Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 169 of 195
Found at i:28189876 original size:22 final size:22
Alignment explanation
Indices: 28189851--28189925 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
28189841 ATAATAATAC
28189851 AATAGTAAATTAAGGATAATTT
1 AATAGTAAATTAAGGATAATTT
* * *
28189873 AATA--AAAATAAGTGATAACTC
1 AATAGTAAATTAAG-GATAATTT
* **
28189894 AGTAGTAAATTAATAATAATTT
1 AATAGTAAATTAAGGATAATTT
28189916 AATAGTAAAT
1 AATAGTAAAT
28189926 AAGATTTAGC
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
20 7 0.17
21 9 0.22
22 18 0.45
23 6 0.15
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.33
Consensus pattern (22 bp):
AATAGTAAATTAAGGATAATTT
Found at i:28189882 original size:43 final size:43
Alignment explanation
Indices: 28189842--28189928 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
28189832 TATAAATATA
*
28189842 TAATAA-TACAATAGTAAATTAAGGATAATTTAATAAAAATAAG
1 TAATAACT-CAATAGTAAATTAAGAATAATTTAATAAAAATAAG
* * * *
28189885 TGATAACTCAGTAGTAAATTAATAATAATTTAATAGTAAATAAG
1 TAATAACTCAATAGTAAATTAAGAATAATTTAATA-AAAATAAG
28189929 ATTTAGCTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 29 0.78
44 8 0.22
ACGTcount: A:0.54, C:0.03, G:0.10, T:0.32
Consensus pattern (43 bp):
TAATAACTCAATAGTAAATTAAGAATAATTTAATAAAAATAAG
Found at i:28190277 original size:22 final size:22
Alignment explanation
Indices: 28190240--28190303 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
28190230 AAAATCATAA
* *
28190240 AGAACTTAATAATAAATTAATG
1 AGAACTTAGTAGTAAATTAATG
* * *
28190262 ATAATTTAGTAGTAAA-TAATTT
1 AGAACTTAGTAGTAAATTAA-TG
28190284 AGAACTTAGTAGT-AATTAAT
1 AGAACTTAGTAGTAAATTAAT
28190304 AATTAAAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
21 6 0.18
22 27 0.82
ACGTcount: A:0.48, C:0.03, G:0.11, T:0.38
Consensus pattern (22 bp):
AGAACTTAGTAGTAAATTAATG
Found at i:28190454 original size:22 final size:22
Alignment explanation
Indices: 28190382--28190887 Score: 199
Period size: 22 Copynumber: 23.0 Consensus size: 22
28190372 ATAATTCTGT
* *
28190382 ATAGTAAATTAGTGATAACTTA
1 ATAGTAAATCAATGATAACTTA
* * * *
28190404 ATAATATATCAATAATAATTTA
1 ATAGTAAATCAATGATAACTTA
**
28190426 ACCGTAAAT-AATTGATAACTTA
1 ATAGTAAATCAA-TGATAACTTA
* *
28190448 GTAGTAAATCAATAATAA-TATA
1 ATAGTAAATCAATGATAACT-TA
*
28190470 ATAGTAAATGC-ATAATAACTTA
1 ATAGTAAAT-CAATGATAACTTA
* *
28190492 ATAGTAAATCAATTATAACATA
1 ATAGTAAATCAATGATAACTTA
* * *
28190514 ATTA-TAAATGC-ATAATAGCATA
1 A-TAGTAAAT-CAATGATAACTTA
* *
28190536 GTAGTAAATCAACGATAACTTA
1 ATAGTAAATCAATGATAACTTA
** * *
28190558 ATAAAAAATAAATAATAACTTA
1 ATAGTAAATCAATGATAACTTA
* * *
28190580 ATAGTTAATCATTGATAATTTA
1 ATAGTAAATCAATGATAACTTA
* *
28190602 ATAGTAAATCAATGAAAATTTA
1 ATAGTAAATCAATGATAACTTA
* * *
28190624 GTAATAAAT-TATAGATAACTTA
1 ATAGTAAATCAAT-GATAACTTA
*** ** **
28190646 ATAGTAAATTTGTTTTAGTTTA
1 ATAGTAAATCAATGATAACTTA
* * *
28190668 ATAGTAATTAAATTATAAACTTA
1 ATAGTAAATCAATGAT-AACTTA
** *
28190691 GCAGTAAATC-ATAAATAACTTA
1 ATAGTAAATCAAT-GATAACTTA
* * *
28190713 AAAATAAATCAATGATAATTTA
1 ATAGTAAATCAATGATAACTTA
* * * * *
28190735 GTAGTTAATCACT-AAAACTCA
1 ATAGTAAATCAATGATAACTTA
* *
28190756 ATAGTAAATCAATGATAACATG
1 ATAGTAAATCAATGATAACTTA
* * * *
28190778 GTAGCAAATGC-ATAAT-A-GTA
1 ATAGTAAAT-CAATGATAACTTA
* * *
28190798 TATAGTAAATCATTGATAATTTT
1 -ATAGTAAATCAATGATAACTTA
* * *
28190821 ATAGTAAATTATTGATAATTTA
1 ATAGTAAATCAATGATAACTTA
* * * *
28190843 GTAGTAAAATCACTAATAA-TGTT
1 ATAGT-AAATCAATGATAACT-TA
* *
28190866 ATAGTAAATTATTGATAACTTA
1 ATAGTAAATCAATGATAACTTA
28190888 GCTGTAAATC
Statistics
Matches: 351, Mismatches: 109, Indels: 48
0.69 0.21 0.09
Matches are distributed among these distances:
20 2 0.01
21 35 0.10
22 273 0.78
23 41 0.12
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (22 bp):
ATAGTAAATCAATGATAACTTA
Found at i:28190862 original size:45 final size:45
Alignment explanation
Indices: 28190800--28190908 Score: 150
Period size: 45 Copynumber: 2.4 Consensus size: 45
28190790 TAATAGTATA
* * *
28190800 TAGTAAATCATTGATAATTTTATAGTAAATTATTGATAATTTAG-
1 TAGTAAATCACTAATAATTTTATAGTAAATTATTGATAACTTAGC
*
28190844 TAGTAAAATCACTAATAATGTTATAGTAAATTATTGATAACTTAGC
1 TAGT-AAATCACTAATAATTTTATAGTAAATTATTGATAACTTAGC
*
28190890 T-GTAAATCAGTAATAATTT
1 TAGTAAATCACTAATAATTT
28190909 AGTATAAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
44 18 0.32
45 38 0.67
46 1 0.02
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (45 bp):
TAGTAAATCACTAATAATTTTATAGTAAATTATTGATAACTTAGC
Found at i:28190939 original size:22 final size:21
Alignment explanation
Indices: 28190825--28190941 Score: 74
Period size: 22 Copynumber: 5.3 Consensus size: 21
28190815 AATTTTATAG
* *
28190825 TAAATTATTGATAATTTAGTA
1 TAAATTAATAATAATTTAGTA
* *
28190846 GTAAAATCACTAATAATGTTA-TA
1 -T-AAATTAATAATAAT-TTAGTA
* * * *
28190869 GTAAATTATTGATAACTTAGCTG
1 -TAAATTAATAATAATTTAG-TA
* *
28190892 TAAATCAGTAATAATTTAGTA
1 TAAATTAATAATAATTTAGTA
*
28190913 TAAATTAATAATGATTTAGTTA
1 TAAATTAATAATAATTTAG-TA
28190935 TAAATTA
1 TAAATTA
28190942 GTTAATTATT
Statistics
Matches: 74, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
21 20 0.27
22 35 0.47
23 16 0.22
24 3 0.04
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.41
Consensus pattern (21 bp):
TAAATTAATAATAATTTAGTA
Found at i:28191011 original size:11 final size:10
Alignment explanation
Indices: 28190988--28191076 Score: 70
Period size: 11 Copynumber: 8.2 Consensus size: 10
28190978 ACTTTATAGC
28190988 AAATTAGTAAT
1 AAATTA-TAAT
*
28190999 AATTTTATAAT
1 AA-ATTATAAT
*
28191010 AAATTATAGT
1 AAATTATAAT
28191020 AAATTAGTAAT
1 AAATTA-TAAT
*
28191031 AACTTTATAAT
1 AA-ATTATAAT
28191042 AAATTATATAT
1 AAATTATA-AT
* *
28191053 AACTTAATAGT
1 AAATT-ATAAT
28191064 AAATTATCAAT
1 AAATTAT-AAT
28191075 AA
1 AA
28191077 TTTAGTAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
10 19 0.31
11 34 0.55
12 9 0.15
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.40
Consensus pattern (10 bp):
AAATTATAAT
Found at i:28191013 original size:22 final size:22
Alignment explanation
Indices: 28190974--28191015 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28190964 GTAAATCATC
*
28190974 AATAACTTTATAGCAAATTAGT
1 AATAACTTTATAACAAATTAGT
* *
28190996 AATAATTTTATAATAAATTA
1 AATAACTTTATAACAAATTA
28191016 TAGTAAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (22 bp):
AATAACTTTATAACAAATTAGT
Found at i:28191021 original size:54 final size:54
Alignment explanation
Indices: 28190962--28191070 Score: 132
Period size: 54 Copynumber: 2.0 Consensus size: 54
28190952 AACAACTTAT
* * *
28190962 TAGTAAATCA-TCAATAACTTTATAGCAAATTAGTA-ATAATTTTATAATAAATTA
1 TAGTAAATCAGT-AATAACTTTATAACAAATTA-TATATAACTTAATAATAAATTA
* * *
28191016 TAGTAAATTAGTAATAACTTTATAATAAATTATATATAACTTAATAGTAAATTA
1 TAGTAAATCAGTAATAACTTTATAACAAATTATATATAACTTAATAATAAATTA
28191070 T
1 T
28191071 CAATAATTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 2 0.04
54 44 0.94
55 1 0.02
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (54 bp):
TAGTAAATCAGTAATAACTTTATAACAAATTATATATAACTTAATAATAAATTA
Found at i:28191024 original size:32 final size:32
Alignment explanation
Indices: 28190981--28191049 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
28190971 ATCAATAACT
*
28190981 TTATAGCAAATTAGTAATAATTTTATAATAAA
1 TTATAGCAAATTAGTAATAACTTTATAATAAA
*
28191013 TTATAGTAAATTAGTAATAACTTTATAATAAA
1 TTATAGCAAATTAGTAATAACTTTATAATAAA
28191045 TTATA
1 TTATA
28191050 TATAACTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (32 bp):
TTATAGCAAATTAGTAATAACTTTATAATAAA
Found at i:28191069 original size:22 final size:21
Alignment explanation
Indices: 28191003--28191110 Score: 96
Period size: 22 Copynumber: 5.0 Consensus size: 21
28190993 AGTAATAATT
*
28191003 TTATAATAAATT-ATAGTAAA
1 TTATAATAACTTAATAGTAAA
* *
28191023 TTAGTAATAACTTTATAATAAA
1 TTA-TAATAACTTAATAGTAAA
28191045 TTATATATAACTTAATAGTAAA
1 TTATA-ATAACTTAATAGTAAA
* *
28191067 TTATCAATAATTTAGTAGT-AA
1 TTAT-AATAACTTAATAGTAAA
*
28191088 TCGT-TTATAACTTAATAGTAAA
1 T--TATAATAACTTAATAGTAAA
28191110 T
1 T
28191111 CATCTATAAC
Statistics
Matches: 72, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
20 3 0.04
21 24 0.33
22 43 0.60
23 2 0.03
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (21 bp):
TTATAATAACTTAATAGTAAA
Found at i:28191118 original size:22 final size:22
Alignment explanation
Indices: 28191029--28191123 Score: 93
Period size: 22 Copynumber: 4.4 Consensus size: 22
28191019 TAAATTAGTA
* * * *
28191029 ATAACTTTATAATAAATTATAT
1 ATAACTTAATAGTAAATCATCT
* *
28191051 ATAACTTAATAGTAAATTATCA
1 ATAACTTAATAGTAAATCATCT
* * * *
28191073 ATAATTTAGTAGT-AATCGTTT
1 ATAACTTAATAGTAAATCATCT
28191094 ATAACTTAATAGTAAATCATCT
1 ATAACTTAATAGTAAATCATCT
28191116 ATAACTTA
1 ATAACTTA
28191124 GTGATAAATT
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
21 15 0.26
22 43 0.74
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.41
Consensus pattern (22 bp):
ATAACTTAATAGTAAATCATCT
Found at i:28191172 original size:21 final size:21
Alignment explanation
Indices: 28191130--28191172 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
28191120 CTTAGTGATA
**
28191130 AATTAATGATAATTTAGAAAT
1 AATTAATGATAAGATAGAAAT
* *
28191151 AATTAGTGATAAGATAGTAAT
1 AATTAATGATAAGATAGAAAT
28191172 A
1 A
28191173 TGTAATTAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35
Consensus pattern (21 bp):
AATTAATGATAAGATAGAAAT
Found at i:28191455 original size:45 final size:46
Alignment explanation
Indices: 28191405--28191493 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 46
28191395 ATTGTAATTT
* *
28191405 ATTGATAAATTAATAATAAAGCATAAATAACTTAGTAG-TAATTGA
1 ATTGATAAATTAATAATAAAGAATAAATAACTTAATAGCTAATTGA
* * * * *
28191450 ATTGATAACTTAGTAGTAAATAATTAATAACTTAATAGCTAATT
1 ATTGATAAATTAATAATAAAGAATAAATAACTTAATAGCTAATT
28191494 ATTAAAAAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
45 31 0.86
46 5 0.14
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.36
Consensus pattern (46 bp):
ATTGATAAATTAATAATAAAGAATAAATAACTTAATAGCTAATTGA
Found at i:28191457 original size:23 final size:22
Alignment explanation
Indices: 28191430--28191508 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
28191420 ATAAAGCATA
28191430 AATAACTTAGTAGTAATTGAATT
1 AATAACTTAGTAGTAATT-AATT
* *
28191453 GATAACTTAGTAGTAAATAATT
1 AATAACTTAGTAGTAATTAATT
*
28191475 AATAACTTAATAGCTAATT-ATT
1 AATAACTTAGTAG-TAATTAATT
* *
28191497 AAAAAGTTAGTA
1 AATAACTTAGTA
28191509 ATTGATCAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
22 27 0.57
23 20 0.43
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (22 bp):
AATAACTTAGTAGTAATTAATT
Found at i:28191666 original size:22 final size:22
Alignment explanation
Indices: 28191641--28191780 Score: 104
Period size: 22 Copynumber: 6.4 Consensus size: 22
28191631 AGTAATAAAT
* * * *
28191641 TAGTTAATCATTGATAATTTTA
1 TAGTAAATCATTAATAACTTAA
* *
28191663 TAGTAAATCATTTATAACTTCA
1 TAGTAAATCATTAATAACTTAA
* * *
28191685 TAGAAAATTAGTT-ATAACTTTA
1 TAGTAAATCA-TTAATAACTTAA
* * *
28191707 TAATAAATTATCAATAACTTAA
1 TAGTAAATCATTAATAACTTAA
* *
28191729 TAGTAAATCATTGATAATTTAA
1 TAGTAAATCATTAATAACTTAA
*
28191751 TAATAAATCATTAATAA-TATAA
1 TAGTAAATCATTAATAACT-TAA
*
28191773 TAATAAAT
1 TAGTAAAT
28191781 TAGTTATAAT
Statistics
Matches: 97, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
21 2 0.02
22 93 0.96
23 2 0.02
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (22 bp):
TAGTAAATCATTAATAACTTAA
Found at i:28191714 original size:44 final size:43
Alignment explanation
Indices: 28191654--28191790 Score: 136
Period size: 44 Copynumber: 3.1 Consensus size: 43
28191644 TTAATCATTG
* * *
28191654 ATAATTTTATAGTAAATCATTTATAACTTCATAGAAAATTAGTT
1 ATAA-TTTATAATAAATCATTAATAACTTAATAGAAAATTAGTT
* * * *
28191698 ATAACTTTATAATAAATTATCAATAACTTAATAGTAAATCA-TT
1 ATAA-TTTATAATAAATCATTAATAACTTAATAGAAAATTAGTT
28191741 GATAATTTAATAATAAATCATTAATAA-TATAATA-ATAAATTAGTT
1 -ATAATTT-ATAATAAATCATTAATAACT-TAATAGA-AAATTAGTT
28191786 ATAAT
1 ATAAT
28191791 AATATATCAG
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
43 6 0.08
44 68 0.89
45 2 0.03
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (43 bp):
ATAATTTATAATAAATCATTAATAACTTAATAGAAAATTAGTT
Found at i:28191850 original size:22 final size:21
Alignment explanation
Indices: 28191674--28191854 Score: 92
Period size: 22 Copynumber: 8.5 Consensus size: 21
28191664 AGTAAATCAT
*
28191674 TTATAACTTCATAGA-AAATTA
1 TTATAACTTAATA-ATAAATTA
*
28191695 GTTATAACTTTATAATAAATTA
1 -TTATAACTTAATAATAAATTA
* * *
28191717 TCAATAACTTAATAGTAAATCA
1 T-TATAACTTAATAATAAATTA
* *
28191739 TTGATAATTTAATAATAAATCA
1 TT-ATAACTTAATAATAAATTA
28191761 TTAATAA-TATAATAATAAATTA
1 TT-ATAACT-TAATAATAAATTA
*
28191783 GTTATAA--TAAT-AT--ATCA
1 -TTATAACTTAATAATAAATTA
* * *
28191800 GTGT-TAACTTAGTCATAATTTA
1 -T-TATAACTTAATAATAAATTA
*
28191822 TTGATAACTTAATGATAAATTA
1 TT-ATAACTTAATAATAAATTA
28191844 GTTATAA-TTAA
1 -TTATAACTTAA
28191855 GTTGTAAATC
Statistics
Matches: 128, Mismatches: 17, Indels: 29
0.74 0.10 0.17
Matches are distributed among these distances:
17 8 0.06
18 1 0.01
19 5 0.04
20 7 0.05
21 8 0.06
22 95 0.74
23 4 0.03
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (21 bp):
TTATAACTTAATAATAAATTA
Found at i:28199214 original size:10 final size:10
Alignment explanation
Indices: 28199194--28199226 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
28199184 TAAAAATATA
28199194 AATAA-TTTT
1 AATAATTTTT
28199203 AATAATTTTT
1 AATAATTTTT
28199213 AATAATTTATT
1 AATAATTT-TT
28199224 AAT
1 AAT
28199227 TTGAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 5 0.23
10 12 0.55
11 5 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
AATAATTTTT
Found at i:28212128 original size:15 final size:15
Alignment explanation
Indices: 28212104--28212133 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28212094 GTAAATAATC
28212104 AAAGTAATATTAAAA
1 AAAGTAATATTAAAA
*
28212119 AAAGTTATATTAAAA
1 AAAGTAATATTAAAA
28212134 TGGATATTTA
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:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
AAAGTAATATTAAAA
Found at i:28215822 original size:15 final size:16
Alignment explanation
Indices: 28215797--28215833 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
28215787 GGTATCATAT
28215797 ATTCATAAATAATTAA
1 ATTCATAAATAATTAA
*
28215813 ATTC-TAAATAATTAG
1 ATTCATAAATAATTAA
28215828 ATTCAT
1 ATTCAT
28215834 GTAATTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (16 bp):
ATTCATAAATAATTAA
Found at i:28219043 original size:14 final size:14
Alignment explanation
Indices: 28219026--28219089 Score: 53
Period size: 14 Copynumber: 4.4 Consensus size: 14
28219016 TAAAATAATT
28219026 TATAAATTAAATAATA
1 TATAAATTAAAT-A-A
28219042 TAATACAATTAAAGTAA
1 T-ATA-AATTAAA-TAA
28219059 T-TAAA-TATAAT-A
1 TATAAATTA-AATAA
28219071 TATAAATTAAATAA
1 TATAAATTAAATAA
28219085 TATAA
1 TATAA
28219090 TAATATTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
12 2 0.05
13 10 0.24
14 12 0.29
15 2 0.05
16 1 0.02
17 5 0.12
18 8 0.20
19 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (14 bp):
TATAAATTAAATAA
Found at i:28219051 original size:45 final size:45
Alignment explanation
Indices: 28219002--28219091 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
28218992 TTCGTGTATC
* *
28219002 CAATTAAATTATATTAAA-ATAATTTATAAATTAAATAATATAATA
1 CAATTAAAGTA-ATTAAATATAATATATAAATTAAATAATATAATA
28219047 CAATTAAAGTAATTAAATATAATATATAAATTAAATAATATAATA
1 CAATTAAAGTAATTAAATATAATATATAAATTAAATAATATAATA
28219092 ATATTTTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 6 0.14
45 36 0.86
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (45 bp):
CAATTAAAGTAATTAAATATAATATATAAATTAAATAATATAATA
Found at i:28219060 original size:27 final size:26
Alignment explanation
Indices: 28219030--28219095 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
28219020 ATAATTTATA
28219030 AATTAAATAATATA-ATACAATTAAAGT
1 AATTAAATAATATATATA-AATTAAA-T
28219057 AATTAAAT-ATAATATATAAATTAAAT
1 AATTAAATAAT-ATATATAAATTAAAT
28219083 AA-TATAATAATAT
1 AATTA-AATAATAT
28219096 TTTAATTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
25 2 0.06
26 10 0.29
27 20 0.57
28 3 0.09
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (26 bp):
AATTAAATAATATATATAAATTAAAT
Found at i:28220579 original size:6 final size:6
Alignment explanation
Indices: 28220568--28220603 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
28220558 ATGGTTACAA
28220568 CTATGG CTATGG CTATGG CTATGG CTATGG CTATGG
1 CTATGG CTATGG CTATGG CTATGG CTATGG CTATGG
28220604 AGATCCTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (6 bp):
CTATGG
Found at i:28222662 original size:3 final size:3
Alignment explanation
Indices: 28222656--28222703 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
28222646 CTTCTGTTTG
28222656 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
28222702 TT
1 TT
28222704 GGTAGTTTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28226276 original size:20 final size:20
Alignment explanation
Indices: 28226228--28226276 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
28226218 AATAATAAAA
28226228 TTTTTAATTTTTTATTACAT
1 TTTTTAATTTTTTATTACAT
*
28226248 ATTTT-ATTTTTTAATTA-AT
1 TTTTTAATTTTTT-ATTACAT
28226267 TTTTTAATTT
1 TTTTTAATTT
28226277 ATCCTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTAATTTTTTATTACAT
Found at i:28233987 original size:3 final size:3
Alignment explanation
Indices: 28233979--28234018 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
28233969 AGAGACAAGG
28233979 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
28234019 TTTTTGTGAA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:28234144 original size:41 final size:42
Alignment explanation
Indices: 28234067--28234145 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 42
28234057 AGAACGTAAA
* * * *
28234067 ATTTAAATCAATTAATTTATACAATTATTTTTAAAAAATAAT
1 ATTTAAATAAATTAATTTATACAATCACTTTAAAAAAATAAT
**
28234109 ATTT-AATAAATTAATTTATACCGTCACTTTAAAAAAA
1 ATTTAAATAAATTAATTTATACAATCACTTTAAAAAAA
28234146 ATTCTAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
41 27 0.87
42 4 0.13
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.42
Consensus pattern (42 bp):
ATTTAAATAAATTAATTTATACAATCACTTTAAAAAAATAAT
Found at i:28234696 original size:2 final size:2
Alignment explanation
Indices: 28234689--28234722 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28234679 AAAACATGTA
28234689 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
28234723 GGTCCTTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28238712 original size:9 final size:9
Alignment explanation
Indices: 28238694--28238729 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
28238684 TAAATGACTG
28238694 AAAAAATAA
1 AAAAAATAA
*
28238703 AAACAATAA
1 AAAAAATAA
28238712 AATAAAATAA
1 AA-AAAATAA
28238722 AAAAAATA
1 AAAAAATA
28238730 GGGACCACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAAAATAA
Found at i:28239918 original size:30 final size:30
Alignment explanation
Indices: 28239812--28239919 Score: 119
Period size: 30 Copynumber: 3.6 Consensus size: 30
28239802 TTTTTATTGC
* *
28239812 ATTTAAATAAGTACTTT-ATTTTTAACTTGT
1 ATTTAAATAAAT-CTTTAATTTTTAACTTAT
** * * *
28239842 GCTTAAATAAGTCTTGAATTTTTAATTTAT
1 ATTTAAATAAATCTTTAATTTTTAACTTAT
*
28239872 ATTCAAATAAATCTTTAATTTTTAACTTAT
1 ATTTAAATAAATCTTTAATTTTTAACTTAT
*
28239902 ATTTAAATAAACCTTTAA
1 ATTTAAATAAATCTTTAA
28239920 AATAATGCAT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 3 0.05
30 61 0.95
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (30 bp):
ATTTAAATAAATCTTTAATTTTTAACTTAT
Found at i:28244049 original size:18 final size:19
Alignment explanation
Indices: 28244011--28244049 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
28244001 AAATAAACAT
*
28244011 ATAAAATTAAAATTTTTTA
1 ATAAAATTAAAATTATTTA
*
28244030 ATAAAA-TAATATTATTTA
1 ATAAAATTAAAATTATTTA
28244048 AT
1 AT
28244050 TTACTGATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATAAAATTAAAATTATTTA
Found at i:28246470 original size:133 final size:136
Alignment explanation
Indices: 28246217--28246607 Score: 538
Period size: 133 Copynumber: 2.9 Consensus size: 136
28246207 CTAATTAAAT
** * *
28246217 ATACACA-ACACATATCTACATGTTTGCCTATATGCAGCATTGCAAGGAATGGGATTTGTGATTT
1 ATACACAGACACATATCTACATGTTTGCCTATATGTTGCATTGCAAGGAATGGGA-CTATGATTT
* * *
28246281 GCATTTCATAACTTAGCTATGGGGAAAATGAATAGGAAAAGAAAAGAAAAGGTGGCCTGCTTCTA
65 GCATTTCAAAACTTAGCTATGAGGAAAATGAATAGGAAAAGAAAAGAAAAGATGGCCTGCTTCTA
* *
28246346 GTTATAT
130 GTCATAC
** * *
28246353 ATACAGTGACACATATCTACATGTTTGCCTATATGTTGTACTGCAAGGAATGGGACT-T-A-TTG
1 ATACACAGACACATATCTACATGTTTGCCTATATGTTGCATTGCAAGGAATGGGACTATGATTTG
* * *
28246415 CATTTCAAAACTTAGCTATGATGAAAATGAATAGGAAAAGAAATGAAAAGATGGCCTGCTTTTAG
66 CATTTCAAAACTTAGCTATGAGGAAAATGAATAGGAAAAGAAAAGAAAAGATGGCCTGCTTCTAG
28246480 TCATAC
131 TCATAC
* * *
28246486 ATACACAGACACACATCTACATGTTTGCCTCTATGTTGCATTGCAAGGAATGAGACTTATGATTT
1 ATACACAGACACATATCTACATGTTTGCCTATATGTTGCATTGCAAGGAATGGGAC-TATGATTT
* * *
28246551 GCATTTCAAAACTTAGCTATTAGGAAAATGAATAGGAAAAGAAAACAAAAGGTGGCC
65 GCATTTCAAAACTTAGCTATGAGGAAAATGAATAGGAAAAGAAAAGAAAAGATGGCC
28246608 AGCTCTTATC
Statistics
Matches: 223, Mismatches: 27, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
133 115 0.52
134 2 0.01
135 2 0.01
136 7 0.03
137 97 0.43
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (136 bp):
ATACACAGACACATATCTACATGTTTGCCTATATGTTGCATTGCAAGGAATGGGACTATGATTTG
CATTTCAAAACTTAGCTATGAGGAAAATGAATAGGAAAAGAAAAGAAAAGATGGCCTGCTTCTAG
TCATAC
Found at i:28247894 original size:15 final size:16
Alignment explanation
Indices: 28247868--28247897 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28247858 ATGAGTCTCA
28247868 AAAAATTAAAATTAAT
1 AAAAATTAAAATTAAT
28247884 AAAAATT-AAATTAA
1 AAAAATTAAAATTAA
28247898 ACATTTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAATTAAAATTAAT
Found at i:28255023 original size:24 final size:26
Alignment explanation
Indices: 28254975--28255024 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
28254965 ATATATGTTA
*
28254975 ATAAATTTATATATATTTTGTCAGTAT
1 ATAAATTTATATATA-TTTGACAGTAT
28255002 ATAAATTT-TATATA-TTGACAGTA
1 ATAAATTTATATATATTTGACAGTA
28255025 AATTAGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
26 6 0.27
27 8 0.36
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (26 bp):
ATAAATTTATATATATTTGACAGTAT
Found at i:28255210 original size:159 final size:159
Alignment explanation
Indices: 28255021--28255315 Score: 484
Period size: 159 Copynumber: 1.9 Consensus size: 159
28255011 ATATATTGAC
* * *
28255021 AGTAAATTAGATAATATCATTTCGTTAATGAGATGAATTAGCTGATACGAAATTTATTGATAAAT
1 AGTAAATTAGATAATATCATTTCGTCAATGAGATGAATTAGATGATAAGAAATTTATTGATAAAT
*
28255086 AAATTTTTTTAAAAAAATT-AATTTTTTGTATATTTATTTTAAGAATTGATGAAATAACATCATA
66 AAATTTTTTTAAAAAAATTAAAATTTTT-TATATTTATTTTAAGAATTGATGAAATAACATCATA
28255150 TGATTTATTGATAATATGTAAAATTTATAT
130 TGATTTATTGATAATATGTAAAATTTATAT
* *
28255180 AGTAAATTAGATAATATCATTTTGTCAATGAGATGAATTAGATGATAATAAATTTATTGATAAAT
1 AGTAAATTAGATAATATCATTTCGTCAATGAGATGAATTAGATGATAAGAAATTTATTGATAAAT
* ** *
28255245 AATTTTTTTTTTAAAAATTAAAATTTTTTATATTTATTTTAAGAATTGATGAAATAATATCATAT
66 AAATTTTTTTAAAAAAATTAAAATTTTTTATATTTATTTTAAGAATTGATGAAATAACATCATAT
28255310 GATTTA
131 GATTTA
28255316 CTAATAATCT
Statistics
Matches: 125, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
159 118 0.94
160 7 0.06
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.44
Consensus pattern (159 bp):
AGTAAATTAGATAATATCATTTCGTCAATGAGATGAATTAGATGATAAGAAATTTATTGATAAAT
AAATTTTTTTAAAAAAATTAAAATTTTTTATATTTATTTTAAGAATTGATGAAATAACATCATAT
GATTTATTGATAATATGTAAAATTTATAT
Found at i:28256574 original size:22 final size:23
Alignment explanation
Indices: 28256536--28256584 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
28256526 TATTTAGTAA
*
28256536 ATAAATTTTTTTATTAAA-TAAT
1 ATAAATTTTATTATTAAATTAAT
28256558 ATAAATTATTATT-TTAAATTAAT
1 ATAAATT-TTATTATTAAATTAAT
28256581 -TAAA
1 ATAAA
28256585 ATTAATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATAAATTTTATTATTAAATTAAT
Found at i:28256579 original size:27 final size:27
Alignment explanation
Indices: 28256533--28256603 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
28256523 ATATATTTAG
* * *
28256533 TAAATAAATTTTTT-TATTAAATAATA
1 TAAATATATTTTTTAAATTAAATAAAA
*
28256559 TAAAT-TATTATTTTAAATTAATTAAAA
1 TAAATATATT-TTTTAAATTAAATAAAA
*
28256586 TTAATATATTTTTTAAAT
1 TAAATATATTTTTTAAAT
28256604 ATATTAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
25 3 0.08
26 9 0.24
27 21 0.57
28 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TAAATATATTTTTTAAATTAAATAAAA
Found at i:28256611 original size:21 final size:21
Alignment explanation
Indices: 28256585--28256630 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
28256575 ATTAATTAAA
*
28256585 ATTAATATAT-TTTTTAAATAT
1 ATTAATATATATTTATAAA-AT
28256606 ATTAATATATATTTATAAAAT
1 ATTAATATATATTTATAAAAT
28256627 ATTA
1 ATTA
28256631 CCTACAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTAATATATATTTATAAAAT
Found at i:28258192 original size:24 final size:23
Alignment explanation
Indices: 28258120--28258192 Score: 58
Period size: 27 Copynumber: 2.9 Consensus size: 23
28258110 GTTAATATAT
28258120 ATTATATTAGTTAATTATATAATA
1 ATTAT-TTAGTTAATTATATAATA
* *
28258144 ATATAATTGGATT-ATGATATAATAATGA
1 AT-TATTTAG-TTAAT--TAT-ATAAT-A
28258172 ATTATTTAGTTAATTATATAA
1 ATTATTTAGTTAATTATATAA
28258193 ATATAATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
24 11 0.29
25 7 0.18
26 5 0.13
27 12 0.32
28 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (23 bp):
ATTATTTAGTTAATTATATAATA
Found at i:28261424 original size:17 final size:18
Alignment explanation
Indices: 28261389--28261426 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
28261379 CTGTACAACA
28261389 ATATACAATCATTAAATT
1 ATATACAATCATTAAATT
* *
28261407 ATATATAAT-ATTATATT
1 ATATACAATCATTAAATT
28261424 ATA
1 ATA
28261427 ACATATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATACAATCATTAAATT
Found at i:28261566 original size:19 final size:19
Alignment explanation
Indices: 28261542--28261600 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
28261532 TAATTTTAAG
28261542 ATATTTATTAAAAAATTAT
1 ATATTTATTAAAAAATTAT
*
28261561 ATATTTATT------TTAAG
1 ATATTTATTAAAAAATT-AT
28261575 ATATTTATTAAAAAATTAT
1 ATATTTATTAAAAAATTAT
28261594 ATATTTA
1 ATATTTA
28261601 AAGATTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
13 2 0.06
14 10 0.32
19 17 0.55
20 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
ATATTTATTAAAAAATTAT
Found at i:28261574 original size:33 final size:33
Alignment explanation
Indices: 28261534--28261600 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
28261524 ATATTTTCTA
28261534 ATTTTAAGATATTTATTAAAAAATTATATATTT
1 ATTTTAAGATATTTATTAAAAAATTATATATTT
28261567 ATTTTAAGATATTTATTAAAAAATTATATATTT
1 ATTTTAAGATATTTATTAAAAAATTATATATTT
28261600 A
1 A
28261601 AAGATTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (33 bp):
ATTTTAAGATATTTATTAAAAAATTATATATTT
Found at i:28261604 original size:29 final size:29
Alignment explanation
Indices: 28261534--28261611 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 29
28261524 ATATTTTCTA
*
28261534 ATTTTAAGATATTTATTAAAAAATTATAT
1 ATTTAAAGATATTTATTAAAAAATTATAT
28261563 ATTTATTTTAAGATATTTATTAAAAAATTATAT
1 ATTTA----AAGATATTTATTAAAAAATTATAT
28261596 ATTTAAAGATTATTTA
1 ATTTAAAGA-TATTTA
28261612 ATTATACAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
29 8 0.19
30 6 0.14
33 29 0.67
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (29 bp):
ATTTAAAGATATTTATTAAAAAATTATAT
Found at i:28263430 original size:25 final size:25
Alignment explanation
Indices: 28263402--28263449 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
28263392 TCTTACTTAA
28263402 AAATTTTATAAAAATTT-ATCATTTG
1 AAATTTT-TAAAAATTTCATCATTTG
*
28263427 AAATTTTTATAAATTTCATCATT
1 AAATTTTTAAAAATTTCATCATT
28263450 GGATAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (25 bp):
AAATTTTTAAAAATTTCATCATTTG
Found at i:28263457 original size:26 final size:25
Alignment explanation
Indices: 28263402--28263457 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
28263392 TCTTACTTAA
*
28263402 AAATTTTATAAAAATTTATCATTTG
1 AAATTTTATAAAAATTTATCATTGG
*
28263427 AAATTTT-TATAAATTTCATCATTGG
1 AAATTTTATAAAAATTT-ATCATTGG
28263452 ATAATT
1 A-AATT
28263458 AATATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 8 0.30
25 15 0.56
26 4 0.15
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.48
Consensus pattern (25 bp):
AAATTTTATAAAAATTTATCATTGG
Found at i:28264316 original size:3 final size:3
Alignment explanation
Indices: 28264296--28264394 Score: 66
Period size: 3 Copynumber: 34.0 Consensus size: 3
28264286 ACAAGAAAAG
* * *
28264296 ATA A-A ATA ATA A-A A-A ATA ATA AAA ATA ATG ATA ATA ATA ATA AAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
28264341 ATAA ATA ATA A-A CAAA AAA ATA ATA ATG CTA ATA ATA ATAA ATA A-A
1 AT-A ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
28264387 ATA A-A ATA
1 ATA ATA ATA
28264395 TGGGTTTATT
Statistics
Matches: 77, Mismatches: 11, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
2 11 0.14
3 59 0.77
4 7 0.09
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (3 bp):
ATA
Found at i:28264363 original size:31 final size:32
Alignment explanation
Indices: 28264286--28264367 Score: 82
Period size: 34 Copynumber: 2.5 Consensus size: 32
28264276 ATTAATCAAG
28264286 ACAAGAAAAGATAA-AATAATAAAAAATAATAA
1 ACAAGAAAA-ATAATAATAATAAAAAATAATAA
*
28264318 A-AATAATGATAATAATAATAA-AAATAAATAATAA
1 ACAAGAA--A-AATAATAATAATAAA-AAATAATAA
28264352 ACAA-AAAAATAATAAT
1 ACAAGAAAAATAATAAT
28264368 GCTAATAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
31 13 0.30
32 2 0.05
33 8 0.19
34 18 0.42
35 2 0.05
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (32 bp):
ACAAGAAAAATAATAATAATAAAAAATAATAA
Found at i:28264378 original size:34 final size:34
Alignment explanation
Indices: 28264296--28264394 Score: 94
Period size: 34 Copynumber: 2.8 Consensus size: 34
28264286 ACAAGAAAAG
* **
28264296 ATAA-AATAATAAAAAATAATAAAAATAATGATA
1 ATAATAATAATAATAAATAATAAAAATAAAAATA
*
28264329 ATAATAATAAAAATAAATAATAAACAA-AAAAATA
1 ATAATAATAATAATAAATAATAAA-AATAAAAATA
*
28264363 ATAATGCTAATAATAATAAATAAAATAAAATA
1 ATAA---TAATAATAATAAATAATA-AAAATA
28264395 TGGGTTTATT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
33 4 0.08
34 26 0.49
35 2 0.04
37 18 0.34
38 3 0.06
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (34 bp):
ATAATAATAATAATAAATAATAAAAATAAAAATA
Found at i:28264679 original size:44 final size:45
Alignment explanation
Indices: 28264577--28264680 Score: 122
Period size: 45 Copynumber: 2.3 Consensus size: 45
28264567 AACTTGATCG
* * * *
28264577 AAGCTCCTCTAATCAGAGTCTCAACGACTTTTGAAAAGATAAACA
1 AAGCTCATCTAAGCAGAGGCTCAACGACTTTGGAAAAGATAAACA
*
28264622 AAGCTCATCTAAGCAGAGGCTCAATGACTTTGGACAAA-A-AAACA
1 AAGCTCATCTAAGCAGAGGCTCAACGACTTTGGA-AAAGATAAACA
* *
28264666 AAGCTCTTTTAAGCA
1 AAGCTCATCTAAGCA
28264681 AAAGCACCAC
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 18 0.35
45 30 0.59
46 3 0.06
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.23
Consensus pattern (45 bp):
AAGCTCATCTAAGCAGAGGCTCAACGACTTTGGAAAAGATAAACA
Found at i:28264867 original size:44 final size:44
Alignment explanation
Indices: 28264699--28265030 Score: 369
Period size: 44 Copynumber: 7.7 Consensus size: 44
28264689 ACAATTTTGG
* * *
28264699 AAATAAATTGCTCCTTTAAACAGAAGC-ACCACAA-ATTTG--A
1 AAATAAATTGCTCCTCTAAACAGAGGCAACCACAACTTTTGAAA
* * * *
28264739 AAATAAATTGCTTCTTTAAACAGAGTC-ACCATAACTTTTG--A
1 AAATAAATTGCTCCTCTAAACAGAGGCAACCACAACTTTTGAAA
* * * *
28264780 AAATAAATTGTTCCTTTATATAGAGGC-ACCACAACTTTTGAAA
1 AAATAAATTGCTCCTCTAAACAGAGGCAACCACAACTTTTGAAA
* *
28264823 AAATAAATTGCTCCTCTAAACAGAGGTAACCACGACTTTTGAAAAA
1 AAATAAATTGCTCCTCTAAACAGAGGCAACCACAACTTTTG--AAA
* *
28264869 AAATAAATTGCTTCTCTAAATAGAGGCAACCACAACTTTTGAAAA
1 AAATAAATTGCTCCTCTAAACAGAGGCAACCACAACTTTTG-AAA
*
28264914 AAATAAATTGCTTCTCT-AACTAGAGGCAACCACAAC-TTTGAAAA
1 AAATAAATTGCTCCTCTAAAC-AGAGGCAACCACAACTTTTG-AAA
* * *
28264958 AAATAAATTGCTCCTCTAAACAAAGGCAACCACGACTTTTGGAA
1 AAATAAATTGCTCCTCTAAACAGAGGCAACCACAACTTTTGAAA
*
28265002 AAATAAATTGCTCTTCTAAACAGAGGCAA
1 AAATAAATTGCTCCTCTAAACAGAGGCAA
28265031 AAAAATAAAT
Statistics
Matches: 255, Mismatches: 28, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
40 30 0.12
41 39 0.15
43 23 0.09
44 80 0.31
45 43 0.17
46 40 0.16
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (44 bp):
AAATAAATTGCTCCTCTAAACAGAGGCAACCACAACTTTTGAAA
Found at i:28264914 original size:89 final size:88
Alignment explanation
Indices: 28264699--28265027 Score: 370
Period size: 89 Copynumber: 3.8 Consensus size: 88
28264689 ACAATTTTGG
* * * * *
28264699 AAATAAATTGCTCCTTTAAACAGAAGCACCACAA-ATTTG--AAAATAAATTGCTTCTTTAAACA
1 AAATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTTGAAAAAATAAATTGCTCCTCTAAACA
* *
28264761 GA-GTCACCATAACTTTTG---A
66 GAGGTAACCACAACTTTTGAAAA
* * * *
28264780 AAATAAATTGTTCCTTTATATAGAGGCACCACAACTTTTGAAAAAATAAATTGCTCCTCTAAACA
1 AAATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTTGAAAAAATAAATTGCTCCTCTAAACA
*
28264845 GAGGTAACCACGACTTTTGAAAAA
66 GAGGTAACCACAACTTTTG-AAAA
* * *
28264869 AAATAAATTGCTTCTCTAAATAGAGGCAACCACAACTTTTGAAAAAAATAAATTGCTTCTCT-AA
1 AAATAAATTGCTCCTCTAAACAGAGGC-ACCACAACTTTTG-AAAAAATAAATTGCTCCTCTAAA
*
28264933 CTAGAGGCAACCACAAC-TTTGAAAA
64 C-AGAGGTAACCACAACTTTTGAAAA
* * * *
28264958 AAATAAATTGCTCCTCTAAACAAAGGCAACCACGACTTTTGGAAAAATAAATTGCTCTTCTAAAC
1 AAATAAATTGCTCCTCTAAACAGAGGC-ACCACAACTTTTGAAAAAATAAATTGCTCCTCTAAAC
28265023 AGAGG
65 AGAGG
28265028 CAAAAAAATA
Statistics
Matches: 212, Mismatches: 24, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
81 30 0.14
82 4 0.02
84 23 0.11
85 13 0.06
88 22 0.10
89 68 0.32
90 20 0.09
91 32 0.15
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (88 bp):
AAATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTTGAAAAAATAAATTGCTCCTCTAAACA
GAGGTAACCACAACTTTTGAAAA
Found at i:28265036 original size:31 final size:31
Alignment explanation
Indices: 28265000--28265061 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
28264990 CGACTTTTGG
*
28265000 AAAAATAAATTGCT-CTTCTAAACAGAGGCAA
1 AAAAATAAATTACTCCTT-TAAACAGAGGCAA
28265031 AAAAATAAATTACTCCTTTAAACAGAGGCAA
1 AAAAATAAATTACTCCTTTAAACAGAGGCAA
28265062 CCATGACTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.23
Consensus pattern (31 bp):
AAAAATAAATTACTCCTTTAAACAGAGGCAA
Found at i:28265039 original size:75 final size:75
Alignment explanation
Indices: 28264954--28265102 Score: 226
Period size: 75 Copynumber: 2.0 Consensus size: 75
28264944 CACAACTTTG
* * *
28264954 AAAAAAATAAATTGCTCCTCTAAACAAAGGCAACCACGACTTTTGGAAAAATAAATTGCTCTTCT
1 AAAAAAATAAATTACTCCTCTAAACAAAGGCAACCACGACTTTTGAAAAAATAAATTGCTCCTCT
28265019 AAACAGAGGC
66 AAACAGAGGC
* * * *
28265029 AAAAAAATAAATTACTCCTTTAAACAGAGGCAACCATGACTTTTGAAAAAATAAATTTCTCCTCT
1 AAAAAAATAAATTACTCCTCTAAACAAAGGCAACCACGACTTTTGAAAAAATAAATTGCTCCTCT
*
28265094 AAATAGAGG
66 AAACAGAGG
28265103 TAACCACGAC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 66 1.00
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.25
Consensus pattern (75 bp):
AAAAAAATAAATTACTCCTCTAAACAAAGGCAACCACGACTTTTGAAAAAATAAATTGCTCCTCT
AAACAGAGGC
Found at i:28265102 original size:44 final size:44
Alignment explanation
Indices: 28265029--28265129 Score: 139
Period size: 44 Copynumber: 2.3 Consensus size: 44
28265019 AAACAGAGGC
* * *
28265029 AAAAAAATAAATTACTCCTTTAAACAGAGGCAACCATGACTTTT
1 AAAAAAATAAATTACTCCTCTAAACAGAGGCAACCACGACTTTA
* * * *
28265073 GAAAAAATAAATTTCTCCTCTAAATAGAGGTAACCACGACTTTA
1 AAAAAAATAAATTACTCCTCTAAACAGAGGCAACCACGACTTTA
28265117 AAAAAAATAAATT
1 AAAAAAATAAATT
28265130 GCTCATCGAC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.49, C:0.16, G:0.09, T:0.27
Consensus pattern (44 bp):
AAAAAAATAAATTACTCCTCTAAACAGAGGCAACCACGACTTTA
Found at i:28265108 original size:119 final size:119
Alignment explanation
Indices: 28264910--28265133 Score: 308
Period size: 119 Copynumber: 1.9 Consensus size: 119
28264900 ACAACTTTTG
* *
28264910 AAAAAAATAAATTGCTTCTCTAACTAGAGGCAACCACAACTTTGAAAAAAATAAATTGCTCCTCT
1 AAAAAAATAAATTACTCCTCTAACTAGAGGCAACCACAACTTTGAAAAAAATAAATTGCTCCTCT
***
28264975 AAACAAAGGCAACCACGACTTTTGGAAAAATAAATTGCTCTTCTAAACAGAGGC
66 AAACAAAGGCAACCACGACTTTAAAAAAAATAAATTGCTCTTCTAAACAGAGGC
* ** *
28265029 AAAAAAATAAATTACTCCTTTAAAC-AGAGGCAACCATGACTTTTG-AAAAAATAAATTTCTCCT
1 AAAAAAATAAATTACTCCTCT-AACTAGAGGCAACCACAAC-TTTGAAAAAAATAAATTGCTCCT
* * *
28265092 CTAAATAGAGGTAACCACGACTTTAAAAAAAATAAATTGCTC
64 CTAAACAAAGGCAACCACGACTTTAAAAAAAATAAATTGCTC
28265134 ATCGACAATC
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
119 84 0.92
120 7 0.08
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.25
Consensus pattern (119 bp):
AAAAAAATAAATTACTCCTCTAACTAGAGGCAACCACAACTTTGAAAAAAATAAATTGCTCCTCT
AAACAAAGGCAACCACGACTTTAAAAAAAATAAATTGCTCTTCTAAACAGAGGC
Found at i:28265425 original size:20 final size:20
Alignment explanation
Indices: 28265400--28265440 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
28265390 CACATCCAGA
*
28265400 AGTTCAAAGCTTCTCATTTG
1 AGTTCAAAGCTTCACATTTG
*
28265420 AGTTCAAAGGTTCACATTTG
1 AGTTCAAAGCTTCACATTTG
28265440 A
1 A
28265441 TAAATTTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (20 bp):
AGTTCAAAGCTTCACATTTG
Found at i:28265534 original size:20 final size:20
Alignment explanation
Indices: 28265506--28265545 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28265496 CACATCGAAA
* *
28265506 AGTTTAAAGCTTCTCATTTG
1 AGTTCAAAGCTTCACATTTG
*
28265526 AGTTCAAAGGTTCACATTTG
1 AGTTCAAAGCTTCACATTTG
28265546 TTAAAACTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (20 bp):
AGTTCAAAGCTTCACATTTG
Found at i:28265540 original size:42 final size:42
Alignment explanation
Indices: 28265450--28265542 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 42
28265440 ATAAATTTAG
* * ***
28265450 GGTTCACATCCAAAAGTTTAAGCTTTTCATTCGAATTTTGGA
1 GGTTCACATCCAAAAGTTTAAGCTTCTCATTCGAAGTTCAAA
* * *
28265492 GATTCACATCGAAAAGTTTAAAGCTTCTCATTTG-AGTTCAAA
1 GGTTCACATCCAAAAGTTT-AAGCTTCTCATTCGAAGTTCAAA
28265534 GGTTCACAT
1 GGTTCACAT
28265543 TTGTTAAAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
42 29 0.71
43 12 0.29
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (42 bp):
GGTTCACATCCAAAAGTTTAAGCTTCTCATTCGAAGTTCAAA
Found at i:28265652 original size:48 final size:49
Alignment explanation
Indices: 28265570--28265665 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 49
28265560 TTCACTTCTA
*
28265570 AGTTCAAAGTTTCTCATTCAAAAATTTAAAGATTCGCATCCAAAAGTTG
1 AGTTCAAAGTTTCTCATTCAAAAATTTAAAGATTCCCATCCAAAAGTTG
* *
28265619 AGTTCAAAGCTTT-TCATT-TAAAATTTGAAGATTCCCATCCAAAAGTT
1 AGTTCAAAG-TTTCTCATTCAAAAATTTAAAGATTCCCATCCAAAAGTT
28265666 CAAATATTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
48 26 0.60
49 14 0.33
50 3 0.07
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (49 bp):
AGTTCAAAGTTTCTCATTCAAAAATTTAAAGATTCCCATCCAAAAGTTG
Found at i:28266798 original size:10 final size:10
Alignment explanation
Indices: 28266783--28266839 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
28266773 CTTTTTCTCC
28266783 TTTCATCTTT
1 TTTCATCTTT
*
28266793 TTTCATTTTT
1 TTTCATCTTT
*
28266803 TTTCAT-TTG
1 TTTCATCTTT
28266812 TTT--TCTTT
1 TTTCATCTTT
*
28266820 TTTCCT-TTT
1 TTTCATCTTT
28266829 TTTCATTCTTT
1 TTTCA-TCTTT
28266840 CACCCATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
7 1 0.03
8 5 0.13
9 12 0.32
10 17 0.45
11 3 0.08
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.75
Consensus pattern (10 bp):
TTTCATCTTT
Found at i:28273487 original size:22 final size:22
Alignment explanation
Indices: 28273462--28273511 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
28273452 TTTAATACTA
28273462 AAAAAACTCAAAAAAAATAAAT
1 AAAAAACTCAAAAAAAATAAAT
** * *
28273484 AAAATGCTTAAATAAAATAAAT
1 AAAAAACTCAAAAAAAATAAAT
28273506 AAAAAA
1 AAAAAA
28273512 ATACCATAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.18
Consensus pattern (22 bp):
AAAAAACTCAAAAAAAATAAAT
Found at i:28274294 original size:3 final size:3
Alignment explanation
Indices: 28274277--28274363 Score: 60
Period size: 3 Copynumber: 30.0 Consensus size: 3
28274267 AAAAGAAAAG
*
28274277 ATA A-A ATA A-A ATA ATA ATA ATA GTA ATA A-A ATAA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
* * * *
28274319 CAAA AAA ATA ATG CTA ATA ATA ATA ATAA ATA A-A ATA A-A ATA ATA
1 -ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA
28274364 TGGATCTATC
Statistics
Matches: 68, Mismatches: 7, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
2 11 0.16
3 50 0.74
4 7 0.10
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (3 bp):
ATA
Found at i:28278687 original size:2 final size:2
Alignment explanation
Indices: 28278682--28278753 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
28278672 AATATATATT
28278682 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
28278724 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
28278754 AGAGAGAGAG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:28278758 original size:2 final size:2
Alignment explanation
Indices: 28278753--28278796 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
28278743 GTGTGTGTGT
28278753 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
28278795 GA
1 GA
28278797 TTGTGAGGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28280629 original size:16 final size:17
Alignment explanation
Indices: 28280595--28280631 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
28280585 AAAATTAATT
28280595 ATTTTTTGAAAAATCAA
1 ATTTTTTGAAAAATCAA
28280612 ATTTTTTGAAAAAT-AA
1 ATTTTTTGAAAAATCAA
28280628 ATTT
1 ATTT
28280632 AACTCTTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (17 bp):
ATTTTTTGAAAAATCAA
Found at i:28282204 original size:2 final size:2
Alignment explanation
Indices: 28282199--28282236 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28282189 CTCTCTCTTG
28282199 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
28282237 CAAGAACAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28282271 original size:2 final size:2
Alignment explanation
Indices: 28282264--28282328 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
28282254 GGTTGGAACG
28282264 TC TC TC TC 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
28282306 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
28282329 ATATATATAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:28282333 original size:2 final size:2
Alignment explanation
Indices: 28282328--28282357 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28282318 TCTCTCTCTC
28282328 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28282358 AATCATGAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28284790 original size:18 final size:18
Alignment explanation
Indices: 28284748--28284791 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
28284738 AATTTTATTC
28284748 AAATTTAA-AAAAATATA
1 AAATTTAATAAAAATATA
*
28284765 AAAATTAATAAAAATATA
1 AAATTTAATAAAAATATA
*
28284783 TAATTTAAT
1 AAATTTAAT
28284792 TCAATGTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTTAATAAAAATATA
Found at i:28293640 original size:15 final size:16
Alignment explanation
Indices: 28293620--28293649 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28293610 AATGAAAACG
28293620 GAAATAGAA-ATTTAA
1 GAAATAGAATATTTAA
28293635 GAAATAGAATATTTA
1 GAAATAGAATATTTA
28293650 CCAGGCTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (16 bp):
GAAATAGAATATTTAA
Found at i:28301094 original size:104 final size:106
Alignment explanation
Indices: 28300958--28301284 Score: 313
Period size: 104 Copynumber: 2.9 Consensus size: 106
28300948 TCCTCTCTCC
* * *
28300958 GTCTCTCTTAATATATATATTTTTTTTGCAAACAAGGGCTGCTCAAAAGGGTGTCTGTCTCTCTT
1 GTCTCTCTTAATATATATATTTTTTTTGCAAACAAGGGCTACTCAAAAGGGGGTCTGTCACTCTT
* *
28301023 AATATATATTTTTTGCAAATAAGGGCTGCTCAAAAGGACTTCT
66 AATAT-TATTTTTTGCAAACAA-GGCTACTCAAAAGGACTTCT
28301066 GTCTCTCTT-A-ATAT-T-TTTTTTTTGCAAACAAGGGCTACTCAAAAGGGGGTCTGTCACTCTT
1 GTCTCTCTTAATATATATATTTTTTTTGCAAACAAGGGCTACTCAAAAGGGGGTCTGTCACTCTT
* *
28301127 AATATTTTTTTTTGCAAACAAGGCTACTCAAAAGGGA-GTCT
66 AATATTATTTTTTGCAAACAAGGCTACTCAAAA-GGACTTCT
* * *
28301168 GTCTCTGCTACTCAAAAGGAGGTCTGTCACTATTTTTTTTTTGCAAACAAGGGCTACTCAAAGGG
1 GTCTCT-CT--T----A--A--TATAT-A-TA-TTT-TTTTTGCAAACAAGGGCTACTCAAAAGG
* * *
28301233 GGGTCTTGTCTCTCTTAATTTTTTTTTTTTGCAAACAAGGGCTACTCAAAAG
51 GGGTC-TGTCACTCTTAA-TATTATTTTTTGCAAACAA-GGCTACTCAAAAG
28301285 AGAGAATTGC
Statistics
Matches: 184, Mismatches: 12, Indels: 31
0.81 0.05 0.14
Matches are distributed among these distances:
102 20 0.11
103 19 0.10
104 48 0.26
105 2 0.01
106 4 0.02
107 1 0.01
108 9 0.05
112 1 0.01
115 2 0.01
118 1 0.01
120 3 0.02
121 32 0.17
122 11 0.06
123 19 0.10
124 12 0.07
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (106 bp):
GTCTCTCTTAATATATATATTTTTTTTGCAAACAAGGGCTACTCAAAAGGGGGTCTGTCACTCTT
AATATTATTTTTTGCAAACAAGGCTACTCAAAAGGACTTCT
Found at i:28301156 original size:50 final size:52
Alignment explanation
Indices: 28300972--28301173 Score: 293
Period size: 52 Copynumber: 3.9 Consensus size: 52
28300962 CTCTTAATAT
* *
28300972 ATATATTTTTTTTGCAAACAAGGGCTGCTCAAAAGGGTGTCTGTCTCTCTTA
1 ATATATTTTTTTTGCAAACAAGGGCTACTCAAAAGGGAGTCTGTCTCTCTTA
* * * *
28301024 ATATATATTTTTTGCAAATAAGGGCTGCTCAAAA-GGACTTCTGTCTCTCTTA
1 ATATATTTTTTTTGCAAACAAGGGCTACTCAAAAGGGA-GTCTGTCTCTCTTA
* * *
28301076 ATATTTTTTTTTTGCAAACAAGGGCTACTCAAAAGGGGGTCTGTCACTCTTA
1 ATATATTTTTTTTGCAAACAAGGGCTACTCAAAAGGGAGTCTGTCTCTCTTA
28301128 ATAT-TTTTTTTTGCAAACAA-GGCTACTCAAAAGGGAGTCTGTCTCT
1 ATATATTTTTTTTGCAAACAAGGGCTACTCAAAAGGGAGTCTGTCTCT
28301174 GCTACTCAAA
Statistics
Matches: 135, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
50 24 0.18
51 18 0.13
52 91 0.67
53 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (52 bp):
ATATATTTTTTTTGCAAACAAGGGCTACTCAAAAGGGAGTCTGTCTCTCTTA
Found at i:28304243 original size:3 final size:3
Alignment explanation
Indices: 28304237--28304310 Score: 75
Period size: 3 Copynumber: 25.7 Consensus size: 3
28304227 GATTTTCATC
* * *
28304237 ATT ATT ATT ACT ATT ATT -TT -TT ATT AGT ATT ATT GTTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
*
28304281 ATT A-T AGT A-T ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
28304311 AGTATAGCTT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
2 8 0.13
3 51 0.84
4 2 0.03
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:28304262 original size:16 final size:16
Alignment explanation
Indices: 28304241--28304328 Score: 72
Period size: 16 Copynumber: 5.6 Consensus size: 16
28304231 TTCATCATTA
*
28304241 TTATTACTATTATTTT
1 TTATTACTATTATTGT
*
28304257 TTATTAGTATTATTGT
1 TTATTACTATTATTGT
* *
28304273 TTATTATTATTATAGT
1 TTATTACTATTATTGT
* * *
28304289 ATATTATTATTATT-A
1 TTATTACTATTATTGT
* * *
28304304 TTATTA-TAGTATAGC
1 TTATTACTATTATTGT
28304319 TTATTACTAT
1 TTATTACTAT
28304329 AGTGTAGTAA
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
14 5 0.09
15 11 0.19
16 42 0.72
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (16 bp):
TTATTACTATTATTGT
Found at i:28304262 original size:19 final size:19
Alignment explanation
Indices: 28304237--28304310 Score: 87
Period size: 19 Copynumber: 3.9 Consensus size: 19
28304227 GATTTTCATC
*
28304237 ATTATTATTACTATTATTT
1 ATTATTATTATTATTATTT
* * *
28304256 TTTATTAGTATTATTGTTT
1 ATTATTATTATTATTATTT
*
28304275 ATTATTATTA-TAGTATATT
1 ATTATTATTATTATTAT-TT
28304294 ATTATTATTATTATTAT
1 ATTATTATTATTATTAT
28304311 AGTATAGCTT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
18 4 0.09
19 35 0.80
20 5 0.11
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (19 bp):
ATTATTATTATTATTATTT
Found at i:28304370 original size:3 final size:3
Alignment explanation
Indices: 28304353--28304394 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
28304343 CGTCGATCAG
28304353 TAT TAT TACT T-T TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
28304395 TATTTTTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 30 0.83
4 2 0.06
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:28304397 original size:9 final size:8
Alignment explanation
Indices: 28304355--28304400 Score: 56
Period size: 9 Copynumber: 5.2 Consensus size: 8
28304345 TCGATCAGTA
28304355 TTATTACTT
1 TTATTA-TT
28304364 TTATTATT
1 TTATTATT
28304372 ATTATTATT
1 -TTATTATT
28304381 ATTATTATT
1 -TTATTATT
28304390 TTATTTATT
1 TTA-TTATT
28304399 TT
1 TT
28304401 TTTCCTAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
8 5 0.14
9 30 0.86
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (8 bp):
TTATTATT
Found at i:28304898 original size:20 final size:20
Alignment explanation
Indices: 28304873--28304921 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
28304863 GGATGAACTA
28304873 TGAATTTTTC-GACAAAAGGT
1 TGAATTTTTCAG-CAAAAGGT
28304893 TGAATTTTTCAGCAAAAGGT
1 TGAATTTTTCAGCAAAAGGT
28304913 TGAATTTTT
1 TGAATTTTT
28304922 TGACCACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (20 bp):
TGAATTTTTCAGCAAAAGGT
Found at i:28305239 original size:6 final size:6
Alignment explanation
Indices: 28305230--28305328 Score: 64
Period size: 6 Copynumber: 16.3 Consensus size: 6
28305220 AGGTTTTCTT
*
28305230 TTTTTA -TTTTA ATTTTA TTTTCTA TTTTTA --TTTA TTATTTA TTTTATA
1 TTTTTA TTTTTA TTTTTA TTTT-TA TTTTTA TTTTTA TT-TTTA TTTT-TA
* * * *
28305278 TTTTGA -TTTTA ATTTTA TTTTCA GTTTTA TTTATT- TCATTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT-TTA T--TTTTA TTTTTA
28305327 TT
1 TT
28305329 GAGTGATTTG
Statistics
Matches: 74, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
4 4 0.05
5 9 0.12
6 36 0.49
7 22 0.30
8 3 0.04
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (6 bp):
TTTTTA
Found at i:28305247 original size:11 final size:11
Alignment explanation
Indices: 28305231--28305328 Score: 76
Period size: 12 Copynumber: 8.6 Consensus size: 11
28305221 GGTTTTCTTT
28305231 TTTTATTTTAA
1 TTTTATTTTAA
*
28305242 TTTTATTTTCTA
1 TTTTATTTT-AA
*
28305254 TTTT-TATTTAT
1 TTTTAT-TTTAA
28305265 TATTTATTTTATA
1 T-TTTATTTTA-A
28305278 TTTTGATTTTAA
1 TTTT-ATTTTAA
*
28305290 TTTTATTTTCAG
1 TTTTATTTT-AA
28305302 TTTTA-TTT-A
1 TTTTATTTTAA
* *
28305311 TTTCATTTTAT
1 TTTTATTTTAA
28305322 TTTTATT
1 TTTTATT
28305329 GAGTGATTTG
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
9 4 0.06
10 3 0.04
11 25 0.36
12 29 0.42
13 8 0.12
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.73
Consensus pattern (11 bp):
TTTTATTTTAA
Found at i:28305257 original size:24 final size:24
Alignment explanation
Indices: 28305223--28305328 Score: 107
Period size: 24 Copynumber: 4.6 Consensus size: 24
28305213 GAATCGTAGG
*
28305223 TTTTCTTTTTTTATTTTAATTTTA
1 TTTTCTATTTTTATTTTAATTTTA
*
28305247 TTTTCTATTTTTA-TTTATTATTTA
1 TTTTCTATTTTTATTTTAAT-TTTA
* *
28305271 TTTTATATTTTGATTTTAATTTTA
1 TTTTCTATTTTTATTTTAATTTTA
* *
28305295 TTTTC-AGTTTTA-TTT-ATTTCA
1 TTTTCTATTTTTATTTTAATTTTA
28305316 -TTT-TATTTTTATT
1 TTTTCTATTTTTATT
28305329 GAGTGATTTG
Statistics
Matches: 68, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
20 9 0.13
21 6 0.09
22 3 0.04
23 10 0.15
24 35 0.51
25 5 0.07
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTTCTATTTTTATTTTAATTTTA
Found at i:28305347 original size:51 final size:48
Alignment explanation
Indices: 28305235--28305329 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 48
28305225 TTCTTTTTTT
* *
28305235 ATTTTAATTTTATTTTCTATTTTTATTTATTATTTATTTTATATTTTG
1 ATTTTAATTTTATTTTCTAGTTTTATTTATTATTTATTTTATATTGTG
28305283 ATTTTAATTTTATTTTC-AGTTTTATTTATTTCATTTTATTTT-TATTG
1 ATTTTAATTTTATTTTCTAGTTTTATTTA-TT-A-TTTATTTTATATTG
28305330 AGTGATTTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
47 10 0.24
48 19 0.45
49 5 0.12
50 8 0.19
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (48 bp):
ATTTTAATTTTATTTTCTAGTTTTATTTATTATTTATTTTATATTGTG
Found at i:28305431 original size:31 final size:30
Alignment explanation
Indices: 28305379--28305436 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
28305369 TTTGGAAAAC
28305379 AAAAAAAAAATAATTAAAAAATAAATTTTA
1 AAAAAAAAAATAATTAAAAAATAAATTTTA
* *
28305409 AAAATAAAAAATCATTACAAAATAAATT
1 AAAA-AAAAAATAATTAAAAAATAAATT
28305437 CATGAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (30 bp):
AAAAAAAAAATAATTAAAAAATAAATTTTA
Found at i:28314650 original size:24 final size:25
Alignment explanation
Indices: 28314608--28314661 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
28314598 ATCCAAATAA
* *
28314608 TTTATTTTTTAGATATTAACTATCT
1 TTTATTTTTTAGATATTAAATATAT
* *
28314633 TTTATTTTTTA-TTTTTAAATATAT
1 TTTATTTTTTAGATATTAAATATAT
28314657 TTTAT
1 TTTAT
28314662 AAAATAAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTATTTTTTAGATATTAAATATAT
Found at i:28314845 original size:32 final size:31
Alignment explanation
Indices: 28314766--28314862 Score: 90
Period size: 32 Copynumber: 3.1 Consensus size: 31
28314756 TTACTTTTAA
* *
28314766 AAAAATTTTTGCATAATATTTTAAAATGATAT
1 AAAAATTTTTGCTTAAT-TTTTAAACTGATAT
* * **
28314798 -AGAGTTTTTATTTAATTTCTTAAACTGATAT
1 AAAAATTTTTGCTTAATTT-TTAAACTGATAT
28314829 AAAAATTTTTGCTTAATTTTTTAAACAT-ATAT
1 AAAAATTTTTGCTTAA-TTTTTAAAC-TGATAT
28314861 AA
1 AA
28314863 TTTTAACAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
30 2 0.04
31 22 0.43
32 23 0.45
33 4 0.08
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.47
Consensus pattern (31 bp):
AAAAATTTTTGCTTAATTTTTAAACTGATAT
Found at i:28320917 original size:10 final size:10
Alignment explanation
Indices: 28320904--28321030 Score: 73
Period size: 10 Copynumber: 12.5 Consensus size: 10
28320894 AAAAAGAAAC
28320904 TAAAAAATTT
1 TAAAAAATTT
*
28320914 TAAAAAACTTC
1 TAAAAAA-TTT
*
28320925 TAAACAATTT
1 TAAAAAATTT
* *
28320935 T-TAAATTTT
1 TAAAAAATTT
28320944 CTAAAAAA-TT
1 -TAAAAAATTT
*
28320954 CAAAACAA-TT
1 TAAAA-AATTT
* *
28320964 CAAAATAGTTT
1 TAAAA-AATTT
28320975 TAAAAAATTT
1 TAAAAAATTT
28320985 T-AAAAATTT
1 TAAAAAATTT
*
28320994 CTAAAAAAATT
1 -TAAAAAATTT
* *
28321005 CAAAACAATTC
1 TAAAA-AATTT
*
28321016 TAAAAAATTC
1 TAAAAAATTT
28321026 TAAAA
1 TAAAA
28321031 TTTTTTAAGT
Statistics
Matches: 91, Mismatches: 18, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
9 17 0.19
10 43 0.47
11 31 0.34
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (10 bp):
TAAAAAATTT
Found at i:28320998 original size:20 final size:21
Alignment explanation
Indices: 28320975--28321030 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
28320965 AAAATAGTTT
*
28320975 TAAAAAATTTT-AAAAATTTC
1 TAAAAAATTTTAAAAAAATTC
* * *
28320995 TAAAAAAATTCAAAACAATTC
1 TAAAAAATTTTAAAAAAATTC
*
28321016 TAAAAAATTCTAAAA
1 TAAAAAATTTTAAAA
28321031 TTTTTTAAGT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAAAATTTTAAAAAAATTC
Found at i:28321037 original size:51 final size:50
Alignment explanation
Indices: 28320905--28321038 Score: 157
Period size: 51 Copynumber: 2.7 Consensus size: 50
28320895 AAAAGAAACT
* *
28320905 AAAA-AATTTTAAAAAACTTCTAAACAATTTTT-AAATTTTCTAAAAAATTC
1 AAAACAATTCTAAAAAA-TTCTAAA-AATTTTTAAAAATTTCTAAAAAATTC
* * *
28320955 AAAACAATTC-AAAATAGTTTTAAAAAATTTTAAAAATTTCTAAAAAAATTC
1 AAAACAATTCTAAAA-AATTCTAAAAATTTTTAAAAATTTCT-AAAAAATTC
*
28321006 AAAACAATTCTAAAAAATTCTAAAATTTTTTAA
1 AAAACAATTCTAAAAAATTCTAAAAATTTTTAA
28321039 GTTTTATAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
49 6 0.09
50 22 0.31
51 38 0.54
52 4 0.06
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.36
Consensus pattern (50 bp):
AAAACAATTCTAAAAAATTCTAAAAATTTTTAAAAATTTCTAAAAAATTC
Found at i:28321051 original size:51 final size:50
Alignment explanation
Indices: 28320905--28321053 Score: 169
Period size: 50 Copynumber: 3.0 Consensus size: 50
28320895 AAAAGAAACT
*
28320905 AAAA-AATTTTAAAAAACTTCTAAACAATTTTTAAATTTTCT-AAAAAATTC
1 AAAACAATTCTAAAAAA-TTCTAAA-AATTTTTAAATTTTCTAAAAAAATTC
* * * *
28320955 AAAACAATTC-AAAATAGTTTTAAAAAATTTTAAAAATTTCTAAAAAAATTC
1 AAAACAATTCTAAAA-AATTCT-AAAAATTTTTAAATTTTCTAAAAAAATTC
* * *
28321006 AAAACAATTCTAAAAAATTCTAAAATTTTTTAAGTTTTATAAAAAAAT
1 AAAACAATTCTAAAAAATTCTAAAAATTTTTAAATTTTCTAAAAAAAT
28321054 AAAAAAATAT
Statistics
Matches: 82, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
50 47 0.57
51 31 0.38
52 4 0.05
ACGTcount: A:0.54, C:0.08, G:0.01, T:0.36
Consensus pattern (50 bp):
AAAACAATTCTAAAAAATTCTAAAAATTTTTAAATTTTCTAAAAAAATTC
Found at i:28321086 original size:26 final size:24
Alignment explanation
Indices: 28321048--28321113 Score: 60
Period size: 26 Copynumber: 2.6 Consensus size: 24
28321038 AGTTTTATAA
* *
28321048 AAAAATAAAAAAATATGAAATATTTT
1 AAAAATTATAAAATATG--ATATTTT
28321074 AAAAATTATAAAAATTATGATATTTT
1 AAAAATTAT-AAAA-TATGATATTTT
* *
28321100 CAAAATTTTAAAAT
1 AAAAATTATAAAAT
28321114 TTTTTAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
24 1 0.03
25 4 0.12
26 21 0.62
27 4 0.12
28 4 0.12
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (24 bp):
AAAAATTATAAAATATGATATTTT
Found at i:28321157 original size:21 final size:22
Alignment explanation
Indices: 28321133--28321173 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28321123 CTTTTAATAA
28321133 AAATT-CAAAAAAATGAAAATT
1 AAATTGCAAAAAAATGAAAATT
* *
28321154 AAATTGTAAAAAAATTAAAA
1 AAATTGCAAAAAAATGAAAA
28321174 AAATACAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.24
Consensus pattern (22 bp):
AAATTGCAAAAAAATGAAAATT
Found at i:28321314 original size:38 final size:37
Alignment explanation
Indices: 28321222--28321303 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 37
28321212 TAAATTTTTA
*
28321222 AAAAAAATTCTAAAAATTTTTAAACTTTTTTGAAAAATT
1 AAAAAATTTC-AAAAA-TTTTAAACTTTTTTGAAAAATT
**
28321261 AATTAATTTCAAAAATTTTAAA-TATTTTT-AAAAATT
1 AAAAAATTTCAAAAATTTTAAACT-TTTTTGAAAAATT
28321297 AAAAAAT
1 AAAAAAT
28321304 ATATGAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
36 13 0.35
37 12 0.32
38 5 0.14
39 7 0.19
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (37 bp):
AAAAAATTTCAAAAATTTTAAACTTTTTTGAAAAATT
Found at i:28321411 original size:26 final size:27
Alignment explanation
Indices: 28321382--28321437 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
28321372 AAATATATAT
*
28321382 AAAAAAT-AAAAAATTGTAGGATTTAA
1 AAAAAATAAAAAAATTGTAGAATTTAA
* *
28321408 AAAATATAAAAAAATTTTAGAATTTAA
1 AAAAAATAAAAAAATTGTAGAATTTAA
28321435 AAA
1 AAA
28321438 CAAAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (27 bp):
AAAAAATAAAAAAATTGTAGAATTTAA
Found at i:28321612 original size:9 final size:9
Alignment explanation
Indices: 28321580--28321683 Score: 65
Period size: 9 Copynumber: 11.7 Consensus size: 9
28321570 TAGCAAATTA
28321580 TTTTAGAATT
1 TTTTAGAA-T
*
28321590 TTTTAAAAT
1 TTTTAGAAT
*
28321599 ATTTAGAAT
1 TTTTAGAAT
28321608 TTTTAGAAT
1 TTTTAGAAT
* * *
28321617 TGCTGAAAAT
1 T-TTTAGAAT
28321627 TTTTAGAAT
1 TTTTAGAAT
28321636 TTTT----T
1 TTTTAGAAT
*
28321641 TTTCA-AAT
1 TTTTAGAAT
* *
28321649 TTTAAAAAT
1 TTTTAGAAT
28321658 GTTTTAGAATT
1 -TTTTAGAA-T
28321669 TTTTAGAAT
1 TTTTAGAAT
28321678 TTTTAG
1 TTTTAG
28321684 TGATGACATA
Statistics
Matches: 73, Mismatches: 14, Indels: 15
0.72 0.14 0.15
Matches are distributed among these distances:
5 4 0.05
8 5 0.07
9 36 0.49
10 27 0.37
11 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.54
Consensus pattern (9 bp):
TTTTAGAAT
Found at i:28321612 original size:28 final size:28
Alignment explanation
Indices: 28321580--28321639 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
28321570 TAGCAAATTA
** *
28321580 TTTTAGAATTTTTTAAAATATTTAGAAT
1 TTTTAGAATTGCTGAAAATATTTAGAAT
*
28321608 TTTTAGAATTGCTGAAAATTTTTAGAAT
1 TTTTAGAATTGCTGAAAATATTTAGAAT
28321636 TTTT
1 TTTT
28321640 TTTTCAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.53
Consensus pattern (28 bp):
TTTTAGAATTGCTGAAAATATTTAGAAT
Found at i:28321639 original size:10 final size:10
Alignment explanation
Indices: 28321575--28321681 Score: 58
Period size: 10 Copynumber: 10.7 Consensus size: 10
28321565 AGTTTTAGCA
28321575 AATTATTTTAG
1 AATT-TTTTAG
28321586 AATTTTTTA-
1 AATTTTTTAG
* *
28321595 AAATATTTAG
1 AATTTTTTAG
28321605 AA-TTTTTAG
1 AATTTTTTAG
** *
28321614 AATTGCTGA-
1 AATTTTTTAG
*
28321623 AAATTTTTAG
1 AATTTTTTAG
**
28321633 AATTTTTTTTTC
1 AA--TTTTTTAG
* * *
28321645 AAATTTTAAA
1 AATTTTTTAG
*
28321655 AATGTTTTAG
1 AATTTTTTAG
28321665 AATTTTTTAG
1 AATTTTTTAG
28321675 AATTTTT
1 AATTTTT
28321682 AGTGATGACA
Statistics
Matches: 69, Mismatches: 22, Indels: 11
0.68 0.22 0.11
Matches are distributed among these distances:
9 20 0.29
10 38 0.55
11 4 0.06
12 7 0.10
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (10 bp):
AATTTTTTAG
Found at i:28321681 original size:19 final size:19
Alignment explanation
Indices: 28321580--28321683 Score: 59
Period size: 19 Copynumber: 5.3 Consensus size: 19
28321570 TAGCAAATTA
* *
28321580 TTTTAGAATTTTTTAAAAT
1 TTTTAGAAATTTTTAGAAT
*
28321599 ATTTAG-AATTTTTAGAAT
1 TTTTAGAAATTTTTAGAAT
**
28321617 TGCT-GAAAATTTTTAGAATTTT
1 TTTTAG-AAATTTTTAGAA---T
** * *
28321639 TTTTTCAAATTTTAAAAAT
1 TTTTAGAAATTTTTAGAAT
*
28321658 GTTTTAGAATTTTTTAGAAT
1 -TTTTAGAAATTTTTAGAAT
28321678 TTTTAG
1 TTTTAG
28321684 TGATGACATA
Statistics
Matches: 62, Mismatches: 16, Indels: 14
0.67 0.17 0.15
Matches are distributed among these distances:
17 1 0.02
18 11 0.18
19 23 0.37
20 14 0.23
22 13 0.21
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.54
Consensus pattern (19 bp):
TTTTAGAAATTTTTAGAAT
Found at i:28322874 original size:2 final size:2
Alignment explanation
Indices: 28322861--28322890 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
28322851 TACTTACTTG
*
28322861 AT AT AT AC 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
28322891 CTTTTAATAT
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28324694 original size:2 final size:2
Alignment explanation
Indices: 28324681--28324720 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
28324671 TCCGTATTAG
* * *
28324681 AT AT AC AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28324721 TTGCTGACTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28325946 original size:4 final size:4
Alignment explanation
Indices: 28325937--28326006 Score: 52
Period size: 4 Copynumber: 17.0 Consensus size: 4
28325927 ATTCATCAAT
* * * *
28325937 TTTA TTTA TTTG TTTG TTTG TTTGT TTTA TTTTA TTTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTT-A TTTA -TTTA -TTTA TTTA TTTA TTTA
* *
28325988 TTAA TTT- GTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA
28326007 AATTTAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
3 2 0.04
4 42 0.75
5 12 0.21
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:28326340 original size:37 final size:38
Alignment explanation
Indices: 28326260--28326340 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 38
28326250 TAAAATGTAT
* ** **
28326260 TAAAATTTTGAGAAAAATAAAAACTATTTCAAAGATGA
1 TAAAATTTTGAAAAAAATAAAAACTATAACAAAGAAAA
28326298 T-AAATTTTGAAAATAAATAAAAA-TATAACAAA-AAAA
1 TAAAATTTTGAAAA-AAATAAAAACTATAACAAAGAAAA
28326334 TAAAATT
1 TAAAATT
28326341 CATAGAAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
36 3 0.08
37 23 0.64
38 10 0.28
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (38 bp):
TAAAATTTTGAAAAAAATAAAAACTATAACAAAGAAAA
Found at i:28337128 original size:22 final size:22
Alignment explanation
Indices: 28337096--28337138 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28337086 TTTTCTGTCT
*
28337096 TTAATTCTAGGGATACAAATAC
1 TTAATTCTAGGAATACAAATAC
*
28337118 TTAATTTTAGGAATACAAATA
1 TTAATTCTAGGAATACAAATA
28337139 TATACAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (22 bp):
TTAATTCTAGGAATACAAATAC
Found at i:28340346 original size:15 final size:15
Alignment explanation
Indices: 28340270--28340346 Score: 50
Period size: 15 Copynumber: 4.9 Consensus size: 15
28340260 TTATTAAAGT
*
28340270 ATATTGAAATTATTTA
1 ATATT-AAAATATTTA
* *
28340286 TTACTAAAAT-TATTA
1 ATATTAAAATAT-TTA
*
28340301 ATATTAAAAAATAATT-
1 ATATT--AAAATATTTA
28340317 ATATTTAATAATATTTA
1 ATA-TTAA-AATATTTA
28340334 ATATTAAAATATT
1 ATATTAAAATATT
28340347 ATATTAATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 15
0.68 0.10 0.22
Matches are distributed among these distances:
14 1 0.02
15 18 0.38
16 16 0.34
17 12 0.26
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (15 bp):
ATATTAAAATATTTA
Found at i:28340365 original size:33 final size:32
Alignment explanation
Indices: 28340298--28340367 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 32
28340288 ACTAAAATTA
*
28340298 TTAATATTAAAAAATAATTATATTTAATAATAT
1 TTAATATT-AAAAATAATTATATTAAATAATAT
28340331 TTAATATT-AAAAT-ATTATATTAATATAAACTAT
1 TTAATATTAAAAATAATTATATTAA-AT-AA-TAT
28340364 TTAA
1 TTAA
28340368 AATGAAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
30 9 0.27
31 7 0.21
32 2 0.06
33 15 0.45
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (32 bp):
TTAATATTAAAAATAATTATATTAAATAATAT
Found at i:28340481 original size:15 final size:15
Alignment explanation
Indices: 28340461--28340501 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
28340451 TTAAAATAAT
28340461 AATATTTATTATTAA
1 AATATTTATTATTAA
*
28340476 AATATTTCTACTATTAA
1 AATA-TT-TATTATTAA
28340493 AATATTTAT
1 AATATTTAT
28340502 ATTTTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 6 0.27
16 4 0.18
17 12 0.55
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (15 bp):
AATATTTATTATTAA
Found at i:28340895 original size:24 final size:24
Alignment explanation
Indices: 28340850--28340895 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
28340840 TGCTAATTTT
*
28340850 TATTTTTAATTAAAATTAAATAAA
1 TATTTTTAATTAAAATAAAATAAA
*
28340874 TATTTTT-ATTAATATAATAATA
1 TATTTTTAATTAAAATAA-AATA
28340896 TTTTAAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TATTTTTAATTAAAATAAAATAAA
Found at i:28341254 original size:22 final size:23
Alignment explanation
Indices: 28341228--28341271 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 23
28341218 ACAGTATCTC
28341228 ATTTTTTA-TAATCAAT-AAATT
1 ATTTTTTATTAATCAATCAAATT
28341249 ATTTTTTATTAATCAATCAAATT
1 ATTTTTTATTAATCAATCAAATT
28341272 TTTACCCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.38
22 8 0.38
23 5 0.24
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTTTTTATTAATCAATCAAATT
Found at i:28346015 original size:29 final size:29
Alignment explanation
Indices: 28345963--28346019 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
28345953 AAGAGGAAAT
* *
28345963 CATGTTAATTTACTTCGCAGTGAGTAATC
1 CATGTTAATTTACTTCGAAATGAGTAATC
*
28345992 CATGTTAATTTACTTTGAAATGAGTAAT
1 CATGTTAATTTACTTCGAAATGAGTAAT
28346020 TATGATCGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (29 bp):
CATGTTAATTTACTTCGAAATGAGTAATC
Found at i:28351630 original size:12 final size:13
Alignment explanation
Indices: 28351608--28351636 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28351598 TTTCTATTGG
28351608 AAAAAGTAAAAGC
1 AAAAAGTAAAAGC
28351621 AAAAAG-AAAAGC
1 AAAAAGTAAAAGC
28351633 AAAA
1 AAAA
28351637 GCACTGACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.76, C:0.07, G:0.14, T:0.03
Consensus pattern (13 bp):
AAAAAGTAAAAGC
Found at i:28369566 original size:27 final size:27
Alignment explanation
Indices: 28369523--28369679 Score: 185
Period size: 27 Copynumber: 5.8 Consensus size: 27
28369513 GGAGGTGATC
28369523 ACTGATGATG-AGATTGATCAGGAGTTG
1 ACTGATGATGAAG-TTGATCAGGAGTTG
*
28369550 ACTGATGATGAAGTTGATCATGAGTTG
1 ACTGATGATGAAGTTGATCAGGAGTTG
* *
28369577 ACTGATGATGAGGTTGATCAGCAGTTG
1 ACTGATGATGAAGTTGATCAGGAGTTG
* *
28369604 ATTGATGATG-AGTTTGATCA-GATGGTG
1 ACTGATGATGAAG-TTGATCAGGA-GTTG
* * *
28369631 ACTGATGATGAGGTTGATCAGGAGCTA
1 ACTGATGATGAAGTTGATCAGGAGTTG
*
28369658 ATTGATGATGAAGTTGATCAGG
1 ACTGATGATGAAGTTGATCAGG
28369680 CCATTGATGA
Statistics
Matches: 111, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
26 2 0.02
27 104 0.94
28 5 0.05
ACGTcount: A:0.29, C:0.08, G:0.32, T:0.31
Consensus pattern (27 bp):
ACTGATGATGAAGTTGATCAGGAGTTG
Found at i:28369597 original size:54 final size:54
Alignment explanation
Indices: 28369523--28369678 Score: 226
Period size: 54 Copynumber: 2.9 Consensus size: 54
28369513 GGAGGTGATC
* * *
28369523 ACTGATGATGAGATTGATCAGGAGTTGACTGATGATGAAGTTGATCATGA-GTTG
1 ACTGATGATGAGGTTGATCAGGAGTTGATTGATGATGAAGTTGATCA-GATGGTG
*
28369577 ACTGATGATGAGGTTGATCAGCAGTTGATTGATGATG-AGTTTGATCAGATGGTG
1 ACTGATGATGAGGTTGATCAGGAGTTGATTGATGATGAAG-TTGATCAGATGGTG
* *
28369631 ACTGATGATGAGGTTGATCAGGAGCTAATTGATGATGAAGTTGATCAG
1 ACTGATGATGAGGTTGATCAGGAGTTGATTGATGATGAAGTTGATCAG
28369679 GCCATTGATG
Statistics
Matches: 92, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
53 4 0.04
54 86 0.93
55 2 0.02
ACGTcount: A:0.29, C:0.08, G:0.32, T:0.31
Consensus pattern (54 bp):
ACTGATGATGAGGTTGATCAGGAGTTGATTGATGATGAAGTTGATCAGATGGTG
Found at i:28369633 original size:81 final size:81
Alignment explanation
Indices: 28369525--28369678 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 81
28369515 AGGTGATCAC
* * * * *
28369525 TGATGATGAGATTGATCAGGAGTTGACTGATGATGAAGTTGATCATGAGTTGACTGATGATGAGG
1 TGATGATGAGATTGATCAGGAGGTGACTGATGATGAAGTTGATCAGGAGCTAACTGATGATGAAG
28369590 TTGATCAGCAGTTGAT
66 TTGATCAGCAGTTGAT
* * *
28369606 TGATGATGAGTTTGATCA-GATGGTGACTGATGATGAGGTTGATCAGGAGCTAATTGATGATGAA
1 TGATGATGAGATTGATCAGGA-GGTGACTGATGATGAAGTTGATCAGGAGCTAACTGATGATGAA
28369670 GTTGATCAG
65 GTTGATCAG
28369679 GCCATTGATG
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
80 2 0.03
81 62 0.97
ACGTcount: A:0.29, C:0.07, G:0.32, T:0.32
Consensus pattern (81 bp):
TGATGATGAGATTGATCAGGAGGTGACTGATGATGAAGTTGATCAGGAGCTAACTGATGATGAAG
TTGATCAGCAGTTGAT
Found at i:28370003 original size:29 final size:29
Alignment explanation
Indices: 28369961--28370018 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
28369951 ATACCAGATG
*
28369961 CCCAGTTGATTCGATTTTGATCTGATCTC
1 CCCAGTTGATTCGATTTTGATCTAATCTC
28369990 CCCAGTTGATTCGATTTTGATCTAATCTC
1 CCCAGTTGATTCGATTTTGATCTAATCTC
28370019 TCAGTCGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.41
Consensus pattern (29 bp):
CCCAGTTGATTCGATTTTGATCTAATCTC
Found at i:28371915 original size:36 final size:36
Alignment explanation
Indices: 28371875--28371947 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
28371865 TGTCTTTTTC
* *
28371875 ACCTCCCAATTGATTCATCATCTACTGCCGTTTCAG
1 ACCTCCCAATTGATTCATCATCTACTGACATTTCAG
*
28371911 ACCTCCCAATTGATTCATCATCTGCTGACATTTCAG
1 ACCTCCCAATTGATTCATCATCTACTGACATTTCAG
28371947 A
1 A
28371948 TGCTTTACGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.25, C:0.32, G:0.11, T:0.33
Consensus pattern (36 bp):
ACCTCCCAATTGATTCATCATCTACTGACATTTCAG
Found at i:28372855 original size:27 final size:27
Alignment explanation
Indices: 28372807--28372858 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
28372797 ATCATGGTCA
* *
28372807 TCATTTTCTTTCTAAAATATATCTTCT
1 TCATTTTCTTTCCAAAACATATCTTCT
28372834 TCATTTTC-TTCCAAAGACATATCTT
1 TCATTTTCTTTCCAAA-ACATATCTT
28372859 ATTCTTGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.27, C:0.21, G:0.02, T:0.50
Consensus pattern (27 bp):
TCATTTTCTTTCCAAAACATATCTTCT
Found at i:28374150 original size:27 final size:27
Alignment explanation
Indices: 28374085--28374140 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
28374075 TTGATCAAAA
* *
28374085 GACAAGGTTGATCAGGTGGTGACTGAT
1 GACAAGGTTGATCAAGTGGTGACTAAT
28374112 GACAAGGTTGATCAAGTGGTGACTAAT
1 GACAAGGTTGATCAAGTGGTGACTAAT
28374139 GA
1 GA
28374141 TGTAGTTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.34, T:0.25
Consensus pattern (27 bp):
GACAAGGTTGATCAAGTGGTGACTAAT
Found at i:28377018 original size:38 final size:40
Alignment explanation
Indices: 28376966--28377055 Score: 114
Period size: 38 Copynumber: 2.3 Consensus size: 40
28376956 CAATAAATAT
* *
28376966 TAAATCATACCATGCAA-AAATTATTATGTAAAAAAT-GTA
1 TAAATCATATCATGCAATAAATTATCATG-AAAAAATAGTA
* *
28377005 -AAATCATATCATGCAATAAATTATCATGCAAATATAGTA
1 TAAATCATATCATGCAATAAATTATCATGAAAAAATAGTA
28377044 TAAATCATATCA
1 TAAATCATATCA
28377056 AATATCATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
38 20 0.45
39 13 0.30
40 11 0.25
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.31
Consensus pattern (40 bp):
TAAATCATATCATGCAATAAATTATCATGAAAAAATAGTA
Found at i:28377174 original size:18 final size:18
Alignment explanation
Indices: 28377153--28377219 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
28377143 ACAATAATGT
28377153 AAATATATAATATCATAC
1 AAATATATAATATCATAC
*
28377171 AAATATAT--TATCATTC
1 AAATATATAATATCATAC
* * *
28377187 AATAATATAAAATACCATGC
1 -A-AATATATAATATCATAC
28377207 AAATATATTAATA
1 AAATATA-TAATA
28377220 ACCATTCATG
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
16 7 0.18
17 1 0.03
18 20 0.51
19 5 0.13
20 6 0.15
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (18 bp):
AAATATATAATATCATAC
Done.