Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167971.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_23, 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: 19268551
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 68000 characters in sequence are not A, C, G, or T
File 111 of 120
Found at i:16386758 original size:11 final size:11
Alignment explanation
Indices: 16386742--16386767 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16386732 CTTTTCCATT
16386742 AATTTGGTTGA
1 AATTTGGTTGA
16386753 AATTTGGTTGA
1 AATTTGGTTGA
16386764 AATT
1 AATT
16386768 CATGTAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (11 bp):
AATTTGGTTGA
Found at i:16389539 original size:27 final size:28
Alignment explanation
Indices: 16389449--16389540 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 28
16389439 TTTGTGCAAA
*
16389449 AAAAATTGATACTTTCAACTTTTTC-CT
1 AAAAATTGATACTTTCAACTTTTTCTCG
* *
16389476 AAAAA-T-ATTATTTTGAAACTTTAATT-TCG
1 AAAAATTGA-TACTTT-CAACTTT--TTCTCG
16389505 AGGAAAATTGATACTTTCAACTTTTTCTC-
1 A--AAAATTGATACTTTCAACTTTTTCTCG
16389534 AAAAATT
1 AAAAATT
16389541 TATTTTTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 20
0.67 0.07 0.27
Matches are distributed among these distances:
25 1 0.02
26 6 0.12
27 17 0.34
29 7 0.14
30 2 0.04
31 10 0.20
32 6 0.12
33 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (28 bp):
AAAAATTGATACTTTCAACTTTTTCTCG
Found at i:16389573 original size:119 final size:118
Alignment explanation
Indices: 16389450--16389667 Score: 343
Period size: 120 Copynumber: 1.8 Consensus size: 118
16389440 TTGTGCAAAA
*
16389450 AAAATTGATACTTTCAACTTTTTC-CTAAAAATATTATTTT-GAAAC-TTTAATTTCGAGGAAAA
1 AAAATTGATACTTTCAAC-TTTTCGCCAAAAATATT-TTTTGGAAACTTTTAATTTCGAGGAAAA
* *
16389512 TTGATACTTTCAACTTTTTCTCAAAAATTTATTTTTTTTAAAAATTTATTTTTAAGG
64 TTGATACTTTCAACTTTTCCCCAAAAA--TATTTTTTTTAAAAATTTATTTTTAAGG
*
16389569 AAAATTGATACTTTTAACTTTTCGCCAAAAATATTTTTTGGAAACTTTTAATTTCGAGGAAAATT
1 AAAATTGATACTTTCAACTTTTCGCCAAAAATATTTTTTGGAAACTTTTAATTTCGAGGAAAATT
16389634 GATACTTTCAACTTTTCCCCAAAAATATTTTTTT
66 GATACTTTCAACTTTTCCCCAAAAATATTTTTTT
16389668 GGATTTTATT
Statistics
Matches: 92, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
118 18 0.20
119 32 0.35
120 42 0.46
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.45
Consensus pattern (118 bp):
AAAATTGATACTTTCAACTTTTCGCCAAAAATATTTTTTGGAAACTTTTAATTTCGAGGAAAATT
GATACTTTCAACTTTTCCCCAAAAATATTTTTTTTAAAAATTTATTTTTAAGG
Found at i:16389635 original size:59 final size:57
Alignment explanation
Indices: 16389450--16389666 Score: 274
Period size: 59 Copynumber: 3.7 Consensus size: 57
16389440 TTGTGCAAAA
*
16389450 AAAATTGATACTTTCAACTTTTTCCTAAAAATATTATTTTGAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATT-TTTTGAAACTTTAATTTCGAGG
* * * * **
16389508 AAAATTGATACTTTCAACTTTTTCTCAAAAATTTATTTTTTTTAAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCCCAAAAA--TA--TTTTTTGAAACTTTAATTTCGAGG
*
16389569 AAAATTGATACTTTTAAC-TTTTCGCCAAAAATATTTTTTGGAAACTTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTTC-CCAAAAATATTTTTT-GAAAC-TTTAATTTCGAGG
*
16389628 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTT
16389667 TGGATTTTAT
Statistics
Matches: 135, Mismatches: 16, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
57 6 0.04
58 32 0.24
59 44 0.33
60 11 0.08
61 40 0.30
62 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.45
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAACTTTAATTTCGAGG
Found at i:16389701 original size:13 final size:13
Alignment explanation
Indices: 16389683--16389707 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16389673 TTATTTAAAG
16389683 AAAACAAAATAAT
1 AAAACAAAATAAT
16389696 AAAACAAAATAA
1 AAAACAAAATAA
16389708 AAGTGAGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAACAAAATAAT
Found at i:16390701 original size:20 final size:21
Alignment explanation
Indices: 16390678--16390720 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
16390668 AAATCAAATG
16390678 AAAATAAATCAGATAAATCAA
1 AAAATAAATCAGATAAATCAA
* *
16390699 AAAATTAA-CAGATAAATTAA
1 AAAATAAATCAGATAAATCAA
16390719 AA
1 AA
16390721 TTAAATAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (21 bp):
AAAATAAATCAGATAAATCAA
Found at i:16390732 original size:22 final size:20
Alignment explanation
Indices: 16390668--16390735 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 20
16390658 TAAATAAAAA
16390668 AAATCAAATGAAAATAAATCAGAT
1 AAATCAAA--AAAAT-AA-CAGAT
*
16390692 AAATCAAAAAATTAACAGAT
1 AAATCAAAAAAATAACAGAT
*
16390712 AAATTAAAATTAAATAACAGAT
1 AAATCAAAA--AAATAACAGAT
16390734 AA
1 AA
16390736 TACATAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
20 13 0.33
21 2 0.05
22 16 0.41
24 8 0.21
ACGTcount: A:0.65, C:0.07, G:0.06, T:0.22
Consensus pattern (20 bp):
AAATCAAAAAAATAACAGAT
Found at i:16390774 original size:15 final size:15
Alignment explanation
Indices: 16390751--16390780 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16390741 AAATATTAAC
16390751 AGAAAAAGAAAAAAA
1 AGAAAAAGAAAAAAA
*
16390766 AGAAGAAGAAAAAAA
1 AGAAAAAGAAAAAAA
16390781 TAATAATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AGAAAAAGAAAAAAA
Found at i:16390865 original size:3 final size:3
Alignment explanation
Indices: 16390859--16390909 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
16390849 GAAGAAAAAA
* * *
16390859 AAT AAT ATAT ATAT AAT AAT AAT AAT AAC AAT AAA AAT AAA AAT AA-
1 AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16390905 AAT AA
1 AAT AA
16390910 AAATGTAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 31 0.77
4 7 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:16390912 original size:6 final size:6
Alignment explanation
Indices: 16390831--16390947 Score: 80
Period size: 6 Copynumber: 19.7 Consensus size: 6
16390821 CCTAAGATAA
* * * * * *
16390831 AAAAAT AATAAT AAAAGAG AAGAAA- AAAAAT -AATAT ATATAT AATAAT
1 AAAAAT AAAAAT AAAA-AT AA-AAAT AAAAAT AAAAAT AAAAAT AAAAAT
* * * *
16390879 AATAAT AACAAT AAAAAT AAAAAT -AAAAT AAAAAT GTAAAAT ACAAA-
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT AAAAAT
*
16390926 AAAAAT AAAAAC AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAA
16390948 TGAAGAAAAA
Statistics
Matches: 88, Mismatches: 16, Indels: 14
0.75 0.14 0.12
Matches are distributed among these distances:
5 16 0.18
6 61 0.69
7 9 0.10
8 2 0.02
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:16390927 original size:16 final size:15
Alignment explanation
Indices: 16390879--16390942 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 15
16390869 ATATAATAAT
* *
16390879 AATAATAACAATAAA
1 AATAAAAACAAAAAA
*
16390894 AATAAAAATAAAATAAA
1 AATAAAAA-CAAA-AAA
16390911 AATGTAAAATACAAAAAA
1 AA--TAAAA-ACAAAAAA
16390929 AATAAAAACAAAAA
1 AATAAAAACAAAAA
16390943 TAAAATGAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.35
16 7 0.17
17 5 0.12
18 5 0.12
19 8 0.20
20 1 0.03
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.16
Consensus pattern (15 bp):
AATAAAAACAAAAAA
Found at i:16391142 original size:13 final size:14
Alignment explanation
Indices: 16391111--16391142 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
16391101 ACCTTTTTAC
16391111 TTTTTATTTTTTTG
1 TTTTTATTTTTTTG
16391125 TTTTT-TTTTTTTG
1 TTTTTATTTTTTTG
16391138 TTTTT
1 TTTTT
16391143 GATCAAAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.03, C:0.00, G:0.06, T:0.91
Consensus pattern (14 bp):
TTTTTATTTTTTTG
Found at i:16391287 original size:41 final size:40
Alignment explanation
Indices: 16391150--16391447 Score: 285
Period size: 41 Copynumber: 7.2 Consensus size: 40
16391140 TTTGATCAAA
** * * * *
16391150 GCTCCTCTAGGCAGAGGCTCAATGACTTTGAGAAACATAAATG
1 GCTCCTCTAAACAGAGGCAC-ACGACTTTG-GAAA-GTAAATT
* * * * *
16391193 GCTCCTCTAATCAGAGGCTCAACAACTTTGAAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCAC-ACGACTTTG--GAAAGTAAATT
16391236 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA-CACGACTTTGGAAAGTAAATT
*
16391277 GCTCCACTAAACAGAGGCA-ACGAAACTTTGGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACACG--ACTTT-GGAAAGTAAATT
* *
16391319 GCTCCTCTAAACAAAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA-CACGACTTTGGAAAGTAAATT
* ** *
16391360 ACTCCTCTAAACAGAGGCAACAATACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGC-ACACGACTTTGGAAAGTAAATT
*
16391401 GCTCCTCTAAACAGAGGCA-ACGAAACTTTGGAAAATAAATT
1 GCTCCTCTAAACAGAGGCACACG--ACTTTGGAAAGTAAATT
16391442 GCTCCT
1 GCTCCT
16391448 TGACAATCAT
Statistics
Matches: 221, Mismatches: 24, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
39 4 0.02
40 1 0.00
41 116 0.52
42 35 0.16
43 57 0.26
44 8 0.04
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (40 bp):
GCTCCTCTAAACAGAGGCACACGACTTTGGAAAGTAAATT
Found at i:16391337 original size:83 final size:82
Alignment explanation
Indices: 16391150--16391446 Score: 325
Period size: 83 Copynumber: 3.6 Consensus size: 82
16391140 TTTGATCAAA
** * * * * * * *
16391150 GCTCCTCTAGGCAGAGGCTCAATGACTTTGAGAAACATAAATGGCTCCTCTAATCAGAGGCTCAA
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAA-GTAAATTGCTCCACTAAACAGAGG--CAA
*
16391215 C-A-ACTTTGAAAAAAATAAATT
62 CAATACTTTG--AAAAGTAAATT
16391236 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCACTAAACAGAGGCAACGAA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCACTAAACAGAGGCAAC-AA
*
16391301 -ACTTTGGGAAAGTAAATT
65 TACTTT-GAAAAGTAAATT
* * * *
16391319 GCTCCTCTAAACAAAGGCACCACGACTTTGAAAAGTAAATTACTCCTCTAAACAGAGGCAACAAT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCACTAAACAGAGGCAACAAT
16391384 ACTTTGAAAAGTAAATT
66 ACTTTGAAAAGTAAATT
*
16391401 GCTCCTCTAAACAGAGGCA--ACGAAACTTTGGAAAATAAATTGCTCC
1 GCTCCTCTAAACAGAGGCACCACG--ACTTTGGAAAGTAAATTGCTCC
16391447 TTGACAATCA
Statistics
Matches: 185, Mismatches: 20, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
80 3 0.02
82 54 0.29
83 72 0.39
84 26 0.14
85 5 0.03
86 25 0.14
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (82 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCACTAAACAGAGGCAACAAT
ACTTTGAAAAGTAAATT
Found at i:16391388 original size:124 final size:124
Alignment explanation
Indices: 16391174--16391447 Score: 379
Period size: 124 Copynumber: 2.2 Consensus size: 124
16391164 AGGCTCAATG
* * * * *
16391174 ACTTTGAGAAACATAAATGGCTCCTCTAATCAGAGGCTCAACAACTTTGAAAAAAATAAATTGCT
1 ACTTTG-GAAA-ATAAATTGCTCCTCTAAACAAAGGCACAACAACTTTG-AAAAAATAAATTACT
* * *
16391239 CCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCACTAAACAGAGGCAACGAA
63 CCTCTAAACAGAGGCAACAAGACTTTGAAAAGTAAATTGCTCCACTAAACAGAGGCAACGAA
* * * *
16391301 ACTTTGGGAAAGTAAATTGCTCCTCTAAACAAAGGCACCACGACTTTG-AAAAGTAAATTACTCC
1 ACTTT-GGAAAATAAATTGCTCCTCTAAACAAAGGCACAACAACTTTGAAAAAATAAATTACTCC
* *
16391365 TCTAAACAGAGGCAACAATACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAA
65 TCTAAACAGAGGCAACAAGACTTTGAAAAGTAAATTGCTCCACTAAACAGAGGCAACGAA
16391425 ACTTTGGAAAATAAATTGCTCCT
1 ACTTTGGAAAATAAATTGCTCCT
16391448 TGACAATCAT
Statistics
Matches: 131, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
123 17 0.13
124 74 0.56
126 30 0.23
127 9 0.07
128 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (124 bp):
ACTTTGGAAAATAAATTGCTCCTCTAAACAAAGGCACAACAACTTTGAAAAAATAAATTACTCCT
CTAAACAGAGGCAACAAGACTTTGAAAAGTAAATTGCTCCACTAAACAGAGGCAACGAA
Found at i:16391775 original size:44 final size:43
Alignment explanation
Indices: 16391734--16391817 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
16391724 CTTATTTGGC
*
16391734 AAACTT-GAAATTCATATCCAAAAA-TCTAAAGCTTTTCATTTG
1 AAACTTGGAAATTCACATCCAAAAATTC-AAAGCTTTTCATTTG
** *
16391776 AATTTTGGAAATTCACATCTAAAAATTCAAAGCTTTTCATTT
1 AAACTTGGAAATTCACATCCAAAAATTCAAAGCTTTTCATTT
16391818 AAGTTCAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 4 0.11
43 30 0.83
44 2 0.06
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.38
Consensus pattern (43 bp):
AAACTTGGAAATTCACATCCAAAAATTCAAAGCTTTTCATTTG
Found at i:16393170 original size:20 final size:19
Alignment explanation
Indices: 16393111--16393190 Score: 67
Period size: 20 Copynumber: 4.2 Consensus size: 19
16393101 AATTTGAATT
*
16393111 TTTTTTTTTCATTTTCTCA-G
1 TTTTTTTTT--TTTTCTCATC
* * *
16393131 TTTTTTCTTCTTTCT-TTC
1 TTTTTTTTTTTTTCTCATC
16393149 TTTTTTTTTTTTTCATCATC
1 TTTTTTTTTTTTTC-TCATC
*
16393169 TTCTTTTTTTTTTCTCAT-
1 TTTTTTTTTTTTTCTCATC
16393187 TTTT
1 TTTT
16393191 CATCTATTGT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
18 20 0.42
19 5 0.10
20 23 0.48
ACGTcount: A:0.06, C:0.16, G:0.01, T:0.76
Consensus pattern (19 bp):
TTTTTTTTTTTTTCTCATC
Found at i:16397100 original size:27 final size:27
Alignment explanation
Indices: 16397070--16397160 Score: 71
Period size: 27 Copynumber: 3.2 Consensus size: 27
16397060 TTTGTGCAGG
16397070 AAAAATTGATACTTTTAACTTTTCTCC
1 AAAAATTGATACTTTTAACTTTTCTCC
* *
16397097 AAAAA-T-ATTA-TTTTGAAACTTTAATTTCG
1 AAAAATTGA-TACTTTT--AACTTT--TCTCC
*
16397126 AGGAAAATTGATACTTTCAACTTTTCTCC
1 A--AAAATTGATACTTTTAACTTTTCTCC
16397155 AAAAAT
1 AAAAAT
16397161 ATGTTTTTGG
Statistics
Matches: 49, Mismatches: 5, Indels: 20
0.66 0.07 0.27
Matches are distributed among these distances:
25 5 0.10
26 3 0.06
27 16 0.33
29 8 0.16
31 10 0.20
32 3 0.06
33 4 0.08
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (27 bp):
AAAAATTGATACTTTTAACTTTTCTCC
Found at i:16397192 original size:5 final size:5
Alignment explanation
Indices: 16397184--16397288 Score: 64
Period size: 5 Copynumber: 21.6 Consensus size: 5
16397174 TTATTTAAAG
16397184 AAAAT AAAAT --AAT AAAAT AAAAT AAAAGT GAGAAAT -AAAT -AAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -A-AAAT AAAAT AAAAT
* * *
16397228 -AAAT -AAAT -AAAT AAAAGT AAAAC AAAA- AAAAT AAAAT GAAGAT AAAAG
1 AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT
* *
16397276 AACAT TAAAT AAA
1 AAAAT AAAAT AAA
16397289 CCTAATCTAA
Statistics
Matches: 82, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
3 3 0.04
4 24 0.29
5 40 0.49
6 10 0.12
7 2 0.02
8 3 0.04
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:16397202 original size:13 final size:13
Alignment explanation
Indices: 16397184--16397208 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16397174 TTATTTAAAG
16397184 AAAATAAAATAAT
1 AAAATAAAATAAT
16397197 AAAATAAAATAA
1 AAAATAAAATAA
16397209 AAGTGAGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:16397225 original size:4 final size:4
Alignment explanation
Indices: 16397216--16397242 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
16397206 TAAAAGTGAG
16397216 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
16397243 AGTAAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:16397314 original size:14 final size:14
Alignment explanation
Indices: 16397216--16397320 Score: 56
Period size: 14 Copynumber: 7.1 Consensus size: 14
16397206 TAAAAGTGAG
16397216 AAATAAATAAAT--
1 AAATAAATAAATAA
16397228 AAATAAATAAATAA
1 AAATAAATAAATAA
* *
16397242 AAGTAAA-ACAAAAA
1 AAATAAATA-AATAA
16397256 AAATAAAATGAAGATAA
1 AAAT-AAAT-AA-ATAA
*
16397273 AAGA-ACATTAAATAA
1 AA-ATA-AATAAATAA
*
16397288 ACCTAATCTAATAAATAA
1 A---AAT-AAATAAATAA
16397306 AAATAAATAAATAA
1 AAATAAATAAATAA
16397320 A
1 A
16397321 TTAATTAATT
Statistics
Matches: 71, Mismatches: 8, Indels: 26
0.68 0.08 0.25
Matches are distributed among these distances:
12 12 0.17
13 1 0.01
14 23 0.32
15 11 0.15
16 4 0.06
17 9 0.13
18 11 0.15
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.20
Consensus pattern (14 bp):
AAATAAATAAATAA
Found at i:16398232 original size:21 final size:22
Alignment explanation
Indices: 16398160--16398241 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 22
16398150 ATTTTCAGCC
*
16398160 AGATAAATTAAAAAAA-AAATAAA
1 AGATAAATCAAAAAAATAAAT--A
*
16398183 AGAAAAAATCAAATAAAAATAAATA
1 AG-ATAAATC-AA-AAAAATAAATA
*
16398208 AGATAAATCAAAAAAATTAAT-
1 AGATAAATCAAAAAAATAAATA
*
16398229 AGATAAATTAAAA
1 AGATAAATCAAAA
16398242 TTAAATAACA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
21 12 0.24
22 9 0.18
23 4 0.08
24 11 0.22
25 5 0.10
26 5 0.10
27 4 0.08
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (22 bp):
AGATAAATCAAAAAAATAAATA
Found at i:16398366 original size:22 final size:21
Alignment explanation
Indices: 16398344--16398455 Score: 81
Period size: 23 Copynumber: 5.2 Consensus size: 21
16398334 AATGCCTAAG
16398344 ATAAAAAAAATAATAATAAAA
1 ATAAAAAAAATAATAATAAAA
*
16398365 GAGAAGAAAAAA-AAT-AT-AAA
1 -ATAA-AAAAAATAATAATAAAA
* * *
16398385 ATAATAACAATAAAAATAAAA
1 ATAAAAAAAATAATAATAAAA
16398406 ATAAAATAGAAATAA-AATAAAA
1 ATAAAA-A-AAATAATAATAAAA
*
16398428 ATGTAAAATAAA-AATAAATAAAA
1 A--TAAAAAAAATAAT-AATAAAA
16398451 ATAAA
1 ATAAA
16398456 TATAAAATGA
Statistics
Matches: 72, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
18 4 0.06
19 5 0.07
20 5 0.07
21 16 0.22
22 18 0.25
23 19 0.26
24 5 0.07
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (21 bp):
ATAAAAAAAATAATAATAAAA
Found at i:16398402 original size:6 final size:6
Alignment explanation
Indices: 16398349--16398462 Score: 85
Period size: 6 Copynumber: 18.7 Consensus size: 6
16398339 CTAAGATAAA
* *
16398349 AAAAAT AATAAT AAAAGAG AAGAAA- AAAAAT ATAAAAT AATAACAAT
1 AAAAAT AAAAAT AAAA-AT AA-AAAT AAAAAT A-AAAAT -A-AA-AAT
* *
16398396 AAAAAT AAAAAT -AAAAT AGAAAT -AAAAT AAAAAT GTAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT AAAAAT
*
16398443 --AAAT AAAAAT AAATAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAA
16398463 TGAAGAAAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
4 4 0.05
5 12 0.14
6 46 0.52
7 16 0.18
8 7 0.08
9 3 0.03
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:16398405 original size:28 final size:26
Alignment explanation
Indices: 16398344--16398462 Score: 96
Period size: 29 Copynumber: 4.2 Consensus size: 26
16398334 AATGCCTAAG
*
16398344 ATAAAAA-AAATAATAATAAAAGAGAAGA
1 ATAAAAATAAA-AATAATAAAATA-AA-A
*
16398372 AAAAAAATATAAAATAATAACAATAAAA
1 ATAAAAATA-AAAATAATAA-AATAAAA
*
16398400 ATAAAAATAAAATAGAAATAAAATAAAA
1 ATAAAAATAAAA-A-TAATAAAATAAAA
* *
16398428 ATGTAAAATAAAAATAAATAAAAATAAAT
1 AT-AAAAATAAAAAT-AAT-AAAATAAAA
16398457 ATAAAA
1 ATAAAA
16398463 TGAAGAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.04
28 32 0.43
29 35 0.47
30 5 0.07
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (26 bp):
ATAAAAATAAAAATAATAAAATAAAA
Found at i:16398462 original size:11 final size:11
Alignment explanation
Indices: 16398371--16398463 Score: 63
Period size: 11 Copynumber: 8.5 Consensus size: 11
16398361 AAAAGAGAAG
*
16398371 AAAAAAAATAT
1 AAAATAAATAT
16398382 AAAAT-AATA-
1 AAAATAAATAT
* *
16398391 ACAATAAAAAT
1 AAAATAAATAT
16398402 AAAAATAAA-AT
1 -AAAATAAATAT
16398413 AGAAATAAA-AT
1 A-AAATAAATAT
16398424 AAAAATGTAAA-AT
1 -AAAA--TAAATAT
16398437 AAAAATAAATA-
1 -AAAATAAATAT
16398448 AAAATAAATAT
1 AAAATAAATAT
16398459 AAAAT
1 AAAAT
16398464 GAAGAAAAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
9 4 0.06
10 18 0.26
11 27 0.39
12 9 0.13
13 11 0.16
ACGTcount: A:0.76, C:0.01, G:0.02, T:0.20
Consensus pattern (11 bp):
AAAATAAATAT
Found at i:16401370 original size:14 final size:14
Alignment explanation
Indices: 16401351--16401399 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
16401341 AGATTCGGAT
*
16401351 TTTAAGTGTTTGGA
1 TTTAAGGGTTTGGA
16401365 TTTAAGGGATTTTGGA
1 TTTAAGGG--TTTGGA
**
16401381 TTTTGGGGTTTGGA
1 TTTAAGGGTTTGGA
16401395 TTTAA
1 TTTAA
16401400 AGGATTTCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 16 0.57
16 12 0.43
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (14 bp):
TTTAAGGGTTTGGA
Found at i:16401380 original size:16 final size:16
Alignment explanation
Indices: 16401359--16401406 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
16401349 ATTTTAAGTG
16401359 TTTGGATTTAAGGGAT
1 TTTGGATTTAAGGGAT
* *
16401375 TTTGGATTT-TGGG-G
1 TTTGGATTTAAGGGAT
*
16401389 TTTGGATTTAAAGGAT
1 TTTGGATTTAAGGGAT
16401405 TT
1 TT
16401407 CAGATTTTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
14 9 0.36
15 5 0.20
16 11 0.44
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (16 bp):
TTTGGATTTAAGGGAT
Found at i:16401392 original size:30 final size:31
Alignment explanation
Indices: 16401348--16401422 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 31
16401338 TGAAGATTCG
* * * **
16401348 GATTTTAAGTGTTTGGATTTAAGGGATTTTG
1 GATTTTAGGGGTTTGGATTTAAAGGATTTCA
16401379 GATTTT-GGGGTTTGGATTTAAAGGATTTCA
1 GATTTTAGGGGTTTGGATTTAAAGGATTTCA
16401409 GATTTTAGGGGTTT
1 GATTTTAGGGGTTT
16401423 TAGAAAACGC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
30 25 0.66
31 13 0.34
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.47
Consensus pattern (31 bp):
GATTTTAGGGGTTTGGATTTAAAGGATTTCA
Found at i:16402843 original size:26 final size:25
Alignment explanation
Indices: 16402800--16402871 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 25
16402790 CTTCTGTTTC
*
16402800 TTTTTT-TTTTATATTTTTTTAGGTA
1 TTTTTTATTTTGTA-TTTTTTAGGTA
**
16402825 TTTTTTTATTTTGTATTTTGTTTTGTA
1 -TTTTTTATTTTGTATTTT-TTAGGTA
**
16402852 TTTCATATTTTGTATTTTTT
1 TTTTTTATTTTGTATTTTTT
16402872 TTCTAGATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 2 0.05
26 26 0.67
27 11 0.28
ACGTcount: A:0.14, C:0.01, G:0.08, T:0.76
Consensus pattern (25 bp):
TTTTTTATTTTGTATTTTTTAGGTA
Found at i:16402848 original size:19 final size:19
Alignment explanation
Indices: 16402826--16402874 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
16402816 TTTTAGGTAT
**
16402826 TTTTTTATTTTGTATTTTG
1 TTTTTTATTTCATATTTTG
*
16402845 TTTTGTATTTCATATTTTG
1 TTTTTTATTTCATATTTTG
16402864 TATTTTT-TTTC
1 T-TTTTTATTTC
16402875 TAGATAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.12, C:0.04, G:0.08, T:0.76
Consensus pattern (19 bp):
TTTTTTATTTCATATTTTG
Found at i:16404475 original size:34 final size:34
Alignment explanation
Indices: 16404395--16404502 Score: 112
Period size: 34 Copynumber: 3.2 Consensus size: 34
16404385 GGATATTCAC
* * * *
16404395 CATTTTTGAGAAGTCATAGCATTTTTTGGAAATGA
1 CATTTTTGAGAAGTAATAACATTTCTTGAAAAT-A
* *
16404430 -ATTTCTAAGAAGCT-ATAACATTTCTTGAAAATA
1 CATTTTTGAGAAG-TAATAACATTTCTTGAAAATA
* *
16404463 CATTTTTGAGAAGTAATAACACTTCTCGAAAATA
1 CATTTTTGAGAAGTAATAACATTTCTTGAAAATA
16404497 CATTTT
1 CATTTT
16404503 GAAAAGTGAA
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
33 2 0.03
34 58 0.95
35 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (34 bp):
CATTTTTGAGAAGTAATAACATTTCTTGAAAATA
Found at i:16407722 original size:123 final size:123
Alignment explanation
Indices: 16407503--16407750 Score: 460
Period size: 123 Copynumber: 2.0 Consensus size: 123
16407493 AAAAGAAATA
16407503 CAGGACAAGCACAGTTAGATAGCAAAAGAACATGCCAACAAGAGTTGTTGAGTTGGTAAGGTTCG
1 CAGGACAAGCACAGTTAGATAGCAAAAGAACATGCCAACAAGAGTTGTTGAGTTGGTAAGGTTCG
*
16407568 AAGACTTCACTTGTAAGATCTAGGTTCGAGTTTTGCTACCAGCAATCCCCTTAGTGGG
66 AAGACTTCACTTGTAAGATCGAGGTTCGAGTTTTGCTACCAGCAATCCCCTTAGTGGG
*
16407626 CAGGACAAGCACTGTTAGATAGCAAAAGAACATGCCAACAAGAGTTGTTGAGTTGGTAAGGTTCG
1 CAGGACAAGCACAGTTAGATAGCAAAAGAACATGCCAACAAGAGTTGTTGAGTTGGTAAGGTTCG
* *
16407691 AAGACTTCACTTGTAAGATCGAGGTTCGAGTTTTGCTGCCAGCAATCTCCTTAGTGGG
66 AAGACTTCACTTGTAAGATCGAGGTTCGAGTTTTGCTACCAGCAATCCCCTTAGTGGG
16407749 CA
1 CA
16407751 ATCCGTAAAT
Statistics
Matches: 121, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 121 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (123 bp):
CAGGACAAGCACAGTTAGATAGCAAAAGAACATGCCAACAAGAGTTGTTGAGTTGGTAAGGTTCG
AAGACTTCACTTGTAAGATCGAGGTTCGAGTTTTGCTACCAGCAATCCCCTTAGTGGG
Found at i:16410914 original size:97 final size:92
Alignment explanation
Indices: 16410743--16410936 Score: 280
Period size: 97 Copynumber: 2.1 Consensus size: 92
16410733 AATTTCAACA
* *
16410743 ACATAACCAATTGCATGCTCCTAACACAAAACTACAGATCATACTTAGCCTTCCAACCCACCCGC
1 ACATAACCAATTGCATGCTCCCAACACAAAACTACAGATCATACTTAGCCTTCCAACCCACCCAC
*
16410808 TCCATATTCCCTATTAGACAGTAATGC
66 TCCATATTCCCCATTAGACAGTAATGC
* * * *
16410835 ACATAACCAATTGCATGCTCCCAACACTAAACTTCTGTTGAATCCATGCTTAGCCTTCCAACCCA
1 ACATAACCAATTGCATGCTCCCAACACAAAACTAC---AG-AT-CATACTTAGCCTTCCAACCCA
16410900 CCCACTCCATATTCCCCATTAGACAGTAATGC
61 CCCACTCCATATTCCCCATTAGACAGTAATGC
16410932 ACATA
1 ACATA
16410937 TGCGTACATG
Statistics
Matches: 90, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
92 32 0.36
95 1 0.01
96 2 0.02
97 55 0.61
ACGTcount: A:0.32, C:0.34, G:0.09, T:0.25
Consensus pattern (92 bp):
ACATAACCAATTGCATGCTCCCAACACAAAACTACAGATCATACTTAGCCTTCCAACCCACCCAC
TCCATATTCCCCATTAGACAGTAATGC
Found at i:16413144 original size:110 final size:110
Alignment explanation
Indices: 16413006--16413227 Score: 417
Period size: 110 Copynumber: 2.0 Consensus size: 110
16412996 GAGTTAACAA
16413006 TTACAAAGAGAATAAAACTTTTGGAAATGAAATTTTCCAGTATCAATAAAATAGCTCAAATTTCT
1 TTACAAAGAGAATAAAACTTTTGGAAATGAAATTTTCCAGTATCAATAAAATAGCTCAAATTTCT
*
16413071 CGAAATGAATTAATTCATCTGTAAATCGCCATTGTGAACAGCCTG
66 CAAAATGAATTAATTCATCTGTAAATCGCCATTGTGAACAGCCTG
*
16413116 TTACAAAGAGCATAAAACTTTTGGAAATGAAATTTTCCAGTATCAATAAAATAGCTCAAATTTCT
1 TTACAAAGAGAATAAAACTTTTGGAAATGAAATTTTCCAGTATCAATAAAATAGCTCAAATTTCT
*
16413181 CAAAATGAATTAATTCATCTGTAAATCGCCATTTTGAACAGCCTG
66 CAAAATGAATTAATTCATCTGTAAATCGCCATTGTGAACAGCCTG
16413226 TT
1 TT
16413228 CCAGACTTAA
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 109 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.32
Consensus pattern (110 bp):
TTACAAAGAGAATAAAACTTTTGGAAATGAAATTTTCCAGTATCAATAAAATAGCTCAAATTTCT
CAAAATGAATTAATTCATCTGTAAATCGCCATTGTGAACAGCCTG
Found at i:16419787 original size:2 final size:2
Alignment explanation
Indices: 16419780--16419811 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
16419770 ACATACCTAC
*
16419780 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16419812 CATAGTGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16420766 original size:2 final size:2
Alignment explanation
Indices: 16420759--16420797 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
16420749 GTTCATTGCT
* * *
16420759 TA TA TA TA AA CA TA AA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16420798 TATTAATAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:16423379 original size:29 final size:29
Alignment explanation
Indices: 16423339--16423398 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
16423329 AAATTATTAT
* * *
16423339 AAAATATTTAATGTGATATTTAAATTGTA
1 AAAATATATAATGTAATATTTAAACTGTA
16423368 AAAATATATAATGTAATATTTAAACTGTA
1 AAAATATATAATGTAATATTTAAACTGTA
16423397 AA
1 AA
16423399 TCTGTTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (29 bp):
AAAATATATAATGTAATATTTAAACTGTA
Found at i:16439728 original size:2 final size:2
Alignment explanation
Indices: 16439721--16439746 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16439711 ATAGATTAGC
16439721 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
16439747 TGGTGTGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16439795 original size:21 final size:21
Alignment explanation
Indices: 16439769--16439813 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
16439759 ATTTAGATTA
16439769 ATTTATGTTTTCAAAG-TTATC
1 ATTTATGTTTTC-AAGCTTATC
16439790 ATTTATGTTTTCAAGCTTATC
1 ATTTATGTTTTCAAGCTTATC
16439811 ATT
1 ATT
16439814 ATTAATAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.53
Consensus pattern (21 bp):
ATTTATGTTTTCAAGCTTATC
Found at i:16442438 original size:19 final size:19
Alignment explanation
Indices: 16442414--16442471 Score: 77
Period size: 20 Copynumber: 3.1 Consensus size: 19
16442404 CTCAAAATTA
16442414 ATAAAATACTTATTTTAAT
1 ATAAAATACTTATTTTAAT
16442433 ATAAAATA-TTATTTTGAAAT
1 ATAAAATACTTATTTT--AAT
16442453 ATAAAAT-CTTA-TTTAAT
1 ATAAAATACTTATTTTAAT
16442470 AT
1 AT
16442472 TATTTTTAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.14
18 7 0.19
19 11 0.31
20 13 0.36
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (19 bp):
ATAAAATACTTATTTTAAT
Found at i:16442520 original size:12 final size:13
Alignment explanation
Indices: 16442499--16442571 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 13
16442489 TTATTTGTTC
16442499 AATATAAATATAA
1 AATATAAATATAA
16442512 AATTAAATAAATATATA
1 AA-T--ATAAATATA-A
*
16442529 AATATGAATATAA
1 AATATAAATATAA
*
16442542 AAT-TAAAGA-AA
1 AATATAAATATAA
16442553 TAATA-AAATATAA
1 -AATATAAATATAA
*
16442566 TATATA
1 AATATA
16442572 TACTGAGTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
11 2 0.04
12 14 0.30
13 9 0.19
14 9 0.19
16 10 0.21
17 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (13 bp):
AATATAAATATAA
Found at i:16442539 original size:30 final size:29
Alignment explanation
Indices: 16442499--16442569 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 29
16442489 TTATTTGTTC
*
16442499 AATATAAATATAAAATTAAATAAAT-ATATA
1 AATAT-AATATAAAATTAAAGAAATAATA-A
16442529 AATATGAATATAAAATTAAAGAAATAATAA
1 AATAT-AATATAAAATTAAAGAAATAATAA
16442559 AATATAATATA
1 AATATAATATA
16442570 TATACTGAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 6 0.16
30 29 0.76
31 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (29 bp):
AATATAATATAAAATTAAAGAAATAATAA
Found at i:16443553 original size:20 final size:20
Alignment explanation
Indices: 16443525--16443583 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 20
16443515 TAATATCATA
* *
16443525 CAAATATATTAATTATCATG
1 CAAAAATATTAATTACCATG
* * * *
16443545 TAATAATATAAAATACCATG
1 CAAAAATATTAATTACCATG
*
16443565 CAAAAATATTAATAACCAT
1 CAAAAATATTAATTACCAT
16443584 TCATTCAAAT
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (20 bp):
CAAAAATATTAATTACCATG
Found at i:16443574 original size:40 final size:38
Alignment explanation
Indices: 16443502--16443577 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 38
16443492 ATAATAACAG
* * *
16443502 TCATGTAAATATATAATATCATACAAATATATTAATTA
1 TCATGTAAATATAAAATACCATACAAAAATATTAATTA
*
16443540 TCATGTAATAATATAAAATACCATGCAAAAATATTAAT
1 TCATGT-A-AATATAAAATACCATACAAAAATATTAAT
16443578 AACCATTCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 6 0.19
39 1 0.03
40 25 0.78
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (38 bp):
TCATGTAAATATAAAATACCATACAAAAATATTAATTA
Found at i:16443753 original size:24 final size:25
Alignment explanation
Indices: 16443714--16443761 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
16443704 ATAATCTTAA
* *
16443714 TCATGCCATAACATATAATATCATT
1 TCATGCAATAACATATAAAATCATT
16443739 TCATGCAATAA-ATATAAAATCAT
1 TCATGCAATAACATATAAAATCAT
16443762 GCAATAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (25 bp):
TCATGCAATAACATATAAAATCATT
Found at i:16443849 original size:88 final size:88
Alignment explanation
Indices: 16443745--16443905 Score: 208
Period size: 88 Copynumber: 1.8 Consensus size: 88
16443735 CATTTCATGC
*
16443745 AATAAATATAAAATCATGCAA-TAATAGTAATA-AA-TAAATAAATAA-CTATGCCAATAA-ATA
1 AATAAATATAAAATCATGCAATTAA-A-T-ATACAATTAAATAAATAATC-ATGCAAATAATA-A
16443805 TATTAATAATCATACAATCACATAAATA
61 TATTAATAATCATACAATCACATAAATA
*
16443833 AATAAAT-TAACAATCATGCAATTAAATATACAATTAAATATATAATCATGCAAATAATAATATT
1 AATAAATATAA-AATCATGCAATTAAATATACAATTAAATAAATAATCATGCAAATAATAATATT
16443897 AATAATCAT
65 AATAATCAT
16443906 GTAAATAAAC
Statistics
Matches: 65, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
86 3 0.05
87 6 0.09
88 51 0.78
89 5 0.08
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (88 bp):
AATAAATATAAAATCATGCAATTAAATATACAATTAAATAAATAATCATGCAAATAATAATATTA
ATAATCATACAATCACATAAATA
Found at i:16443880 original size:56 final size:56
Alignment explanation
Indices: 16443820--16443931 Score: 136
Period size: 56 Copynumber: 2.0 Consensus size: 56
16443810 ATAATCATAC
* * *
16443820 AATCACATAAATAAATAA-ATTAACAATCATGCAATTAAATATACAATTAAATATAT
1 AATCACACAAAT-AATAATATTAACAATCATGCAAATAAACATACAATTAAATATAT
** * * *
16443876 AATCATGCAAATAATAATATTAATAATCATGTAAATAAACATGCAATTAAATATAT
1 AATCACACAAATAATAATATTAACAATCATGCAAATAAACATACAATTAAATATAT
16443932 TAATAATCAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
55 5 0.11
56 42 0.89
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.31
Consensus pattern (56 bp):
AATCACACAAATAATAATATTAACAATCATGCAAATAAACATACAATTAAATATAT
Found at i:16443920 original size:36 final size:36
Alignment explanation
Indices: 16443874--16443942 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
16443864 AATTAAATAT
*
16443874 ATAATCATGCAAAT-AATAATATTAATAATCATGTAA
1 ATAAACATGCAAATAAAT-ATATTAATAATCATGTAA
*
16443910 ATAAACATGCAATTAAATATATTAATAATCATG
1 ATAAACATGCAAATAAATATATTAATAATCATG
16443943 CAATCAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 27 0.90
37 3 0.10
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (36 bp):
ATAAACATGCAAATAAATATATTAATAATCATGTAA
Found at i:16443936 original size:24 final size:24
Alignment explanation
Indices: 16443909--16444046 Score: 82
Period size: 21 Copynumber: 6.0 Consensus size: 24
16443899 TAATCATGTA
*
16443909 AATAAACATGCAATTAAATATATT
1 AATAAACATGCAAATAAATATATT
*
16443933 AATAATCATGC-AATCAAAT-TA--
1 AATAAACATGCAAAT-AAATATATT
**
16443954 AATATAATCATATAAATAAATATATT
1 AATA-AA-CATGCAAATAAATATATT
* *
16443980 AACAATCATGC----AAATATATT
1 AATAAACATGCAAATAAATATATT
**
16444000 AATAAATCACACAAATAAATATATT
1 AATAAA-CATGCAAATAAATATATT
*
16444025 AAT---CATGCAAACAAATATATT
1 AATAAACATGCAAATAAATATATT
16444046 A
1 A
16444047 GGCAAATAAA
Statistics
Matches: 86, Mismatches: 16, Indels: 27
0.67 0.12 0.21
Matches are distributed among these distances:
20 13 0.15
21 23 0.27
22 1 0.01
23 11 0.13
24 22 0.26
25 13 0.15
26 3 0.03
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (24 bp):
AATAAACATGCAAATAAATATATT
Found at i:16443954 original size:56 final size:55
Alignment explanation
Indices: 16443833--16443973 Score: 131
Period size: 56 Copynumber: 2.5 Consensus size: 55
16443823 CACATAAATA
* * * * * *
16443833 AATAAATTAACAATCATGCAATTAAATATACAATTAAATATATAATCATGCAAAT
1 AATAAATTAATAATCATGTAAATAAACATACAATTAAATATATAATAATGCAAAC
* **
16443888 AATAATATTAATAATCATGTAAATAAACATGCAATTAAATATATTAATAAT-CATGC
1 AATAA-ATTAATAATCATGTAAATAAACATACAATTAAATATA-TAATAATGCAAAC
*
16443944 AATCAAATTAAATATAATCATATAAATAAA
1 AAT-AAATT--A-ATAATCATGTAAATAAA
16443974 TATATTAACA
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
55 5 0.07
56 40 0.57
57 8 0.11
58 1 0.01
59 16 0.23
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (55 bp):
AATAAATTAATAATCATGTAAATAAACATACAATTAAATATATAATAATGCAAAC
Found at i:16443956 original size:45 final size:46
Alignment explanation
Indices: 16443907--16444027 Score: 149
Period size: 47 Copynumber: 2.7 Consensus size: 46
16443897 AATAATCATG
* *
16443907 TAAATAAA-CATGCAATTAAATATATTAATAATCATGC-AATCAAAT
1 TAAATAAATCATACAAATAAATATATTAATAATCATGCAAAT-AAAT
* * *
16443952 TAAATATAATCATATAAATAAATATATTAACAATCATGCAAATATAT
1 TAAATA-AATCATACAAATAAATATATTAATAATCATGCAAATAAAT
*
16443999 T-AATAAATCACACAAATAAATATATTAAT
1 TAAATAAATCATACAAATAAATATATTAAT
16444028 CATGCAAACA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
45 27 0.42
46 6 0.09
47 29 0.45
48 3 0.05
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.32
Consensus pattern (46 bp):
TAAATAAATCATACAAATAAATATATTAATAATCATGCAAATAAAT
Found at i:16444014 original size:21 final size:20
Alignment explanation
Indices: 16443971--16444016 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
16443961 TCATATAAAT
* **
16443971 AAATATATTAACAATCATGC
1 AAATATATTAAAAATCACAC
16443991 AAATATATTAATAAATCACAC
1 AAATATATTAA-AAATCACAC
16444012 AAATA
1 AAATA
16444017 AATATATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (20 bp):
AAATATATTAAAAATCACAC
Found at i:16444038 original size:25 final size:25
Alignment explanation
Indices: 16443991--16444041 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
16443981 ACAATCATGC
*
16443991 AAATATATTAATAAATCACACAAAT
1 AAATATATTAATAAATCAAACAAAT
*
16444016 AAATATATTAAT-CATGCAAACAAAT
1 AAATATATTAATAAAT-CAAACAAAT
16444041 A
1 A
16444042 TATTAGGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (25 bp):
AAATATATTAATAAATCAAACAAAT
Found at i:16445837 original size:12 final size:12
Alignment explanation
Indices: 16445820--16445858 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
16445810 TTTGTCAAAG
16445820 AAAAAAAAG-AGA
1 AAAAAAAAGCA-A
*
16445832 AAAAAATAGCAA
1 AAAAAAAAGCAA
16445844 AAAAAAAAGCAA
1 AAAAAAAAGCAA
16445856 AAA
1 AAA
16445859 GAGAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 23 0.96
13 1 0.04
ACGTcount: A:0.82, C:0.05, G:0.10, T:0.03
Consensus pattern (12 bp):
AAAAAAAAGCAA
Found at i:16446267 original size:23 final size:23
Alignment explanation
Indices: 16446237--16446294 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
16446227 TAGCTAGCCC
16446237 CTAA-ATTTTAAGTCCAAATTAG
1 CTAACATTTTAAGTCCAAATTAG
*
16446259 CTAACATTTTAAGTTCAAATTAG
1 CTAACATTTTAAGTCCAAATTAG
* *
16446282 TTGACATTTTAAG
1 CTAACATTTTAAG
16446295 CTCAAGTGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 4 0.12
23 28 0.88
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (23 bp):
CTAACATTTTAAGTCCAAATTAG
Found at i:16446321 original size:22 final size:22
Alignment explanation
Indices: 16446291--16446333 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
16446281 GTTGACATTT
*
16446291 TAAGCTCAAGTGAGCTGGCACC
1 TAAGCTCAAATGAGCTGGCACC
* *
16446313 TAAGTTCAAATTAGCTGGCAC
1 TAAGCTCAAATGAGCTGGCAC
16446334 TCAAATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (22 bp):
TAAGCTCAAATGAGCTGGCACC
Found at i:16447611 original size:14 final size:14
Alignment explanation
Indices: 16447592--16447619 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16447582 TCTAATGGCC
16447592 CAAAAAAATAAAAA
1 CAAAAAAATAAAAA
16447606 CAAAAAAATAAAAA
1 CAAAAAAATAAAAA
16447620 AGAGACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (14 bp):
CAAAAAAATAAAAA
Found at i:16448089 original size:35 final size:35
Alignment explanation
Indices: 16448019--16448108 Score: 92
Period size: 35 Copynumber: 2.6 Consensus size: 35
16448009 CTCACAGTTT
*
16448019 AATCTCGATCATTTTTATTTATCAACTTACAGCTC
1 AATCCCGATCATTTTTATTTATCAACTTACAGCTC
* * * *
16448054 AATCCCGATCATTCTTATTTCTCGATTTA-AGGCTC
1 AATCCCGATCATTTTTATTTATCAACTTACA-GCTC
* * *
16448089 AGTCCTGATTATTTTTATTT
1 AATCCCGATCATTTTTATTT
16448109 TTTTATTTGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
34 1 0.02
35 44 0.98
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.46
Consensus pattern (35 bp):
AATCCCGATCATTTTTATTTATCAACTTACAGCTC
Found at i:16448378 original size:35 final size:35
Alignment explanation
Indices: 16448339--16448423 Score: 91
Period size: 35 Copynumber: 2.4 Consensus size: 35
16448329 GTTCAATCTT
*
16448339 AATCATTTTTATT-TTCTAATTCGCGATTAAGTCCC
1 AATCATTTTTATTCTTC-AACTCGCGATTAAGTCCC
* ** * *
16448374 AATCATATTTATTCTTCGGCTCGTGATTTAGTCCC
1 AATCATTTTTATTCTTCAACTCGCGATTAAGTCCC
*
16448409 TATCATTTTTATTCT
1 AATCATTTTTATTCT
16448424 AGTCATTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
35 38 0.93
36 3 0.07
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.48
Consensus pattern (35 bp):
AATCATTTTTATTCTTCAACTCGCGATTAAGTCCC
Found at i:16448628 original size:35 final size:35
Alignment explanation
Indices: 16448589--16448656 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
16448579 TATATTTATA
* * *
16448589 GCTCAACCCTGGTAATTCTTATCTCTTAACTTGTG
1 GCTCAACCCTGATAACTCTTATCTCTCAACTTGTG
* *
16448624 GCTCAATCCTGATCACTCTTATCTCTCAACTTG
1 GCTCAACCCTGATAACTCTTATCTCTCAACTTG
16448657 CAGCTTATCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (35 bp):
GCTCAACCCTGATAACTCTTATCTCTCAACTTGTG
Found at i:16449274 original size:2 final size:2
Alignment explanation
Indices: 16449267--16449297 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
16449257 TTTCAAGTCT
16449267 TA TA TA TA TA TA T- 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
16449298 AAATCATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16451669 original size:21 final size:22
Alignment explanation
Indices: 16451623--16451670 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
16451613 CCCAACTTTG
*
16451623 TTTTTGAAGACCTATAAATATC
1 TTTTTGAAAACCTATAAATATC
16451645 -TTTTGATAAACC-ATAAAT-TC
1 TTTTTGA-AAACCTATAAATATC
16451665 TTTTTG
1 TTTTTG
16451671 CGATTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 2 0.09
21 17 0.74
22 4 0.17
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.46
Consensus pattern (22 bp):
TTTTTGAAAACCTATAAATATC
Found at i:16452134 original size:17 final size:18
Alignment explanation
Indices: 16452099--16452135 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
16452089 CTTAAAAGAG
16452099 TTACAATGCATTGAGTTT
1 TTACAATGCATTGAGTTT
16452117 TTACAAT-CA-TGAAGTTT
1 TTACAATGCATTG-AGTTT
16452134 TT
1 TT
16452136 TCCCCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.11
17 9 0.50
18 7 0.39
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (18 bp):
TTACAATGCATTGAGTTT
Found at i:16459238 original size:43 final size:43
Alignment explanation
Indices: 16459177--16459274 Score: 169
Period size: 43 Copynumber: 2.3 Consensus size: 43
16459167 ATAATTTGGT
* * *
16459177 GAATATTTGAATCTTGGTTGGCTATGCATTTGCATCATGTAGC
1 GAATATTTGAATCTTGGTTAGCTATACATTTGCATCATGTAAC
16459220 GAATATTTGAATCTTGGTTAGCTATACATTTGCATCATGTAAC
1 GAATATTTGAATCTTGGTTAGCTATACATTTGCATCATGTAAC
16459263 GAATATTTGAAT
1 GAATATTTGAAT
16459275 AATAGTGTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (43 bp):
GAATATTTGAATCTTGGTTAGCTATACATTTGCATCATGTAAC
Found at i:16459250 original size:23 final size:23
Alignment explanation
Indices: 16459181--16459251 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
16459171 TTTGGTGAAT
* *
16459181 ATTTGAATCTTGGTTGGCTATGC
1 ATTTGAATCTTGGTTAGCTATAC
* * * *
16459204 ATTTGCATCAT-G-TAGCGA-AT
1 ATTTGAATCTTGGTTAGCTATAC
16459224 ATTTGAATCTTGGTTAGCTATAC
1 ATTTGAATCTTGGTTAGCTATAC
16459247 ATTTG
1 ATTTG
16459252 CATCATGTAA
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
20 9 0.26
21 5 0.14
22 6 0.17
23 15 0.43
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (23 bp):
ATTTGAATCTTGGTTAGCTATAC
Found at i:16459576 original size:24 final size:23
Alignment explanation
Indices: 16459549--16459662 Score: 124
Period size: 24 Copynumber: 4.9 Consensus size: 23
16459539 AAGAATATTT
* *
16459549 GAATTTTAGATGAAAATCTTTAA
1 GAATTTTAAATGAGAATCTTTAA
*
16459572 GGAATTTTAAATGAGAATATTT--
1 -GAATTTTAAATGAGAATCTTTAA
* *
16459594 GAGTTTTAAATAAGAATCTTTAA
1 GAATTTTAAATGAGAATCTTTAA
16459617 GAAGTTTTAAATGAGAATCTTTAA
1 GAA-TTTTAAATGAGAATCTTTAA
* *
16459641 GAAATTCTATATGAGAATCTTT
1 G-AATTTTAAATGAGAATCTTT
16459663 GAATGAGAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
21 18 0.24
23 2 0.03
24 54 0.71
25 2 0.03
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.39
Consensus pattern (23 bp):
GAATTTTAAATGAGAATCTTTAA
Found at i:16459594 original size:45 final size:45
Alignment explanation
Indices: 16459540--16459634 Score: 140
Period size: 45 Copynumber: 2.1 Consensus size: 45
16459530 AAAAATGATA
*
16459540 AGAATATTTGAATTTTAGATGAA-AATCTTTAAGGAA-TTTTAAATG
1 AGAATATTTGAATTTTAAAT-AAGAATCTTTAA-GAAGTTTTAAATG
*
16459585 AGAATATTTGAGTTTTAAATAAGAATCTTTAAGAAGTTTTAAATG
1 AGAATATTTGAATTTTAAATAAGAATCTTTAAGAAGTTTTAAATG
16459630 AGAAT
1 AGAAT
16459635 CTTTAAGAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
44 5 0.11
45 41 0.89
ACGTcount: A:0.43, C:0.02, G:0.16, T:0.39
Consensus pattern (45 bp):
AGAATATTTGAATTTTAAATAAGAATCTTTAAGAAGTTTTAAATG
Found at i:16459602 original size:21 final size:22
Alignment explanation
Indices: 16459540--16459666 Score: 89
Period size: 24 Copynumber: 5.6 Consensus size: 22
16459530 AAAAATGATA
*
16459540 AGAATATTT-GAATTTTAGATG
1 AGAATATTTAGAATTTTAAATG
* *
16459561 AAAATCTTTAAGGAATTTTAAATG
1 AGAATATTT-A-GAATTTTAAATG
* *
16459585 AGAATATTT-GAGTTTTAAATA
1 AGAATATTTAGAATTTTAAATG
*
16459606 AGAATCTTTAAGAAGTTTTAAATG
1 AGAATATTT-AGAA-TTTTAAATG
* * *
16459630 AGAATCTTTAAGAAATTCTATATG
1 AGAATATTT-AG-AATTTTAAATG
*
16459654 AGAATCTTT-GAAT
1 AGAATATTTAGAAT
16459667 GAGAATCTTC
Statistics
Matches: 87, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
21 28 0.32
22 1 0.01
23 2 0.02
24 54 0.62
25 2 0.02
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.39
Consensus pattern (22 bp):
AGAATATTTAGAATTTTAAATG
Found at i:16459636 original size:69 final size:66
Alignment explanation
Indices: 16459537--16459664 Score: 166
Period size: 69 Copynumber: 1.9 Consensus size: 66
16459527 GTTAAAAATG
* * *
16459537 ATAAGAATATTTGAATTTTAGATGAAAATCTTTAAGGAATTTTAAATGAGAATATTTGAGTTTTA
1 ATAAGAATATTTGAATTTTAAATGAAAATCTTTAAGAAATTCTAAATGAGAATATTTGAGTTTTA
16459602 A
66 A
* * * *
16459603 ATAAGAATCTTTAAGAAGTTTTAAATGAGAATCTTTAAGAAATTCTATATGAGAATCTTTGA
1 ATAAGAATATTT--GAA-TTTTAAATGAAAATCTTTAAGAAATTCTAAATGAGAATATTTGA
16459665 ATGAGAATCT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
66 11 0.21
68 3 0.06
69 38 0.73
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.39
Consensus pattern (66 bp):
ATAAGAATATTTGAATTTTAAATGAAAATCTTTAAGAAATTCTAAATGAGAATATTTGAGTTTTA
A
Found at i:16459639 original size:14 final size:14
Alignment explanation
Indices: 16459598--16459675 Score: 55
Period size: 14 Copynumber: 6.1 Consensus size: 14
16459588 ATATTTGAGT
*
16459598 TTTAAATAAGAATC
1 TTTAAATGAGAATC
*
16459612 TTT-AA-GA-AGT-
1 TTTAAATGAGAATC
16459622 TTTAAATGAGAATC
1 TTTAAATGAGAATC
16459636 TTT-AA-GA-AAT-
1 TTTAAATGAGAATC
* *
16459646 TCTATATGAGAATC
1 TTTAAATGAGAATC
*
16459660 TTTGAATGAGAATC
1 TTTAAATGAGAATC
16459674 TT
1 TT
16459676 CGTCTTTTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
10 5 0.10
11 8 0.17
12 7 0.15
13 9 0.19
14 19 0.40
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.38
Consensus pattern (14 bp):
TTTAAATGAGAATC
Found at i:16460041 original size:18 final size:18
Alignment explanation
Indices: 16460020--16460070 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
16460010 TAATTTTGTG
*
16460020 AATCTTGAAATTCTTGCA
1 AATCTTAAAATTCTTGCA
* *
16460038 AATC-TAAAATTCTTACG
1 AATCTTAAAATTCTTGCA
*
16460055 AATCTTAAAAATCTTG
1 AATCTTAAAATTCTTG
16460071 TGAAACTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (18 bp):
AATCTTAAAATTCTTGCA
Found at i:16460047 original size:17 final size:17
Alignment explanation
Indices: 16460027--16460083 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
16460017 GTGAATCTTG
16460027 AAATTCTTGCAAATCTA
1 AAATTCTTGCAAATCTA
* *
16460044 AAATTCTTACGAATCTTA
1 AAATTCTTGCAAATC-TA
* *
16460062 AAAATCTTGTGAAA-CTA
1 AAATTCTTG-CAAATCTA
16460079 AAATT
1 AAATT
16460084 TTGAGAATCA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
17 19 0.61
18 10 0.32
19 2 0.06
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (17 bp):
AAATTCTTGCAAATCTA
Found at i:16460124 original size:82 final size:82
Alignment explanation
Indices: 16460027--16460267 Score: 204
Period size: 82 Copynumber: 2.9 Consensus size: 82
16460017 GTGAATCTTG
** **
16460027 AAATTCTTGCAAATCTAAAATTCTTACGAATCTTAAAAATCTTGTGAAACTAAAATTTTGA-GAA
1 AAATTCTTGTGAATCTAAAATTCTTACGAATCTTAAAAATCTTGCAAAACTAAAATTTT-ATGAA
* *
16460091 TCAAATTCTTTTGAAATT
65 TCAAATTCTTCTGAAACT
* * * * * *
16460109 GAATTCTTGTGAATCTCAAAATT-TTATGAAT-TTGAAAATTCTTACAAAACTGATATTTTATGA
1 AAATTCTTGTGAATCT-AAAATTCTTACGAATCTT-AAAAATCTTGCAAAACTAAAATTTTATGA
*
16460172 ATCATATTCTTCTGAAACT
64 ATCAAATTCTTCTGAAACT
* * * * * *
16460191 AAAGTT-TTATGAATTTAAAATTCTTGCGAATC-TGAAAATCTTGCAAATCTAAAAAATCTTATG
1 AAA-TTCTTGTGAATCTAAAATTCTTACGAATCTTAAAAATCTTGCAAAACT--AAAATTTTATG
16460254 AATCTAAAATTCTT
63 AATC--AAATTCTT
16460268 ACAAATCTGA
Statistics
Matches: 123, Mismatches: 26, Indels: 17
0.74 0.16 0.10
Matches are distributed among these distances:
81 22 0.18
82 74 0.60
83 20 0.16
85 7 0.06
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (82 bp):
AAATTCTTGTGAATCTAAAATTCTTACGAATCTTAAAAATCTTGCAAAACTAAAATTTTATGAAT
CAAATTCTTCTGAAACT
Found at i:16460232 original size:17 final size:18
Alignment explanation
Indices: 16460207--16460279 Score: 69
Period size: 17 Copynumber: 4.2 Consensus size: 18
16460197 TTATGAATTT
* *
16460207 AAAATTCTTGCGAATCTG
1 AAAATTCTTACAAATCTG
* *
16460225 AAAA-TCTTGCAAATCTA
1 AAAATTCTTACAAATCTG
* **
16460242 AAAAATCTTATGAATCT-
1 AAAATTCTTACAAATCTG
16460259 AAAATTCTTACAAATCTG
1 AAAATTCTTACAAATCTG
16460277 AAA
1 AAA
16460280 TATTGTAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
17 29 0.64
18 16 0.36
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (18 bp):
AAAATTCTTACAAATCTG
Found at i:16461525 original size:20 final size:20
Alignment explanation
Indices: 16461479--16461526 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
16461469 GCTAAGCCGA
* * *
16461479 TTTTTTTTTTGTTATTTTTG
1 TTTTTTTTATGTTATTCTTC
*
16461499 TTATTTTTATGTTATTCTTC
1 TTTTTTTTATGTTATTCTTC
16461519 TTTTTTTT
1 TTTTTTTT
16461527 TAGGTATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.08, C:0.04, G:0.06, T:0.81
Consensus pattern (20 bp):
TTTTTTTTATGTTATTCTTC
Found at i:16462440 original size:16 final size:18
Alignment explanation
Indices: 16462413--16462447 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
16462403 AATTAGCTAT
16462413 ATTTTCAAT-AAAATAAA
1 ATTTTCAATAAAAATAAA
16462430 ATTTT-AATAAAAATAAA
1 ATTTTCAATAAAAATAAA
16462447 A
1 A
16462448 AATAAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
ATTTTCAATAAAAATAAA
Found at i:16462605 original size:15 final size:15
Alignment explanation
Indices: 16462585--16462618 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
16462575 TTTTTTCAAT
*
16462585 ATTAAATTTAAGACC
1 ATTAAAATTAAGACC
16462600 ATTAAAATTAAGACC
1 ATTAAAATTAAGACC
16462615 -TTAA
1 ATTAA
16462619 GATAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.32
Consensus pattern (15 bp):
ATTAAAATTAAGACC
Found at i:16463801 original size:29 final size:30
Alignment explanation
Indices: 16463696--16463801 Score: 117
Period size: 30 Copynumber: 3.6 Consensus size: 30
16463686 ATATACAATA
* * *
16463696 ATTAAATTTTTTAAAAGTAATATTATAAAA
1 ATTAAATTTCTTAAAAATAATATTATAAAG
16463726 ATTAAATTTCTTAAAAATAATATTATAAAG
1 ATTAAATTTCTTAAAAATAATATTATAAAG
*** * * *
16463756 ATTAAATCGGTT-TAAATACTATTATAAGG
1 ATTAAATTTCTTAAAAATAATATTATAAAG
16463785 ATTAAA-TTCTTAAAAAT
1 ATTAAATTTCTTAAAAAT
16463802 TGAAGAATAT
Statistics
Matches: 62, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
28 2 0.03
29 24 0.39
30 36 0.58
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.41
Consensus pattern (30 bp):
ATTAAATTTCTTAAAAATAATATTATAAAG
Found at i:16464119 original size:52 final size:54
Alignment explanation
Indices: 16464046--16464170 Score: 148
Period size: 52 Copynumber: 2.3 Consensus size: 54
16464036 TGTAAAATTT
* * * *
16464046 ATTTTTTTTAATGAAAGATTACATTTCTA-TTTATAAAAACATAAT-TTT-TATA
1 ATTTTTTTTAATAAAAAATTACATCTCTACTTTA-AAAAACATAATCTTTGTAAA
*
16464098 ATTTTTTTTAATAAAAAATTACGTCTCTACTTTAAAAAACATAATCTTTGTAAA
1 ATTTTTTTTAATAAAAAATTACATCTCTACTTTAAAAAACATAATCTTTGTAAA
* *
16464152 ATTTTATTTCAATCAAAAA
1 ATTTT-TTTTAATAAAAAA
16464171 GAATGTTTCT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
52 36 0.58
53 7 0.11
54 8 0.13
55 11 0.18
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (54 bp):
ATTTTTTTTAATAAAAAATTACATCTCTACTTTAAAAAACATAATCTTTGTAAA
Found at i:16468170 original size:16 final size:19
Alignment explanation
Indices: 16468134--16468174 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 19
16468124 TCATTATTTG
16468134 AAATAAGTTTTTTGATGAA
1 AAATAAGTTTTTTGATGAA
16468153 AAATAA-TTTTTT-AT-AA
1 AAATAAGTTTTTTGATGAA
16468169 AAATAA
1 AAATAA
16468175 AAGAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.36
17 2 0.09
18 6 0.27
19 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (19 bp):
AAATAAGTTTTTTGATGAA
Found at i:16468973 original size:2 final size:2
Alignment explanation
Indices: 16468966--16469036 Score: 60
Period size: 2 Copynumber: 37.5 Consensus size: 2
16468956 GTTCATTGCT
* * *
16468966 TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA -A T- TG TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
16469006 TA TA -A T- TG TA TA TA CA TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16469037 TATGAATAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
1 4 0.07
2 53 0.93
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16468987 original size:12 final size:12
Alignment explanation
Indices: 16468970--16469036 Score: 79
Period size: 12 Copynumber: 5.9 Consensus size: 12
16468960 ATTGCTTATA
16468970 TATATATATATG
1 TATATATATATG
*
16468982 TATATATATATA
1 TATATATATATG
*
16468994 TATA-AT-TGTG
1 TATATATATATG
16469004 TATATA-AT-TG
1 TATATATATATG
*
16469014 TATATACATATG
1 TATATATATATG
16469026 TATATATATAT
1 TATATATATAT
16469037 TATGAATAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
10 14 0.30
11 6 0.13
12 27 0.57
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.49
Consensus pattern (12 bp):
TATATATATATG
Found at i:16469792 original size:12 final size:12
Alignment explanation
Indices: 16469771--16469796 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16469761 CACCAAAACC
16469771 AAAAAAAAAAGA
1 AAAAAAAAAAGA
16469783 AAAAAAAAAAGA
1 AAAAAAAAAAGA
16469795 AA
1 AA
16469797 CCCTTCTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:16471054 original size:29 final size:26
Alignment explanation
Indices: 16471025--16471127 Score: 90
Period size: 26 Copynumber: 4.1 Consensus size: 26
16471015 ATTTTTATTA
16471025 ATTAA-ATAATAATATTATATAATTC
1 ATTAATATAATAATATTATATAATTC
* *
16471050 ATTAATATAGTAATATTATATAATTT
1 ATTAATATAATAATATTATATAATTC
* * *
16471076 ATTGATAATATATAAAATT-TATAAATC
1 ATTAAT-ATA-ATAATATTATATAATTC
* *
16471103 AATAATATATTAA-A-TATA-AATTC
1 ATTAATATAATAATATTATATAATTC
16471126 AT
1 AT
16471128 ATTAAAAATG
Statistics
Matches: 62, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
23 6 0.10
24 3 0.05
25 8 0.13
26 26 0.42
27 13 0.21
28 6 0.10
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (26 bp):
ATTAATATAATAATATTATATAATTC
Found at i:16475731 original size:2 final size:2
Alignment explanation
Indices: 16475726--16475751 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16475716 TTTTTTTCTT
16475726 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
16475752 AATTTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16479078 original size:37 final size:39
Alignment explanation
Indices: 16479018--16479096 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 39
16479008 TGAAAAAATG
** * *
16479018 TTTTAAATAAATTTTTTTATATTT-TTATAAATGAATTA
1 TTTTAAATAAATCCTTTTATATTTGTTAAAAAAGAATTA
*
16479056 TTTTAAAT-AATCCTTTTATATTTGTTAAAAAAGTATTA
1 TTTTAAATAAATCCTTTTATATTTGTTAAAAAAGAATTA
16479094 TTT
1 TTT
16479097 CATGTGTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
37 13 0.37
38 22 0.63
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.56
Consensus pattern (39 bp):
TTTTAAATAAATCCTTTTATATTTGTTAAAAAAGAATTA
Found at i:16479271 original size:62 final size:63
Alignment explanation
Indices: 16479200--16479352 Score: 193
Period size: 62 Copynumber: 2.4 Consensus size: 63
16479190 ATTTAGGTTA
* *
16479200 ATATTTTTATAAAAAGATTATTTAAGACATTTT-TATAAATAAAATACCTTAAA-AATATTTTT
1 ATATTTTTATAAAAAGATTATTTAAAACATTTTCTACAAA-AAAATACCTTAAATAATATTTTT
* * * * * *
16479262 ATATTTTTATAAAAATATTATTTAAAACGTTTTCTGCACAAAAATATCTTAAATAATTTTTTT
1 ATATTTTTATAAAAAGATTATTTAAAACATTTTCTACAAAAAAATACCTTAAATAATATTTTT
*
16479325 ATATATTTTATAAATAGATTATTTAAAA
1 ATAT-TTTTATAAAAAGATTATTTAAAA
16479353 ATATTTTAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
62 42 0.54
63 15 0.19
64 21 0.27
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.46
Consensus pattern (63 bp):
ATATTTTTATAAAAAGATTATTTAAAACATTTTCTACAAAAAAATACCTTAAATAATATTTTT
Found at i:16480001 original size:17 final size:18
Alignment explanation
Indices: 16479979--16480012 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
16479969 TCGACTACTG
16479979 TATTTTTTC-AAAAATCA
1 TATTTTTTCTAAAAATCA
16479996 TATTTTTTCTAAAAATC
1 TATTTTTTCTAAAAATC
16480013 CAAGATTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTTTTTCTAAAAATCA
Found at i:16480458 original size:1 final size:1
Alignment explanation
Indices: 16480452--16480476 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
16480442 AAACAGAAAG
16480452 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
16480477 GAAAGAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16486549 original size:4 final size:4
Alignment explanation
Indices: 16486540--16486568 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
16486530 CAACCTTTTC
16486540 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
16486569 AATATATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:16493148 original size:22 final size:22
Alignment explanation
Indices: 16493122--16493165 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
16493112 TTGTATATTT
*
16493122 ATATTTGTATCTCTAAAATTAA
1 ATATTTGTATCCCTAAAATTAA
*
16493144 ATATTTGTATCCCTAGAATTAA
1 ATATTTGTATCCCTAAAATTAA
16493166 GGACAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (22 bp):
ATATTTGTATCCCTAAAATTAA
Found at i:16506988 original size:17 final size:18
Alignment explanation
Indices: 16506966--16507001 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
16506956 AATCTTAGAG
16506966 AGAGAAG-AAAAGAAAAT
1 AGAGAAGAAAAAGAAAAT
16506983 AGAGAAGAAAAAGAAAAT
1 AGAGAAGAAAAAGAAAAT
16507001 A
1 A
16507002 TTTTATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (18 bp):
AGAGAAGAAAAAGAAAAT
Found at i:16523986 original size:2 final size:2
Alignment explanation
Indices: 16523979--16524007 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16523969 ACTATCTTTC
16523979 AT AT 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 AT AT A
16524008 AACCATTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16524561 original size:3 final size:3
Alignment explanation
Indices: 16524548--16524577 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
16524538 TGCCACCGCT
*
16524548 TCC TGC TCC TCC TCC TCC TCC TCC TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
16524578 GCCCAACGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.63, G:0.03, T:0.33
Consensus pattern (3 bp):
TCC
Found at i:16527329 original size:22 final size:23
Alignment explanation
Indices: 16527290--16527333 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
16527280 AAATTATAGA
*
16527290 TATTAAAATTTTAATTTTAAATT
1 TATTAAAATATTAATTTTAAATT
*
16527313 TATT-AAATATTACTTTTAAAT
1 TATTAAAATATTAATTTTAAAT
16527334 AGTATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAAAATATTAATTTTAAATT
Found at i:16527339 original size:23 final size:24
Alignment explanation
Indices: 16527285--16527339 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
16527275 AAAATAAATT
*
16527285 ATAGATATTAAAATTTTAATTTTAA
1 ATAG-TATTAAAATATTAATTTTAA
* *
16527310 AT-TTATT-AAATATTACTTTTAA
1 ATAGTATTAAAATATTAATTTTAA
16527332 ATAGTATT
1 ATAGTATT
16527340 TATATGAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 15 0.60
23 8 0.32
25 2 0.08
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (24 bp):
ATAGTATTAAAATATTAATTTTAA
Found at i:16535702 original size:22 final size:22
Alignment explanation
Indices: 16535670--16535722 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
16535660 AGTTTCCTAA
* *
16535670 AATTTTAAAATTTTTAAAATAT
1 AATTTTAAAATATATAAAATAT
* *
16535692 AATTTTGAAATATATAAAATAAA
1 AATTTTAAAATATATAAAAT-AT
16535715 AATTTTAA
1 AATTTTAA
16535723 CGATTCAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATTTTAAAATATATAAAATAT
Found at i:16538262 original size:16 final size:16
Alignment explanation
Indices: 16538241--16538293 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
16538231 TATTTTTTAA
16538241 ATATAAATATTTAAAT
1 ATATAAATATTTAAAT
* **
16538257 ATATAATTATAGAAAT
1 ATATAAATATTTAAAT
16538273 ATATATAATTAATTTAAAT
1 ATATA-AA-T-ATTTAAAT
16538292 AT
1 AT
16538294 TATTTTTATA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 1 0.04
19 8 0.29
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
ATATAAATATTTAAAT
Found at i:16538764 original size:19 final size:18
Alignment explanation
Indices: 16538731--16538768 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
16538721 AAAAACATAA
*
16538731 AATATAATTTATTTATAT
1 AATACAATTTATTTATAT
16538749 AATACAATTATATTTATAT
1 AATACAATT-TATTTATAT
16538768 A
1 A
16538769 TTCTAATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
AATACAATTTATTTATAT
Found at i:16542953 original size:2 final size:2
Alignment explanation
Indices: 16542946--16542994 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
16542936 TATTATGAGA
16542946 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16542988 AT AT AT A
1 AT AT AT A
16542995 GAGGATAAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16545033 original size:13 final size:13
Alignment explanation
Indices: 16545015--16545049 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
16545005 AAAAGTTTAA
16545015 GTTTAAAAAATAC
1 GTTTAAAAAATAC
*
16545028 GTTTAAAAAATAT
1 GTTTAAAAAATAC
*
16545041 GATTAAAAA
1 GTTTAAAAA
16545050 TTTTAATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (13 bp):
GTTTAAAAAATAC
Found at i:16546051 original size:19 final size:19
Alignment explanation
Indices: 16546029--16546097 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 19
16546019 ATGAATGATT
16546029 TTTAAATTATAATAAAATA
1 TTTAAATTATAATAAAATA
* *
16546048 TTTAATTTGAT-ATTAAAT-
1 TTTAAATT-ATAATAAAATA
* * **
16546066 TTAAAAATTTTAATATTATA
1 TT-TAAATTATAATAAAATA
16546086 TTTAAATTATAA
1 TTTAAATTATAA
16546098 ATTTATTAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
18 3 0.08
19 29 0.81
20 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (19 bp):
TTTAAATTATAATAAAATA
Found at i:16546070 original size:26 final size:28
Alignment explanation
Indices: 16546029--16546098 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 28
16546019 ATGAATGATT
16546029 TTTAAATTATAATAAAATATTTAAT-TTGATA
1 TTTAAATTAT-A-AAAAT-TTTAATATT-ATA
16546060 -TTAAATT-TAAAAATTTTAATATTATA
1 TTTAAATTATAAAAATTTTAATATTATA
16546086 TTTAAATTATAAA
1 TTTAAATTATAAA
16546099 TTTATTAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
26 9 0.25
27 14 0.39
28 5 0.14
29 1 0.03
30 7 0.19
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
TTTAAATTATAAAAATTTTAATATTATA
Found at i:16546238 original size:29 final size:29
Alignment explanation
Indices: 16546197--16546256 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
16546187 AATTAATAGA
* *
16546197 TTTATAATTTAAATATCACATTAAATATT
1 TTTAAAATATAAATATCACATTAAATATT
*
16546226 TTTAAAATATAAATATCATATTAAATATT
1 TTTAAAATATAAATATCACATTAAATATT
16546255 TT
1 TT
16546257 ATTATAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTAAAATATAAATATCACATTAAATATT
Found at i:16561676 original size:13 final size:13
Alignment explanation
Indices: 16561658--16561690 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
16561648 TACTTTTCTC
16561658 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
16561671 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
*
16561684 AAGAAAA
1 AAAAAAA
16561691 CTACCATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:16567538 original size:14 final size:13
Alignment explanation
Indices: 16567501--16567526 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16567491 CTGTCTCATT
16567501 AAAAAAAGAAAGA
1 AAAAAAAGAAAGA
16567514 AAAAAAAGAAAGA
1 AAAAAAAGAAAGA
16567527 GGAAAAGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAGA
Found at i:16569194 original size:2 final size:2
Alignment explanation
Indices: 16569182--16569229 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
16569172 TAACTCCCCA
*
16569182 TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
16569224 TC -C TC T
1 TC TC TC T
16569230 TTTCTCCTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:16570100 original size:18 final size:18
Alignment explanation
Indices: 16570079--16570135 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 18
16570069 AAATAAATAA
16570079 ATAATTGATGATAAAATT
1 ATAATTGATGATAAAATT
*
16570097 ATAATT-ACT-TTAAAATT
1 ATAATTGA-TGATAAAATT
16570114 -TAAATATGATGATAAAATT
1 AT-AAT-TGATGATAAAATT
16570133 ATA
1 ATA
16570136 TCAATTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
16 1 0.03
17 11 0.35
18 9 0.29
19 9 0.29
20 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (18 bp):
ATAATTGATGATAAAATT
Found at i:16570496 original size:2 final size:2
Alignment explanation
Indices: 16570489--16570517 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
16570479 ACAAATTTAT
16570489 TA TA TA TA T- 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
16570518 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16571313 original size:56 final size:58
Alignment explanation
Indices: 16571247--16571368 Score: 178
Period size: 57 Copynumber: 2.1 Consensus size: 58
16571237 TAATATAAAA
* * *
16571247 ATTTTAAATTTGAATTCAA-TGATCA-CTCATTTTAAATTATTAAATAT-AGATATTTT
1 ATTTTGAATTTAAATTCAATTGATCATCT-ATTTTAAATTATTAAATATGACATATTTT
16571303 ATTTTGAATTTAAATTCAATTGATCATCTATTTTAAATTATTAAATATGACATATTTT
1 ATTTTGAATTTAAATTCAATTGATCATCTATTTTAAATTATTAAATATGACATATTTT
*
16571361 ATCTTGAA
1 ATTTTGAA
16571369 ATAATTAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
56 17 0.29
57 25 0.42
58 17 0.29
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (58 bp):
ATTTTGAATTTAAATTCAATTGATCATCTATTTTAAATTATTAAATATGACATATTTT
Found at i:16576651 original size:192 final size:192
Alignment explanation
Indices: 16576324--16576711 Score: 722
Period size: 192 Copynumber: 2.0 Consensus size: 192
16576314 TATATCTGTG
16576324 GAACTTGGATGCGAGATAAGGAATGAGGATGGAATACATTGCTCTTCTAATAGTTATATCGTAGG
1 GAACTTGGATGCGAGATAAGGAATGAGGATGGAATACATTGCTCTTCTAATAGTTATATCGTAGG
* * * *
16576389 CGACTCCTTCATATGCATGTATAGCTTTACTTTCATTCACCATATTCAATAGCGCTCTTGTTTTT
66 AGACTCCTTCATATGCATGTATAGCTTCACTTTCATTCACCATAATCAATAGCGCTCTTCTTTTT
16576454 TCAGGAAAAACTGATCCATATGTTGTTCTAAGCCTGGGGGATCAAGTTATATGCAGTAAAAA
131 TCAGGAAAAACTGATCCATATGTTGTTCTAAGCCTGGGGGATCAAGTTATATGCAGTAAAAA
* *
16576516 GAACTTGGATGTGAGATAAGGAATGAGGATGGAATACATTGCTCTTCTAATAGTTATATTGTAGG
1 GAACTTGGATGCGAGATAAGGAATGAGGATGGAATACATTGCTCTTCTAATAGTTATATCGTAGG
16576581 AGACTCCTTCATATGCATGTATAGCTTCACTTTCATTCACCATAATCAATAGCGCTCTTCTTTTT
66 AGACTCCTTCATATGCATGTATAGCTTCACTTTCATTCACCATAATCAATAGCGCTCTTCTTTTT
16576646 TCAGGAAAAACTGATCCATATGTTGTTCTAAGCCTGGGGGATCAAGTTATATGCAGTAAAAA
131 TCAGGAAAAACTGATCCATATGTTGTTCTAAGCCTGGGGGATCAAGTTATATGCAGTAAAAA
16576708 GAAC
1 GAAC
16576712 AGTCAAACTA
Statistics
Matches: 190, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
192 190 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.33
Consensus pattern (192 bp):
GAACTTGGATGCGAGATAAGGAATGAGGATGGAATACATTGCTCTTCTAATAGTTATATCGTAGG
AGACTCCTTCATATGCATGTATAGCTTCACTTTCATTCACCATAATCAATAGCGCTCTTCTTTTT
TCAGGAAAAACTGATCCATATGTTGTTCTAAGCCTGGGGGATCAAGTTATATGCAGTAAAAA
Found at i:16589483 original size:2 final size:2
Alignment explanation
Indices: 16589478--16589505 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16589468 ATATATATAT
16589478 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
16589506 TAAAATGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:16599070 original size:2 final size:2
Alignment explanation
Indices: 16599065--16599093 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16599055 CGCGTGTGTG
16599065 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16599094 TTAACTAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16616445 original size:2 final size:2
Alignment explanation
Indices: 16616438--16616463 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16616428 ATCATATGTG
16616438 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
16616464 ATTTCGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16619362 original size:9 final size:9
Alignment explanation
Indices: 16619348--16619390 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
16619338 ATTGATACTG
16619348 AATTTGTGA
1 AATTTGTGA
16619357 AATTTGTGGA
1 AATTTGT-GA
*
16619367 GAATTTTTTGA
1 -AA-TTTGTGA
16619378 AATTTGTGA
1 AATTTGTGA
16619387 AATT
1 AATT
16619391 GATGCGGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 17 0.59
10 4 0.14
11 4 0.14
12 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.47
Consensus pattern (9 bp):
AATTTGTGA
Found at i:16619401 original size:30 final size:33
Alignment explanation
Indices: 16619348--16619426 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 33
16619338 ATTGATACTG
16619348 AATTTGTGAAATTTG-TG-GAGAATT-TT-TTGA
1 AATTTGTGAAA-TTGATGCGAGAATTATTGTTGA
16619378 AATTTGTGAAATTGATGCG-GAATTATTGTTGA
1 AATTTGTGAAATTGATGCGAGAATTATTGTTGA
*
16619410 AA-TTGTAAAATTGATGC
1 AATTTGTGAAATTGATGC
16619427 TAAATTAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
29 3 0.07
30 18 0.41
31 17 0.39
32 6 0.14
ACGTcount: A:0.33, C:0.03, G:0.23, T:0.42
Consensus pattern (33 bp):
AATTTGTGAAATTGATGCGAGAATTATTGTTGA
Found at i:16619424 original size:31 final size:30
Alignment explanation
Indices: 16619367--16619426 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
16619357 AATTTGTGGA
*
16619367 GAATTTTTTGAAATTTGTGAAATTGATGCG
1 GAATTTTTTGAAATTTGTAAAATTGATGCG
16619397 GAATTATTGTTGAAA-TTGTAAAATTGATGC
1 GAATT-TT-TTGAAATTTGTAAAATTGATGC
16619427 TAAATTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 5 0.19
31 16 0.59
32 6 0.22
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.42
Consensus pattern (30 bp):
GAATTTTTTGAAATTTGTAAAATTGATGCG
Found at i:16619433 original size:31 final size:33
Alignment explanation
Indices: 16619374--16619442 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 33
16619364 GGAGAATTTT
* *
16619374 TTGAAATTTGTGAAATTGATGCGGAATT-ATTG
1 TTGAAATTTGTAAAATTGATGCGAAATTAATTG
*
16619406 TTGAAA-TTGTAAAATTGATGCTAAATTAATTG
1 TTGAAATTTGTAAAATTGATGCGAAATTAATTG
*
16619438 GTGAA
1 TTGAA
16619443 CTTAAATTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 18 0.56
32 14 0.44
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (33 bp):
TTGAAATTTGTAAAATTGATGCGAAATTAATTG
Done.