTCATTTTATTTTTTCTAACTTCTGATTCAATCCCGATCATTCATATT
CA
Found at i:16554701 original size:18 final size:18
Alignment explanation
Indices: 16554666--16554717 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 18
16554656 ATATATCAAT
*
16554666 TATCATACAAT-A-ATAA
1 TATCATGCAATAATATAA
*
16554682 TAATCATGTAA-AATATAA
1 T-ATCATGCAATAATATAA
16554700 TATCATGCAATAATATAA
1 TATCATGCAATAATATAA
16554718 AATACCATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 1 0.03
17 16 0.55
18 12 0.41
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (18 bp):
TATCATGCAATAATATAA
Found at i:16554893 original size:7 final size:7
Alignment explanation
Indices: 16554881--16554905 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16554871 TTAATCATGC
16554881 AATAATA
1 AATAATA
16554888 AATAATA
1 AATAATA
16554895 AATAATA
1 AATAATA
16554902 AATA
1 AATA
16554906 GCCATGCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAATA
Found at i:16556057 original size:44 final size:42
Alignment explanation
Indices: 16555942--16556091 Score: 201
Period size: 43 Copynumber: 3.5 Consensus size: 42
16555932 CTAAGACTTT
* *
16555942 AACTTTGAAAAAATAAAATGCTTTCCCATAACTGAAGCTTTGA
1 AACTTTGAAAAAATAAAATGC-TCCCCATAACTGAGGCTTTGA
* * * *
16555985 AACTTTTAGAAAATAAAATGCTCTCCCATAACTGAGGTTTTGG
1 AACTTTGAAAAAATAAAATGCTC-CCCATAACTGAGGCTTTGA
*
16556028 AACTTTGAAGAAAATAAAAATGCTCCCCATAACTAAGGCTTTGA
1 AACTTTGAA-AAAAT-AAAATGCTCCCCATAACTGAGGCTTTGA
16556072 AACTTTGAAAAAATAAAATG
1 AACTTTGAAAAAATAAAATG
16556092 AGATATCTAA
Statistics
Matches: 93, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
42 7 0.08
43 47 0.51
44 30 0.32
45 9 0.10
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (42 bp):
AACTTTGAAAAAATAAAATGCTCCCCATAACTGAGGCTTTGA
Found at i:16561684 original size:19 final size:20
Alignment explanation
Indices: 16561640--16561685 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
16561630 AAGGGTTAGT
*
16561640 CAATATAATATATACAATGAA
1 CAATATAATATATA-AATAAA
16561661 CAATATAATATAT-AATAAA
1 CAATATAATATATAAATAAA
*
16561680 TAATAT
1 CAATAT
16561686 GAAGGGTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 10 0.43
21 13 0.57
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (20 bp):
CAATATAATATATAAATAAA
Found at i:16562826 original size:22 final size:22
Alignment explanation
Indices: 16562801--16562869 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
16562791 TTATCATGTA
16562801 ATAATAATAATCATGTC-A-AT
1 ATAATAATAATCATGTCAATAT
*
16562821 AT-ATAAT-ATCATG-CAAATGT
1 ATAATAATAATCATGTC-AATAT
16562841 AATAATAATAATCATGTCAATAT
1 -ATAATAATAATCATGTCAATAT
16562864 ATAATA
1 ATAATA
16562870 TCATGCAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
17 1 0.03
18 6 0.15
19 6 0.15
20 3 0.08
21 2 0.05
22 11 0.28
23 10 0.25
24 1 0.03
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.35
Consensus pattern (22 bp):
ATAATAATAATCATGTCAATAT
Found at i:16562833 original size:35 final size:35
Alignment explanation
Indices: 16562776--16562882 Score: 124
Period size: 41 Copynumber: 2.8 Consensus size: 35
16562766 CAAGAATGTT
*
16562776 ATGTAAATATATTAATTATCATGTAATAATAATAATC
1 ATGTCAATATA-TAA-TATCATGTAATAATAATAATC
16562813 ATGTCAATATATAATATCATGCAAATGTAATAATAATAATC
1 ATGTCAATATAT-A-AT-AT-C--ATGTAATAATAATAATC
*
16562854 ATGTCAATATATAATATCATGCAATAATA
1 ATGTCAATATATAATATCATGTAATAATA
16562883 TAAAATACCA
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
35 10 0.16
36 1 0.02
37 13 0.21
38 5 0.08
39 3 0.05
40 1 0.02
41 29 0.47
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (35 bp):
ATGTCAATATATAATATCATGTAATAATAATAATC
Found at i:16562843 original size:16 final size:18
Alignment explanation
Indices: 16562776--16562885 Score: 93
Period size: 18 Copynumber: 5.8 Consensus size: 18
16562766 CAAGAATGTT
*
16562776 ATGTAAATATATTAATTATC
1 ATGTCAATATA-TAA-TATC
16562796 ATGT-AATA-ATAATAATC
1 ATGTCAATATATAAT-ATC
16562813 ATGTCAATATATAATATC
1 ATGTCAATATATAATATC
16562831 ATG-CAAATGTAATAATAATAATC
1 ATGTC-AA--T-AT-ATAAT-ATC
16562854 ATGTCAATATATAATATC
1 ATGTCAATATATAATATC
16562872 ATG-CAATAATATAA
1 ATGTCAAT-ATATAA
16562886 AATACCATGC
Statistics
Matches: 79, Mismatches: 0, Indels: 24
0.77 0.00 0.23
Matches are distributed among these distances:
16 1 0.01
17 15 0.19
18 25 0.32
19 14 0.18
20 7 0.09
21 3 0.04
22 5 0.06
23 8 0.10
24 1 0.01
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.36
Consensus pattern (18 bp):
ATGTCAATATATAATATC
Found at i:16562843 original size:41 final size:41
Alignment explanation
Indices: 16562796--16562877 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
16562786 ATTAATTATC
16562796 ATGTAATAATAATAATCATGTCAATATATAATATCATGCAA
1 ATGTAATAATAATAATCATGTCAATATATAATATCATGCAA
16562837 ATGTAATAATAATAATCATGTCAATATATAATATCATGCAA
1 ATGTAATAATAATAATCATGTCAATATATAATATCATGCAA
16562878 TAATATAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (41 bp):
ATGTAATAATAATAATCATGTCAATATATAATATCATGCAA
Found at i:16562884 original size:20 final size:20
Alignment explanation
Indices: 16562818--16562897 Score: 69
Period size: 20 Copynumber: 4.0 Consensus size: 20
16562808 TAATCATGTC
16562818 AATATATAATATCATGCAAATGT
1 AATATATAATATCATGC-AA--T
16562841 AATA-ATAATAATCATG---T
1 AATATATAAT-ATCATGCAAT
16562858 CAATATATAATATCATGCAAT
1 -AATATATAATATCATGCAAT
* *
16562879 AATATAAAATACCATGCAA
1 AATATATAATATCATGCAA
16562898 ATTTATTAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
17 1 0.02
18 10 0.20
19 5 0.10
20 17 0.35
21 1 0.02
22 5 0.10
23 10 0.20
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.31
Consensus pattern (20 bp):
AATATATAATATCATGCAAT
Found at i:16563128 original size:32 final size:32
Alignment explanation
Indices: 16563081--16563228 Score: 107
Period size: 32 Copynumber: 4.8 Consensus size: 32
16563071 AATAGTCATG
**
16563081 CAAATAAATGTATTAATAATCATGCAATCACA
1 CAAATAAATAAATTAATAATCATGCAATCACA
* * *
16563113 CAAATAAATAAATTAATAATCATACAATTAAA
1 CAAATAAATAAATTAATAATCATGCAATCACA
*** *
16563145 CATGCAATTAAA-TATATAATCATGC-A--A-A
1 CAAATAAATAAATTA-ATAATCATGCAATCACA
*
16563173 -TAAT-AAT--ATTAATAATCATGCAATCACA
1 CAAATAAATAAATTAATAATCATGCAATCACA
* *
16563201 CAAATAAATATATTAGGTAATCATGCAA
1 CAAATAAATAAATTA-ATAATCATGCAA
16563229 ACAAATATTA
Statistics
Matches: 88, Mismatches: 17, Indels: 21
0.70 0.13 0.17
Matches are distributed among these distances:
24 11 0.12
25 3 0.03
26 2 0.02
27 1 0.01
28 2 0.02
29 4 0.05
30 3 0.03
31 3 0.03
32 48 0.55
33 11 0.12
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (32 bp):
CAAATAAATAAATTAATAATCATGCAATCACA
Found at i:16563131 original size:44 final size:42
Alignment explanation
Indices: 16563091--16563215 Score: 110
Period size: 44 Copynumber: 2.9 Consensus size: 42
16563081 CAAATAAATG
16563091 TATTAATAATCATGCAATCACACAAATAAATAAATTAATAAT
1 TATTAATAATCATGCAATCACACAAATAAATAAATTAATAAT
* * * * * * *
16563133 CATACAATTAAACATGCAATTAAATATATAATCATGCAAA-TAATAA-
1 TAT-TAA-TAATCATGCAATCACACAAATAA--AT--AAATTAATAAT
*
16563179 TATTAATAATCATGCAATCACACAAATAAATATATTA
1 TATTAATAATCATGCAATCACACAAATAAATAAATTA
16563216 GGTAATCATG
Statistics
Matches: 61, Mismatches: 15, Indels: 15
0.67 0.16 0.16
Matches are distributed among these distances:
40 2 0.03
41 2 0.03
42 4 0.07
43 2 0.03
44 36 0.59
45 2 0.03
46 4 0.07
47 6 0.10
48 3 0.05
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.30
Consensus pattern (42 bp):
TATTAATAATCATGCAATCACACAAATAAATAAATTAATAAT
Found at i:16563170 original size:20 final size:23
Alignment explanation
Indices: 16563145--16563196 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
16563135 TACAATTAAA
*
16563145 CATGCAATTA-AATA-T-ATAAT
1 CATGCAATAATAATATTAATAAT
16563165 CATGCAAATAATAATATTAATAAT
1 CATGC-AATAATAATATTAATAAT
16563189 CATGCAAT
1 CATGCAAT
16563197 CACACAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.19
21 4 0.15
22 4 0.15
23 4 0.15
24 10 0.37
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.33
Consensus pattern (23 bp):
CATGCAATAATAATATTAATAAT
Found at i:16563257 original size:20 final size:19
Alignment explanation
Indices: 16563218--16563269 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
16563208 ATATATTAGG
*
16563218 TAATCATGCAAACAAATAT
1 TAATCATGCAAATAAATAT
*
16563237 TAATCATACAAATATAATAT
1 TAATCATGCAAATA-AATAT
*
16563257 TAGTCATGCAAAT
1 TAATCATGCAAAT
16563270 TCATACAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.50, C:0.13, G:0.06, T:0.31
Consensus pattern (19 bp):
TAATCATGCAAATAAATAT
Found at i:16563320 original size:25 final size:24
Alignment explanation
Indices: 16563292--16563343 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
16563282 AAGTACAATG
* * *
16563292 CAATAACTATAAAAATAAAAATAAA
1 CAATAACCA-AAAAAAAAAAAAAAA
*
16563317 CAATATCCAAAAAAAAAAAAAAAA
1 CAATAACCAAAAAAAAAAAAAAAA
16563341 CAA
1 CAA
16563344 AACAACAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.75, C:0.12, G:0.00, T:0.13
Consensus pattern (24 bp):
CAATAACCAAAAAAAAAAAAAAAA
Found at i:16563861 original size:12 final size:12
Alignment explanation
Indices: 16563821--16563863 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
16563811 TTTGACCAAT
16563821 AAAA-TAAAATC
1 AAAATTAAAATC
* *
16563832 ACAATCAAAATC
1 AAAATTAAAATC
*
16563844 AAAATTAAAATT
1 AAAATTAAAATC
16563856 AAAATTAA
1 AAAATTAA
16563864 GATTTTCAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 3 0.12
12 23 0.88
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATTAAAATC
Found at i:16564275 original size:129 final size:129
Alignment explanation
Indices: 16564043--16564279 Score: 352
Period size: 129 Copynumber: 1.8 Consensus size: 129
16564033 TGCAAAGTAT
* * * *
16564043 TTAAGACAAAATTTACCATTATATTATGCGAATGTTCAGTTTATTATTGTACTTCAATTTCATTA
1 TTAAGACAAAATTTACCACTATATTACGAGAATGTTCAGTTTATTATTGCACTTCAATTTCATTA
*
16564108 TTGAATTTTCATTTTTATACTTCTAAGTTTATTGATTTTTAATTTAAAAAAACAATGAAATTGA
66 TTGAAATTTCATTTTTATACTTCTAAGTTTATTGATTTTTAATTTAAAAAAACAATGAAATTGA
* *
16564172 TTAAGACAAAATTTACTACTATATTACGAGAATGTTCAATTTTATTATAT-CACTTCAATTTCAT
1 TTAAGACAAAATTTACCACTATATTACGAGAATGTTC-AGTTTATTAT-TGCACTTCAATTTCAT
* * *
16564236 TATTGAAATTTC-TTTTTATACTTTTAATTTTATTTATTTTTAAT
64 TATTGAAATTTCATTTTTATACTTCTAAGTTTATTGATTTTTAAT
16564280 AAAAATAGCG
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
129 62 0.65
130 33 0.34
131 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.49
Consensus pattern (129 bp):
TTAAGACAAAATTTACCACTATATTACGAGAATGTTCAGTTTATTATTGCACTTCAATTTCATTA
TTGAAATTTCATTTTTATACTTCTAAGTTTATTGATTTTTAATTTAAAAAAACAATGAAATTGA
Found at i:16567272 original size:13 final size:13
Alignment explanation
Indices: 16567254--16567283 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
16567244 ATAGTAGGGA
*
16567254 TTTGATTCAAATC
1 TTTGATTCAAAGC
16567267 TTTGATTCAAAGC
1 TTTGATTCAAAGC
16567280 TTTG
1 TTTG
16567284 GTAGTTTGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (13 bp):
TTTGATTCAAAGC
Found at i:16567389 original size:14 final size:14
Alignment explanation
Indices: 16567370--16567406 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
16567360 CTTCCAATAA
16567370 TTTTTAAAATTTTG
1 TTTTTAAAATTTTG
**
16567384 TTTTTAATTTTTTG
1 TTTTTAAAATTTTG
16567398 TTTTTAAAA
1 TTTTTAAAA
16567407 CAAAGAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (14 bp):
TTTTTAAAATTTTG
Found at i:16567653 original size:29 final size:29
Alignment explanation
Indices: 16567589--16567654 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
16567579 CACGTCATTT
*
16567589 AATATTTTTATAATTCAAGTAATATATTA
1 AATATTTTTATAATTCAAATAATATATTA
* * * *
16567618 TAGATTTTTA-AATTTTAAATATTATATTA
1 AATATTTTTATAA-TTCAAATAATATATTA
16567647 AATATTTT
1 AATATTTT
16567655 ATTATAGTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (29 bp):
AATATTTTTATAATTCAAATAATATATTA
Found at i:16568467 original size:23 final size:23
Alignment explanation
Indices: 16568439--16568484 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
16568429 CAAAATTAAT
* * *
16568439 AAAATATTATTTTTTAAAATATA
1 AAAATATAATTATATAAAATATA
16568462 AAAATATAATTATATAAAATATA
1 AAAATATAATTATATAAAATATA
16568485 TATAAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAATATAATTATATAAAATATA
Found at i:16568502 original size:23 final size:22
Alignment explanation
Indices: 16568452--16568503 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
16568442 ATATTATTTT
*
16568452 TTAAAATATAAAAATATAATTA
1 TTAAAATATAAAAATATAATAA
16568474 TATAAAATATATATAAATA-AATAA
1 T-TAAAATATA-A-AAATATAATAA
16568498 TTAAAA
1 TTAAAA
16568504 AATTAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 1 0.04
23 14 0.54
24 6 0.23
25 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
TTAAAATATAAAAATATAATAA
Found at i:16568914 original size:35 final size:36
Alignment explanation
Indices: 16568871--16568961 Score: 107
Period size: 36 Copynumber: 2.5 Consensus size: 36
16568861 TTATTTTAAA
16568871 TATATTATTTAATAAAAATT-TTCAAATATATATTTT
1 TATATTATTTAATAAAAATTATTCAAATATAT-TTTT
* * *
16568907 TA-ATTATTTCAATCAAAGTTATTCAATTATATTTTT
1 TATATTATTT-AATAAAAATTATTCAAATATATTTTT
16568943 TATATT-TTTAATAATAAAT
1 TATATTATTTAATAA-AAAT
16568962 AAAAAAAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
35 11 0.24
36 22 0.48
37 13 0.28
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (36 bp):
TATATTATTTAATAAAAATTATTCAAATATATTTTT
Found at i:16576868 original size:52 final size:52
Alignment explanation
Indices: 16576782--16576925 Score: 184
Period size: 52 Copynumber: 2.8 Consensus size: 52
16576772 TATAACCATA
* * * *
16576782 CAAACTTGCCCATTAAGAATCTCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCAATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* * *
16576834 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCAATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* *
16576886 CAAACTTACCAATTAAGAAT-CCTTTTCTCTT-GAAATTCTT
1 CAAACTTGCCAATTAAGAATCCCTTTCCTCTTAG-AATTCTT
16576926 TTTTTGCAAG
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
50 1 0.01
51 16 0.20
52 64 0.79
ACGTcount: A:0.27, C:0.26, G:0.08, T:0.39
Consensus pattern (52 bp):
CAAACTTGCCAATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:16576972 original size:21 final size:22
Alignment explanation
Indices: 16576954--16577000 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
16576944 TCCATCAAGC
*
16576954 AATATCTGACAAATCTCAAACA
1 AATATCTAACAAATCTCAAACA
* *
16576976 AATCTCTAACAAATCCCAAACA
1 AATATCTAACAAATCTCAAACA
16576998 AAT
1 AAT
16577001 CTCTTATGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.26, G:0.02, T:0.21
Consensus pattern (22 bp):
AATATCTAACAAATCTCAAACA
Found at i:16576978 original size:11 final size:11
Alignment explanation
Indices: 16576962--16577003 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
16576952 GCAATATCTG
16576962 ACAAATCTCAA
1 ACAAATCTCAA
*
16576973 ACAAATCTCTA
1 ACAAATCTCAA
*
16576984 ACAAATCCCAA
1 ACAAATCTCAA
16576995 ACAAATCTC
1 ACAAATCTC
16577004 TTATGAGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:16576987 original size:22 final size:22
Alignment explanation
Indices: 16576962--16577004 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
16576952 GCAATATCTG
*
16576962 ACAAATCTCAAACAAATCTCTA
1 ACAAATCCCAAACAAATCTCTA
16576984 ACAAATCCCAAACAAATCTCT
1 ACAAATCCCAAACAAATCTCT
16577005 TATGAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (22 bp):
ACAAATCCCAAACAAATCTCTA
Found at i:16577208 original size:18 final size:19
Alignment explanation
Indices: 16577175--16577211 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
16577165 ATCTTCAAAA
16577175 CTCGAACTCGAACTCTTCT
1 CTCGAACTCGAACTCTTCT
*
16577194 CTCGAA-TCGAGCTCTTCT
1 CTCGAACTCGAACTCTTCT
16577212 GAACTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.19, C:0.35, G:0.14, T:0.32
Consensus pattern (19 bp):
CTCGAACTCGAACTCTTCT
Found at i:16577323 original size:25 final size:25
Alignment explanation
Indices: 16577268--16577363 Score: 122
Period size: 25 Copynumber: 3.9 Consensus size: 25
16577258 TAGCTTTTCC
*
16577268 CACATCTCGAACTTTCAGCTC-TTT
1 CACATCTCGAACCTTCAGCTCTTTT
*
16577292 CACATCTCGAACCTTCGGCTCTTTT
1 CACATCTCGAACCTTCAGCTCTTTT
* * *
16577317 CACATCTTGAATCTTCAACTCTTTT
1 CACATCTCGAACCTTCAGCTCTTTT
* *
16577342 CACGTTTCGAACCTTCAGCTCT
1 CACATCTCGAACCTTCAGCTCT
16577364 GATACCATTT
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
24 19 0.32
25 41 0.68
ACGTcount: A:0.20, C:0.33, G:0.09, T:0.38
Consensus pattern (25 bp):
CACATCTCGAACCTTCAGCTCTTTT
Found at i:16577981 original size:52 final size:52
Alignment explanation
Indices: 16577895--16578039 Score: 195
Period size: 52 Copynumber: 2.8 Consensus size: 52
16577885 TATAACCATA
* * *
16577895 CAAACTTACCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTACCAATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* * * *
16577947 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTACCAATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
16577999 CAAACTTACCAATTAAGAATCCTCTTT-CTCTT-GAAATTCTT
1 CAAACTTACCAATTAAGAATCC-CTTTCCTCTTAG-AATTCTT
16578040 TTTTTGCAAG
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
51 1 0.01
52 77 0.94
53 4 0.05
ACGTcount: A:0.28, C:0.27, G:0.08, T:0.38
Consensus pattern (52 bp):
CAAACTTACCAATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:16578092 original size:11 final size:11
Alignment explanation
Indices: 16578076--16578117 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
16578066 GCAATATCTG
16578076 ACAAATCTCAA
1 ACAAATCTCAA
*
16578087 ACAAATCTCTA
1 ACAAATCTCAA
* *
16578098 ATAAATCCCAA
1 ACAAATCTCAA
16578109 ACAAATCTC
1 ACAAATCTC
16578118 TTATGGGATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:16583767 original size:16 final size:15
Alignment explanation
Indices: 16583733--16583784 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
16583723 TGATATAAAT
* *
16583733 ATTTTTCATCTTTTT
1 ATTTTTTATCTTTTC
*
16583748 ATTTTTTTTCTTTTC
1 ATTTTTTATCTTTTC
*
16583763 AATTTTGTATCTTTTC
1 -ATTTTTTATCTTTTC
16583779 ATTTTT
1 ATTTTT
16583785 AATTCATCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 17 0.57
16 13 0.43
ACGTcount: A:0.13, C:0.12, G:0.02, T:0.73
Consensus pattern (15 bp):
ATTTTTTATCTTTTC
Found at i:16589706 original size:17 final size:18
Alignment explanation
Indices: 16589668--16589707 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
16589658 CAAAATAGAC
*
16589668 TCAAATTAAAACATCGAA
1 TCAAATTAAAAAATCGAA
*
16589686 TCAAGTTAAAAAATC-AA
1 TCAAATTAAAAAATCGAA
16589703 TCAAA
1 TCAAA
16589708 ATTGCTCATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.57, C:0.15, G:0.05, T:0.23
Consensus pattern (18 bp):
TCAAATTAAAAAATCGAA
Found at i:16591231 original size:21 final size:20
Alignment explanation
Indices: 16591181--16591242 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
16591171 ATTTAGAAAT
*
16591181 AATAAT-AATAATAACTAAATA
1 AATAATAAATAA-AAC-AAAAA
16591202 AATAA-AAATAAAACAAAAA
1 AATAATAAATAAAACAAAAA
16591221 AATTAATAAATGAAAA-AAAAA
1 AA-TAATAAAT-AAAACAAAAA
16591242 A
1 A
16591243 CTTTAACGCG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 6 0.17
20 6 0.17
21 20 0.56
22 4 0.11
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.19
Consensus pattern (20 bp):
AATAATAAATAAAACAAAAA
Found at i:16592028 original size:18 final size:19
Alignment explanation
Indices: 16592005--16592061 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
16591995 AAAATACAAA
16592005 AAATAATAATAGTAA-T-AT
1 AAATAATAATA-TAACTAAT
16592023 AAATAATAATATAACTAAT
1 AAATAATAATATAACTAAT
*
16592042 AAATAATAGTA-AA-TAAT
1 AAATAATAATATAACTAAT
16592059 AAA
1 AAA
16592062 ACAAAATAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
17 10 0.28
18 14 0.39
19 12 0.33
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (19 bp):
AAATAATAATATAACTAAT
Found at i:16592076 original size:12 final size:12
Alignment explanation
Indices: 16592052--16592111 Score: 77
Period size: 12 Copynumber: 4.8 Consensus size: 12
16592042 AAATAATAGT
16592052 AAATAATAAAACA
1 AAATAA-AAAACA
16592065 AAATAAAAAACA
1 AAATAAAAAACA
*
16592077 AAATAAAATAATA
1 AAATAAAA-AACA
16592090 AAA-ATAAAAACA
1 AAATA-AAAAACA
16592102 AAATAAAAAA
1 AAATAAAAAA
16592112 GGGCCCATCT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
12 26 0.62
13 16 0.38
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.13
Consensus pattern (12 bp):
AAATAAAAAACA
Found at i:16592091 original size:20 final size:20
Alignment explanation
Indices: 16592046--16592111 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
16592036 ACTAATAAAT
*
16592046 AATAGTAAATAAT-AAAACAA
1 AATAATAAA-AATAAAAACAA
* *
16592066 AAT-A-AAAAA-CAAAATAA
1 AATAATAAAAATAAAAACAA
16592083 AATAATAAAAATAAAAACAA
1 AATAATAAAAATAAAAACAA
16592103 AATAA-AAAA
1 AATAATAAAA
16592112 GGGCCCATCT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
17 11 0.29
18 4 0.11
19 9 0.24
20 14 0.37
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.15
Consensus pattern (20 bp):
AATAATAAAAATAAAAACAA
Found at i:16592352 original size:44 final size:44
Alignment explanation
Indices: 16592297--16592389 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
16592287 TTAAAGCTTT
* *
16592297 TCTAATTAGAGGCTCAACGACTTTTG-AAAAGTGAACAAAGCTCC
1 TCTAATTAGAGGCTCAACGAC-TTTGAAAAAATAAACAAAGCTCC
*
16592341 TCTAATTAGAGGCTCAACGACTTTGAAAAAATAAATAAAGCTCC
1 TCTAATTAGAGGCTCAACGACTTTGAAAAAATAAACAAAGCTCC
16592385 TCTAA
1 TCTAA
16592390 ACAGAGGCAC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 4 0.09
44 41 0.91
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (44 bp):
TCTAATTAGAGGCTCAACGACTTTGAAAAAATAAACAAAGCTCC
Found at i:16592472 original size:40 final size:40
Alignment explanation
Indices: 16592381--16592506 Score: 164
Period size: 40 Copynumber: 3.1 Consensus size: 40
16592371 ATAAATAAAG
* * *
16592381 CTCCTCTAAACAGAGGCACCATAACTTTAGAAAATAAATTG
1 CTCCTCTAAACAGAAGCACCACAACTTT-GAAAATAAATTA
* *
16592422 CTCATTTAAACAGAAGCACCACAACTTTGAAAATAAATTA
1 CTCCTCTAAACAGAAGCACCACAACTTTGAAAATAAATTA
16592462 CTCCTCTAAACAG-AGACACCACAACTTTTGAAAAATAAATTA
1 CTCCTCTAAACAGAAG-CACCACAAC-TTTG-AAAATAAATTA
16592504 CTC
1 CTC
16592507 ATTGATCATG
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.41
41 28 0.37
42 14 0.19
ACGTcount: A:0.44, C:0.23, G:0.09, T:0.25
Consensus pattern (40 bp):
CTCCTCTAAACAGAAGCACCACAACTTTGAAAATAAATTA
Found at i:16604275 original size:61 final size:58
Alignment explanation
Indices: 16604197--16604365 Score: 166
Period size: 59 Copynumber: 2.8 Consensus size: 58
16604187 TTTTTAAAGG
* *
16604197 AAAATTGATACTTTCAACTTTTCCTCAAAATGCTTTCTTTTAAA-A-TTTAAT-TTCAAGAAAA
1 AAAATTGATACTTTCAACTTTTCCT-AAAAT-ATTT-TTTAAAATATTTTAATCTTCAAG---A
*
16604258 AAAATTGATACTTTCAACTTTTTCCTAAAATATTTTTTAAAATATTTTTATCTTCAAGA
1 AAAATTGATACTTTCAAC-TTTTCCTAAAATATTTTTTAAAATATTTTAATCTTCAAGA
* * * *
16604317 GAAATTGATACTTTCAACTTTCTGCCCAAAATGTTTTTGAAAAT-TTTTA
1 AAAATTGATACTTTCAACTTT-T-CCTAAAATATTTTTTAAAATATTTTA
16604366 TTTTAGAAAC
Statistics
Matches: 94, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
58 3 0.03
59 29 0.31
60 21 0.22
61 28 0.30
62 13 0.14
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.44
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTAAAATATTTTTTAAAATATTTTAATCTTCAAGA
Found at i:16604499 original size:18 final size:18
Alignment explanation
Indices: 16604476--16604516 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
16604466 ACTTTCCCTT
16604476 AAAAATATTTT-TTTTAAA
1 AAAAAT-TTTTATTTTAAA
16604494 AAAAATTTTTATTTTAAA
1 AAAAATTTTTATTTTAAA
16604512 AAAAA
1 AAAAA
16604517 ATTGATACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAAATTTTTATTTTAAA
Found at i:16604597 original size:62 final size:62
Alignment explanation
Indices: 16604376--16604605 Score: 233
Period size: 62 Copynumber: 3.7 Consensus size: 62
16604366 TTTTAGAAAC
** **
16604376 TTTATTTTTGAGAAAAATTGATACTTTCAAC-TTTTC-CCTAAAAATA--TTTTTTAAAACTTTT
1 TTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAAAATATTTTTTTTAAAA----T
16604437 T
62 T
* **
16604438 TTTATTTTCAAG-AAAATTGATACTTTCAAC--TTTCCCTTAAAAATATTTTTTTTAAAAAAAAT
1 TTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAAAATATTTTTTTT----AAAAT
16604500 T
62 T
* *
16604501 TTTATTTTAAAAAAAAATTGATACTTTCAACTTTTTCTCAAAAAAATATTTTTTTCTAAAA-T
1 TTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAAAATATTTTTTT-TAAAATT
*
16604563 TTTAATTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAA
1 TTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAA
16604606 TACTTTTTGG
Statistics
Matches: 146, Mismatches: 11, Indels: 22
0.82 0.06 0.12
Matches are distributed among these distances:
60 4 0.03
61 27 0.18
62 51 0.35
63 22 0.15
64 18 0.12
66 19 0.13
67 5 0.03
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (62 bp):
TTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAAAATATTTTTTTTAAAATT
Found at i:16604606 original size:125 final size:121
Alignment explanation
Indices: 16604388--16604613 Score: 285
Period size: 125 Copynumber: 1.8 Consensus size: 121
16604378 TATTTTTGAG
** *
16604388 AAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTAAAACTTTTTTTTATTTTCAAGAAA
1 AAAAATTGATACTTTCAACTTTTCCAAAAAAATATTTTTTAAAA----TTTTTAATTTCAAGAAA
*
16604453 ATTGATACTTTCAACTTTCCCTTAAAAATATTTTTTTTAAAAAAAATTTTTATTTTAAAA
62 ATTGATACTTTCAACTTTCCCTTAAAAATACTTTTTTTAAAAAAAATTTTTATTTTAAAA
16604513 AAAAATTGATACTTTCAACTTTTTCTCAAAAAAATATTTTTTTCTAAAA-TTTTAATTTCAAGAA
1 AAAAATTGATACTTTCAAC-TTTTC-CAAAAAAATA--TTTTT-TAAAATTTTTAATTTCAAG-A
** *
16604577 AAATTGATACTTTCAACTTTTTC-TCAAAATACTTTTT
60 AAATTGATACTTTCAACTTTCCCTTAAAAATACTTTTT
16604614 GGAAAAATTT
Statistics
Matches: 88, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
125 43 0.49
126 27 0.31
127 8 0.09
129 5 0.06
130 5 0.06
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.46
Consensus pattern (121 bp):
AAAAATTGATACTTTCAACTTTTCCAAAAAAATATTTTTTAAAATTTTTAATTTCAAGAAAATTG
ATACTTTCAACTTTCCCTTAAAAATACTTTTTTTAAAAAAAATTTTTATTTTAAAA
Found at i:16604707 original size:12 final size:12
Alignment explanation
Indices: 16604690--16604743 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
16604680 TAGAAATTTC
*
16604690 ATTAAAAAGAAA
1 ATTAAAAATAAA
16604702 ATT-AAAATAAA
1 ATTAAAAATAAA
* *
16604713 A-CAAAATTAAA
1 ATTAAAAATAAA
*
16604724 ATTAAAATTAAA
1 ATTAAAAATAAA
16604736 ATTAAAAA
1 ATTAAAAA
16604744 AATTTAAGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 16 0.46
12 19 0.54
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (12 bp):
ATTAAAAATAAA
Found at i:16604708 original size:6 final size:6
Alignment explanation
Indices: 16604699--16604742 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
16604689 CATTAAAAAG
*
16604699 AAAATT AAAA-T AAAA-C AAAATT AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAA
16604743 AAATTTAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 9 0.26
6 26 0.74
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (6 bp):
AAAATT
Found at i:16604718 original size:22 final size:23
Alignment explanation
Indices: 16604693--16604736 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
16604683 AAATTTCATT
16604693 AAAAAGAAAATTAAAA-TAAAAC
1 AAAAAGAAAATTAAAATTAAAAC
**
16604715 AAAATTAAAATTAAAATTAAAA
1 AAAAAGAAAATTAAAATTAAAA
16604737 TTAAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (23 bp):
AAAAAGAAAATTAAAATTAAAAC
Found at i:16604722 original size:28 final size:27
Alignment explanation
Indices: 16604690--16604747 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
16604680 TAGAAATTTC
16604690 ATTAAAAAGAAAATTAAAATAAAACAAA
1 ATTAAAAAGAAAATTAAAATAAAA-AAA
** *
16604718 ATTAAAATTAAAATTAAAATTAAAAAA
1 ATTAAAAAGAAAATTAAAATAAAAAAA
16604745 ATT
1 ATT
16604748 TAAGGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (27 bp):
ATTAAAAAGAAAATTAAAATAAAAAAA
Found at i:16604802 original size:12 final size:11
Alignment explanation
Indices: 16604776--16604814 Score: 55
Period size: 10 Copynumber: 3.6 Consensus size: 11
16604766 TCTAATTTAG
16604776 AAAT-AATAAT
1 AAATAAATAAT
16604786 AAATAAATAACT
1 AAATAAATAA-T
16604798 AAATAAATAA-
1 AAATAAATAAT
16604808 AAATAAA
1 AAATAAA
16604815 ACAAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 11 0.41
11 5 0.19
12 11 0.41
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:16605632 original size:3 final size:3
Alignment explanation
Indices: 16605624--16605699 Score: 59
Period size: 3 Copynumber: 24.7 Consensus size: 3
16605614 TAAAATCAAA
*
16605624 AAT AAT AAT AAT AAT AAT AGT AAT -AT AAAT AAT AAT -AT AACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA-T AAT
* *
16605669 AA- ATAT AGT AAAT AAT AAA AAT AAAT AAT AA
1 AAT A-AT AAT -AAT AAT AAT AAT -AAT AAT AA
16605700 ACGAGAAAAC
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
2 5 0.08
3 43 0.73
4 11 0.19
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:16605762 original size:6 final size:6
Alignment explanation
Indices: 16605677--16605762 Score: 52
Period size: 7 Copynumber: 14.0 Consensus size: 6
16605667 ATAAATATAG
* * * * *
16605677 TAAATAA TAAAAA TAAATAA TAAACGA GAAAACA AAAAACA AAAAAA TAATAA
1 TAAA-AA TAAAAA TAAA-AA TAAA-AA TAAAA-A TAAAA-A TAAAAA TAAAAA
*
16605730 TAAAAA T-AAAA TAAAAA -CAAAA T-AAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
16605763 AAGGGCTCAT
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
5 14 0.22
6 25 0.38
7 26 0.40
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.15
Consensus pattern (6 bp):
TAAAAA
Found at i:16605763 original size:12 final size:11
Alignment explanation
Indices: 16605719--16605761 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
16605709 CAAAAAACAA
16605719 AAAAATAATAAT
1 AAAAATAA-AAT
16605731 AAAAATAAAAT
1 AAAAATAAAAT
*
16605742 AAAAACAAAAT
1 AAAAATAAAAT
16605753 -AAAATAAAA
1 AAAAATAAAA
16605762 AAAGGGCTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 8 0.28
11 13 0.45
12 8 0.28
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:16606655 original size:26 final size:26
Alignment explanation
Indices: 16606619--16606668 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
16606609 CTCAAGCCAA
16606619 AACAATTTATTCATAATTAGGGTCAG
1 AACAATTTATTCATAATTAGGGTCAG
*
16606645 AACAATTTATTTATAATTAGGGTC
1 AACAATTTATTCATAATTAGGGTC
16606669 TCATCAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (26 bp):
AACAATTTATTCATAATTAGGGTCAG
Found at i:16606887 original size:19 final size:19
Alignment explanation
Indices: 16606863--16606900 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
16606853 AATTATTTAA
16606863 AATTATAAAATTAATAAAT
1 AATTATAAAATTAATAAAT
* *
16606882 AATTATTAAATTATTAAAT
1 AATTATAAAATTAATAAAT
16606901 TATTTTATAT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTATAAAATTAATAAAT
Found at i:16608117 original size:33 final size:32
Alignment explanation
Indices: 16608077--16608156 Score: 81
Period size: 33 Copynumber: 2.4 Consensus size: 32
16608067 CTCATCTTAT
** *
16608077 TTATATAATAAAATTTATTTATTTATTAGTT-TA
1 TTATATAATAAAAGAT-TTTATTTATTA-TTAAA
*
16608110 TTATATAACAACAAGATTTTATTTATTATTAAA
1 TTATATAATAA-AAGATTTTATTTATTATTAAA
16608143 TTATATAATTAAAA
1 TTATATAA-TAAAA
16608157 ATAAAAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
32 2 0.05
33 32 0.82
34 5 0.13
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (32 bp):
TTATATAATAAAAGATTTTATTTATTATTAAA
Found at i:16608627 original size:17 final size:19
Alignment explanation
Indices: 16608602--16608648 Score: 64
Period size: 17 Copynumber: 2.6 Consensus size: 19
16608592 ATATCTTGAC
16608602 TTAAATTTT-ATTAAAA-TA
1 TTAAATTTTCA-TAAAATTA
16608620 TT-AATTTTCATAAAATTA
1 TTAAATTTTCATAAAATTA
16608638 TTAAATTTTCA
1 TTAAATTTTCA
16608649 CTTGCAACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 11 0.42
18 7 0.27
19 8 0.31
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAATTTTCATAAAATTA
Found at i:16613918 original size:30 final size:30
Alignment explanation
Indices: 16613875--16613935 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
16613865 CCAAATGTAC
* *
16613875 TAAAGAAACCTCAATACGCGTGCTTTGCTT
1 TAAAAAAAACTCAATACGCGTGCTTTGCTT
*
16613905 TAAAAAAAACTCAATATGCGTGCTTTGCTT
1 TAAAAAAAACTCAATACGCGTGCTTTGCTT
16613935 T
1 T
16613936 TATATATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (30 bp):
TAAAAAAAACTCAATACGCGTGCTTTGCTT
Found at i:16614683 original size:144 final size:144
Alignment explanation
Indices: 16614524--16614808 Score: 333
Period size: 144 Copynumber: 2.0 Consensus size: 144
16614514 TAAAAGCATT
* * ** *
16614524 ATCTTCATTAAAATTTCATAATTTTAAAAATAAAGTTTCAACATTTATTACATTTATTT-TCTTA
1 ATCTTCATTAAAATTTCAGAATTTAAAAAATAAAGTTTCAACATCCATTACATTT-TTTAGCTTA
* * * * * * *
16614588 AAAGCGCAATCTTTGTTAAAATTTTATCA-TTTAAAAAATATAACTTT-AACATCCATTACGTTT
65 AAAACGCAATCTTTATTAAAATATCA-AATTTTAAAAAATATAA-TTTCAACATCCACTACATTT
16614651 TTTATCTTAAAAATGTG
128 TTTATCTTAAAAATGTG
* * * **
16614668 ATCTTTATTAAAATTTTAGAATTTAAAAAATAGAGTTTCATTATCCATTACATTTTTTAGCTTAA
1 ATCTTCATTAAAATTTCAGAATTTAAAAAATAAAGTTTCAACATCCATTACATTTTTTAGCTTAA
* * * *
16614733 AAATGCAGTCTTTATTAAAATATCAAATTTTCAAAAATATAATTTCAACATCCACTATATTTTTT
66 AAACGCAATCTTTATTAAAATATCAAATTTTAAAAAATATAATTTCAACATCCACTACATTTTTT
16614798 ATCTTAAAAAT
131 ATCTTAAAAAT
16614809 ACAGTACTGG
Statistics
Matches: 117, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
143 7 0.06
144 110 0.94
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.44
Consensus pattern (144 bp):
ATCTTCATTAAAATTTCAGAATTTAAAAAATAAAGTTTCAACATCCATTACATTTTTTAGCTTAA
AAACGCAATCTTTATTAAAATATCAAATTTTAAAAAATATAATTTCAACATCCACTACATTTTTT
ATCTTAAAAATGTG
Found at i:16614807 original size:72 final size:73
Alignment explanation
Indices: 16614525--16614813 Score: 277
Period size: 72 Copynumber: 4.0 Consensus size: 73
16614515 AAAAGCATTA
* * * **
16614525 TCTTCATTAAAATTTCATAATTTTAAAAATA-AAGTTTCAACATTTATTACATTTATTT-TCTTA
1 TCTTTATTAAAATTTCATAATTTAAAAAATATAACTTTCAACATCCATTACATTT-TTTATCTTA
** *
16614588 AAAGCGCAA
65 AAAATGCAG
* * * *
16614597 TCTTTGTTAAAATTTTATCATTTAAAAAATATAACTTT-AACATCCATTACGTTTTTTATCTTAA
1 TCTTTATTAAAATTTCATAATTTAAAAAATATAACTTTCAACATCCATTACATTTTTTATCTTAA
*
16614661 AAATG-TG
66 AAATGCAG
* * * * ** *
16614668 ATCTTTATTAAAATTTTAGAATTTAAAAAATA-GAGTTTCATTATCCATTACATTTTTTAGCTTA
1 -TCTTTATTAAAATTTCATAATTTAAAAAATATAACTTTCAACATCCATTACATTTTTTATCTTA
16614732 AAAATGCAG
65 AAAATGCAG
* * * *
16614741 TCTTTATTAAAATATCA-AATTTTCAAAAATATAA-TTTCAACATCCACTATATTTTTTATCTTA
1 TCTTTATTAAAATTTCATAA-TTTAAAAAATATAACTTTCAACATCCATTACATTTTTTATCTTA
*
16614804 AAAATACAG
65 AAAATGCAG
16614813 T
1 T
16614814 ACTGGTTGAA
Statistics
Matches: 177, Mismatches: 33, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
71 9 0.05
72 161 0.91
73 7 0.04
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.44
Consensus pattern (73 bp):
TCTTTATTAAAATTTCATAATTTAAAAAATATAACTTTCAACATCCATTACATTTTTTATCTTAA
AAATGCAG
Found at i:16615756 original size:22 final size:22
Alignment explanation
Indices: 16615728--16615770 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
16615718 CTATAGGAGC
* *
16615728 AGTTGATTGTTTTATCAAGAGT
1 AGTTGATTGTCTTAGCAAGAGT
16615750 AGTTGATTGTCTTAGCAAGAG
1 AGTTGATTGTCTTAGCAAGAG
16615771 CAGTCAATTG
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:0.28, C:0.07, G:0.26, T:0.40
Consensus pattern (22 bp):
AGTTGATTGTCTTAGCAAGAGT
Found at i:16616067 original size:27 final size:26
Alignment explanation
Indices: 16616037--16616112 Score: 66
Period size: 27 Copynumber: 3.0 Consensus size: 26
16616027 AGTATATAAA
16616037 ATTTTTTATTAAATAATATAAATTATT
1 ATTTTTTATTAAATAATATAAATTA-T
** * * *
16616064 ATTTTAGATTAATTAACATTAA-TAT
1 ATTTTTTATTAAATAATATAAATTAT
* *
16616089 A-TTTTTATTAAAAAATATATATTA
1 ATTTTTTATTAAATAATATAAATTA
16616113 ATATATATAT
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
24 13 0.36
25 4 0.11
26 2 0.06
27 17 0.47
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (26 bp):
ATTTTTTATTAAATAATATAAATTAT
Found at i:16617147 original size:19 final size:18
Alignment explanation
Indices: 16617123--16617163 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
16617113 GAAAATTACA
* *
16617123 AAAATAAAATTAGAAAATG
1 AAAATAAAA-AAGAAAAAG
16617142 AAAATAAAAAAGAAAAAG
1 AAAATAAAAAAGAAAAAG
16617160 AAAA
1 AAAA
16617164 ACCTACGATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (18 bp):
AAAATAAAAAAGAAAAAG
Found at i:16617581 original size:15 final size:15
Alignment explanation
Indices: 16617561--16617631 Score: 90
Period size: 15 Copynumber: 4.7 Consensus size: 15
16617551 TAGAAATATC
16617561 AAACCCAAAAACTTT
1 AAACCCAAAAACTTT
*
16617576 AAACCCAAAAA-TTCA
1 AAACCCAAAAACTT-T
* *
16617591 AAACCCATAAATTTT
1 AAACCCAAAAACTTT
*
16617606 AAACCCAGAAACTTT
1 AAACCCAAAAACTTT
16617621 AAACCCAAAAA
1 AAACCCAAAAA
16617632 GTTTTCCCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
14 2 0.04
15 44 0.92
16 2 0.04
ACGTcount: A:0.55, C:0.25, G:0.01, T:0.18
Consensus pattern (15 bp):
AAACCCAAAAACTTT
Found at i:16617866 original size:3 final size:3
Alignment explanation
Indices: 16617858--16617882 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16617848 TAACACAGAT
16617858 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
16617883 CATTTAACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:16619188 original size:73 final size:73
Alignment explanation
Indices: 16619013--16619205 Score: 234
Period size: 72 Copynumber: 2.7 Consensus size: 73
16619003 TAGCATTTTG
* * ***
16619013 AAAATATAATTTCAACATCCACTACA-TTTTTTATCTTTAAAATGTGGTCTTTATTAAAATTTCA
1 AAAATATAGTTTCAACATCCACTACATTTTTTTATCTTAAAAATACAGTCTTTATTAAAATTTCA
*
16619077 GGATTTAA
66 GAATTTAA
*
16619085 AAAATATAGTTTCAATATCCA-TCACATTTTTTTATCTTAAAAATACAGT-TTTCA-TAAAATAT
1 AAAATATAGTTTCAACATCCACT-ACATTTTTTTATCTTAAAAATACAGTCTTT-ATTAAAAT-T
*
16619147 T-AGAATTTCA
63 TCAGAATTTAA
* *
16619157 AAAATATAGTTTCTACATCCACTATATTTTTTTATCTTAAAAATACAGT
1 AAAATATAGTTTCAACATCCACTACATTTTTTTATCTTAAAAATACAGT
16619206 ATTTGTTGAA
Statistics
Matches: 105, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
71 1 0.01
72 82 0.78
73 22 0.21
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.42
Consensus pattern (73 bp):
AAAATATAGTTTCAACATCCACTACATTTTTTTATCTTAAAAATACAGTCTTTATTAAAATTTCA
GAATTTAA
Found at i:16620248 original size:21 final size:21
Alignment explanation
Indices: 16620222--16620262 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
16620212 GATAAATAAG
16620222 TCAATTGTTATAAATTTTATT
1 TCAATTGTTATAAATTTTATT
*
16620243 TCAATTGTTATGAATTTTAT
1 TCAATTGTTATAAATTTTAT
16620263 CTATATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (21 bp):
TCAATTGTTATAAATTTTATT
Found at i:16620583 original size:3 final size:3
Alignment explanation
Indices: 16620575--16620621 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
16620565 AATATTTTAG
16620575 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
16620622 TTAAGTTATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:16623889 original size:17 final size:17
Alignment explanation
Indices: 16623867--16623899 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16623857 TTCCTTTTAA
16623867 TTATTTAAGAAAAATAT
1 TTATTTAAGAAAAATAT
*
16623884 TTATTTAGGAAAAATA
1 TTATTTAAGAAAAATA
16623900 ATTCTATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (17 bp):
TTATTTAAGAAAAATAT
Found at i:16624281 original size:25 final size:26
Alignment explanation
Indices: 16624242--16624302 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 26
16624232 TATTACTTTT
* *
16624242 ATTTATTTTTATATTTATTGATAATA
1 ATTTAATTTTATATTTATTGAAAATA
*
16624268 GTTTAATTTT-TATTTATTGAAAATA
1 ATTTAATTTTATATTTATTGAAAATA
16624293 ATTTAATTTT
1 ATTTAATTTT
16624303 CCGTAAAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 23 0.74
26 8 0.26
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (26 bp):
ATTTAATTTTATATTTATTGAAAATA
Found at i:16629607 original size:17 final size:17
Alignment explanation
Indices: 16629585--16629620 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
16629575 TTCCTTTTAA
16629585 TTATTTAAGAAAAATAT
1 TTATTTAAGAAAAATAT
*
16629602 TTATTTAGGAAAAATAT
1 TTATTTAAGAAAAATAT
16629619 TT
1 TT
16629621 CTATAGTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (17 bp):
TTATTTAAGAAAAATAT
Found at i:16629999 original size:25 final size:25
Alignment explanation
Indices: 16629959--16630019 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
16629949 TTATTACTTT
* *
16629959 TATTTATTTTTATATTTATTGATAA
1 TATTTAATTTTATATTTATTGAAAA
16629984 TAGTTTAATTTT-TATTTATTGAAAA
1 TA-TTTAATTTTATATTTATTGAAAA
16630009 TATTTAATTTT
1 TATTTAATTTT
16630020 CCGTAAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 9 0.27
25 16 0.48
26 8 0.24
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (25 bp):
TATTTAATTTTATATTTATTGAAAA
Found at i:16640461 original size:3 final size:3
Alignment explanation
Indices: 16640444--16640597 Score: 130
Period size: 3 Copynumber: 54.3 Consensus size: 3
16640434 TGGCATAGTA
* * *
16640444 TAT TAT T-T TAG TAT TAT TAT TA- TAT TA- TAT TA- TCT TA- TCT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
16640487 TAT CA- TAG TA- TAG TA- TAT TAA TA- TAT TA- TAT TAT TAC TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
16640530 TAT CAC TAT TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
16640576 TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
16640598 TGCATAATAT
Statistics
Matches: 125, Mismatches: 15, Indels: 22
0.77 0.09 0.14
Matches are distributed among these distances:
2 17 0.14
3 105 0.84
4 3 0.02
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:16641443 original size:14 final size:13
Alignment explanation
Indices: 16641421--16641455 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
16641411 CGATCGAAGG
16641421 TTTTTTTTTTCAT
1 TTTTTTTTTTCAT
*
16641434 TTTATTTTTTTTAT
1 TTT-TTTTTTTCAT
16641448 TTTTTTTT
1 TTTTTTTT
16641456 AGTTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTTCAT
Found at i:16641444 original size:18 final size:19
Alignment explanation
Indices: 16641421--16641468 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
16641411 CGATCGAAGG
16641421 TTTTTTTTTTCATTTTA-T
1 TTTTTTTTTTCATTTTAGT
**
16641439 TTTTTTTATTTTTTTTTAGT
1 TTTTTTT-TTTCATTTTAGT
16641459 TTTTTATTTT
1 TTTTT-TTTT
16641469 GCTAACTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 7 0.28
19 8 0.32
20 8 0.32
21 2 0.08
ACGTcount: A:0.10, C:0.02, G:0.02, T:0.85
Consensus pattern (19 bp):
TTTTTTTTTTCATTTTAGT
Found at i:16641478 original size:27 final size:28
Alignment explanation
Indices: 16641449--16641512 Score: 78
Period size: 26 Copynumber: 2.3 Consensus size: 28
16641439 TTTTTTTATT
*
16641449 TTTTTTTAGTT-TTTTA-TTTTGCTAAC
1 TTTTATTAGTTATTTTATTTTTGCTAAC
*
16641475 TTTTATTATTTATTTTATTTTTGCTAAGC
1 TTTTATTAGTTATTTTATTTTTGCTAA-C
16641504 TATTTATTA
1 T-TTTATTA
16641513 TTTGTTAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 9 0.28
27 5 0.16
28 9 0.28
29 2 0.06
30 7 0.22
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.67
Consensus pattern (28 bp):
TTTTATTAGTTATTTTATTTTTGCTAAC
Found at i:16641478 original size:28 final size:28
Alignment explanation
Indices: 16641460--16641515 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 28
16641450 TTTTTTAGTT
16641460 TTTTA-TTTTGCTAACTTTTATTATTTA
1 TTTTATTTTTGCTAACTTTTATTATTTA
16641487 TTTTATTTTTGCTAAGCTATTTATTATTT
1 TTTTATTTTTGCTAA-CT-TTTATTATTT
16641516 GTTAAGCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 5 0.19
28 9 0.35
29 2 0.08
30 10 0.38
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.66
Consensus pattern (28 bp):
TTTTATTTTTGCTAACTTTTATTATTTA
Found at i:16641509 original size:18 final size:18
Alignment explanation
Indices: 16641488--16641526 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16641478 TATTATTTAT
16641488 TTTATT-TTTGCTAAGCTA
1 TTTATTATTTGCTAAGC-A
*
16641506 TTTATTATTTGTTAAGCA
1 TTTATTATTTGCTAAGCA
16641524 TTT
1 TTT
16641527 TACAAAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.23, C:0.08, G:0.10, T:0.59
Consensus pattern (18 bp):
TTTATTATTTGCTAAGCA
Found at i:16641528 original size:19 final size:18
Alignment explanation
Indices: 16641486--16641528 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
16641476 TTTATTATTT
16641486 ATTTTATTTTTGCTAAGC
1 ATTTTATTTTTGCTAAGC
*
16641504 -TATTTATTATTTGTTAAGC
1 AT-TTTATT-TTTGCTAAGC
16641523 ATTTTA
1 ATTTTA
16641529 CAAAATTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
17 1 0.05
18 6 0.29
19 13 0.62
20 1 0.05
ACGTcount: A:0.26, C:0.07, G:0.09, T:0.58
Consensus pattern (18 bp):
ATTTTATTTTTGCTAAGC
Found at i:16646267 original size:10 final size:10
Alignment explanation
Indices: 16646252--16646348 Score: 51
Period size: 10 Copynumber: 9.8 Consensus size: 10
16646242 GGTGTGCCAA
16646252 AAAAAAAGAG
1 AAAAAAAGAG
** *
16646262 AAAAAATTAC
1 AAAAAAAGAG
16646272 AAAAAAA-ATG
1 AAAAAAAGA-G
**
16646282 AAAGCAAG-G
1 AAAAAAAGAG
16646291 AAAAAAA-AG
1 AAAAAAAGAG
*
16646300 ATTAAAAAAGGG
1 A--AAAAAAGAG
16646312 TAAAAAAA-AG
1 -AAAAAAAGAG
*
16646322 AAAAAAAAAG
1 AAAAAAAGAG
*
16646332 -AAAAAAGAA
1 AAAAAAAGAG
16646341 AAAAAAAG
1 AAAAAAAG
16646349 GGGAAGACTT
Statistics
Matches: 65, Mismatches: 13, Indels: 18
0.68 0.14 0.19
Matches are distributed among these distances:
9 23 0.35
10 28 0.43
11 12 0.18
12 1 0.02
13 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.06
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:16646335 original size:17 final size:17
Alignment explanation
Indices: 16646315--16646348 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16646305 AAAAGGGTAA
16646315 AAAAAAGAAAAAAAAAG
1 AAAAAAGAAAAAAAAAG
16646332 AAAAAAGAAAAAAAAAG
1 AAAAAAGAAAAAAAAAG
16646349 GGGAAGACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAAAAG
Found at i:16647725 original size:14 final size:13
Alignment explanation
Indices: 16647701--16647832 Score: 52
Period size: 13 Copynumber: 9.9 Consensus size: 13
16647691 TAGTATGGCA
16647701 TAGTATATTATTT
1 TAGTATATTATTT
*
16647714 TAGTACTATTATTA
1 TAGTA-TATTATTT
* *
16647728 TATTATATTATCT
1 TAGTATATTATTT
* * * *
16647741 TATTACCA-TAGTA
1 TAGTA-TATTATTT
* * *
16647754 TGGTATATTAATA
1 TAGTATATTATTT
* *
16647767 TATTATATTA-TA
1 TAGTATATTATTT
*
16647779 TAGTATATTATAT
1 TAGTATATTATTT
* *
16647792 TATTACTACTATTAT
1 TAGTA-TATTATT-T
*
16647807 TATTATTATTATTT
1 TAGTA-TATTATTT
*
16647821 TATTATATTATT
1 TAGTATATTATT
16647833 ATTATCATCA
Statistics
Matches: 91, Mismatches: 22, Indels: 12
0.73 0.18 0.10
Matches are distributed among these distances:
12 12 0.13
13 44 0.48
14 23 0.25
15 12 0.13
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (13 bp):
TAGTATATTATTT
Found at i:16647733 original size:5 final size:5
Alignment explanation
Indices: 16647704--16647837 Score: 69
Period size: 5 Copynumber: 25.6 Consensus size: 5
16647694 TATGGCATAG
* * * * * *
16647704 TATAT TATTT TAGTAC TATTAT TATAT TATAT TATCT TATTAC CATAG
1 TATAT TATAT TA-TAT TA-TAT TATAT TATAT TATAT TA-TAT TATAT
** *
16647752 TATGG TATAT TA-A- TATAT TATAT TATAT AGTATAT TATAT TATTAC
1 TATAT TATAT TATAT TATAT TATAT TATAT --TATAT TATAT TA-TAT
16647798 TACTAT TATTAT TATTAT TAT-T T-TAT TATAT TATTAT TAT
1 TA-TAT TA-TAT TA-TAT TATAT TATAT TATAT TA-TAT TAT
16647838 CATCATCATC
Statistics
Matches: 101, Mismatches: 18, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
3 3 0.03
4 6 0.06
5 54 0.53
6 33 0.33
7 5 0.05
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:16647785 original size:12 final size:12
Alignment explanation
Indices: 16647756--16647791 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
16647746 CCATAGTATG
16647756 GTATATTAATATA
1 GTATATT-ATATA
*
16647769 TTATATTATATA
1 GTATATTATATA
16647781 GTATATTATAT
1 GTATATTATAT
16647792 TATTACTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (12 bp):
GTATATTATATA
Found at i:16647787 original size:17 final size:15
Alignment explanation
Indices: 16647759--16647834 Score: 68
Period size: 17 Copynumber: 4.9 Consensus size: 15
16647749 TAGTATGGTA
16647759 TATTAATATATTATAT
1 TATT-ATATATTATAT
16647775 TATATAGTATATTATAT
1 TAT-TA-TATATTATAT
16647792 TATTACTACTA-T-TAT
1 TATTA-TA-TATTATAT
*
16647807 TATTAT-TATTATTT
1 TATTATATATTATAT
16647821 TATTATATTATTAT
1 TATTATA-TATTAT
16647835 TATCATCATC
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
12 2 0.04
13 1 0.02
14 9 0.18
15 8 0.16
16 15 0.29
17 16 0.31
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (15 bp):
TATTATATATTATAT
Found at i:16647807 original size:3 final size:3
Alignment explanation
Indices: 16647767--16647871 Score: 76
Period size: 3 Copynumber: 36.3 Consensus size: 3
16647757 TATATTAATA
* * *
16647767 TAT TA- TAT TAT ATAG TA- TAT TA- TAT TAT TAC TAC TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
16647810 TAT TAT TAT T-T TAT TA- TAT TAT TAT TAT CAT CAT CAT CAT CAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
16647856 TAG TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
16647872 TTGCAAATTT
Statistics
Matches: 89, Mismatches: 7, Indels: 12
0.82 0.06 0.11
Matches are distributed among these distances:
2 10 0.11
3 77 0.87
4 2 0.02
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:16647814 original size:51 final size:48
Alignment explanation
Indices: 16647699--16647828 Score: 113
Period size: 51 Copynumber: 2.6 Consensus size: 48
16647689 TATAGTATGG
* * * *
16647699 CATAGTATAT-TATT-TTAGTACTATTATTATATTATATTATCTTATTAC
1 CATAGTATGTATATTATTATTA-TATTA-TATAGTATATTATATTATTAC
16647747 CATAGTATGGTATATTAATATATTATATTATATAGTATATTATATTATTAC
1 CATAGTAT-GTATATT-AT-TATTATATTATATAGTATATTATATTATTAC
* * *
16647798 TACTATTAT-TATTATTATTATTTTATTATAT
1 CA-TAGTATGTA-TATTATTATTATATTATAT
16647829 TATTATTATC
Statistics
Matches: 68, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
48 8 0.12
49 13 0.19
50 8 0.12
51 24 0.35
52 11 0.16
53 4 0.06
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (48 bp):
CATAGTATGTATATTATTATTATATTATATAGTATATTATATTATTAC
Found at i:16648729 original size:13 final size:13
Alignment explanation
Indices: 16648692--16648730 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
16648682 GTAGGTTTTC
* *
16648692 TTTTTTATTTTTAT
1 TTTTTTA-TTTCAA
16648706 TTTTTTATTTCAA
1 TTTTTTATTTCAA
16648719 TTTTTTATTTCA
1 TTTTTTATTTCA
16648731 CCAACTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTATTTCAA
Found at i:16648750 original size:29 final size:29
Alignment explanation
Indices: 16648718--16648775 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
16648708 TTTTATTTCA
*
16648718 ATTT-TTTA-TTTCACCAA-CT-TTTATT
1 ATTTATTTATTTTTACCAAGCTATTTATT
*
16648743 ATTTATTTATTTTTACTAAGCTATTTATT
1 ATTTATTTATTTTTACCAAGCTATTTATT
16648772 ATTT
1 ATTT
16648776 GTTAAACATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 4 0.15
26 4 0.15
27 7 0.26
28 2 0.07
29 10 0.37
ACGTcount: A:0.26, C:0.10, G:0.02, T:0.62
Consensus pattern (29 bp):
ATTTATTTATTTTTACCAAGCTATTTATT
Found at i:16648943 original size:6 final size:6
Alignment explanation
Indices: 16648927--16648965 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
16648917 AAAAATTAAC
* *
16648927 AAAAAT AAAAAGT AAAAAT AAAAAC AAAAAT AAATAT AA
1 AAAAAT AAAAA-T AAAAAT AAAAAT AAAAAT AAAAAT AA
16648966 TATTTGTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:16650089 original size:27 final size:26
Alignment explanation
Indices: 16650051--16650111 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 26
16650041 GCGGGTCAAC
16650051 AAACTAGTGATTACGAAAATTATACTT
1 AAACTAGTGATTACGAAAATTATA-TT
*
16650078 AAACTAGTGATTATGAAAATTATATT
1 AAACTAGTGATTACGAAAATTATATT
*
16650104 TAACTAGT
1 AAACTAGT
16650112 AAGTACTGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 9 0.28
27 23 0.72
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (26 bp):
AAACTAGTGATTACGAAAATTATATT
Found at i:16655785 original size:33 final size:34
Alignment explanation
Indices: 16655704--16655796 Score: 152
Period size: 35 Copynumber: 2.7 Consensus size: 34
16655694 TTTAGATTAA
16655704 TTTCATGTTTATTTGTATTTAAATAAATATACAAT
1 TTTCATGTTTATTTGTATTTAAATAAATATA-AAT
*
16655739 TTTCATGTTTATTTGTATTTAAATAAATAT-ATT
1 TTTCATGTTTATTTGTATTTAAATAAATATAAAT
*
16655772 TTTCATGTCTATTTGTATTTAAATA
1 TTTCATGTTTATTTGTATTTAAATA
16655797 GACCTCATGA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 26 0.46
35 30 0.54
ACGTcount: A:0.33, C:0.05, G:0.06, T:0.55
Consensus pattern (34 bp):
TTTCATGTTTATTTGTATTTAAATAAATATAAAT
Found at i:16656469 original size:18 final size:18
Alignment explanation
Indices: 16656443--16656478 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
16656433 AGCTTTGTTT
16656443 TTATGATTATGATTTTTA
1 TTATGATTATGATTTTTA
*
16656461 TTATTATTATGATTTTTA
1 TTATGATTATGATTTTTA
16656479 GGAAGCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (18 bp):
TTATGATTATGATTTTTA
Found at i:16663938 original size:2 final size:2
Alignment explanation
Indices: 16663931--16663955 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16663921 ACATACATAC
16663931 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
16663956 GACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16663962 original size:2 final size:2
Alignment explanation
Indices: 16663957--16663981 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16663947 ATATATATAG
16663957 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
16663982 AATATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:16671833 original size:19 final size:20
Alignment explanation
Indices: 16671804--16671842 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
16671794 GATATGGGCG
*
16671804 TTGATTTTGTTGACGTGATA
1 TTGATTTTGTTGACATGATA
16671824 TTGA-TTTGTTGACATGATA
1 TTGATTTTGTTGACATGATA
16671843 ATTAAGATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (20 bp):
TTGATTTTGTTGACATGATA
Found at i:16671949 original size:31 final size:29
Alignment explanation
Indices: 16671905--16671970 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 29
16671895 TATGGAACTC
* *
16671905 GAAATTTAGTTTTTATATTCACATGAAATTT
1 GAAATTAAATTTTTATATTCACA--AAATTT
* *
16671936 GAAATTAAATTTTTGTATTTACAAAATTT
1 GAAATTAAATTTTTATATTCACAAAATTT
16671965 GAAATT
1 GAAATT
16671971 TAATCCTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 12 0.39
31 19 0.61
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (29 bp):
GAAATTAAATTTTTATATTCACAAAATTT
Found at i:16672401 original size:26 final size:25
Alignment explanation
Indices: 16672350--16672405 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
16672340 TATCACTATC
**
16672350 TAATTTAATAAATAAATATTTTTTA
1 TAATTTAATAAATAAATATTAATTA
*
16672375 TTAATTTATTAAATAAAT-TATAATTA
1 -TAATTTAATAAATAAATAT-TAATTA
16672401 TAATT
1 TAATT
16672406 CTATCTCCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TAATTTAATAAATAAATATTAATTA
Found at i:16672596 original size:16 final size:14
Alignment explanation
Indices: 16672561--16672602 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
16672551 AATTTTGATA
16672561 TATTAAT-TTAAAT
1 TATTAATATTAAAT
16672574 TATTAATATTATAAT
1 TATTAATATTA-AAT
16672589 TGATTAATA-TAAAT
1 T-ATTAATATTAAAT
16672603 GATAATAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.27
14 6 0.23
15 6 0.23
16 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TATTAATATTAAAT
Found at i:16674154 original size:2 final size:2
Alignment explanation
Indices: 16674147--16674178 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16674137 AAAGATTTAC
16674147 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16674179 AAAGAAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16681106 original size:19 final size:20
Alignment explanation
Indices: 16681077--16681115 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
16681067 GATATGGTCG
*
16681077 TTGATTTTGTTGACGTGATA
1 TTGATTTTGTTGACATGATA
16681097 TTGA-TTTGTTGACATGATA
1 TTGATTTTGTTGACATGATA
16681116 ATTAGGATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (20 bp):
TTGATTTTGTTGACATGATA
Found at i:16681675 original size:25 final size:25
Alignment explanation
Indices: 16681622--16681676 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
16681612 TATCACTATC
**
16681622 TAATTTAATAAATAAATATTTTTAT
1 TAATTTAATAAATAAATATAATTAT
*
16681647 TAATTTATTAAATAAATTATAATTA-
1 TAATTTAATAAATAAA-TATAATTAT
16681672 TAATT
1 TAATT
16681677 CTATCTCCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 20 0.77
26 6 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TAATTTAATAAATAAATATAATTAT
Found at i:16681866 original size:16 final size:14
Alignment explanation
Indices: 16681831--16681872 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
16681821 AATTTTGATA
16681831 TATTAAT-TTAAAT
1 TATTAATATTAAAT
16681844 TATTAATATTATAAT
1 TATTAATATTA-AAT
16681859 TGATTAATA-TAAAT
1 T-ATTAATATTAAAT
16681873 GATAATAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.27
14 6 0.23
15 6 0.23
16 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TATTAATATTAAAT
Found at i:16682083 original size:31 final size:32
Alignment explanation
Indices: 16682028--16682104 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 32
16682018 ATTAAAAAGA
* * *
16682028 CTAAATTTTAAATCTCGTGCAAATA-TA-GAT
1 CTAAATTTTAAATTTCATGCAAATACAAGGAT
*
16682058 GCTAAATTTTAAATTTCATGTAAATACAAGGAT
1 -CTAAATTTTAAATTTCATGCAAATACAAGGAT
16682091 -TAAATTTTAAATTT
1 CTAAATTTTAAATTT
16682105 TATATAAGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 36 0.90
32 1 0.03
33 3 0.08
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (32 bp):
CTAAATTTTAAATTTCATGCAAATACAAGGAT
Found at i:16685993 original size:20 final size:20
Alignment explanation
Indices: 16685968--16686008 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
16685958 AAATTAGCAT
16685968 AGTAAAAATAT-ATTAAAATA
1 AGTAAAAAT-TCATTAAAATA
*
16685988 AGTAAATATTCATTAAAATA
1 AGTAAAAATTCATTAAAATA
16686008 A
1 A
16686009 TATAACTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (20 bp):
AGTAAAAATTCATTAAAATA
Found at i:16687876 original size:14 final size:15
Alignment explanation
Indices: 16687857--16687887 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
16687847 CATTACTTTC
16687857 CAAATTTCA-ATGAT
1 CAAATTTCACATGAT
16687871 CAAATTTCACATGAT
1 CAAATTTCACATGAT
16687886 CA
1 CA
16687888 TTTCACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (15 bp):
CAAATTTCACATGAT
Found at i:16691288 original size:29 final size:29
Alignment explanation
Indices: 16691223--16691289 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
16691213 TATTATTACG
* **
16691223 AAATCATATTCAAAAATCAAAACAATATC
1 AAATCATATTCAAAAATCAAAACAAAAAA
* * * *
16691252 AAACCATATTCCAAACTCATAACAAAAAA
1 AAATCATATTCAAAAATCAAAACAAAAAA
16691281 AAATCATAT
1 AAATCATAT
16691290 ATACATTTTG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.22
Consensus pattern (29 bp):
AAATCATATTCAAAAATCAAAACAAAAAA
Found at i:16701763 original size:61 final size:62
Alignment explanation
Indices: 16701641--16701765 Score: 191
Period size: 61 Copynumber: 2.0 Consensus size: 62
16701631 CTTGTACCAC
* *
16701641 TTGTTATATTTTCAGATATGGAAAACTTTGTGACCAGGATGTCTATTTTCTTCTTTACTGTAG
1 TTGTTACATTTTCAGATATGGAAAAC-TTGTGACCAGGATGTCTATTTTCATCTTTACTGTAG
*
16701704 TTGTTACATTTTCAGATATGGAAAAC-TGTGACCAGTATGT-TGATTTTCATCTTTACTGTAG
1 TTGTTACATTTTCAGATATGGAAAACTTGTGACCAGGATGTCT-ATTTTCATCTTTACTGTAG
16701765 T
1 T
16701766 AGCTTGTGTT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
60 1 0.02
61 32 0.55
63 25 0.43
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.45
Consensus pattern (62 bp):
TTGTTACATTTTCAGATATGGAAAACTTGTGACCAGGATGTCTATTTTCATCTTTACTGTAG
Found at i:16704892 original size:25 final size:24
Alignment explanation
Indices: 16704838--16704895 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
16704828 ACATGTTAAA
*
16704838 ATTTTAATAAAAATTATATATATG
1 ATTTTAATAAAAATAATATATATG
*
16704862 AGTTTAATAAAAATAAATATATAT-
1 ATTTTAATAAAAAT-AATATATATG
16704886 ATTTTTAATA
1 A-TTTTAATA
16704896 TCGACACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.48
25 15 0.52
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (24 bp):
ATTTTAATAAAAATAATATATATG
Found at i:16707865 original size:51 final size:51
Alignment explanation
Indices: 16707768--16707886 Score: 125
Period size: 51 Copynumber: 2.3 Consensus size: 51
16707758 ATTTAAGGTA
* * *
16707768 CTTAAATTATCTTTTTAATAGATTATTTAAGGTGTTTTAGTACAAAAATAT
1 CTTAAATAATCTTTTTAATAGATCATTAAAGGTGTTTTAGTACAAAAATAT
* * * *
16707819 TTTAAATAATCTTTTTAAT-GACTCATTAAAGGTTTTTTTA-TTCAAAAATGT
1 CTTAAATAATCTTTTTAATAGA-TCATTAAAGG-TGTTTTAGTACAAAAATAT
* *
16707870 CTTAACTAATTTTTTTA
1 CTTAAATAATCTTTTTA
16707887 TAAAAAAATT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
50 2 0.04
51 48 0.86
52 6 0.11
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (51 bp):
CTTAAATAATCTTTTTAATAGATCATTAAAGGTGTTTTAGTACAAAAATAT
Found at i:16709436 original size:5 final size:5
Alignment explanation
Indices: 16709426--16709453 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
16709416 AAGCATATTC
16709426 AATTT AATTT AATTT AATTT AATTT AAT
1 AATTT AATTT AATTT AATTT AATTT AAT
16709454 ATATTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
AATTT
Done.