Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 22 of 126
Found at i:4953790 original size:9 final size:10
Alignment explanation
Indices: 4953776--4953815 Score: 59
Period size: 9 Copynumber: 4.3 Consensus size: 10
4953766 AGATCCTACA
4953776 ATTTA-TATT
1 ATTTATTATT
4953785 ATTTATTATT
1 ATTTATTATT
4953795 A-TTATTATT
1 ATTTATTATT
4953804 A-TTATTATT
1 ATTTATTATT
4953813 ATT
1 ATT
4953816 GTTGTTGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 23 0.79
10 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
ATTTATTATT
Found at i:4953793 original size:3 final size:3
Alignment explanation
Indices: 4953781--4953815 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
4953771 CTACAATTTA
4953781 TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4953816 GTTGTTGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:4953820 original size:3 final size:3
Alignment explanation
Indices: 4953814--4953842 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4953804 ATTATTATTA
4953814 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
4953843 ATGGATAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:4954033 original size:15 final size:14
Alignment explanation
Indices: 4953998--4954030 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
4953988 AAATAAATCC
*
4953998 ATTTTAAAAAAATT
1 ATTTTAAAAAAACT
4954012 ATTTTAAAAAAACT
1 ATTTTAAAAAAACT
4954026 ATTTT
1 ATTTT
4954031 TAATGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAAAAAAACT
Found at i:4955474 original size:22 final size:22
Alignment explanation
Indices: 4955431--4955496 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
4955421 ATTTCATATA
*
4955431 AAAAAATTGATAATTTAATTTT
1 AAAAAATTGATAATTGAATTTT
*
4955453 AAAAAATT-ATAATATGACTTTT
1 AAAAAATTGATAAT-TGAATTTT
** * *
4955475 AATCAATTGATATTTGATTTTT
1 AAAAAATTGATAATTGAATTTT
4955497 TTTACTAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 5 0.14
22 27 0.75
23 4 0.11
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (22 bp):
AAAAAATTGATAATTGAATTTT
Found at i:4955581 original size:17 final size:16
Alignment explanation
Indices: 4955559--4955594 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
4955549 TAGTATTAAA
4955559 AATTATAAAATTTTGAT
1 AATTATAAAATTTT-AT
*
4955576 AATTATAAGATTTTAT
1 AATTATAAAATTTTAT
4955592 AAT
1 AAT
4955595 GTATCATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
AATTATAAAATTTTAT
Found at i:4962314 original size:23 final size:23
Alignment explanation
Indices: 4962270--4962314 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4962260 AATTTGAAGG
* *
4962270 AAAATTCTTTCTAGACATCCTTA
1 AAAATTCTTTCTAAACACCCTTA
4962293 AAAATT-TTTCCTAAACACCCTT
1 AAAATTCTTT-CTAAACACCCTT
4962315 TTTGTTTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (23 bp):
AAAATTCTTTCTAAACACCCTTA
Found at i:4965952 original size:3 final size:3
Alignment explanation
Indices: 4965944--4965983 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
4965934 TTCGTTTAAT
4965944 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4965984 CTTTATGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4967045 original size:14 final size:13
Alignment explanation
Indices: 4967012--4967053 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
4967002 ATTTATGAAT
4967012 TTATTTAAAAAATA
1 TTATTTAAAAAA-A
4967026 TT-TTTAAAAAAA
1 TTATTTAAAAAAA
4967038 TTAATTTAAATAAAA
1 TT-ATTTAAA-AAAA
4967053 T
1 T
4967054 GAGTAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.12
13 9 0.36
14 8 0.32
15 5 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TTATTTAAAAAAA
Found at i:4967067 original size:24 final size:24
Alignment explanation
Indices: 4967040--4967088 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
4967030 TAAAAAAATT
* *
4967040 AATTTAAATAAAATGAGTAAATAA
1 AATTTAAATAAAATAAATAAATAA
*
4967064 AATTTACATAAAATAAATAAATAA
1 AATTTAAATAAAATAAATAAATAA
4967088 A
1 A
4967089 TAACAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (24 bp):
AATTTAAATAAAATAAATAAATAA
Found at i:4967880 original size:44 final size:44
Alignment explanation
Indices: 4967799--4968152 Score: 194
Period size: 44 Copynumber: 8.0 Consensus size: 44
4967789 AAAGGCTTAA
** *
4967799 CAATAACTTTAAAAAATT-TAAAAGGCTTTTCTCATCAAAGGTT
1 CAATAACTTTAAAAAATTATAAAAGGCTCATCTTATCAAAGGTT
* *
4967842 CAATAACTTCAAAAAATTATAAAAGGCTCATCTTATCAAAGGCT
1 CAATAACTTTAAAAAATTATAAAAGGCTCATCTTATCAAAGGTT
* * * * *
4967886 CAACAACTTTAGCAAATTTATAAAAGGCTTAT-TTAACTAAAGGTT
1 CAATAACTTTA-AAAAATTATAAAAGGCTCATCTTATC-AAAGGTT
* * * * * * *
4967931 --ATGAAACTTT-GAATATTTTAAAAAGGCTAAT-TTCACCAAAAGCT
1 CAAT--AACTTTAAAAAATTAT-AAAAGGCTCATCTT-ATCAAAGGTT
* *
4967975 CAATAACTTTAAAAAATTATAAAAGGCTCAT-TTCATTAGAGGCTT
1 CAATAACTTTAAAAAATTATAAAAGGCTCATCTT-ATCAAAGG-TT
* * * *
4968020 -AATAACTTTGAAAAATTATAAAATGGTTC-TCTTATTAGAGGCTT
1 CAATAACTTTAAAAAATTATAAAA-GGCTCATCTTATCAAAGG-TT
* * * *
4968064 -AACAACTTCAAAAAAATTATAAAAGGCTTC-TCTTAAACAAAAGTT
1 CAATAACTT-TAAAAAATTATAAAAGGC-TCATCTT-ATCAAAGGTT
* ** * *
4968109 CAACAACTTTTGGAAAAGTATAAAAAGGCTC--CTTAACAAAGGTT
1 CAATAAC-TTTAAAAAATTAT-AAAAGGCTCATCTTATCAAAGGTT
4968153 TATCAATTTT
Statistics
Matches: 247, Mismatches: 45, Indels: 37
0.75 0.14 0.11
Matches are distributed among these distances:
43 23 0.09
44 126 0.51
45 68 0.28
46 21 0.09
47 9 0.04
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (44 bp):
CAATAACTTTAAAAAATTATAAAAGGCTCATCTTATCAAAGGTT
Found at i:4967928 original size:89 final size:86
Alignment explanation
Indices: 4967803--4968092 Score: 232
Period size: 89 Copynumber: 3.3 Consensus size: 86
4967793 GCTTAACAAT
*
4967803 AACTTTAAAAAATT-TAAAAGGCTT-TTCTCA-TCAAAGGTTCAATAACTTCAAAAAATTATAAA
1 AACTTTAAAAAATTATAAAAGGCTTATT-TAACT-AAAGGTT-AATAACTT-AAAAAATTATAAA
4967865 AGGCTCATCTTATCAAAGGCTCAAC
62 AGGCTCATCTTATCAAAGGCTCAAC
* * ** * *
4967890 AACTTTAGCAAATTTATAAAAGGCTTATTTAACTAAAGGTT-ATGAAACTTTGAATATTTTAAAA
1 AACTTTA-AAAAATTATAAAAGGCTTATTTAACTAAAGGTTAAT--AACTTAAAAAATTAT-AAA
* * * *
4967954 AGGCTAAT-TTCACCAAAAGCTCAAT
62 AGGCTCATCTT-ATCAAAGGCTCAAC
* * * * *
4967979 AACTTTAAAAAATTATAAAAGGCTCATTTCATTAGAGGCTTAATAACTTTGAAAAATTATAAAAT
1 AACTTTAAAAAATTATAAAAGGCTTATTTAACTAAAGG-TTAATAAC-TTAAAAAATTATAAAA-
* * * *
4968044 GGTTC-TCTTATTAGAGGCTTAAC
63 GGCTCATCTTATCAAAGGCTCAAC
*
4968067 AACTTCAAAAAAATTATAAAAGGCTT
1 AACTT-TAAAAAATTATAAAAGGCTT
4968093 CTCTTAAACA
Statistics
Matches: 158, Mismatches: 31, Indels: 26
0.73 0.14 0.12
Matches are distributed among these distances:
87 9 0.06
88 59 0.37
89 85 0.54
90 5 0.03
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.32
Consensus pattern (86 bp):
AACTTTAAAAAATTATAAAAGGCTTATTTAACTAAAGGTTAATAACTTAAAAAATTATAAAAGGC
TCATCTTATCAAAGGCTCAAC
Found at i:4969299 original size:9 final size:10
Alignment explanation
Indices: 4969285--4969317 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
4969275 TTTCATTTTT
4969285 TTTTTC-TCA
1 TTTTTCATCA
4969294 TTTTTCATCA
1 TTTTTCATCA
*
4969304 CTTTTCATCA
1 TTTTTCATCA
4969314 TTTT
1 TTTT
4969318 ATTTCATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 6 0.29
10 15 0.71
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTTCATCA
Found at i:4974415 original size:8 final size:9
Alignment explanation
Indices: 4974377--4974425 Score: 52
Period size: 8 Copynumber: 5.9 Consensus size: 9
4974367 TTAAACAACC
4974377 AAAAT-AAT
1 AAAATAAAT
4974385 AAAA-AAA-
1 AAAATAAAT
* *
4974392 AAACTCAAT
1 AAAATAAAT
4974401 AAAATAAAT
1 AAAATAAAT
4974410 -AAATAAAT
1 AAAATAAAT
4974418 AAAATAAA
1 AAAATAAA
4974426 AATTTAACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
7 3 0.09
8 16 0.48
9 14 0.42
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (9 bp):
AAAATAAAT
Found at i:4981044 original size:22 final size:22
Alignment explanation
Indices: 4981019--4981090 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
4981009 CTCATACTTA
*
4981019 ATTTAATTTAATCCAAAATA-TT
1 ATTTAATTTAAT-AAAAATATTT
*
4981041 ATTTTA-TTAATAAAAATATTTT
1 ATTTAATTTAATAAAAATA-TTT
*
4981063 ATTTAATTTTAATTAAAAA-ATTA
1 ATTTAA-TTTAA-TAAAAATATTT
4981086 ATTTA
1 ATTTA
4981091 TTAATATTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
20 6 0.15
21 5 0.12
22 12 0.29
23 7 0.17
24 5 0.12
25 6 0.15
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTAATTTAATAAAAATATTT
Found at i:4981072 original size:27 final size:27
Alignment explanation
Indices: 4981041--4981092 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
4981031 CCAAAATATT
*
4981041 ATTTT-ATTAATAAAAATATTTTATTTA
1 ATTTTAATTAA-AAAAATAATTTATTTA
*
4981068 ATTTTAATTAAAAAATTAATTTATT
1 ATTTTAATTAAAAAAATAATTTATT
4981093 AATATTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTTTAATTAAAAAAATAATTTATTTA
Found at i:4981124 original size:24 final size:24
Alignment explanation
Indices: 4981091--4981143 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
4981081 AATTAATTTA
4981091 TTAATATTAGA-AGTTTTT-TATATT
1 TTAATATTAGATA-TTTTTATA-ATT
*
4981115 TTAATTTTAGATATTTTTATAATT
1 TTAATATTAGATATTTTTATAATT
4981139 TTAAT
1 TTAAT
4981144 CAAGTCAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (24 bp):
TTAATATTAGATATTTTTATAATT
Found at i:4981440 original size:42 final size:45
Alignment explanation
Indices: 4981355--4981449 Score: 108
Period size: 42 Copynumber: 2.2 Consensus size: 45
4981345 ATAAATAGTT
*
4981355 TTATATTATATATTTTAATAATAAATAATTATATAGTAGATAAT-
1 TTATTTTATATATTTTAATAATAAATAATTATATAGTAGATAATA
* * * *
4981399 TT-TTTTAT-TATTTTAATAATTAAT-ATTGTTTATTAGAATAATA
1 TTATTTTATATATTTTAATAATAAATAATTATATAGTAG-ATAATA
4981442 TTATTTTA
1 TTATTTTA
4981450 ATAATATGAC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
41 9 0.21
42 20 0.47
43 7 0.16
44 7 0.16
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (45 bp):
TTATTTTATATATTTTAATAATAAATAATTATATAGTAGATAATA
Found at i:4981835 original size:25 final size:24
Alignment explanation
Indices: 4981779--4981838 Score: 93
Period size: 25 Copynumber: 2.5 Consensus size: 24
4981769 ATGCATAATA
*
4981779 ATTTTAACAATAAATAATTTCAAT
1 ATTTTAATAATAAATAATTTCAAT
*
4981803 ATTTTAATAATAAATAAATTTGAAT
1 ATTTTAATAATAAAT-AATTTCAAT
4981828 ATTTTAATAAT
1 ATTTTAATAAT
4981839 TATGTTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
24 14 0.42
25 19 0.58
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (24 bp):
ATTTTAATAATAAATAATTTCAAT
Found at i:4983862 original size:18 final size:19
Alignment explanation
Indices: 4983839--4983875 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4983829 TAAAGATAGT
4983839 GATATAA-TAATTTAAATG
1 GATATAATTAATTTAAATG
4983857 GATATAATTAATTTAAATG
1 GATATAATTAATTTAAATG
4983876 ATCTAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.41
Consensus pattern (19 bp):
GATATAATTAATTTAAATG
Found at i:4986786 original size:27 final size:27
Alignment explanation
Indices: 4986748--4986805 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
4986738 TCTTCGAAAG
4986748 TAAATGAAATTCTTCCAAAAATTAAAA
1 TAAATGAAATTCTTCCAAAAATTAAAA
4986775 TAAATGAAATTCTTCCAAAAATTAAAA
1 TAAATGAAATTCTTCCAAAAATTAAAA
4986802 TAAA
1 TAAA
4986806 ATCAACAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.29
Consensus pattern (27 bp):
TAAATGAAATTCTTCCAAAAATTAAAA
Found at i:4987633 original size:74 final size:77
Alignment explanation
Indices: 4987496--4987644 Score: 187
Period size: 74 Copynumber: 2.0 Consensus size: 77
4987486 ATTTACATTA
* * **
4987496 AATTTTTATTTTTAGAATTTAAATAAAATTAATCCATTCAATTTTACTTATTTTCTTTATAGTTA
1 AATTTTTATTTTCAGAATCTAAATAAAATTAATCCATT-AATTTTACTTATTTTCTGAATAGTTA
4987561 TATTTAACAACTT
65 TATTTAACAACTT
* * *
4987574 AATTTTTATTTTCAG-A-CTAAATAAAATTAATCTATT-TTTTTATTTATTTTCTGAATAGTTAT
1 AATTTTTATTTTCAGAATCTAAATAAAATTAATCCATTAATTTTACTTATTTTCTGAATAGTTAT
* *
4987636 GTTTCACAA
66 ATTTAACAA
4987645 AAACAACTGC
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
74 29 0.47
76 18 0.29
77 1 0.02
78 14 0.23
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (77 bp):
AATTTTTATTTTCAGAATCTAAATAAAATTAATCCATTAATTTTACTTATTTTCTGAATAGTTAT
ATTTAACAACTT
Found at i:4989489 original size:2 final size:2
Alignment explanation
Indices: 4989482--4989514 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4989472 GGATCGAGTT
4989482 TA TA 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 TA TA T
4989515 GTATGTATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4989967 original size:2 final size:2
Alignment explanation
Indices: 4989962--4989991 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4989952 ATTTTTTCTT
*
4989962 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4989992 CACACACACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4995710 original size:7 final size:7
Alignment explanation
Indices: 4995696--4995728 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
4995686 TAACAAGAAC
4995696 AATGAAG
1 AATGAAG
*
4995703 ATTGAAG
1 AATGAAG
4995710 AATGAAG
1 AATGAAG
4995717 AATGAAG
1 AATGAAG
4995724 AATGA
1 AATGA
4995729 GCAATTACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.27, T:0.18
Consensus pattern (7 bp):
AATGAAG
Found at i:4997914 original size:23 final size:24
Alignment explanation
Indices: 4997888--4997957 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 24
4997878 AGTTATTATT
4997888 TATTATATTTATTAAAATAT-AAA
1 TATTATATTTATTAAAATATAAAA
4997911 TATTATATCTAACTATTAAAATATAAAA
1 TATTATAT-T---TATTAAAATATAAAA
* *
4997939 TATGAT-TTTAATAAAATAT
1 TATTATATTTATTAAAATAT
4997958 TAAGTAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
23 18 0.45
24 1 0.03
26 1 0.03
27 12 0.30
28 8 0.20
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (24 bp):
TATTATATTTATTAAAATATAAAA
Found at i:4998892 original size:23 final size:25
Alignment explanation
Indices: 4998865--4998934 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 25
4998855 ATTTCAATAT
*
4998865 AATAAA-ATAC-TTTTTTTATTAAA
1 AATAAATATACATTCTTTTATTAAA
4998888 AATAAATTATACATTCTTTTATTAAA
1 AATAAA-TATACATTCTTTTATTAAA
4998914 AATAAATTATACATTCTTTTA
1 AATAAA-TATACATTCTTTTA
4998935 AACGAAACAA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
23 6 0.14
25 4 0.09
26 33 0.77
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (25 bp):
AATAAATATACATTCTTTTATTAAA
Found at i:4998907 original size:26 final size:26
Alignment explanation
Indices: 4998878--4998934 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
4998868 AAAATACTTT
4998878 TTTTATTAAAAATAAATTATACATTC
1 TTTTATTAAAAATAAATTATACATTC
4998904 TTTTATTAAAAATAAATTATACATTC
1 TTTTATTAAAAATAAATTATACATTC
4998930 TTTTA
1 TTTTA
4998935 AACGAAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (26 bp):
TTTTATTAAAAATAAATTATACATTC
Found at i:5002032 original size:3 final size:3
Alignment explanation
Indices: 5002024--5002066 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
5002014 CTTACATTTA
5002024 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5002067 GTAACAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5002585 original size:17 final size:16
Alignment explanation
Indices: 5002557--5002600 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
5002547 AATACCTAAC
5002557 ATAAATATTTTATTTAAA
1 ATAAA-ATTTTATTT-AA
5002575 ATAAAATTTTATTTAA
1 ATAAAATTTTATTTAA
5002591 ATACAAATTT
1 ATA-AAATTT
5002601 AAAAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.20
17 15 0.60
18 5 0.20
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAAAATTTTATTTAA
Found at i:5010196 original size:41 final size:42
Alignment explanation
Indices: 5010112--5010207 Score: 103
Period size: 41 Copynumber: 2.4 Consensus size: 42
5010102 TATTATTATA
* *
5010112 TTATTATTTTAATAA-TAAAATCAATATAGTAAATAATATTT
1 TTATTATTTTAATAATTAAAATCAATATAATAAATAATAATT
* * *
5010153 TTATTATTTTAATAATTAATA-CTATTTAATATAATAA-AATT
1 TTATTATTTTAATAATTAAAATCAATATAATA-AATAATAATT
5010194 TTA--ATTTTAATAAT
1 TTATTATTTTAATAAT
5010208 ACAAATATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
39 11 0.23
41 28 0.58
42 9 0.19
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (42 bp):
TTATTATTTTAATAATTAAAATCAATATAATAAATAATAATT
Found at i:5010597 original size:16 final size:15
Alignment explanation
Indices: 5010521--5010632 Score: 63
Period size: 16 Copynumber: 7.1 Consensus size: 15
5010511 TGTATAATAT
5010521 TAATATAATATTTTAA
1 TAATA-AATATTTTAA
*
5010537 TATTAAATATTATTATTA
1 TAATAAATATT-TTA--A
*
5010555 AAATATAATTATTTTTTAA
1 TAATA-AA-TA--TTTTAA
*
5010574 T-ATTAATATTTTTAA
1 TAATAAATA-TTTTAA
*
5010589 TAATAAATAATTT--
1 TAATAAATATTTTAA
5010602 TAAT--ATATTTTAA
1 TAATAAATATTTTAA
5010615 TAATAAATAATTTTAA
1 TAATAAAT-ATTTTAA
5010631 TA
1 TA
5010633 TTTTAATAGT
Statistics
Matches: 75, Mismatches: 8, Indels: 26
0.69 0.07 0.24
Matches are distributed among these distances:
11 6 0.08
13 8 0.11
15 19 0.25
16 24 0.32
17 2 0.03
18 6 0.08
19 3 0.04
20 2 0.03
21 3 0.04
22 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATAAATATTTTAA
Found at i:5010599 original size:36 final size:37
Alignment explanation
Indices: 5010531--5010600 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
5010521 TAATATAATA
*
5010531 TTTTAATATTAAATATTATTATTAAAATATAATTATT
1 TTTTAATATTAAATATTATTAATAAAATATAATTATT
*
5010568 TTTTAATATT-AATATTTTTAATAATAA-ATAATT
1 TTTTAATATTAAATATTATTAATAA-AATATAATT
5010601 TTAATATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 18 0.60
37 12 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (37 bp):
TTTTAATATTAAATATTATTAATAAAATATAATTATT
Found at i:5010611 original size:10 final size:9
Alignment explanation
Indices: 5010571--5010640 Score: 60
Period size: 9 Copynumber: 8.2 Consensus size: 9
5010561 AATTATTTTT
*
5010571 TAATATTAA
1 TAATTTTAA
*
5010580 TATTTTTAA
1 TAATTTTAA
*
5010589 TAA--TAAA
1 TAATTTTAA
5010596 TAATTTTAA
1 TAATTTTAA
5010605 TATATTTTAA
1 TA-ATTTTAA
*
5010615 TAA--TAAA
1 TAATTTTAA
5010622 TAATTTTAA
1 TAATTTTAA
5010631 T-ATTTTAA
1 TAATTTTAA
5010639 TA
1 TA
5010641 GTTACATCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
7 12 0.25
8 8 0.17
9 19 0.40
10 9 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TAATTTTAA
Found at i:5010612 original size:26 final size:26
Alignment explanation
Indices: 5010571--5010640 Score: 110
Period size: 26 Copynumber: 2.8 Consensus size: 26
5010561 AATTATTTTT
*
5010571 TAATATTAATAT-TTTTAATAATAAA
1 TAATTTTAATATATTTTAATAATAAA
5010596 TAATTTTAATATATTTTAATAATAAA
1 TAATTTTAATATATTTTAATAATAAA
5010622 TAATTTT-A-ATATTTTAATA
1 TAATTTTAATATATTTTAATA
5010641 GTTACATCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
24 11 0.26
25 12 0.28
26 20 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TAATTTTAATATATTTTAATAATAAA
Found at i:5011915 original size:80 final size:80
Alignment explanation
Indices: 5011817--5011977 Score: 277
Period size: 80 Copynumber: 2.0 Consensus size: 80
5011807 AAATCACTTT
**
5011817 TGAAAATGGGTAAAATAATACACAGAGAGTCACCCAACTTTGGGCGACATTTTATTTTGGTCACT
1 TGAAAATGGGTAAAATAATACACAGAGAGTCACCCAACTTTGAACGACATTTTATTTTGGTCACT
5011882 CAACTATAAAATCTA
66 CAACTATAAAATCTA
* * *
5011897 TGAAAATGGGTAAAATAATACACGGAGAGTCACCCAACTTTGAACGACTTTTTCTTTTGGTCACT
1 TGAAAATGGGTAAAATAATACACAGAGAGTCACCCAACTTTGAACGACATTTTATTTTGGTCACT
5011962 CAACTATAAAATCTA
66 CAACTATAAAATCTA
5011977 T
1 T
5011978 CAGCATAGCC
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (80 bp):
TGAAAATGGGTAAAATAATACACAGAGAGTCACCCAACTTTGAACGACATTTTATTTTGGTCACT
CAACTATAAAATCTA
Found at i:5016330 original size:8 final size:8
Alignment explanation
Indices: 5016317--5016379 Score: 63
Period size: 8 Copynumber: 7.9 Consensus size: 8
5016307 ATCATATGCC
5016317 TACATATA
1 TACATATA
*
5016325 TACATACA
1 TACATATA
*
5016333 TACATACA
1 TACATATA
*
5016341 TACATACA
1 TACATATA
5016349 TACATATA
1 TACATATA
* *
5016357 TATATAGA
1 TACATATA
*
5016365 TATATATA
1 TACATATA
*
5016373 TATATAT
1 TACATAT
5016380 TCTATAACAC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 50 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.37
Consensus pattern (8 bp):
TACATATA
Found at i:5016332 original size:12 final size:12
Alignment explanation
Indices: 5016317--5016374 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
5016307 ATCATATGCC
5016317 TACATATATACA
1 TACATATATACA
*
5016329 TACATACATACA
1 TACATATATACA
*
5016341 TACATACATACA
1 TACATATATACA
* *
5016353 TATATATATAGA
1 TACATATATACA
*
5016365 TATATATATA
1 TACATATATA
5016375 TATATTCTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.34
Consensus pattern (12 bp):
TACATATATACA
Found at i:5016374 original size:4 final size:4
Alignment explanation
Indices: 5016317--5016354 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
5016307 ATCATATGCC
*
5016317 TACA TATA TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
5016355 TATATATAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (4 bp):
TACA
Found at i:5016792 original size:2 final size:2
Alignment explanation
Indices: 5016785--5016809 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5016775 CCCTCCTTCA
5016785 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
5016810 GAGAGAGAGA
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:5016818 original size:6 final size:6
Alignment explanation
Indices: 5016813--5016847 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
5016803 ATATATAGAG
*
5016813 AGAGAG AGAGAC AGAGAC AGAGAC AGAGAC AGAGA
1 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAGA
5016848 TGCAGTAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.51, C:0.11, G:0.37, T:0.00
Consensus pattern (6 bp):
AGAGAC
Found at i:5018008 original size:2 final size:2
Alignment explanation
Indices: 5018001--5018052 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
5017991 ATCAGCTGAC
5018001 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
5018043 GT GT GT GT GT
1 GT GT GT GT GT
5018053 TTATATGTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:5026481 original size:2 final size:2
Alignment explanation
Indices: 5026474--5026498 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5026464 GGATCGAGTT
5026474 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 T
5026499 GTGTGTGTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5032666 original size:7 final size:7
Alignment explanation
Indices: 5032652--5032684 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
5032642 TAACAAGAAC
5032652 AATGAAG
1 AATGAAG
*
5032659 ATTGAAG
1 AATGAAG
5032666 AATGAAG
1 AATGAAG
5032673 AATGAAG
1 AATGAAG
5032680 AATGA
1 AATGA
5032685 GCAATTACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.27, T:0.18
Consensus pattern (7 bp):
AATGAAG
Found at i:5034680 original size:33 final size:34
Alignment explanation
Indices: 5034610--5034674 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
5034600 AATGATTTTA
* *
5034610 ATTTCCTTTTTACTAATTTTCATATAATATAAAT
1 ATTTCATTTTTACTAATTTTCATATAAGATAAAT
*
5034644 ATTTCATTTTTATTAATTTT-ATATATAGATA
1 ATTTCATTTTTACTAATTTTCATATA-AGATA
5034675 TTATTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 5 0.19
34 22 0.81
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (34 bp):
ATTTCATTTTTACTAATTTTCATATAAGATAAAT
Found at i:5034705 original size:21 final size:21
Alignment explanation
Indices: 5034654--5034711 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 21
5034644 ATTTCATTTT
*
5034654 TATTA-ATTTT-ATATATAGA
1 TATTATATTTTAATAAATAGA
5034673 TATTAT-TTTTAATAAATA-A
1 TATTATATTTTAATAAATAGA
5034692 TATTCATATTTTAATAAATA
1 TATT-ATATTTTAATAAATA
5034712 TAAATAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 14 0.41
20 8 0.24
21 12 0.35
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TATTATATTTTAATAAATAGA
Found at i:5034731 original size:13 final size:13
Alignment explanation
Indices: 5034715--5034762 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
5034705 ATAAATATAA
5034715 ATAATTA-TTATTT
1 ATAATTATTTA-TT
5034728 ATAATTATTTATT
1 ATAATTATTTATT
*
5034741 ATTATTATTTATT
1 ATAATTATTTATT
*
5034754 ATATTTATT
1 ATAATTATT
5034763 AAAATATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
13 28 0.90
14 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATAATTATTTATT
Found at i:5034731 original size:23 final size:23
Alignment explanation
Indices: 5034705--5034752 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
5034695 TCATATTTTA
5034705 ATAAATATAAATAATTATTATTT
1 ATAAATATAAATAATTATTATTT
* ** *
5034728 ATAATTATTTATTATTATTATTT
1 ATAAATATAAATAATTATTATTT
5034751 AT
1 AT
5034753 TATATTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATAAATATAAATAATTATTATTT
Found at i:5034752 original size:10 final size:10
Alignment explanation
Indices: 5034718--5034755 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
5034708 AATATAAATA
5034718 ATTATTATTT
1 ATTATTATTT
*
5034728 ATAATTATTT
1 ATTATTATTT
5034738 ATTATTA-TT
1 ATTATTATTT
5034747 ATTTATTAT
1 A-TTATTAT
5034756 ATTTATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 3 0.12
10 21 0.88
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
ATTATTATTT
Found at i:5037899 original size:3 final size:3
Alignment explanation
Indices: 5037887--5037919 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
5037877 CTTACATTTA
5037887 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5037920 GTAACAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:5038438 original size:17 final size:19
Alignment explanation
Indices: 5038410--5038451 Score: 70
Period size: 17 Copynumber: 2.3 Consensus size: 19
5038400 AATACCTAAC
5038410 ATAAATATTTTATTTAAA-
1 ATAAATATTTTATTTAAAT
5038428 ATAAA-ATTTTATTTAAAT
1 ATAAATATTTTATTTAAAT
5038446 ATAAAT
1 ATAAAT
5038452 TTAAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAAATATTTTATTTAAAT
Found at i:5038445 original size:30 final size:31
Alignment explanation
Indices: 5038411--5038477 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
5038401 ATACCTAACA
** *
5038411 TAAATATTTTATTT-AAAATAAAATTTTATT
1 TAAATATTAAATTTAAAAATAAAAATTTATT
5038441 TAAATA-TAAATTTAAAAATAAAAATTTATT
1 TAAATATTAAATTTAAAAATAAAAATTTATT
*
5038471 TGAATAT
1 TAAATAT
5038478 AATAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (31 bp):
TAAATATTAAATTTAAAAATAAAAATTTATT
Found at i:5038478 original size:30 final size:29
Alignment explanation
Indices: 5038421--5038479 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
5038411 TAAATATTTT
*
5038421 ATTTAAAATAAAATTTTATTTAAATATAA
1 ATTTAAAATAAAAATTTATTTAAATATAA
*
5038450 ATTTAAAAATAAAAATTTATTTGAATATAA
1 ATTT-AAAATAAAAATTTATTTAAATATAA
5038480 TAAAAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (29 bp):
ATTTAAAATAAAAATTTATTTAAATATAA
Found at i:5038492 original size:35 final size:30
Alignment explanation
Indices: 5038425--5038492 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
5038415 TATTTTATTT
* *
5038425 AAAATAAAATTTTATTTAAATATAAATTTA
1 AAAATAAAAATTTATTTAAATATAAATATA
*
5038455 AAAATAAAAATTTATTTGAATAT-AATA-A
1 AAAATAAAAATTTATTTAAATATAAATATA
5038483 AAATATAAAA
1 AAA-ATAAAA
5038493 TCTTACTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 4 0.12
29 9 0.26
30 21 0.62
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (30 bp):
AAAATAAAAATTTATTTAAATATAAATATA
Found at i:5045289 original size:20 final size:21
Alignment explanation
Indices: 5045252--5045290 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5045242 AACTCGACTC
5045252 AAAATATTATTATATTAATAA
1 AAAATATTATTATATTAATAA
*
5045273 AAAATATTTTTAT-TTAAT
1 AAAATATTATTATATTAAT
5045291 TTTGATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATATTATTATATTAATAA
Found at i:5045905 original size:16 final size:16
Alignment explanation
Indices: 5045829--5045941 Score: 64
Period size: 15 Copynumber: 7.1 Consensus size: 16
5045819 TGTATAATAT
5045829 TAATATAATA-TTTTAA
1 TAATA-AATATTTTTAA
*
5045845 TATTAAATATTATTATTAA
1 TAATAAATA-T-TT-TTAA
5045864 -AATATAATTATTTTTTAA
1 TAATA-AA-TA-TTTTTAA
*
5045882 T-ATTAATATTTTTAA
1 TAATAAATATTTTTAA
*
5045897 TAATAAATA-ATTT--
1 TAATAAATATTTTTAA
5045910 TAAT--ATA-TTTTAA
1 TAATAAATATTTTTAA
5045923 TAATAAATCATTTTTAA
1 TAATAAAT-ATTTTTAA
5045940 TA
1 TA
5045942 TTTTAATAGT
Statistics
Matches: 77, Mismatches: 6, Indels: 27
0.70 0.05 0.25
Matches are distributed among these distances:
11 6 0.08
13 8 0.10
15 17 0.22
16 13 0.17
17 10 0.13
18 11 0.14
19 8 0.10
20 4 0.05
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATAAATATTTTTAA
Found at i:5045907 original size:36 final size:37
Alignment explanation
Indices: 5045839--5045908 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
5045829 TAATATAATA
*
5045839 TTTTAATATTAAATATTATTATTAAAATATAATTATT
1 TTTTAATATTAAATATTATTAATAAAATATAATTATT
*
5045876 TTTTAATATT-AATATTTTTAATAATAA-ATAATT
1 TTTTAATATTAAATATTATTAATAA-AATATAATT
5045909 TTAATATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 18 0.60
37 12 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (37 bp):
TTTTAATATTAAATATTATTAATAAAATATAATTATT
Found at i:5045920 original size:26 final size:26
Alignment explanation
Indices: 5045879--5045949 Score: 101
Period size: 25 Copynumber: 2.8 Consensus size: 26
5045869 AATTATTTTT
*
5045879 TAATATTAATAT-TTTTAATAATAAA
1 TAATTTTAATATATTTTAATAATAAA
5045904 TAATTTTAATATATTTTAATAATAAA
1 TAATTTTAATATATTTTAATAATAAA
* *
5045930 TCATTTTTA-ATATTTTAATA
1 TAATTTTAATATATTTTAATA
5045950 GTTACATCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
25 22 0.52
26 20 0.48
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (26 bp):
TAATTTTAATATATTTTAATAATAAA
Found at i:5047224 original size:80 final size:80
Alignment explanation
Indices: 5047126--5047286 Score: 259
Period size: 80 Copynumber: 2.0 Consensus size: 80
5047116 AAATCACTTT
*
5047126 TGAAAATGGGTAAAATAATACACAGAGAGTCACCCAACTTTGGGCGACATTTTATTTTGGTCACT
1 TGAAAATGGGTAAAATAATACACAGAGAGTCACCCAACTTTGGACGACATTTTATTTTGGTCACT
5047191 CAACTATAAAATCTA
66 CAACTATAAAATCTA
* * * *
5047206 TGAAAATGGGTAAAATAATACACGGAGAGTCACCCAACTTTGGATGACTTTTTCTTTTGGTCACT
1 TGAAAATGGGTAAAATAATACACAGAGAGTCACCCAACTTTGGACGACATTTTATTTTGGTCACT
**
5047271 TGACTATAAAATCTA
66 CAACTATAAAATCTA
5047286 T
1 T
5047287 CAGCATAGTC
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 74 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (80 bp):
TGAAAATGGGTAAAATAATACACAGAGAGTCACCCAACTTTGGACGACATTTTATTTTGGTCACT
CAACTATAAAATCTA
Found at i:5051588 original size:8 final size:8
Alignment explanation
Indices: 5051575--5051629 Score: 56
Period size: 8 Copynumber: 6.9 Consensus size: 8
5051565 ATCATATGCC
5051575 TACATATA
1 TACATATA
*
5051583 TACATACA
1 TACATATA
*
5051591 TACATACA
1 TACATATA
*
5051599 TACATACA
1 TACATATA
*
5051607 TATATATA
1 TACATATA
*
5051615 TATATATA
1 TACATATA
*
5051623 TATATAT
1 TACATAT
5051630 TCTATAACAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 44 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (8 bp):
TACATATA
Found at i:5051591 original size:4 final size:4
Alignment explanation
Indices: 5051575--5051608 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
5051565 ATCATATGCC
*
5051575 TACA TATA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TA
5051609 TATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (4 bp):
TACA
Found at i:5051613 original size:4 final size:4
Alignment explanation
Indices: 5051578--5051629 Score: 50
Period size: 4 Copynumber: 13.0 Consensus size: 4
5051568 ATATGCCTAC
* * * * * *
5051578 ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
5051626 ATAT
1 ATAT
5051630 TCTATAACAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (4 bp):
ATAT
Found at i:5051629 original size:12 final size:12
Alignment explanation
Indices: 5051575--5051620 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
5051565 ATCATATGCC
5051575 TACATATATACA
1 TACATATATACA
*
5051587 TACATACATACA
1 TACATATATACA
* *
5051599 TACATACATATA
1 TACATATATACA
*
5051611 TATATATATA
1 TACATATATA
5051621 TATATATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (12 bp):
TACATATATACA
Found at i:5052060 original size:6 final size:6
Alignment explanation
Indices: 5052051--5052085 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
5052041 ATATATAGAG
5052051 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAGA
1 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAGA
5052086 TGCAGTAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.34, T:0.00
Consensus pattern (6 bp):
AGAGAC
Found at i:5059634 original size:26 final size:26
Alignment explanation
Indices: 5059595--5059645 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
5059585 AACTATTAAA
* *
5059595 ATATTAAAAATATTTATAATTAAAAT
1 ATATTAAAAATATTCATAATCAAAAT
*
5059621 ATATTAAAATTATTCATAATCAAAA
1 ATATTAAAAATATTCATAATCAAAA
5059646 ATTATGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (26 bp):
ATATTAAAAATATTCATAATCAAAAT
Found at i:5060108 original size:26 final size:26
Alignment explanation
Indices: 5060062--5060118 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
5060052 TAATATTATT
* * *
5060062 TAATATATTATTATATCTTATTAAAA
1 TAATATAATACTATATCTTATCAAAA
*
5060088 TAATATAATACTAT-TCATTATCGAAA
1 TAATATAATACTATATC-TTATCAAAA
5060114 TAATA
1 TAATA
5060119 AAAAGATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (26 bp):
TAATATAATACTATATCTTATCAAAA
Found at i:5061627 original size:41 final size:41
Alignment explanation
Indices: 5061558--5061641 Score: 100
Period size: 41 Copynumber: 2.0 Consensus size: 41
5061548 TATGTTAAAT
*
5061558 ATATATAAAATATAAAAATTATTATATTACAATTTGTAT-TA
1 ATATATAAAATATAAAAATTATTATATTA-AATTTATATATA
* * *
5061599 ATATATTAAATA-AAAAATATTTTTTATTAAATTTATATATA
1 ATATATAAAATATAAAAAT-TATTATATTAAATTTATATATA
5061640 AT
1 AT
5061642 TTTTATCAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
40 14 0.38
41 23 0.62
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (41 bp):
ATATATAAAATATAAAAATTATTATATTAAATTTATATATA
Found at i:5061702 original size:16 final size:16
Alignment explanation
Indices: 5061681--5061724 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
5061671 ACATAAATTT
5061681 TTATATCATTTTTATA
1 TTATATCATTTTTATA
*
5061697 TTATATTATATTTTATA
1 TTATATCAT-TTTTATA
*
5061714 TATGTATCATT
1 T-TATATCATT
5061725 CTCCAAAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 9 0.39
18 6 0.26
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (16 bp):
TTATATCATTTTTATA
Found at i:5062247 original size:23 final size:23
Alignment explanation
Indices: 5062220--5062273 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
5062210 CCAAAATCCC
5062220 ATTTAGATTCAAA-TAAAA-TGATT
1 ATTTAGATTCAAATTAAAACT--TT
*
5062243 ATTTA-AGTCAAATTAAAACTTT
1 ATTTAGATTCAAATTAAAACTTT
5062265 ATTTAGATT
1 ATTTAGATT
5062274 GATAATGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 13 0.50
23 12 0.46
24 1 0.04
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (23 bp):
ATTTAGATTCAAATTAAAACTTT
Found at i:5064721 original size:26 final size:23
Alignment explanation
Indices: 5064692--5064748 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 23
5064682 ATTTTATTAA
5064692 TAAAATAAATTAAATGATATTATTTT
1 TAAAATAAATTAAAT-ATA-TA-TTT
* *
5064718 TAAAA-AATTTTAATATATATTT
1 TAAAATAAATTAAATATATATTT
5064740 TAAAATAAA
1 TAAAATAAA
5064749 AATAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 8 0.30
23 4 0.15
24 3 0.11
25 7 0.26
26 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TAAAATAAATTAAATATATATTT
Found at i:5066180 original size:18 final size:19
Alignment explanation
Indices: 5066147--5066182 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5066137 TTTGATAAGA
5066147 TAAAATATAATAATTATAG
1 TAAAATATAATAATTATAG
*
5066166 TAAAAT-TAATTATTATA
1 TAAAATATAATAATTATA
5066183 ATGAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAAATATAATAATTATAG
Found at i:5066483 original size:18 final size:18
Alignment explanation
Indices: 5066460--5066500 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5066450 GCTTTAAATT
5066460 ATAAAAAGGAAAAA-TAAA
1 ATAAAAAGGAAAAACT-AA
*
5066478 ATAAAAATGAAAAACTAA
1 ATAAAAAGGAAAAACTAA
5066496 ATAAA
1 ATAAA
5066501 TAAAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (18 bp):
ATAAAAAGGAAAAACTAA
Found at i:5067019 original size:22 final size:21
Alignment explanation
Indices: 5066970--5067022 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
5066960 GATATTTTTA
5066970 AATA-TTTATATTTAAAAAAT
1 AATATTTTATATTTAAAAAAT
5066990 AATATTTTATATTTAAAAAAT
1 AATATTTTATATTTAAAAAAT
*
5067011 AGTATTTT-TATT
1 AATATTTTATATT
5067023 AATTTCGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 8 0.26
21 23 0.74
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
AATATTTTATATTTAAAAAAT
Found at i:5069541 original size:22 final size:22
Alignment explanation
Indices: 5069516--5069562 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5069506 TTTGGTTCAA
*
5069516 AATTTTAATTTAGAATTT-TTAT
1 AATTTT-ATTTACAATTTCTTAT
*
5069538 AATTTTTTTTACAATTTCTTAT
1 AATTTTATTTACAATTTCTTAT
5069560 AAT
1 AAT
5069563 AATTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (22 bp):
AATTTTATTTACAATTTCTTAT
Found at i:5069568 original size:22 final size:21
Alignment explanation
Indices: 5069524--5069568 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
5069514 AAAATTTTAA
* **
5069524 TTTAGAATTTTTATAATTTTT
1 TTTACAATTTTTATAATAATT
5069545 TTTACAATTTCTTATAATAATT
1 TTTACAATTT-TTATAATAATT
5069567 TT
1 TT
5069569 ATTTCAATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTACAATTTTTATAATAATT
Found at i:5075302 original size:19 final size:19
Alignment explanation
Indices: 5075279--5075314 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
5075269 CTATAAAGGT
5075279 TTTTTTATTTT-ATTTTGA
1 TTTTTTATTTTAATTTTGA
5075297 TTTTTTATTTTAATTTTG
1 TTTTTTATTTTAATTTTG
5075315 GCTTTCGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (19 bp):
TTTTTTATTTTAATTTTGA
Found at i:5076366 original size:20 final size:20
Alignment explanation
Indices: 5076341--5076381 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5076331 TACCATTTAA
5076341 ATTTATTTTTGTTGGAAGAG
1 ATTTATTTTTGTTGGAAGAG
5076361 ATTTATTTTTGTTGGAAGAG
1 ATTTATTTTTGTTGGAAGAG
5076381 A
1 A
5076382 GTCGATTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (20 bp):
ATTTATTTTTGTTGGAAGAG
Found at i:5077499 original size:16 final size:16
Alignment explanation
Indices: 5077478--5077508 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5077468 CAATCATCGG
*
5077478 CTTTTTTTTTTTTAAT
1 CTTTTTATTTTTTAAT
5077494 CTTTTTATTTTTTAA
1 CTTTTTATTTTTTAA
5077509 AATTAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (16 bp):
CTTTTTATTTTTTAAT
Found at i:5077972 original size:14 final size:14
Alignment explanation
Indices: 5077921--5077971 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
5077911 GAGTTTCAAA
5077921 ATTTTTAAAATGTAT
1 ATTTTTAAAAT-TAT
*
5077936 ATTTTTAAAAATTTT
1 ATTTTT-AAAATTAT
* *
5077951 A-ATTTAATATTAT
1 ATTTTTAAAATTAT
5077964 ATTTTTAA
1 ATTTTTAA
5077972 TTATAAGATA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
13 7 0.24
14 8 0.28
15 9 0.31
16 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
ATTTTTAAAATTAT
Found at i:5082294 original size:19 final size:19
Alignment explanation
Indices: 5082272--5082372 Score: 84
Period size: 19 Copynumber: 5.4 Consensus size: 19
5082262 TTTGGTTTAA
*
5082272 GGTTTAGGGTTTGGTGGGT
1 GGTTTAGGGTTTGATGGGT
* *
5082291 GGTTTGGGGTTT-ATTGGT
1 GGTTTAGGGTTTGATGGGT
* *
5082309 GGTTTAAGGTTTCAAT-GGT
1 GGTTTAGGGTTT-GATGGGT
*
5082328 GGTTTAAGGTTTCG-TGGGT
1 GGTTTAGGGTTT-GATGGGT
*
5082347 GG-TTAGGGATTTGAAGGGT
1 GGTTTAGGG-TTTGATGGGT
5082366 GGTTTAG
1 GGTTTAG
5082373 CATTTGAAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
18 21 0.31
19 41 0.60
20 6 0.09
ACGTcount: A:0.13, C:0.02, G:0.44, T:0.42
Consensus pattern (19 bp):
GGTTTAGGGTTTGATGGGT
Found at i:5088137 original size:20 final size:20
Alignment explanation
Indices: 5088112--5088151 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5088102 ATTAAACGTG
*
5088112 TAAAAAATATATAAATATTT
1 TAAAAAATATAAAAATATTT
*
5088132 TAAAAAATTTAAAAATATTT
1 TAAAAAATATAAAAATATTT
5088152 AAATATGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAAAATATAAAAATATTT
Found at i:5088142 original size:9 final size:10
Alignment explanation
Indices: 5088114--5088154 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
5088104 TAAACGTGTA
*
5088114 AAAAATATAT
1 AAAAATATTT
*
5088124 AAATAT-TTT
1 AAAAATATTT
5088133 AAAAA-ATTT
1 AAAAATATTT
5088142 AAAAATATTT
1 AAAAATATTT
5088152 AAA
1 AAA
5088155 TATGAAGGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 14 0.54
10 12 0.46
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAAATATTT
Found at i:5089886 original size:8 final size:8
Alignment explanation
Indices: 5089849--5089900 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
5089839 TTAAATATAC
*
5089849 AAAAAATT
1 AAAAAAAT
*
5089857 AACAAAAT
1 AAAAAAAT
*
5089865 AAAAAAAG
1 AAAAAAAT
*
5089873 ACAAAAAT
1 AAAAAAAT
5089881 AAAAAAAT
1 AAAAAAAT
5089889 AAAAAAAAT
1 -AAAAAAAT
5089898 AAA
1 AAA
5089901 TAAAGGAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
8 28 0.78
9 8 0.22
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:5089897 original size:33 final size:32
Alignment explanation
Indices: 5089849--5089914 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
5089839 TTAAATATAC
* *
5089849 AAAAAATTAACAAAATAAAAAAAGACAAAAATA
1 AAAAAATAAAAAAAATAAAAAAAG-CAAAAATA
* *
5089882 AAAAAATAAAAAAAATAAATAAAGGAAAAATA
1 AAAAAATAAAAAAAATAAAAAAAGCAAAAATA
5089914 A
1 A
5089915 GAAGCACCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 8 0.28
33 21 0.72
ACGTcount: A:0.80, C:0.03, G:0.05, T:0.12
Consensus pattern (32 bp):
AAAAAATAAAAAAAATAAAAAAAGCAAAAATA
Found at i:5089910 original size:17 final size:16
Alignment explanation
Indices: 5089860--5089911 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
5089850 AAAAATTAAC
*
5089860 AAAATAAAAAAAGACA
1 AAAATAAAAAAAGAAA
*
5089876 AAAATAAAAAAATAAAA
1 AAAATAAAAAAA-GAAA
*
5089893 AAAATAAATAAAGGAAA
1 AAAATAAA-AAAAGAAA
5089910 AA
1 AA
5089912 TAAGAAGCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 12 0.40
17 15 0.50
18 3 0.10
ACGTcount: A:0.83, C:0.02, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATAAAAAAAGAAA
Found at i:5090081 original size:16 final size:17
Alignment explanation
Indices: 5090059--5090103 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
5090049 GGGAAAAGAG
5090059 AACAAAGAAAAAAAGCA
1 AACAAAGAAAAAAAGCA
5090076 AA-AAAG-AAAAAAGCA
1 AACAAAGAAAAAAAGCA
5090091 AACAAA-AAAAAAA
1 AACAAAGAAAAAAA
5090104 ATGGACTGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.42
16 13 0.50
17 2 0.08
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (17 bp):
AACAAAGAAAAAAAGCA
Found at i:5090085 original size:15 final size:16
Alignment explanation
Indices: 5090059--5090102 Score: 65
Period size: 15 Copynumber: 2.8 Consensus size: 16
5090049 GGGAAAAGAG
5090059 AACAAAGAAAAAAAGCA
1 AACAAAG-AAAAAAGCA
5090076 AA-AAAGAAAAAAGCA
1 AACAAAGAAAAAAGCA
5090091 AACAAA-AAAAAA
1 AACAAAGAAAAAA
5090103 AATGGACTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 17 0.65
16 7 0.27
17 2 0.08
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (16 bp):
AACAAAGAAAAAAGCA
Found at i:5092701 original size:40 final size:39
Alignment explanation
Indices: 5092657--5093194 Score: 704
Period size: 40 Copynumber: 13.2 Consensus size: 39
5092647 ATGATTGTCA
5092657 AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-TCGTTGCCTCTGTTTAG
5092697 AGGAGCAATTTACTTTTCAAAGTCGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTTGCCTCTGTTTAG
5092736 AGGAGCAATTTACTTTTCCAAAGTCGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTCGTTGCCTCTGTTTAG
*
5092776 AGGAGCAATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGT--TGCCTCTGTTTAG
5092817 AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-TCGTTGCCTCTGTTTAG
*
5092857 AGGAGCAATTTACTTTCCAAAGTCG-TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTTGCCTCTGTTTAG
5092895 AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-TCGTTGCCTCTGTTTAG
5092935 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGT--TGCCTCTGTTTAG
5092976 AGGAGCAATTTACTTTTCCAAAGTTCGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAG-TCGTTGCCTCTGTTTAG
* *
5093017 AGGAGCAATTTACTTTCCAAAGTTCGTGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-TCGT-TGCCTCTGTTTAG
*
5093058 AGGAGCAATTTACTTTTCCAAAGGTCGTGGTAACCTCTGTTTAAAGGG
1 AGGAGCAATTTACTTTT-CAAA-GTCGT--T-GCCTCTGTTT--A--G
* * *
5093106 ACGAGCAA-TTACTCTTCCAATGTCGTTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACT-TTTCAAAGTCG-T--TGCCTCTGTTTAG
* * *
5093148 AGGAGCAATTTA-TGTTTCTCAAGTCGTTGAGCTCTATTTAG
1 AGGAGCAATTTACT-TTTC-AAAGTCGTTG-CCTCTGTTTAG
5093189 AGGAGC
1 AGGAGC
5093195 TTTGATAAAA
Statistics
Matches: 456, Mismatches: 18, Indels: 47
0.88 0.03 0.09
Matches are distributed among these distances:
38 34 0.07
39 53 0.12
40 141 0.31
41 136 0.30
42 30 0.07
43 15 0.03
44 11 0.02
46 14 0.03
47 12 0.03
48 10 0.02
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (39 bp):
AGGAGCAATTTACTTTTCAAAGTCGTTGCCTCTGTTTAG
Found at i:5092946 original size:159 final size:159
Alignment explanation
Indices: 5092657--5093194 Score: 796
Period size: 160 Copynumber: 3.3 Consensus size: 159
5092647 ATGATTGTCA
*
5092657 AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCG
1 AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCG
5092722 TTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTTGCCTCTGTTTAGAGGAGCAATTT
66 -TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTTGCCTCTGTTTAGAGGAGCAATTT
*
5092787 ACTTTTCAAAGTCGTGGTACCTCTGTTTAG
130 ACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
5092817 AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCG
1 AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCG
5092882 TGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTT
66 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAG-TCGTTGCCTCTGTTTAGAGGAGCAATTT
5092946 ACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
130 ACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
5092976 AGGAGCAATTTACTTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTT
1 AGGAGCAATTTACTTTT-CAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAG-T
*
5093041 CGTGTACCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGGTCGTGGTAACCTCTGTTTAAAGGG
64 CGTG--CCTCTGTTTAGAGGAGCAATTTACTTTTCCAAA-GTCGT--T-GCCTCTGTTT--A--G
* * *
5093106 ACGAGCAA-TTACTCTTCCAATGTCGTTGGTGCCTCTGTTTAG
119 AGGAGCAATTTACT-TTTCAAAGTCG-TGGTGCCTCTGTTTAG
* * *
5093148 AGGAGCAATTTA-TGTTTCTCAAG-TCGTTGAGCTCTATTTAGAGGAGC
1 AGGAGCAATTTACT-TTTC-AAAGTTCGTTG-CCTCTGTTTAGAGGAGC
5093195 TTTGATAAAA
Statistics
Matches: 350, Mismatches: 9, Indels: 26
0.91 0.02 0.07
Matches are distributed among these distances:
158 5 0.01
159 104 0.30
160 109 0.31
161 5 0.01
163 28 0.08
164 8 0.02
165 1 0.00
166 1 0.00
167 9 0.03
169 1 0.00
170 5 0.01
171 25 0.07
172 49 0.14
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (159 bp):
AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCG
TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTTGCCTCTGTTTAGAGGAGCAATTTA
CTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:5093448 original size:8 final size:8
Alignment explanation
Indices: 5093435--5093473 Score: 69
Period size: 8 Copynumber: 4.8 Consensus size: 8
5093425 TCCTGTATTT
5093435 TTTTTTTC
1 TTTTTTTC
5093443 TTTTTTTC
1 TTTTTTTC
5093451 TTTTTTTC
1 TTTTTTTC
5093459 TTTTTTTTC
1 -TTTTTTTC
5093468 TTTTTT
1 TTTTTT
5093474 ATATATCTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 22 0.73
9 8 0.27
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTC
Found at i:5093454 original size:16 final size:17
Alignment explanation
Indices: 5093435--5093473 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
5093425 TCCTGTATTT
5093435 TTTTTTTC-TTTTTTTC
1 TTTTTTTCTTTTTTTTC
5093451 TTTTTTTCTTTTTTTTC
1 TTTTTTTCTTTTTTTTC
5093468 TTTTTT
1 TTTTTT
5093474 ATATATCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (17 bp):
TTTTTTTCTTTTTTTTC
Found at i:5093544 original size:3 final size:3
Alignment explanation
Indices: 5093528--5093580 Score: 62
Period size: 3 Copynumber: 19.3 Consensus size: 3
5093518 TATAGTGTTA
*
5093528 TAT T-T TAT TA- TAT TAT TA- TAT TAT TAT TAT TAC TAT T-T T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5093571 TAT TAT TAT T
1 TAT TAT TAT T
5093581 TTTTTTAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 10 0.23
3 34 0.77
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5093571 original size:22 final size:22
Alignment explanation
Indices: 5093528--5093580 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5093518 TATAGTGTTA
5093528 TATT-TTATTATATTATTATAT
1 TATTATTATTATATTATTATAT
*
5093549 TATTATTATTACTATT-TTTTAT
1 TATTATTATTA-TATTATTATAT
5093571 TATTATTATT
1 TATTATTATT
5093581 TTTTTTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 4 0.14
22 21 0.72
23 4 0.14
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (22 bp):
TATTATTATTATATTATTATAT
Found at i:5093577 original size:19 final size:18
Alignment explanation
Indices: 5093530--5093587 Score: 66
Period size: 19 Copynumber: 3.3 Consensus size: 18
5093520 TAGTGTTATA
*
5093530 TTTTATTA-TATTAT-TA
1 TTTTATTATTATTATATT
*
5093546 TATTATTATTATTACTATT
1 TTTTATTATTATTA-TATT
*
5093565 TTTTATTATTATTATTTT
1 TTTTATTATTATTATATT
5093583 TTTTA
1 TTTTA
5093588 ATATATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
16 7 0.20
17 5 0.14
18 9 0.26
19 14 0.40
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATTATTATTATATT
Found at i:5093580 original size:16 final size:16
Alignment explanation
Indices: 5093528--5093597 Score: 74
Period size: 16 Copynumber: 4.4 Consensus size: 16
5093518 TATAGTGTTA
5093528 TATTTTATTA-TATTAT
1 TATTTT-TTATTATTAT
* *
5093544 TATATTATTATTATTAC
1 TAT-TTTTTATTATTAT
5093561 TATTTTTTATTATTAT
1 TATTTTTTATTATTAT
*
5093577 TATTTTTT-TTAATA-
1 TATTTTTTATTATTAT
5093591 TATTTTT
1 TATTTTT
5093598 GGGTTTATCT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
14 7 0.15
15 5 0.11
16 25 0.53
17 10 0.21
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTTTTATTATTAT
Found at i:5096205 original size:16 final size:17
Alignment explanation
Indices: 5096167--5096205 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
5096157 TGAAAGTATC
*
5096167 AATTTTTCTTAAAAATA
1 AATTTTTCTAAAAAATA
5096184 AA-TTTTC-AAAAAATA
1 AATTTTTCTAAAAAATA
5096199 AATTTTT
1 AATTTTT
5096206 GAGGAAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 9 0.45
16 9 0.45
17 2 0.10
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTTTTCTAAAAAATA
Found at i:5096283 original size:116 final size:115
Alignment explanation
Indices: 5096059--5096411 Score: 552
Period size: 116 Copynumber: 3.0 Consensus size: 115
5096049 TAAAAAAACA
* *
5096059 TAAAATAAAATTTCCAAAAA-AAATGTTTTCGAGGAAAAGTTGAAAGTATCAATTTTT-TCGAAA
1 TAAAATAAATTTTCAAAAAATAAAT-TTTT-GAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAA
* *
5096122 TTGAAAGTTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCT
64 TT-AAAGTTT-CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCC
5096176 TAAAAATAAATTTTCAAAAAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAAT
1 T-AAAATAAATTTTCAAAAAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAAT
5096241 TAAAGTTTCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCC
65 TAAAGTTTCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCC
*
5096292 T--AATAAATTTTCAAAAAAAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAA
1 TAAAATAAATTTTC--AAAAAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAA
*
5096355 TTAAAATTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCC
64 TTAAAGTTTC-AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCC
5096408 TAAA
1 TAAA
5096412 CAAGAAAAAT
Statistics
Matches: 222, Mismatches: 6, Indels: 15
0.91 0.02 0.06
Matches are distributed among these distances:
113 11 0.05
115 57 0.26
116 85 0.38
117 35 0.16
118 30 0.14
119 4 0.02
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (115 bp):
TAAAATAAATTTTCAAAAAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATT
AAAGTTTCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCC
Found at i:5096405 original size:58 final size:58
Alignment explanation
Indices: 5096064--5096406 Score: 428
Period size: 58 Copynumber: 5.9 Consensus size: 58
5096054 AAACATAAAA
*
5096064 TAAAATTTCCAAAAAAA-ATGTTTTCGAGGAAAAGTTGAAAGTATCAATTTT-TTCGAAAT
1 TAAAATTT-CAAAAAAATAT-TTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAT
* * * * ** *
5096123 TGAAAGTTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAA
1 T-AAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAT
* * *
5096182 TAAATTTTCAAAAAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAAT
1 TAAAATTTCAAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAT
* * *
5096241 TAAAGTTTC-AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC-C-TAA-
1 TAAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAT
*
5096295 TAAATTTTCAAAAAAAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAT
1 TAAAATTTC-AAAAAAAT--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAT
*
5096356 TAAAATTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 TAAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
5096407 CTAAACAAGA
Statistics
Matches: 249, Mismatches: 24, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
54 8 0.03
55 2 0.01
56 8 0.03
57 33 0.13
58 108 0.43
59 64 0.26
60 18 0.07
61 8 0.03
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.35
Consensus pattern (58 bp):
TAAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAT
Found at i:5099739 original size:46 final size:46
Alignment explanation
Indices: 5099679--5099863 Score: 146
Period size: 46 Copynumber: 4.1 Consensus size: 46
5099669 AACTCTAAAC
* * *
5099679 TTTTCAAATCAAAATCTTTAGAATCTTATATGTGAATTTCTAAAGT
1 TTTTCAAATAAAAATCTTTAGAATCTTAGATGTGAATTTCTAAAAT
* * * * * * **
5099725 TTTTCAAATAAAAATTTTTAAAATTTTGGATATAAAACTC-AAAAT
1 TTTTCAAATAAAAATCTTTAGAATCTTAGATGTGAATTTCTAAAAT
* * * *
5099770 TTTT-TAATCAAAATCTATAGAATCTTAGATGTGAATTTCTAAACT
1 TTTTCAAATAAAAATCTTTAGAATCTTAGATGTGAATTTCTAAAAT
* * * *
5099815 TTTTTAAATAAAATTCTTT-GAAT-TATGGGTGTGAATCTT-TAAAAT
1 TTTTCAAATAAAAATCTTTAGAATCT-TAGATGTGAAT-TTCTAAAAT
5099860 TTTT
1 TTTT
5099864 TAAGGTGAAT
Statistics
Matches: 105, Mismatches: 30, Indels: 9
0.73 0.21 0.06
Matches are distributed among these distances:
44 25 0.24
45 38 0.36
46 42 0.40
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (46 bp):
TTTTCAAATAAAAATCTTTAGAATCTTAGATGTGAATTTCTAAAAT
Found at i:5099783 original size:90 final size:91
Alignment explanation
Indices: 5099658--5099827 Score: 261
Period size: 90 Copynumber: 1.9 Consensus size: 91
5099648 ATATTTGAAA
* * * *
5099658 TTTGGATGTAAAACTCTAAACTTTTCAAATCAAAATCTTTAGAATCTTATATGTGAATTTCTAAA
1 TTTGGATATAAAACTCTAAAATTTTCAAATCAAAATCTATAGAATCTTAGATGTGAATTTCTAAA
*
5099723 GTTTTTCAAATAAAAATTTTTAAAAT
66 CTTTTTCAAATAAAAATTTTTAAAAT
**
5099749 TTTGGATATAAAACTC-AAAATTTTTTAATCAAAATCTATAGAATCTTAGATGTGAATTTCTAAA
1 TTTGGATATAAAACTCTAAAATTTTCAAATCAAAATCTATAGAATCTTAGATGTGAATTTCTAAA
*
5099813 CTTTTTTAAATAAAA
66 CTTTTTCAAATAAAA
5099828 TTCTTTGAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 56 0.79
91 15 0.21
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (91 bp):
TTTGGATATAAAACTCTAAAATTTTCAAATCAAAATCTATAGAATCTTAGATGTGAATTTCTAAA
CTTTTTCAAATAAAAATTTTTAAAAT
Found at i:5099828 original size:45 final size:46
Alignment explanation
Indices: 5099672--5099837 Score: 153
Period size: 46 Copynumber: 3.7 Consensus size: 46
5099662 GATGTAAAAC
*
5099672 TCTAAAC-TTTTCAAATCAAAATCTTTAGAATCTTATATGTGAATT
1 TCTAAACTTTTTCAAATCAAAATCTTTAGAATCTTAGATGTGAATT
* * * * * * * * **
5099717 TCTAAAGTTTTTCAAATAAAAATTTTTAAAATTTTGGATATAAAAC
1 TCTAAACTTTTTCAAATCAAAATCTTTAGAATCTTAGATGTGAATT
* * *
5099763 TC-AAAATTTTT-TAATCAAAATCTATAGAATCTTAGATGTGAATT
1 TCTAAACTTTTTCAAATCAAAATCTTTAGAATCTTAGATGTGAATT
*
5099807 TCTAAACTTTTTTAAAT-AAAATTCTTT-GAAT
1 TCTAAACTTTTTCAAATCAAAA-TCTTTAGAAT
5099838 TATGGGTGTG
Statistics
Matches: 91, Mismatches: 26, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
44 24 0.26
45 30 0.33
46 37 0.41
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.43
Consensus pattern (46 bp):
TCTAAACTTTTTCAAATCAAAATCTTTAGAATCTTAGATGTGAATT
Found at i:5100199 original size:17 final size:17
Alignment explanation
Indices: 5100156--5100203 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
5100146 ATCTTTGAGT
*
5100156 TTCTTGCAAATCT-AAA
1 TTCTTGCGAATCTAAAA
* *
5100172 TTATTGTGAATCTAAAA
1 TTCTTGCGAATCTAAAA
5100189 TTCTTGCGAATCTAA
1 TTCTTGCGAATCTAA
5100204 GTTTTTGTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (17 bp):
TTCTTGCGAATCTAAAA
Found at i:5100201 original size:33 final size:33
Alignment explanation
Indices: 5100156--5100232 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
5100146 ATCTTTGAGT
* * *
5100156 TTCTTGCAAATCTAAATTATTGTGAATCTAAAA
1 TTCTTGCGAATCTAAATTATTGTAAATATAAAA
* * *
5100189 TTCTTGCGAATCTAAGTTTTTGTAAATATGAAA
1 TTCTTGCGAATCTAAATTATTGTAAATATAAAA
5100222 TTCTTGCGAAT
1 TTCTTGCGAAT
5100233 ATAAGTTCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.42
Consensus pattern (33 bp):
TTCTTGCGAATCTAAATTATTGTAAATATAAAA
Found at i:5100254 original size:33 final size:33
Alignment explanation
Indices: 5100186--5100265 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
5100176 TGTGAATCTA
* * **
5100186 AAATTCTTGCGAATCTAAGTTTTTGTAAATATG
1 AAATTCTTGCGAATATAAGTTCTTACAAATATG
* *
5100219 AAATTCTTGCGAATATAAGTTCTTACGAATTTG
1 AAATTCTTGCGAATATAAGTTCTTACAAATATG
5100252 AAAGTT-TTGCGAAT
1 AAA-TTCTTGCGAAT
5100266 TTGAATTTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
33 38 0.95
34 2 0.05
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (33 bp):
AAATTCTTGCGAATATAAGTTCTTACAAATATG
Found at i:5103732 original size:16 final size:16
Alignment explanation
Indices: 5103713--5103748 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
5103703 AAAAAATTCA
5103713 AATTATTGTAAATTTG
1 AATTATTGTAAATTTG
*
5103729 AATTATTTTAAATTTG
1 AATTATTGTAAATTTG
5103745 AATT
1 AATT
5103749 TGAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (16 bp):
AATTATTGTAAATTTG
Found at i:5103758 original size:21 final size:22
Alignment explanation
Indices: 5103723--5103764 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
5103713 AATTATTGTA
5103723 AATTTGAATTATTTTAAATTTG
1 AATTTGAATTATTTTAAATTTG
5103745 AATTTGAA-TATTTTAAATTT
1 AATTTGAATTATTTTAAATTT
5103765 TACATTCGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
AATTTGAATTATTTTAAATTTG
Found at i:5104366 original size:3 final size:3
Alignment explanation
Indices: 5104358--5104391 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5104348 AGCGTTTCCA
5104358 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5104392 TATTTGTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5105973 original size:13 final size:13
Alignment explanation
Indices: 5105955--5105980 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5105945 CCAAACAAAG
5105955 AGAAAGAGAAAAA
1 AGAAAGAGAAAAA
5105968 AGAAAGAGAAAAA
1 AGAAAGAGAAAAA
5105981 CAGCTTGATT
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:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AGAAAGAGAAAAA
Found at i:5108385 original size:31 final size:31
Alignment explanation
Indices: 5108295--5108385 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 31
5108285 GAATCCATAT
* * *
5108295 TGAGGTGATTTATATTGAGCTAAATATATACC
1 TGAGGTGATTTACACTAAGCTAAATATATA-C
* *
5108327 T-AAGTGATTTACAC-GAGCTAAATATATAC
1 TGAGGTGATTTACACTAAGCTAAATATATAC
* *
5108356 TGAGGTGATTTACACTAAGGTGAATATATA
1 TGAGGTGATTTACACTAAGCTAAATATATA
5108386 ATAAATGTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.04
30 26 0.52
31 21 0.42
32 1 0.02
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (31 bp):
TGAGGTGATTTACACTAAGCTAAATATATAC
Found at i:5109047 original size:30 final size:30
Alignment explanation
Indices: 5108956--5109047 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 30
5108946 TTTAAAGCCT
* * * **
5108956 TTTGGCCAAGCTAAGCCTTTATGAAGGCGA
1 TTTGGCTAAGTTAAGCTTTTATGAAGGAAA
* *
5108986 -TTGGCTAAGTTAATCTTTTATGAAAGAAA
1 TTTGGCTAAGTTAAGCTTTTATGAAGGAAA
* * *
5109015 TTTGGTTGAGTTAAGCTTTTATGAAGGTAA
1 TTTGGCTAAGTTAAGCTTTTATGAAGGAAA
5109045 TTT
1 TTT
5109048 ATTGAGCAAA
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 22 0.45
30 27 0.55
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (30 bp):
TTTGGCTAAGTTAAGCTTTTATGAAGGAAA
Found at i:5109125 original size:30 final size:30
Alignment explanation
Indices: 5109061--5109255 Score: 143
Period size: 30 Copynumber: 6.5 Consensus size: 30
5109051 GAGCAAATTA
* ** *
5109061 TTTATGAAGATAATTTTGTCAAACTAATCC
1 TTTATGAAGGTAATTTTGTCAAGTTGATCC
* **
5109091 TTTATGAAGGTAATTTTGTCGAGTTGATAT
1 TTTATGAAGGTAATTTTGTCAAGTTGATCC
* *
5109121 TTTATAAAGGT-ATTTTGTAAAGTTGATCC
1 TTTATGAAGGTAATTTTGTCAAGTTGATCC
* * *
5109150 TTTATAAAGGAAATTGATTG--AA-TTGATCTT
1 TTTATGAAGGTAATT--TTGTCAAGTTGATC-C
*
5109180 TTTATGAAAGGT-ATTTGGTCAAGTTGATCC
1 TTTATG-AAGGTAATTTTGTCAAGTTGATCC
* *
5109210 TTTATGAAAGTAA-TTTGACTCAA-TTGAGCC
1 TTTATGAAGGTAATTTTG--TCAAGTTGATCC
*
5109240 TTTATGAAGGCAATTT
1 TTTATGAAGGTAATTT
5109256 AGCTAAGCTA
Statistics
Matches: 130, Mismatches: 23, Indels: 23
0.74 0.13 0.13
Matches are distributed among these distances:
28 2 0.02
29 37 0.28
30 72 0.55
31 16 0.12
32 3 0.02
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (30 bp):
TTTATGAAGGTAATTTTGTCAAGTTGATCC
Found at i:5109144 original size:29 final size:30
Alignment explanation
Indices: 5109090--5109164 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
5109080 CAAACTAATC
* **
5109090 CTTTATGAAGGTAATTTTGTCGAGTTGATA
1 CTTTATAAAGGTAATTTTGTAAAGTTGATA
* *
5109120 TTTTATAAAGGT-ATTTTGTAAAGTTGATC
1 CTTTATAAAGGTAATTTTGTAAAGTTGATA
*
5109149 CTTTATAAAGGAAATT
1 CTTTATAAAGGTAATT
5109165 GATTGAATTG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
29 24 0.65
30 13 0.35
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (30 bp):
CTTTATAAAGGTAATTTTGTAAAGTTGATA
Found at i:5109244 original size:60 final size:60
Alignment explanation
Indices: 5109121--5109247 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 60
5109111 GAGTTGATAT
* * * * *
5109121 TTTAT-AAAGGTATTTTGTAAAGTTGATCCTTTATAAAGGAAATTGATTGAATTGATCTT
1 TTTATGAAAGGTATTTGGTAAAGTTGATCCTTTATAAAGGAAATTGACTCAATTGAGCTC
* * *
5109180 TTTATGAAAGGTATTTGGTCAAGTTGATCCTTTATGAAAGTAATTTGACTCAATTGAGC-C
1 TTTATGAAAGGTATTTGGTAAAGTTGATCCTTTAT-AAAGGAAATTGACTCAATTGAGCTC
5109240 TTTATGAA
1 TTTATGAA
5109248 GGCAATTTAG
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 5 0.09
60 35 0.60
61 18 0.31
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (60 bp):
TTTATGAAAGGTATTTGGTAAAGTTGATCCTTTATAAAGGAAATTGACTCAATTGAGCTC
Found at i:5109418 original size:30 final size:30
Alignment explanation
Indices: 5109357--5109432 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
5109347 GATCTAATCA
*
5109357 TTTATGAAAGAATTTGACTGAACTAATTC-
1 TTTATGAAAGAATTTGACTGAACTAAGTCT
* *
5109386 TTTATGAAAGAAATTTGA-TTAAGCTGAGTCT
1 TTTATGAAAG-AATTTGACTGAA-CTAAGTCT
5109417 TTTATGAAAGTAATTT
1 TTTATGAAAG-AATTT
5109433 CCCTAAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
29 13 0.32
30 12 0.30
31 15 0.38
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.41
Consensus pattern (30 bp):
TTTATGAAAGAATTTGACTGAACTAAGTCT
Found at i:5109732 original size:47 final size:47
Alignment explanation
Indices: 5109689--5109957 Score: 138
Period size: 47 Copynumber: 5.7 Consensus size: 47
5109679 TTTTTTGTCG
* *
5109689 AGTTAGGCCTTTATAAAGGTAATTTGTTAAGCTGAAATCTTTTGCCA
1 AGTTAGGCCTTTATAAAGGCAATTTGTTAAGATGAAATCTTTTGCCA
* * * * *
5109736 AGCT-GGCCTTGTATGAAGGCAATTTGTTGAGATGGATTCTTTTGCCA
1 AGTTAGGCCTT-TATAAAGGCAATTTGTTAAGATGAAATCTTTTGCCA
* * *
5109783 AGTTAAGCCTTTA-AGTAGGCAATTTGTCTAA-CT-AAACTCTTTTGCCA
1 AGTTAGGCCTTTATA-AAGGCAATTTGT-TAAGATGAAA-TCTTTTGCCA
* * ** * * * * * *
5109830 AGCTAAGTTTTTATGAAGACAATTTGTCAAGTTG--AGCTATTTGCCT
1 AGTTAGGCCTTTATAAAGGCAATTTGTTAAGATGAAATCT-TTTGCCA
* * * ** * * *
5109876 AGCTAGGCCTTTGTGAAA-ACAATTTGTTAAGATGAGTTATATTGCTA
1 AGTTAGGCCTTTAT-AAAGGCAATTTGTTAAGATGAAATCTTTTGCCA
* * * * *
5109923 AGTTGGGCCTTTATGAAGGTAATTTATCAAGATGA
1 AGTTAGGCCTTTATAAAGGCAATTTGTTAAGATGA
5109958 GCTATTTTAC
Statistics
Matches: 163, Mismatches: 46, Indels: 26
0.69 0.20 0.11
Matches are distributed among these distances:
45 2 0.01
46 42 0.26
47 111 0.68
48 8 0.05
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (47 bp):
AGTTAGGCCTTTATAAAGGCAATTTGTTAAGATGAAATCTTTTGCCA
Found at i:5109845 original size:94 final size:94
Alignment explanation
Indices: 5109649--5109857 Score: 219
Period size: 94 Copynumber: 2.2 Consensus size: 94
5109639 TTTAGCTGAG
* * * * * * *
5109649 CTTTTATGAATGTAATTTGTCGAGATAAATTTTTTTGTCGAGTTAGGCCTTTATAAAGGTAATTT
1 CTTTTATGAAGGCAATTTGTCGAGATAAATTCTTTTGCCAAGTTAAGCCTTTATAAAGGCAATTT
*
5109714 GTTAAGCTGAAATCTTTTGCCAAGCTGGC
66 GTTAAGCTGAAATCTTTTGCCAAGCTAGC
* * ** *
5109743 CTTGTATGAAGGCAATTTGTTGAGATGGATTCTTTTGCCAAGTTAAGCCTTTA-AGTAGGCAATT
1 CTTTTATGAAGGCAATTTGTCGAGATAAATTCTTTTGCCAAGTTAAGCCTTTATA-AAGGCAATT
5109807 TGTCTAA-CT-AAACTCTTTTGCCAAGCTAAG-
65 TGT-TAAGCTGAAA-TCTTTTGCCAAGCT-AGC
* *
5109837 TTTTTATGAAGACAATTTGTC
1 CTTTTATGAAGGCAATTTGTC
5109858 AAGTTGAGCT
Statistics
Matches: 94, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
93 4 0.04
94 86 0.91
95 4 0.04
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (94 bp):
CTTTTATGAAGGCAATTTGTCGAGATAAATTCTTTTGCCAAGTTAAGCCTTTATAAAGGCAATTT
GTTAAGCTGAAATCTTTTGCCAAGCTAGC
Found at i:5109958 original size:47 final size:47
Alignment explanation
Indices: 5109895--5109994 Score: 110
Period size: 47 Copynumber: 2.1 Consensus size: 47
5109885 TTTGTGAAAA
* * * * * * *
5109895 CAATTTGTTAAGATGAGTTATATTGCTAAGTTGGGCCTTTATGAAGG
1 CAATTTATCAAGATGAGCTATATTACCAAATTGGGCCTATATGAAGG
* * *
5109942 TAATTTATCAAGATGAGCTATTTTACCAAATTGGGCCTATGTGAAGG
1 CAATTTATCAAGATGAGCTATATTACCAAATTGGGCCTATATGAAGG
5109989 CAATTT
1 CAATTT
5109995 CATTGAGTTG
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (47 bp):
CAATTTATCAAGATGAGCTATATTACCAAATTGGGCCTATATGAAGG
Found at i:5110286 original size:93 final size:94
Alignment explanation
Indices: 5110118--5110298 Score: 215
Period size: 93 Copynumber: 1.9 Consensus size: 94
5110108 TAGTTGGGCT
* * * ** *
5110118 TTTATGAAAGAAATTTTGTCAAGTTGAGCTCTTTTGTTGAACTCTGCCTTTATAAAGGTAATTTT
1 TTTATGAAAGAAATTTTGTCAAGCTAAGCTCTTTTGTCGAACTAGGCCTTTATAAAGGTAATTTG
* **
5110183 TTTAGCTGAGCTC-TTTATCGAGATTACC
66 TTGAAATGAGCTCTTTTATCGAGATTACC
* * *
5110211 TTTATGAAAGCAA-TTTGTCATGCTAAGCTCTTTTGTCGAACTAGGCCTTTTATGATA-GTAATT
1 TTTATGAAAGAAATTTTGTCAAGCTAAGCTCTTTTGTCGAACTAGGCC-TTTAT-AAAGGTAATT
5110274 TGTTGAAATGAGCTCTTTTATCGAG
64 TGTTGAAATGAGCTCTTTTATCGAG
5110299 TTAGATCTTT
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
92 28 0.38
93 34 0.47
94 11 0.15
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (94 bp):
TTTATGAAAGAAATTTTGTCAAGCTAAGCTCTTTTGTCGAACTAGGCCTTTATAAAGGTAATTTG
TTGAAATGAGCTCTTTTATCGAGATTACC
Found at i:5113573 original size:20 final size:20
Alignment explanation
Indices: 5113550--5113590 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5113540 ATAATTATTT
5113550 TTAT-TTAAATATATTAAAAA
1 TTATATTAAATA-ATTAAAAA
*
5113570 TTATATTAAATAATTTAAAA
1 TTATATTAAATAATTAAAAA
5113590 T
1 T
5113591 ACCAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTATATTAAATAATTAAAAA
Found at i:5117429 original size:16 final size:14
Alignment explanation
Indices: 5117401--5117471 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 14
5117391 GATTAAAATT
5117401 TAATATTATTTAAA
1 TAATATTATTTAAA
5117415 TAATATTATAATTAAA
1 TAATATTAT--TTAAA
**
5117431 TAAT-TTAACT-AA
1 TAATATTATTTAAA
5117443 -AATA-TATTTAAA
1 TAATATTATTTAAA
* * *
5117455 AAATAATATTTATA
1 TAATATTATTTAAA
5117469 TAA
1 TAA
5117472 AAATTAAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
11 6 0.13
12 4 0.09
13 5 0.11
14 18 0.40
15 3 0.07
16 9 0.20
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (14 bp):
TAATATTATTTAAA
Done.