Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, 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: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 18 of 117
Found at i:5289861 original size:21 final size:20
Alignment explanation
Indices: 5289819--5289861 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
5289809 AGTTCGAGGA
* * *
5289819 GTGAATTCAGGTTTTTGGAG
1 GTGAATTCAGGTTGTAGAAG
5289839 GTGAATTCAGGGTTGTAGAAG
1 GTGAATTCA-GGTTGTAGAAG
5289860 GT
1 GT
5289862 TTGGGAAGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.23, C:0.05, G:0.37, T:0.35
Consensus pattern (20 bp):
GTGAATTCAGGTTGTAGAAG
Found at i:5293455 original size:37 final size:34
Alignment explanation
Indices: 5293414--5293515 Score: 98
Period size: 34 Copynumber: 2.9 Consensus size: 34
5293404 TGTAAGAATG
5293414 TCATGCAAATATATTAATTATCATGC-AATAATAACTA
1 TCATGCAAATATATT-A-TATCATGCAAAT-AT-ACTA
* *
5293451 TCATGTAAATATATTATATCATGCAAATATATTA
1 TCATGCAAATATATTATATCATGCAAATATACTA
* ** * *
5293485 TTATGCAAATATAAAATACCATACAAATATA
1 TCATGCAAATATATTATATCATGCAAATATA
5293516 TTAATAACCA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
34 28 0.50
35 10 0.18
36 4 0.07
37 14 0.25
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.35
Consensus pattern (34 bp):
TCATGCAAATATATTATATCATGCAAATATACTA
Found at i:5293490 original size:16 final size:18
Alignment explanation
Indices: 5293414--5293518 Score: 101
Period size: 18 Copynumber: 5.9 Consensus size: 18
5293404 TGTAAGAATG
5293414 TCATGCAAATATATTAATTA
1 TCATGCAAATATATT-A-TA
*
5293434 TCATGC-AATA-ATAACTA
1 TCATGCAAATATATTA-TA
*
5293451 TCATGTAAATATATTATA
1 TCATGCAAATATATTATA
5293469 TCATGCAAATATATTAT-
1 TCATGCAAATATATTATA
**
5293486 T-ATGCAAATATAAAATA
1 TCATGCAAATATATTATA
* *
5293503 CCATACAAATATATTA
1 TCATGCAAATATATTA
5293519 ATAACCATTC
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
16 13 0.19
17 9 0.13
18 35 0.50
19 7 0.10
20 6 0.09
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (18 bp):
TCATGCAAATATATTATA
Found at i:5293660 original size:17 final size:17
Alignment explanation
Indices: 5293592--5293687 Score: 72
Period size: 19 Copynumber: 5.4 Consensus size: 17
5293582 ATTATGCACA
*
5293592 CAATAAATATAGAAACATG
1 CAATAAATAT--AATCATG
* *
5293611 CAATCAA-AT-ATCATT
1 CAATAAATATAATCATG
5293626 CAAATATAATATTAATCATG
1 C-AATA-AATA-TAATCATG
5293646 CAATAACATAT-ATCATG
1 CAATAA-ATATAATCATG
5293663 CAATAAATATAAAATCATG
1 CAATAAATAT--AATCATG
5293682 CAATAA
1 CAATAA
5293688 TAATAAATAA
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
15 5 0.08
16 7 0.11
17 14 0.22
18 5 0.08
19 26 0.41
20 6 0.10
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (17 bp):
CAATAAATATAATCATG
Found at i:5293686 original size:36 final size:36
Alignment explanation
Indices: 5293592--5293687 Score: 110
Period size: 36 Copynumber: 2.7 Consensus size: 36
5293582 ATTATGCACA
*
5293592 CAATAAATATAGAAA-CATGCAAT--CAAATATCATT
1 CAATAAATATA-AAATCATGCAATAACAAATATCATG
* *
5293626 CAAATATAATAT-TAATCATGCAATAACATATATCATG
1 C-AATA-AATATAAAATCATGCAATAACAAATATCATG
5293663 CAATAAATATAAAATCATGCAATAA
1 CAATAAATATAAAATCATGCAATAA
5293688 TAATAAATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
34 3 0.06
35 17 0.33
36 22 0.42
37 10 0.19
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (36 bp):
CAATAAATATAAAATCATGCAATAACAAATATCATG
Found at i:5293693 original size:19 final size:18
Alignment explanation
Indices: 5293639--5293694 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
5293629 ATATAATATT
*
5293639 AATCATGCAATAACAT-A
1 AATCATGCAATAAAATAA
*
5293656 TATCATGCAATAAATATAA
1 AATCATGCAATAAA-ATAA
5293675 AATCATGCAATAATAATAA
1 AATCATGCAATAA-AATAA
5293694 A
1 A
5293695 TAAATAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 12 0.36
18 2 0.06
19 18 0.55
20 1 0.03
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.27
Consensus pattern (18 bp):
AATCATGCAATAAAATAA
Found at i:5293841 original size:22 final size:23
Alignment explanation
Indices: 5293816--5293860 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
5293806 CATGCAATTT
*
5293816 AATATATAATC-ATACAAATAAA
1 AATATATAAACAATACAAATAAA
*
5293838 AATATATAAACAATGCAAATAAA
1 AATATATAAACAATACAAATAAA
5293861 CATGCAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.24
Consensus pattern (23 bp):
AATATATAAACAATACAAATAAA
Found at i:5293845 original size:55 final size:54
Alignment explanation
Indices: 5293786--5294002 Score: 267
Period size: 55 Copynumber: 3.9 Consensus size: 54
5293776 ATATAATTAA
* *
5293786 ATATATAAATGTGTAATAAACATGCAATTTAATATATAATCATACAAATAAAAAT
1 ATATATAAATGT-AAATAAACATGCAATTAAATATATAATCATACAAATAAAAAT
* * * *
5293841 ATATAAACAATGCAAATAAACATGCAATTAAATATATAATCAAACAAATAATAAT
1 ATATATA-AATGTAAATAAACATGCAATTAAATATATAATCATACAAATAAAAAT
* * *
5293896 ATAT-TAATTATATAAATAAACATGCAATTAAATATATAATCATGCAAATAATAAT
1 ATATATAA--ATGTAAATAAACATGCAATTAAATATATAATCATACAAATAAAAAT
* *
5293951 ATATA-AATCATGTAAATAAATATGCAATTAAATATATAATCATGCAAATAAA
1 ATATATAA--ATGTAAATAAACATGCAATTAAATATATAATCATACAAATAAA
5294003 CATGCAATTA
Statistics
Matches: 143, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
53 1 0.01
54 1 0.01
55 137 0.96
56 4 0.03
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (54 bp):
ATATATAAATGTAAATAAACATGCAATTAAATATATAATCATACAAATAAAAAT
Found at i:5293920 original size:110 final size:110
Alignment explanation
Indices: 5293800--5294001 Score: 325
Period size: 110 Copynumber: 1.8 Consensus size: 110
5293790 ATAAATGTGT
*
5293800 AATAAACATGCAATTTAATATATAATCATACAAATAAAAATATATAAA-CAATGCAAATAAACAT
1 AATAAACATGCAATTAAATATATAATCATACAAATAAAAATATATAAATC-ATGCAAATAAACAT
5293864 GCAATTAAATATATAATCAAACAAATAATAATATATTAATTATATA
65 GCAATTAAATATATAATCAAACAAATAATAATATATTAATTATATA
* * * *
5293910 AATAAACATGCAATTAAATATATAATCATGCAAATAATAATATATAAATCATGTAAATAAATATG
1 AATAAACATGCAATTAAATATATAATCATACAAATAAAAATATATAAATCATGCAAATAAACATG
**
5293975 CAATTAAATATATAATCATGCAAATAA
66 CAATTAAATATATAATCAAACAAATAA
5294002 ACATGCAATT
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
110 83 0.99
111 1 0.01
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (110 bp):
AATAAACATGCAATTAAATATATAATCATACAAATAAAAATATATAAATCATGCAAATAAACATG
CAATTAAATATATAATCAAACAAATAATAATATATTAATTATATA
Found at i:5293967 original size:23 final size:22
Alignment explanation
Indices: 5293926--5294085 Score: 91
Period size: 20 Copynumber: 7.4 Consensus size: 22
5293916 CATGCAATTA
5293926 AATATATAATCATGCAAATAAT
1 AATATATAATCATGCAAATAAT
*
5293948 AATATATAAATCATGTAAAT-A-
1 AATATAT-AATCATGCAAATAAT
** * *** *
5293969 AATATGCAATTAAATATATAAT
1 AATATATAATCATGCAAATAAT
* * * *
5293991 CATGCAAATAAACATGC-AATTA-
1 AAT--ATATAATCATGCAAATAAT
* *
5294013 AATAAATAGTCATGCAAATAAT
1 AATATATAATCATGCAAATAAT
5294035 AATATATAAATCATGCAAAT-AT
1 AATATAT-AATCATGCAAATAAT
* *
5294057 AATAT-TAGTCATGCAAAAAAT
1 AATATATAATCATGCAAATAAT
5294078 AA-ATATAA
1 AATATATAA
5294086 AAATAAGAGT
Statistics
Matches: 101, Mismatches: 27, Indels: 21
0.68 0.18 0.14
Matches are distributed among these distances:
20 30 0.30
21 17 0.17
22 25 0.25
23 25 0.25
24 4 0.04
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (22 bp):
AATATATAATCATGCAAATAAT
Found at i:5294000 original size:32 final size:32
Alignment explanation
Indices: 5293948--5294033 Score: 127
Period size: 32 Copynumber: 2.7 Consensus size: 32
5293938 TGCAAATAAT
* *
5293948 AATATATAAATCATGTAAATAAATATGCAATTA
1 AATATAT-AATCATGCAAATAAACATGCAATTA
5293981 AATATATAATCATGCAAATAAACATGCAATTA
1 AATATATAATCATGCAAATAAACATGCAATTA
* *
5294013 AATAAATAGTCATGCAAATAA
1 AATATATAATCATGCAAATAA
5294034 TAATATATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 42 0.86
33 7 0.14
ACGTcount: A:0.55, C:0.09, G:0.07, T:0.29
Consensus pattern (32 bp):
AATATATAATCATGCAAATAAACATGCAATTA
Found at i:5294020 original size:20 final size:20
Alignment explanation
Indices: 5293901--5294002 Score: 58
Period size: 20 Copynumber: 5.3 Consensus size: 20
5293891 ATAATATATT
*
5293901 AATTATATAAATAAACATGC
1 AATTAAATAAATAAACATGC
* *
5293921 AATTAAATATATAATCATGC
1 AATTAAATAAATAAACATGC
*
5293941 AAAT-AATAATATATAA-AT-C
1 AATTAAATAA-ATA-AACATGC
5293960 -ATGTAAATAAAT----ATGC
1 AAT-TAAATAAATAAACATGC
* *
5293976 AATTAAATATATAATCATGC
1 AATTAAATAAATAAACATGC
*
5293996 AAATAAA
1 AATTAAA
5294003 CATGCAATTA
Statistics
Matches: 63, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
15 2 0.03
16 9 0.14
17 2 0.03
18 1 0.02
19 8 0.13
20 40 0.63
21 1 0.02
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (20 bp):
AATTAAATAAATAAACATGC
Found at i:5294047 original size:110 final size:111
Alignment explanation
Indices: 5293800--5294061 Score: 322
Period size: 110 Copynumber: 2.4 Consensus size: 111
5293790 ATAAATGTGT
* * *
5293800 AATAAACATGCAAT-TTAATATATAATCATACAAATAAAAATATATAAACAATGCAAATAAACAT
1 AATAAACATGCAATAATAATATATAATCATGCAAATAATAATATATAAACAATGCAAATAAACAT
* ** *
5293864 GCAATTAAATATATAATCAAACAAATAATAATATATTAATTATATA
66 GCAATTAAATATATAATCAAACAAATAATAACATAGCAATTAAATA
* * *
5293910 AATAAACATGCAATTA-AATATATAATCATGCAAATAATAATATATAAATC-ATGTAAATAAATA
1 AATAAACATGCAATAATAATATATAATCATGCAAATAATAATATATAAA-CAATGCAAATAAACA
**
5293973 TGCAATTAAATATATAATCATGCAAAT-A-AACAT-GCAATTAAATA
65 TGCAATTAAATATATAATCAAACAAATAATAACATAGCAATTAAATA
**
5294017 AATAGTCATGCAAATAATAATATATAAATCATGCAAAT-ATAATAT
1 AATAAACATGC-AATAATAATATAT-AATCATGCAAATAATAATAT
5294062 TAGTCATGCA
Statistics
Matches: 133, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
107 17 0.13
108 8 0.06
109 15 0.11
110 92 0.69
111 1 0.01
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (111 bp):
AATAAACATGCAATAATAATATATAATCATGCAAATAATAATATATAAACAATGCAAATAAACAT
GCAATTAAATATATAATCAAACAAATAATAACATAGCAATTAAATA
Found at i:5295074 original size:42 final size:43
Alignment explanation
Indices: 5294964--5295660 Score: 300
Period size: 42 Copynumber: 15.6 Consensus size: 43
5294954 TTGACAAAGG
** *** * *
5294964 TTTGAAACTTTCAAAAAAATAAAATGCTTTTCCACAATTTAGGC
1 TTTGAAACTTT-TGAAAAATAAAATGCTCCCCCACAACTGAGGC
* * * * * *
5295008 CTTGAAACTTTTTGCAAAAGAAAATACTCCCCCATAACTGAGTC
1 TTTGAAAC-TTTTGAAAAATAAAATGCTCCCCCACAACTGAGGC
* * * *
5295052 TTTGGAA-TTTTGAAACATAAAATACTCCCTCACAA-TCGAGGC
1 TTTGAAACTTTTGAAAAATAAAATGCTCCCCCACAACT-GAGGC
* ** * ** *
5295094 TTTGAAAC-TTTGAAAAATAAAATGCTCTCATATAACCAAAGC
1 TTTGAAACTTTTGAAAAATAAAATGCTCCCCCACAACTGAGGC
*
5295136 TTTGAAACTTTTGAAAAAAATAAAATGCTCCCCCACAATTGAGGC
1 TTTGAAACTTTTG--AAAAATAAAATGCTCCCCCACAACTGAGGC
*
5295181 TTTGAAACTTTATGAAAAATAAAATGCT-TCCCACAACTGAGGC
1 TTTGAAACTTT-TGAAAAATAAAATGCTCCCCCACAACTGAGGC
* * * *
5295224 TTTGAAACTTTTTAAAAAATAAAATGCTCCCCCATAATTGAGGT
1 TTTGAAAC-TTTTGAAAAATAAAATGCTCCCCCACAACTGAGGC
* * *
5295268 TTTGGAACTTTTGAAAAATAAAATG-T-TCCC-TAACTGAGGC
1 TTTGAAACTTTTGAAAAATAAAATGCTCCCCCACAACTGAGGC
* * * * ** ** **** * * * *
5295308 TTTGAAACTCCTTCATAACTGAGACTTTGAAACTTTGAAAAATAAAATGC
1 TTTGAAACT-TTTGAAAAAT-A-A-AATG-CTCCCCCACAACT--GAGGC
** * **
5295358 TCCCCCACAGCTAAGGCTTTGGAAATATTGAAAAATAAAATGCT-TTCCACAACTGAGGC
1 T------TTG--AA-AC-TT-------TTGAAAAATAAAATGCTCCCCCACAACTGAGGC
* * * *
5295417 ATTGAAACTTTTGAAAAATAAAAAGCTCTCCCACAATTGAGGC
1 TTTGAAACTTTTGAAAAATAAAATGCTCCCCCACAACTGAGGC
* ** *
5295460 ATTGAAACTTATAAAAAAATAAAATGCTCCCCCACAATTGAGGC
1 TTTGAAACTT-TTGAAAAATAAAATGCTCCCCCACAACTGAGGC
* ** * * *
5295504 ATTGAAACTTTAAAAAATAAAATAAAATGCT-CCTCACAACTGTGGT
1 TTTGAAACTTT---TGA-AAAATAAAATGCTCCCCCACAACTGAGGC
* * * *
5295550 TTTGAAATTTTTGAAAAATAAAATGCTTCTCCACAATTGAGGC
1 TTTGAAACTTTTGAAAAATAAAATGCTCCCCCACAACTGAGGC
* *
5295593 TTTGAAACTTTGGAAAAATAAAAT-CTTCCCCA-AACCTGAGGC
1 TTTGAAACTTTTGAAAAATAAAATGCTCCCCCACAA-CTGAGGC
*
5295635 TTTAAAACTTTTGAAAAATTAAAATG
1 TTTGAAACTTTTGAAAAA-TAAAATG
5295661 AGATCATTCT
Statistics
Matches: 493, Mismatches: 113, Indels: 94
0.70 0.16 0.13
Matches are distributed among these distances:
40 16 0.03
41 12 0.02
42 125 0.25
43 120 0.24
44 108 0.22
45 36 0.07
46 25 0.05
47 14 0.03
48 3 0.01
49 2 0.00
50 5 0.01
51 2 0.00
53 1 0.00
56 1 0.00
58 2 0.00
59 4 0.01
60 1 0.00
61 6 0.01
63 2 0.00
64 1 0.00
65 1 0.00
66 6 0.01
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (43 bp):
TTTGAAACTTTTGAAAAATAAAATGCTCCCCCACAACTGAGGC
Found at i:5295163 original size:45 final size:43
Alignment explanation
Indices: 5294964--5295316 Score: 299
Period size: 44 Copynumber: 8.2 Consensus size: 43
5294954 TTGACAAAGG
** * * * *
5294964 TTTGAAACTTTCAAAAAAATAAAATGCTTTTCCACAATTTAGGC
1 TTTGAAACTTT-TGAAAAATAAAATGCTCTCCCACAACTGAGGC
* * * * * * *
5295008 CTTGAAACTTTTTGCAAAAGAAAATACTCCCCCATAACTGAGTC
1 TTTGAAAC-TTTTGAAAAATAAAATGCTCTCCCACAACTGAGGC
* * *
5295052 TTTGGAA-TTTTGAAACATAAAATACTC-CCTCACAA-TCGAGGC
1 TTTGAAACTTTTGAAAAATAAAATGCTCTCC-CACAACT-GAGGC
** * ** *
5295094 TTTGAAAC-TTTGAAAAATAAAATGCTCTCATATAACCAAAGC
1 TTTGAAACTTTTGAAAAATAAAATGCTCTCCCACAACTGAGGC
* *
5295136 TTTGAAACTTTTGAAAAAAATAAAATGCTCCCCCACAATTGAGGC
1 TTTGAAACTTTTG--AAAAATAAAATGCTCTCCCACAACTGAGGC
5295181 TTTGAAACTTTATGAAAAATAAAATGCT-TCCCACAACTGAGGC
1 TTTGAAACTTT-TGAAAAATAAAATGCTCTCCCACAACTGAGGC
* * * * *
5295224 TTTGAAACTTTTTAAAAAATAAAATGCTCCCCCATAATTGAGGT
1 TTTGAAAC-TTTTGAAAAATAAAATGCTCTCCCACAACTGAGGC
* *
5295268 TTTGGAACTTTTGAAAAATAAAATG-T-TCCC-TAACTGAGGC
1 TTTGAAACTTTTGAAAAATAAAATGCTCTCCCACAACTGAGGC
5295308 TTTGAAACT
1 TTTGAAACT
5295317 CCTTCATAAC
Statistics
Matches: 247, Mismatches: 50, Indels: 28
0.76 0.15 0.09
Matches are distributed among these distances:
40 16 0.06
41 6 0.02
42 63 0.26
43 57 0.23
44 67 0.27
45 36 0.15
46 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (43 bp):
TTTGAAACTTTTGAAAAATAAAATGCTCTCCCACAACTGAGGC
Found at i:5295173 original size:87 final size:86
Alignment explanation
Indices: 5294958--5295292 Score: 309
Period size: 87 Copynumber: 3.9 Consensus size: 86
5294948 TTTTCCTTGA
* * *** * * *
5294958 CAAAGGTTTGAAACTTTCAAAAAAATAAAATGCTTTTCCACAATTTAGGCCTTGAAACTTTTTGC
1 CAAAGCTTTGAAACTTTTAAAAAAATAAAATGCTCCCCCACAATTGAGGCTTTGAAAC-TTTTGA
* * * * *
5295023 AAAAGAAAATAC-TCCCCCATAA
65 AAAATAAAATGCTTCACACA-AC
** * * * * * *
5295045 CTGAGTCTTTGGAA-TTTT-GAAACATAAAATACTCCCTCACAATCGAGGCTTTGAAAC-TTTGA
1 CAAAG-CTTTGAAACTTTTAAAAAAATAAAATGCTCCCCCACAATTGAGGCTTTGAAACTTTTGA
* *
5295107 AAAATAAAATGCTCTCATATAAC
65 AAAATAAAATGCT-TCACACAAC
5295130 CAAAGCTTTGAAACTTTTGAAAAAAATAAAATGCTCCCCCACAATTGAGGCTTTGAAACTTTATG
1 CAAAGCTTTGAAACTTTT-AAAAAAATAAAATGCTCCCCCACAATTGAGGCTTTGAAACTTT-TG
*
5295195 AAAAATAAAATGCTTCCCACAAC
64 AAAAATAAAATGCTTCACACAAC
** * * * * *
5295218 TGAGGCTTTGAAACTTTTTAAAAAATAAAATGCTCCCCCATAATTGAGGTTTTGGAACTTTTGAA
1 CAAAGCTTTGAAACTTTTAAAAAAATAAAATGCTCCCCCACAATTGAGGCTTTGAAACTTTTGAA
5295283 AAATAAAATG
66 AAATAAAATG
5295293 TTCCCTAACT
Statistics
Matches: 199, Mismatches: 41, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
84 21 0.11
85 8 0.04
86 46 0.23
87 79 0.40
88 29 0.15
89 16 0.08
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.30
Consensus pattern (86 bp):
CAAAGCTTTGAAACTTTTAAAAAAATAAAATGCTCCCCCACAATTGAGGCTTTGAAACTTTTGAA
AAATAAAATGCTTCACACAAC
Found at i:5295465 original size:43 final size:43
Alignment explanation
Indices: 5295324--5295658 Score: 272
Period size: 43 Copynumber: 7.8 Consensus size: 43
5295314 ACTCCTTCAT
* * *
5295324 AACTGAGACTTTGAAAC-TTTGAAAAATAAAATGCTCCCCCAC
1 AACTGAGGCTTTGAAACTTTTGAAAAATAAAAAGCTCTCCCAC
* * * * *
5295366 AGCTAAGGCTTTGGAAA-TATTGAAAAATAAAATGCT-TTCCAC
1 AACTGAGGCTTT-GAAACTTTTGAAAAATAAAAAGCTCTCCCAC
*
5295408 AACTGAGGCATTGAAACTTTTGAAAAATAAAAAGCTCTCCCAC
1 AACTGAGGCTTTGAAACTTTTGAAAAATAAAAAGCTCTCCCAC
* * ** * *
5295451 AATTGAGGCATTGAAACTTATAAAAAAATAAAATGCTCCCCCAC
1 AACTGAGGCTTTGAAACTT-TTGAAAAATAAAAAGCTCTCCCAC
* * * **
5295495 AATTGAGGCATTGAAAC-TTTAAAAAATAAAATAAAATGCTCCTCAC
1 AACTGAGGCTTTGAAACTTTTGAAAAAT-AAA-AAGCT-CTCC-CAC
* * * *
5295541 AACTGTGGTTTTGAAATTTTTGAAAAATAAAATGCT-TCTCCAC
1 AACTGAGGCTTTGAAACTTTTGAAAAATAAAAAGCTCTC-CCAC
* * *
5295584 AATTGAGGCTTTGAAACTTTGGAAAAAT-AAAATCT-TCCC-C
1 AACTGAGGCTTTGAAACTTTTGAAAAATAAAAAGCTCTCCCAC
* *
5295624 AAACCTGAGGCTTTAAAACTTTTGAAAAATTAAAA
1 -AA-CTGAGGCTTTGAAACTTTTGAAAAATAAAAA
5295659 TGAGATCATT
Statistics
Matches: 238, Mismatches: 41, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
40 1 0.00
41 8 0.03
42 77 0.32
43 80 0.34
44 40 0.17
45 5 0.02
46 18 0.08
47 9 0.04
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.27
Consensus pattern (43 bp):
AACTGAGGCTTTGAAACTTTTGAAAAATAAAAAGCTCTCCCAC
Found at i:5295481 original size:193 final size:196
Alignment explanation
Indices: 5295135--5295490 Score: 506
Period size: 193 Copynumber: 1.8 Consensus size: 196
5295125 ATAACCAAAG
* * *
5295135 CTTTGAAACTTTTGAAAAAAATAAAATGCTCCCCCACAATTGAGGCTTTGAAACTTTATGAAAAA
1 CTTTGAAACTTTTG-AAAAAATAAAATGCTCCCCCACAACTAAGGCTTTGAAACTATATGAAAAA
* * *
5295200 TAAAATGCTTCCCACAACTGAGGCTTTGAAACTTTTTAAAAAATAAAATGCTCCCCCATAATTGA
65 TAAAATGCTTCCCACAACTGAGGCATTGAAACTTTTTAAAAAATAAAAAGCTCCCCCACAATTGA
** * ** *
5295265 GGTTTTGGAACTTTTGAAAAATAAAATGTTCCCTAACTGAGGCTTTGAAACTCCTTCATAACTGA
130 GGCATTGAAACTTTAAAAAAATAAAATGCTCCCTAACTGAGGCTTTGAAACTCCTTCATAACTGA
5295330 GA
195 GA
*
5295332 CTTTGAAAC-TTTG-AAAAATAAAATGCTCCCCCACAGCTAAGGCTTTGGAAA-TAT-TGAAAAA
1 CTTTGAAACTTTTGAAAAAATAAAATGCTCCCCCACAACTAAGGCTTT-GAAACTATATGAAAAA
* * *
5295393 TAAAATGCTTTCCACAACTGAGGCATTGAAAC-TTTTGAAAAATAAAAAGCTCTCCCACAATTGA
65 TAAAATGCTTCCCACAACTGAGGCATTGAAACTTTTTAAAAAATAAAAAGCTCCCCCACAATTGA
5295457 GGCATTGAAACTTATAAAAAAATAAAATGCTCCC
130 GGCATTGAAACTT-TAAAAAAATAAAATGCTCCC
5295491 CCACAATTGA
Statistics
Matches: 141, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
192 38 0.27
193 54 0.38
194 32 0.23
195 4 0.03
196 4 0.03
197 9 0.06
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (196 bp):
CTTTGAAACTTTTGAAAAAATAAAATGCTCCCCCACAACTAAGGCTTTGAAACTATATGAAAAAT
AAAATGCTTCCCACAACTGAGGCATTGAAACTTTTTAAAAAATAAAAAGCTCCCCCACAATTGAG
GCATTGAAACTTTAAAAAAATAAAATGCTCCCTAACTGAGGCTTTGAAACTCCTTCATAACTGAG
A
Found at i:5295566 original size:133 final size:133
Alignment explanation
Indices: 5295389--5295659 Score: 336
Period size: 133 Copynumber: 2.0 Consensus size: 133
5295379 GAAATATTGA
*
5295389 AAAATAAAATGCTTTCCACAACTGAGGCATTGAAACTTTTGAAAAATAAAAAGC-TCTCCCACAA
1 AAAATAAAATGCTCTCCACAACTGAGGCATTGAAACTTTTGAAAAATAAAAAGCTTCT-CCACAA
* *
5295453 TTGAGGCATTGAAACTTATAAAAAAATAAAATGCTCCCCCACAA-TTGAGGCATTGAAAC-TTT-
65 TTGAGGCATTGAAACTT-TAAAAAAATAAAAT-CTCCCCCA-AACCTGAGGCATTAAAACTTTTG
5295515 AAAAAAT
127 AAAAAAT
* ** * *
5295522 AAAATAAAATGCTC-CTCACAACTGTGGTTTTGAAATTTTTGAAAAATAAAATGCTTCTCCACAA
1 AAAATAAAATGCTCTC-CACAACTGAGGCATTGAAACTTTTGAAAAATAAAAAGCTTCTCCACAA
* ** * *
5295586 TTGAGGCTTTGAAACTTTGGAAAAATAAAATCTTCCCCAAACCTGAGGCTTTAAAACTTTTGAAA
65 TTGAGGCATTGAAACTTTAAAAAAATAAAATCTCCCCCAAACCTGAGGCATTAAAACTTTTGAAA
*
5295651 AATT
130 AAAT
5295655 AAAAT
1 AAAAT
5295660 GAGATCATTC
Statistics
Matches: 119, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
130 2 0.02
131 19 0.16
132 16 0.13
133 79 0.66
134 3 0.03
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (133 bp):
AAAATAAAATGCTCTCCACAACTGAGGCATTGAAACTTTTGAAAAATAAAAAGCTTCTCCACAAT
TGAGGCATTGAAACTTTAAAAAAATAAAATCTCCCCCAAACCTGAGGCATTAAAACTTTTGAAAA
AAT
Found at i:5297119 original size:21 final size:20
Alignment explanation
Indices: 5297093--5297131 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
5297083 TTTTAAACTT
*
5297093 TTTTCTTGTTTCTTTTTTTGC
1 TTTTCTTGCTT-TTTTTTTGC
5297114 TTTTCTTGCTTTTTTTTT
1 TTTTCTTGCTTTTTTTTT
5297132 ACACATTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (20 bp):
TTTTCTTGCTTTTTTTTTGC
Found at i:5303073 original size:34 final size:33
Alignment explanation
Indices: 5303009--5303083 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 33
5302999 GAATGTCACA
5303009 CAAATATATTAATTATCATGCAATAATATCATG
1 CAAATATATTAATTATCATGCAATAATATCATG
* *
5303042 TAAATATATT-A-TATTATGCAAATATATTATCATG
1 CAAATATATTAATTATCATGC-AATA-A-TATCATG
5303076 CAAATATA
1 CAAATATA
5303084 AAATACCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 7 0.19
32 5 0.14
33 10 0.28
34 14 0.39
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (33 bp):
CAAATATATTAATTATCATGCAATAATATCATG
Found at i:5303076 original size:16 final size:16
Alignment explanation
Indices: 5303020--5303083 Score: 71
Period size: 16 Copynumber: 4.1 Consensus size: 16
5303010 AAATATATTA
5303020 ATTATCATGC-AATA-
1 ATTATCATGCAAATAT
*
5303034 A-TATCATGTAAATAT
1 ATTATCATGCAAATAT
*
5303049 ATTATATTATGCAAATAT
1 A-T-TATCATGCAAATAT
5303067 ATTATCATGCAAATAT
1 ATTATCATGCAAATAT
5303083 A
1 A
5303084 AAATACCATA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
13 7 0.17
14 5 0.12
15 1 0.02
16 14 0.34
17 1 0.02
18 13 0.32
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTATCATGCAAATAT
Found at i:5303374 original size:31 final size:32
Alignment explanation
Indices: 5303314--5303402 Score: 110
Period size: 31 Copynumber: 2.8 Consensus size: 32
5303304 CACACCAATA
* * *
5303314 AATAAATTA-ATAATCATGTAAATAGACATGG
1 AATAAAATATATAATCATGTAAATAAACATGC
*
5303345 AATAAAATATATAAACATGT-AATAAACATGC
1 AATAAAATATATAATCATGTAAATAAACATGC
**
5303376 AATTTAATATATAATCATGTAAATAAA
1 AATAAAATATATAATCATGTAAATAAA
5303403 AATATATAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
31 34 0.69
32 15 0.31
ACGTcount: A:0.55, C:0.07, G:0.08, T:0.30
Consensus pattern (32 bp):
AATAAAATATATAATCATGTAAATAAACATGC
Found at i:5303409 original size:22 final size:23
Alignment explanation
Indices: 5303381--5303425 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
5303371 CATGCAATTT
* *
5303381 AATATATAATC-ATGTAAATAAA
1 AATATATAAACTATGCAAATAAA
5303403 AATATATAAACTATGCAAATAAA
1 AATATATAAACTATGCAAATAAA
5303426 CATGCACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (23 bp):
AATATATAAACTATGCAAATAAA
Found at i:5303478 original size:55 final size:54
Alignment explanation
Indices: 5303348--5303478 Score: 165
Period size: 55 Copynumber: 2.4 Consensus size: 54
5303338 GACATGGAAT
* * *
5303348 AAAATATATAAACATGT-AATAAACATGCAATTTAATATATAATCATGTAAATA
1 AAAATATATAAACATGTAAATAAACATGCAATTAAATATATAATCACGCAAATA
* * * *
5303401 AAAATATATAAACTATGCAAATAAACATGCACTTAAATATATAGTCACGCAATTA
1 AAAATATATAAAC-ATGTAAATAAACATGCAATTAAATATATAATCACGCAAATA
*
5303456 ATAATATATAAATCATGTAAATA
1 AAAATATATAAA-CATGTAAATA
5303479 TAATATTAGT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
53 13 0.20
54 3 0.05
55 49 0.74
56 1 0.02
ACGTcount: A:0.53, C:0.10, G:0.06, T:0.31
Consensus pattern (54 bp):
AAAATATATAAACATGTAAATAAACATGCAATTAAATATATAATCACGCAAATA
Found at i:5306857 original size:59 final size:58
Alignment explanation
Indices: 5306780--5306901 Score: 208
Period size: 59 Copynumber: 2.1 Consensus size: 58
5306770 TTGTATATTT
* *
5306780 ATTTATGTTATTTAGTTGTTTCTCTTTCTTCTTTATTTAAAATAAATTTTTATAATAAA
1 ATTTTTGTTACTTAGTTGTTTCTCTTTCTTCTTTATTTAAAATAAATTTTTAT-ATAAA
*
5306839 CTTTTTGTTACTTAGTTGTTTCTCTTTCTTCTTTATTTAAAATAAATTTTTATATAAA
1 ATTTTTGTTACTTAGTTGTTTCTCTTTCTTCTTTATTTAAAATAAATTTTTATATAAA
5306897 ATTTT
1 ATTTT
5306902 CAACCTTACC
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
58 9 0.15
59 50 0.85
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (58 bp):
ATTTTTGTTACTTAGTTGTTTCTCTTTCTTCTTTATTTAAAATAAATTTTTATATAAA
Found at i:5318762 original size:43 final size:43
Alignment explanation
Indices: 5318715--5318932 Score: 192
Period size: 43 Copynumber: 5.1 Consensus size: 43
5318705 TTTACATTAC
* * * *
5318715 TTTTTTAAAATCGTTGAGCCTTTGTTTAGATGAACTTTATTTA
1 TTTTTCAAAATCGTTGAGCCTCTGTTTAGAAGAACCTTATTTA
* * * *
5318758 TTTTTCAAAAGTCG-TGAGCCTTTGTTTAGAGGAGCCTTATTCA
1 TTTTTCAAAA-TCGTTGAGCCTCTGTTTAGAAGAACCTTATTTA
* * ** * *
5318801 TTTTTTAAAGTTATTGAGCCTATGTTTAGAAGAGCCTTATTTA
1 TTTTTCAAAATCGTTGAGCCTCTGTTTAGAAGAACCTTATTTA
* * *
5318844 TTTTTCAAAATCG-TAAGCCTCTATTTA-AAGAAGCCTTATTCA
1 TTTTTCAAAATCGTTGAGCCTCTGTTTAGAAGAA-CCTTATTTA
* * * *
5318886 TTTTTCAAAGTCATTGAGCCTCTATTTA-AAGAAGCTTTATTTA
1 TTTTTCAAAATCGTTGAGCCTCTGTTTAGAAGAA-CCTTATTTA
5318929 TTTT
1 TTTT
5318933 GTTACGCCTC
Statistics
Matches: 145, Mismatches: 26, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
41 4 0.03
42 31 0.21
43 107 0.74
44 3 0.02
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (43 bp):
TTTTTCAAAATCGTTGAGCCTCTGTTTAGAAGAACCTTATTTA
Found at i:5318904 original size:85 final size:86
Alignment explanation
Indices: 5318728--5318932 Score: 270
Period size: 85 Copynumber: 2.4 Consensus size: 86
5318718 TTTAAAATCG
* * * * * * * *
5318728 TTGAGCCTTTGTTTAGATGAACTTTATTTATTTTTCAAAAGTCGTGAGCCTTTGTTTAGAGGAGC
1 TTGAGCCTATGTTTAGAAGAGCTTTATTTATTTTTCAAAAGTCGTAAGCCTCTATTTAAAGAAGC
* *
5318793 CTTATTCATTTTTTAAAGTTA
66 CTTATTCATTTTTCAAAGTCA
*
5318814 TTGAGCCTATGTTTAGAAGAGCCTTATTTATTTTTCAAAA-TCGTAAGCCTCTATTTAAAGAAGC
1 TTGAGCCTATGTTTAGAAGAGCTTTATTTATTTTTCAAAAGTCGTAAGCCTCTATTTAAAGAAGC
5318878 CTTATTCATTTTTCAAAGTCA
66 CTTATTCATTTTTCAAAGTCA
* *
5318899 TTGAGCCTCTATTTA-AAGAAGCTTTATTTATTTT
1 TTGAGCCTATGTTTAGAAG-AGCTTTATTTATTTT
5318933 GTTACGCCTC
Statistics
Matches: 104, Mismatches: 14, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
84 3 0.03
85 65 0.62
86 36 0.35
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (86 bp):
TTGAGCCTATGTTTAGAAGAGCTTTATTTATTTTTCAAAAGTCGTAAGCCTCTATTTAAAGAAGC
CTTATTCATTTTTCAAAGTCA
Found at i:5319000 original size:44 final size:44
Alignment explanation
Indices: 5318938--5319059 Score: 137
Period size: 44 Copynumber: 2.8 Consensus size: 44
5318928 ATTTTGTTAC
* * *
5318938 GCCTCTATCT-AGAGGAGTTTTATTTATTTTTTAATAA-TTGTTGA
1 GCCTCTAT-TGAGAAGAGTTTTATTTATTTTTCAA-AAGTTATTGA
5318982 GCCTCTATTGAGAAGAGTTTTATTTATTTTTCAAAAGTTATTGA
1 GCCTCTATTGAGAAGAGTTTTATTTATTTTTCAAAAGTTATTGA
*
5319026 GCCTCTGTTGAG-AGAAGCTTTTA--TATTTTTCAAA
1 GCCTCTATTGAGAAG-AG-TTTTATTTATTTTTCAAA
5319060 GTAATAAACT
Statistics
Matches: 70, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
43 16 0.23
44 49 0.70
45 5 0.07
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (44 bp):
GCCTCTATTGAGAAGAGTTTTATTTATTTTTCAAAAGTTATTGA
Found at i:5319958 original size:18 final size:18
Alignment explanation
Indices: 5319935--5319975 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5319925 AAAACTTATG
*
5319935 ATTTTTA-AATAAAAATTA
1 ATTTTTAGAA-AAAAAATA
5319953 ATTTTTAGAAAAAAAATA
1 ATTTTTAGAAAAAAAATA
5319971 ATTTT
1 ATTTT
5319976 CATAAAATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
ATTTTTAGAAAAAAAATA
Found at i:5319982 original size:18 final size:19
Alignment explanation
Indices: 5319940--5319982 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
5319930 TTATGATTTT
*
5319940 TAAATAAAAATTAATTTTTA
1 TAAA-AAAAATTAATTTTCA
*
5319960 GAAAAAAAA-TAATTTTCA
1 TAAAAAAAATTAATTTTCA
5319978 TAAAA
1 TAAAA
5319983 TCCTACCAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 12 0.60
19 5 0.25
20 3 0.15
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
TAAAAAAAATTAATTTTCA
Found at i:5320763 original size:90 final size:89
Alignment explanation
Indices: 5320650--5320817 Score: 205
Period size: 90 Copynumber: 1.9 Consensus size: 89
5320640 TTTTTTATGA
* * * *
5320650 ATTTTTTAAAAAAATGATTATTAAATTTTTCAATAGTTTGGTAATATTTAACTT-AGAGATTTAA
1 ATTTTTTAAAAAAA-GATTATTAAATTCTCCAATAGTTTAGTAATACTTAA-TTCA-AGATTTAA
5320714 ATCCTCCAATCGTTTAATACAAAATTT
63 ATCCTCCAATCGTTTAATACAAAATTT
* * *
5320741 ATTTTTTAAAAAAA-ATTCATTAAGTTCTCCAATAGTTTAGTAGTACTTAATTCAAGATTTGAAT
1 ATTTTTTAAAAAAAGATT-ATTAAATTCTCCAATAGTTTAGTAATACTTAATTCAAGATTTAAAT
* *
5320805 CTTTCAATCGTTT
65 CCTCCAATCGTTT
5320818 GGTAGGATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
89 25 0.38
90 27 0.41
91 14 0.21
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (89 bp):
ATTTTTTAAAAAAAGATTATTAAATTCTCCAATAGTTTAGTAATACTTAATTCAAGATTTAAATC
CTCCAATCGTTTAATACAAAATTT
Found at i:5323669 original size:11 final size:11
Alignment explanation
Indices: 5323644--5323677 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
5323634 TATAACTTGT
*
5323644 TATATATATATA
1 TATA-ATATAAA
5323656 TATAATATAAA
1 TATAATATAAA
5323667 TATAATATAAA
1 TATAATATAAA
5323678 GTTATTATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TATAATATAAA
Found at i:5324004 original size:14 final size:14
Alignment explanation
Indices: 5323985--5324013 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5323975 TTAAATTGTT
5323985 TATGTGATAGCATA
1 TATGTGATAGCATA
5323999 TATGTGATAGCATA
1 TATGTGATAGCATA
5324013 T
1 T
5324014 CTTTAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (14 bp):
TATGTGATAGCATA
Found at i:5324909 original size:19 final size:18
Alignment explanation
Indices: 5324869--5324918 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
5324859 TTTATACTAA
* *
5324869 AAAATATTATTTTTTTCC
1 AAAATATTATTTATTTAC
*
5324887 AAAATATTATTTGATTTAG
1 AAAATATTATTT-ATTTAC
5324906 AAAATATT-TTTAT
1 AAAATATTATTTAT
5324919 AAAATTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 2 0.07
18 15 0.54
19 11 0.39
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (18 bp):
AAAATATTATTTATTTAC
Found at i:5325609 original size:21 final size:22
Alignment explanation
Indices: 5325578--5325625 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
5325568 AAAGGATTGA
* * *
5325578 CCATTTATGAACATGGATCTAT
1 CCATTTATGAAAATGAATCAAT
5325600 CCATTT-TGAAAATGAATCAAT
1 CCATTTATGAAAATGAATCAAT
5325621 CCATT
1 CCATT
5325626 ATCTTACAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (22 bp):
CCATTTATGAAAATGAATCAAT
Found at i:5330551 original size:23 final size:23
Alignment explanation
Indices: 5330491--5330539 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
5330481 TTTTTTTATT
*
5330491 TTTATTATTAATTATTAATAATA
1 TTTATTATTAAATATTAATAATA
*
5330514 TTTATTATTAAATATTATTAATA
1 TTTATTATTAAATATTAATAATA
5330537 TTT
1 TTT
5330540 TCTATTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTATTATTAAATATTAATAATA
Found at i:5341581 original size:13 final size:13
Alignment explanation
Indices: 5341549--5341581 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
5341539 TCAACGCCGA
5341549 TTCGGCTCGACGG
1 TTCGGCTCGACGG
5341562 TTC-GCTCGACGG
1 TTCGGCTCGACGG
5341574 TTCGGCTC
1 TTCGGCTC
5341582 AATCTAGGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.06, C:0.33, G:0.33, T:0.27
Consensus pattern (13 bp):
TTCGGCTCGACGG
Found at i:5342507 original size:6 final size:6
Alignment explanation
Indices: 5342489--5342534 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
5342479 AAACGGGAAG
* *
5342489 AAAAGA AATAGA AAAAGA AAAAGA AAGAAAA AAAAGA AAAA-A AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AA-AAGA AAAAGA AAAAGA AAAA
5342535 TAATAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
5 5 0.14
6 25 0.71
7 5 0.14
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:5342516 original size:27 final size:24
Alignment explanation
Indices: 5342486--5342534 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 24
5342476 CAGAAACGGG
5342486 AAGAAAAGAAATAGAAAAAGAAAAAGA
1 AAGAAAA-AAA-AGAAAAA-AAAAAGA
5342513 AAGAAAAAAAAGAAAAAAAAAA
1 AAGAAAAAAAAGAAAAAAAAAA
5342535 TAATAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.23
25 7 0.32
26 3 0.14
27 7 0.32
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (24 bp):
AAGAAAAAAAAGAAAAAAAAAAGA
Found at i:5342524 original size:9 final size:9
Alignment explanation
Indices: 5342500--5342532 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
5342490 AAAGAAATAG
5342500 AAAAAGAAA
1 AAAAAGAAA
5342509 AAGAAAGAAA
1 AA-AAAGAAA
5342519 AAAAAGAAA
1 AAAAAGAAA
5342528 AAAAA
1 AAAAA
5342533 AATAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:5342832 original size:46 final size:45
Alignment explanation
Indices: 5342724--5342925 Score: 232
Period size: 46 Copynumber: 4.4 Consensus size: 45
5342714 TTAAAAGTTT
* * * * *
5342724 AAAAGGCTCATCTCAGCAGATGCTTAATAACTTTAAAATTCTCTTG
1 AAAAAGCTCATCTCAACAGAGGCTCAACAA-TTTAAAATTCTCTTG
* *
5342770 AAAAAACTCCTCTCAACAGAGGCTCAACAA-TTAAAATCTCATCTT-
1 AAAAAGCTCATCTCAACAGAGGCTCAACAATTTAAAAT-TC-TCTTG
*
5342815 AGAAAAGCTCATCTCAACAAAGGCTCAACAATTTTAAAATTCTCTTG
1 A-AAAAGCTCATCTCAACAGAGGCTCAACAA-TTTAAAATTCTCTTG
5342862 AAAAAGCTCATCTCAACAGAGGCTCAACAACTTTAAAATTTCATCTTG
1 AAAAAGCTCATCTCAACAGAGGCTCAACAA-TTTAAAA-TTC-TCTTG
5342910 AAAAAGCTC--CTCAACA
1 AAAAAGCTCATCTCAACA
5342926 AAAAAAGGGA
Statistics
Matches: 136, Mismatches: 12, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
44 7 0.05
45 3 0.02
46 99 0.73
47 6 0.04
48 21 0.15
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (45 bp):
AAAAAGCTCATCTCAACAGAGGCTCAACAATTTAAAATTCTCTTG
Found at i:5342851 original size:92 final size:91
Alignment explanation
Indices: 5342755--5342927 Score: 269
Period size: 92 Copynumber: 1.9 Consensus size: 91
5342745 GCTTAATAAC
*
5342755 TTTAAAATTCTCTTGAAAAAACTCCTCTCAACAGAGGCTCAACAA-TTAAAATCTCATCTT-AGA
1 TTTAAAATTCTCTTGAAAAAACTCATCTCAACAGAGGCTCAACAACTTAAAATCTCATCTTGA-A
5342818 AAAGCTCATCTCAACAAAGGCTCAACAAT
65 AAAGCTC--CTCAACAAAGGCTCAACAAT
* *
5342847 TTTAAAATTCTCTTGAAAAAGCTCATCTCAACAGAGGCTCAACAACTTTAAAATTTCATCTTGAA
1 TTTAAAATTCTCTTGAAAAAACTCATCTCAACAGAGGCTCAACAAC-TTAAAATCTCATCTTGAA
5342912 AAAGCTCCTCAACAAA
65 AAAGCTCCTCAACAAA
5342928 AAAAGGGAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
92 52 0.69
94 22 0.29
95 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27
Consensus pattern (91 bp):
TTTAAAATTCTCTTGAAAAAACTCATCTCAACAGAGGCTCAACAACTTAAAATCTCATCTTGAAA
AAGCTCCTCAACAAAGGCTCAACAAT
Found at i:5343569 original size:75 final size:75
Alignment explanation
Indices: 5343402--5343661 Score: 236
Period size: 75 Copynumber: 3.4 Consensus size: 75
5343392 CTTCTGTTTT
* * * * * * * * *
5343402 ATTCTCTGATG-TAAACAGCATGATCATGGAAGACAACGAGTCAGCGCCAGAGACTGCTTTCAAG
1 ATTCTCTGATGTTAAA-AGCATAATCATGGAAG---ATGAATCAACTCCAGAGATTGGTTTGAAC
5343466 CAGAAGAAGGTCTC
62 CAGAAGAAGGTCTC
* * * *
5343480 ATTCTCTGATGTTAAAAGCGTCATCATGGAGGATGAATCAAC-CCGGAAGATTGGTTTGAACCAG
1 ATTCTCTGATGTTAAAAGCATAATCATGGAAGATGAATCAACTCCAG-AGATTGGTTTGAACCAG
*
5343544 AAGAAGGTTTC
65 AAGAAGGTCTC
* * * *
5343555 TTTTTCTGATGTTAAAAGCATAATCATGGAAGATGAGTCCACTCCAGAGATTGGTTTGAACCAGA
1 ATTCTCTGATGTTAAAAGCATAATCATGGAAGATGAATCAACTCCAGAGATTGGTTTGAACCAGA
* *
5343620 ATAAGGTGTC
66 AGAAGGTCTC
* * ** *
5343630 ATTCGCTGATGTAAAAAGTGTAGTCATGGAAG
1 ATTCTCTGATGTTAAAAGCATAATCATGGAAG
5343662 GTAACGAGCC
Statistics
Matches: 150, Mismatches: 29, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
74 3 0.02
75 116 0.77
76 3 0.02
78 24 0.16
79 4 0.03
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.26
Consensus pattern (75 bp):
ATTCTCTGATGTTAAAAGCATAATCATGGAAGATGAATCAACTCCAGAGATTGGTTTGAACCAGA
AGAAGGTCTC
Found at i:5352298 original size:23 final size:23
Alignment explanation
Indices: 5352278--5352326 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
5352268 ATAAAATAGA
*
5352278 AAATATTAATAATATTTAATAAT
1 AAATATTAATAATAATTAATAAT
*
5352301 AAATATTATTAATAATTAATAAT
1 AAATATTAATAATAATTAATAAT
5352324 AAA
1 AAA
5352327 AATAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATATTAATAATAATTAATAAT
Found at i:5355572 original size:17 final size:18
Alignment explanation
Indices: 5355535--5355572 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5355525 TATTAAAAAG
*
5355535 ATATTAGAAAAACAATTA
1 ATATTAGAAAAACAATAA
*
5355553 ATATTGGAAAAA-AATAA
1 ATATTAGAAAAACAATAA
5355570 ATA
1 ATA
5355573 CTATGTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (18 bp):
ATATTAGAAAAACAATAA
Found at i:5357218 original size:21 final size:22
Alignment explanation
Indices: 5357192--5357239 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
5357182 GTTGTAAGAT
* *
5357192 AATGGATTGATTCATTTTCA-A
1 AATGGATAGATCCATTTTCATA
5357213 AATGGATAGATCCATTTTCATA
1 AATGGATAGATCCATTTTCATA
5357235 AATGG
1 AATGG
5357240 TCAATCCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (22 bp):
AATGGATAGATCCATTTTCATA
Found at i:5357922 original size:20 final size:18
Alignment explanation
Indices: 5357897--5357942 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
5357887 AATTTTTAAA
*
5357897 AATATTTTCTAAAATCAAAT
1 AATATTTTCGAAAA--AAAT
*
5357917 AATATTTTGGAAAAAAAT
1 AATATTTTCGAAAAAAAT
5357935 AATATTTT
1 AATATTTT
5357943 TTAGTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.50
20 12 0.50
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (18 bp):
AATATTTTCGAAAAAAAT
Found at i:5359168 original size:13 final size:13
Alignment explanation
Indices: 5359150--5359182 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5359140 AGATAATAAC
5359150 TTTATA-TGTTATA
1 TTTATATTG-TATA
5359163 TTTATATTGTATA
1 TTTATATTGTATA
5359176 TTTATAT
1 TTTATAT
5359183 ATATATATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 17 0.89
14 2 0.11
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (13 bp):
TTTATATTGTATA
Found at i:5359169 original size:6 final size:6
Alignment explanation
Indices: 5359150--5359188 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
5359140 AGATAATAAC
*
5359150 TTTATA TGTTATA TTTATA TTGTATA TTTATA TATATA T
1 TTTATA T-TTATA TTTATA TT-TATA TTTATA TTTATA T
5359189 ATAGACAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 18 0.60
7 12 0.40
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (6 bp):
TTTATA
Found at i:5363666 original size:75 final size:74
Alignment explanation
Indices: 5363587--5363765 Score: 214
Period size: 75 Copynumber: 2.4 Consensus size: 74
5363577 AGCGAATGAC
* * * *
5363587 ACCTTATTCTGGTTCAAACCAATCTCTGGAGTGGACTCATCTTCCATGATTATGCTTTTAACATC
1 ACCTTCTTCTGGTTCAAACCAATCTCTGG-GTGGACTCATCCTCCATGATGACGCTTTTAACATC
5363652 AGAAAAAGAA
65 AGAAAAAGAA
* * *
5363662 ACCTTCTTCTGGTTCAAACCAATCTCCCGGGTTGATTCATCCTCCATGATGACGCTTTTAACATC
1 ACCTTCTTCTGGTTCAAACCAATCT-CTGGGTGGACTCATCCTCCATGATGACGCTTTTAACATC
* * *
5363727 AGAGAATGAG
65 AGAAAAAGAA
* * * *
5363737 ACCTTCTTCTGCTTGAAAGCAGTCTCTGG
1 ACCTTCTTCTGGTTCAAACCAATCTCTGG
5363766 CGCTGACTCG
Statistics
Matches: 88, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
74 3 0.03
75 82 0.93
76 3 0.03
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (74 bp):
ACCTTCTTCTGGTTCAAACCAATCTCTGGGTGGACTCATCCTCCATGATGACGCTTTTAACATCA
GAAAAAGAA
Found at i:5369231 original size:16 final size:16
Alignment explanation
Indices: 5369189--5369235 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5369179 AGTTACTTTA
*
5369189 TATTTATAGTATATAT
1 TATTTATATTATATAT
* *
5369205 TATATAAATTATAT-T
1 TATTTATATTATATAT
5369220 GTATTTATATTATATA
1 -TATTTATATTATATA
5369236 AAAAATTATT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
15 1 0.04
16 23 0.96
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (16 bp):
TATTTATATTATATAT
Found at i:5377981 original size:2 final size:2
Alignment explanation
Indices: 5377974--5377998 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5377964 TACAGGAAGT
5377974 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
5377999 TTTGGAAAAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5382090 original size:25 final size:25
Alignment explanation
Indices: 5382062--5382118 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 25
5382052 GATTAAAAAA
*
5382062 ATTAATAAAATTTATTATATTTATG
1 ATTAATAAAATTTATTATAATTATG
*
5382087 A-T--TAAAATTTATTATAATTGTG
1 ATTAATAAAATTTATTATAATTATG
*
5382109 ATTAAAAAAA
1 ATTAATAAAA
5382119 ATTTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
22 19 0.73
23 1 0.04
24 1 0.04
25 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (25 bp):
ATTAATAAAATTTATTATAATTATG
Found at i:5382092 original size:22 final size:22
Alignment explanation
Indices: 5382067--5382115 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
5382057 AAAAAATTAA
*
5382067 TAAAATTTATTATATTTATGAT
1 TAAAATTTATTATAATTATGAT
*
5382089 TAAAATTTATTATAATTGTGAT
1 TAAAATTTATTATAATTATGAT
5382111 TAAAA
1 TAAAA
5382116 AAAATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (22 bp):
TAAAATTTATTATAATTATGAT
Found at i:5385052 original size:27 final size:26
Alignment explanation
Indices: 5385021--5385104 Score: 71
Period size: 28 Copynumber: 3.1 Consensus size: 26
5385011 TACTATGTTT
5385021 TTTATGTTGGTCA-TGTTTGATTGTAAG
1 TTTATGTTGGT-AGTGTTTGATTGT-AG
* *
5385048 TTTATTTTTGTAGTTGTTTGATTGTAG
1 TTTATGTTGGTAG-TGTTTGATTGTAG
* * *
5385075 TTAATGTTTGAATAGTATTTGATTGTAG
1 TTTATG-TTG-GTAGTGTTTGATTGTAG
5385103 TT
1 TT
5385105 AATATTTGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
26 1 0.02
27 15 0.33
28 27 0.59
29 3 0.07
ACGTcount: A:0.20, C:0.01, G:0.23, T:0.56
Consensus pattern (26 bp):
TTTATGTTGGTAGTGTTTGATTGTAG
Found at i:5385095 original size:28 final size:28
Alignment explanation
Indices: 5385064--5385117 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
5385054 TTTGTAGTTG
*
5385064 TTTGATTGTAGTTAATGTTTGAATAGTA
1 TTTGATTGTAGTTAATATTTGAATAGTA
5385092 TTTGATTGTAGTTAATATTTGAATAG
1 TTTGATTGTAGTTAATATTTGAATAG
5385118 ACAGAGCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (28 bp):
TTTGATTGTAGTTAATATTTGAATAGTA
Found at i:5385770 original size:16 final size:16
Alignment explanation
Indices: 5385750--5385785 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5385740 TGTAAAAAAA
5385750 AAAAAGTATAAAATTAT
1 AAAAA-TATAAAATTAT
*
5385767 AAAAATTTAAAATTAT
1 AAAAATATAAAATTAT
5385783 AAA
1 AAA
5385786 GATAAAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AAAAATATAAAATTAT
Found at i:5403987 original size:29 final size:29
Alignment explanation
Indices: 5403954--5404014 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
5403944 AACATGATGA
5403954 AGAACATTAGTGCAACATAAAACTATCAC
1 AGAACATTAGTGCAACATAAAACTATCAC
*
5403983 AGAACATTGGTGCAACATAAAACTATCAC
1 AGAACATTAGTGCAACATAAAACTATCAC
5404012 AGA
1 AGA
5404015 CAAAAAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.48, C:0.20, G:0.13, T:0.20
Consensus pattern (29 bp):
AGAACATTAGTGCAACATAAAACTATCAC
Found at i:5419471 original size:16 final size:17
Alignment explanation
Indices: 5419450--5419482 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5419440 TAATAATTAT
*
5419450 TTTGTAT-TATATTTAA
1 TTTGTATCTATAGTTAA
5419466 TTTGTATCTATAGTTAA
1 TTTGTATCTATAGTTAA
5419483 AGTTATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (17 bp):
TTTGTATCTATAGTTAA
Found at i:5420324 original size:20 final size:23
Alignment explanation
Indices: 5420299--5420353 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
5420289 TTTTTTTATT
5420299 TTAATTT-TA-AAAT-AATTTTA
1 TTAATTTATATAAATAAATTTTA
5420319 TTAATTTAATATAAATAAATTTTA
1 TTAATTT-ATATAAATAAATTTTA
5420343 TT-A-TTATATAA
1 TTAATTTATATAA
5420354 TAATAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
20 7 0.23
21 6 0.19
22 4 0.13
23 5 0.16
24 9 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTAATTTATATAAATAAATTTTA
Found at i:5420356 original size:24 final size:24
Alignment explanation
Indices: 5420308--5420365 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 24
5420298 TTTAATTTTA
5420308 AAAT-AATTTTATTAATTTAATAT
1 AAATAAATTTTATTAATTTAATAT
*
5420331 AAATAAATTTTATTATTATATAATAAT
1 AAATAAATTTTATTA--ATTTAAT-AT
5420358 AAATAAAT
1 AAATAAAT
5420366 AATATGTATC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 4 0.13
24 10 0.33
26 6 0.20
27 10 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATAAATTTTATTAATTTAATAT
Found at i:5422993 original size:2 final size:2
Alignment explanation
Indices: 5422980--5423020 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
5422970 CATGCAAAAC
* * *
5422980 TA TA TA TT TA TA TA TA TA TA TA TA TA TT TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5423021 CGATAGTTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (2 bp):
TA
Found at i:5422995 original size:10 final size:10
Alignment explanation
Indices: 5422980--5423014 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
5422970 CATGCAAAAC
5422980 TATATATTTA
1 TATATATTTA
*
5422990 TATATATATA
1 TATATATTTA
5423000 TATATATTTA
1 TATATATTTA
5423010 TATAT
1 TATAT
5423015 TTATATCGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TATATATTTA
Found at i:5425166 original size:14 final size:14
Alignment explanation
Indices: 5425147--5425187 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
5425137 GAATATCATT
*
5425147 TATAATTATTTTAA
1 TATAATTATTATAA
5425161 TATAATTAATTATAA
1 TATAATT-ATTATAA
5425176 T-TAATTATTATA
1 TATAATTATTATA
5425188 TAAAATTCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 6 0.24
14 12 0.48
15 7 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATAATTATTATAA
Found at i:5432258 original size:16 final size:16
Alignment explanation
Indices: 5432198--5432259 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
5432188 TATCCCTAAT
5432198 TAATTAGATTCATGAA
1 TAATTAGATTCATGAA
* * *
5432214 TATCTTAGATTCTTTAA
1 TA-ATTAGATTCATGAA
*
5432231 TGATTA-AGTTCATGAA
1 TAATTAGA-TTCATGAA
5432247 TAATTAGATTCAT
1 TAATTAGATTCAT
5432260 TAAATTTGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
15 1 0.03
16 21 0.60
17 13 0.37
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (16 bp):
TAATTAGATTCATGAA
Found at i:5443009 original size:28 final size:28
Alignment explanation
Indices: 5442952--5443015 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
5442942 TGATAAAAGT
* *
5442952 ATTTTAAAATTTTTTATGTAATTATTAA
1 ATTTTAAAATTTTTAATATAATTATTAA
*
5442980 ATTTTAAAATTTTTAATATGA-TATTGAA
1 ATTTTAAAATTTTTAATATAATTATT-AA
5443008 ATTATTAA
1 ATT-TTAA
5443016 TTATATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 4 0.13
28 23 0.74
29 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (28 bp):
ATTTTAAAATTTTTAATATAATTATTAA
Found at i:5443485 original size:2 final size:2
Alignment explanation
Indices: 5443478--5443502 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5443468 CAAATAAATA
5443478 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
5443503 ATCTTCTCAG
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:5447569 original size:23 final size:21
Alignment explanation
Indices: 5447526--5447574 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
5447516 AAATTATTTT
5447526 TATATTAATAATATAAAACAA
1 TATATTAATAATATAAAACAA
**
5447547 TATATATAATAATAGTAGTACAA
1 TATAT-TAATAATA-TAAAACAA
5447570 TATAT
1 TATAT
5447575 CATTATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.21
22 8 0.33
23 11 0.46
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (21 bp):
TATATTAATAATATAAAACAA
Found at i:5447998 original size:22 final size:23
Alignment explanation
Indices: 5447964--5448011 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
5447954 ATGAATATAT
* * *
5447964 AATAATATATTATATTGATAATA
1 AATAACATATTATAATGATAAGA
5447987 AATAACAT-TTATAATGATAAGA
1 AATAACATATTATAATGATAAGA
5448009 AAT
1 AAT
5448012 TATGTGATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (23 bp):
AATAACATATTATAATGATAAGA
Found at i:5449259 original size:18 final size:19
Alignment explanation
Indices: 5449227--5449264 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
5449217 TTATTCGTAT
*
5449227 TTATTTATGTATATT-TTA
1 TTATTTATATATATTATTA
*
5449245 TTATTTATATTTATTATTA
1 TTATTTATATATATTATTA
5449264 T
1 T
5449265 CATATTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TTATTTATATATATTATTA
Found at i:5451284 original size:2 final size:2
Alignment explanation
Indices: 5451273--5451310 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
5451263 TGTAAATTAC
5451273 TA TA TA -A 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 TA TA TA T
5451311 TAGATTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5454444 original size:42 final size:42
Alignment explanation
Indices: 5454397--5454476 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
5454387 CCAACGATGA
*
5454397 TATTGATTTAAGAAAAAAAAAAGGATAAAATATTTGTTATGG
1 TATTGATTTAAAAAAAAAAAAAGGATAAAATATTTGTTATGG
*
5454439 TATTGATTTAAAAAAAAAAAAAGGGTAAAATATTTGTT
1 TATTGATTTAAAAAAAAAAAAAGGATAAAATATTTGTT
5454477 CTTTAAACGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (42 bp):
TATTGATTTAAAAAAAAAAAAAGGATAAAATATTTGTTATGG
Found at i:5461257 original size:21 final size:22
Alignment explanation
Indices: 5461219--5461263 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
5461209 TTACTGATTT
* *
5461219 TAAAATTTTTATATTATTTTAA
1 TAAAATTTTAATATTATTTAAA
5461241 TAAAATTTTAATA-TATTTAAA
1 TAAAATTTTAATATTATTTAAA
5461262 TA
1 TA
5461264 GATTTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAAAATTTTAATATTATTTAAA
Found at i:5461314 original size:19 final size:18
Alignment explanation
Indices: 5461292--5461330 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
5461282 TTAATTATTT
*
5461292 TATAAAAATTTAAAAAATA
1 TATAAAAATAT-AAAAATA
5461311 TATAAAAATATAAAAATA
1 TATAAAAATATAAAAATA
5461329 TA
1 TA
5461331 ATTCGATTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TATAAAAATATAAAAATA
Found at i:5466838 original size:18 final size:16
Alignment explanation
Indices: 5466820--5466858 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
5466810 ATTTAGTTAT
5466820 TATTTTTATTTATTGTA
1 TATTTTTATTT-TTGTA
5466837 T-TTTTTATTTTTGTAA
1 TATTTTTATTTTTGT-A
5466853 TATTTT
1 TATTTT
5466859 ACTTCTGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.20
16 11 0.55
17 5 0.25
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (16 bp):
TATTTTTATTTTTGTA
Found at i:5470695 original size:13 final size:13
Alignment explanation
Indices: 5470677--5470701 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5470667 AACTCTCCCT
5470677 TCTATCTTTTCTC
1 TCTATCTTTTCTC
5470690 TCTATCTTTTCT
1 TCTATCTTTTCT
5470702 GGTTCTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (13 bp):
TCTATCTTTTCTC
Found at i:5471665 original size:34 final size:34
Alignment explanation
Indices: 5471617--5471682 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
5471607 AAAAAAAAAT
*
5471617 GTTTCGATCAAGCATTTCATCAAACACTTTTTGA
1 GTTTCAATCAAGCATTTCATCAAACACTTTTTGA
* *
5471651 GTTTCAATCGAGCATTTCATCAAATACTTTTT
1 GTTTCAATCAAGCATTTCATCAAACACTTTTT
5471683 AAGCTTCATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.41
Consensus pattern (34 bp):
GTTTCAATCAAGCATTTCATCAAACACTTTTTGA
Found at i:5472701 original size:21 final size:21
Alignment explanation
Indices: 5472675--5472716 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5472665 TCATAGCAAC
5472675 AACCTTGTATACTCCCCTTTG
1 AACCTTGTATACTCCCCTTTG
5472696 AACCTTGTATACTCCCCTTTG
1 AACCTTGTATACTCCCCTTTG
5472717 GAGTGCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.10, T:0.38
Consensus pattern (21 bp):
AACCTTGTATACTCCCCTTTG
Found at i:5475626 original size:17 final size:16
Alignment explanation
Indices: 5475604--5475638 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
5475594 ATTTTTATTA
5475604 TTATTTATCTATTTCTT
1 TTATTTATCTATTT-TT
5475621 TTATTTATCTATTTTT
1 TTATTTATCTATTTTT
5475637 TT
1 TT
5475639 GTTGTTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTTATCTATTTTT
Found at i:5476072 original size:6 final size:6
Alignment explanation
Indices: 5476061--5476125 Score: 57
Period size: 6 Copynumber: 11.5 Consensus size: 6
5476051 TTTAATATTC
* * * * *
5476061 TTTTAT TTTTAT TTTTA- TTTTAC TTTTCT TTAT-T TTTTAT TTTCAC
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
5476107 TTTTA- TTTTA- TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTT
5476126 CTTTAAATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
5 19 0.39
6 30 0.61
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:5476075 original size:5 final size:5
Alignment explanation
Indices: 5476061--5476125 Score: 58
Period size: 5 Copynumber: 11.8 Consensus size: 5
5476051 TTTAATATTC
* *
5476061 TTTTA TTTTTA TTTTTA TTTTA CTTTTC TTTATT TTTTA TTTTCA CTTTTA
1 TTTTA -TTTTA -TTTTA TTTTA -TTTTA TTT-TA TTTTA TTTT-A -TTTTA
5476112 TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTT
5476126 CTTTAAATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
5 27 0.52
6 21 0.40
7 4 0.08
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:5476089 original size:28 final size:28
Alignment explanation
Indices: 5476058--5476125 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
5476048 TTGTTTAATA
*
5476058 TTCTTTTATTTTTATTTTTA-TTTTACTT
1 TTCTTTTATTTTTATTTTCACTTTTA-TT
5476086 TTC-TTTATTTTTTATTTTCACTTTTATT
1 TTCTTTTA-TTTTTATTTTCACTTTTATT
*
5476114 TTATTTTATTTT
1 TTCTTTTATTTT
5476126 CTTTAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 4 0.11
28 22 0.63
29 9 0.26
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (28 bp):
TTCTTTTATTTTTATTTTCACTTTTATT
Found at i:5476100 original size:22 final size:22
Alignment explanation
Indices: 5476060--5476129 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
5476050 GTTTAATATT
*
5476060 CTTTTATTTTTATTTTTATTTTA
1 CTTTTATTTAT-TTTTTATTTTA
*
5476083 CTTTTCTTTATTTTTTATTTTCA
1 CTTTTATTTATTTTTTATTTT-A
*
5476106 CTTTTATTT-TATTTTATTTT-
1 CTTTTATTTATTTTTTATTTTA
5476126 CTTT
1 CTTT
5476130 AAATAAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 4 0.10
22 20 0.48
23 18 0.43
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (22 bp):
CTTTTATTTATTTTTTATTTTA
Found at i:5476111 original size:34 final size:34
Alignment explanation
Indices: 5476056--5476120 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
5476046 ATTTGTTTAA
* *
5476056 TATTCTTTTATTTTTATTTTTATTTTACTTTTCTT
1 TATTCTTTTATTTTCACTTTTATTTTA-TTTTCTT
5476091 TATT-TTTTATTTTCACTTTTATTTTATTTT
1 TATTCTTTTATTTTCACTTTTATTTTATTTT
5476121 ATTTTCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 4 0.14
34 20 0.71
35 4 0.14
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (34 bp):
TATTCTTTTATTTTCACTTTTATTTTATTTTCTT
Found at i:5476193 original size:59 final size:58
Alignment explanation
Indices: 5476122--5476823 Score: 664
Period size: 59 Copynumber: 12.1 Consensus size: 58
5476112 TTTTATTTTA
* *
5476122 TTTTCTT-TAAATAAA-ATTAAAAAATATATATTTTTGGGAAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAAATAAATTTTAAAAAA-A-ATATTTTTGGGAAAAAGTTGAAAGTATCAAT
* * ** **
5476180 TTTCCTTGAAAATAAGCTTTCCAAAAAATATTTTTAGGG-AAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAAATAAATTTTAAAAAAAATATTTTT-GGGAAAAAGTTGAAAGTATCAAT
* * *
5476238 TTTCCTTAAAAATAAATTTTTAAAAAAAAAAGTTTTGAGGAAAAAGTTGAAAGTATCAA-
1 TTTTCTTAAAAATAAA-TTTTAAAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAAT
* * *
5476297 TTTTCTTAAAAATAAGTTTTTAAAAAAAGATTTTTGAGG-AAAAGTTGAAAGTATCAA-
1 TTTTCTTAAAAATAAATTTTAAAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAAT
* * * * *
5476354 TTTTCTTGAAAATAAACTTTT-TAAAAAATATTTTTAGAAAAAAATTGAAAGTATCAA-
1 TTTTCTTAAAAATAAA-TTTTAAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAAT
** * * *
5476411 TTTTCTTTAAAAATAAATTTTCAAAAAAGTTTTTTTTTTAGG-AAAAGTTAAAAGTATCAAT
1 TTTTC-TTAAAAATAAATTTT-AAAAAA--AATATTTTTGGGAAAAAGTTGAAAGTATCAAT
* * * ** * *
5476472 TTTTCTTGAAATTAAAGTTTCCAAAAAATATTTTTGGGGAAATGTTGAAAGTATCAAT
1 TTTTCTTAAAAATAAATTTTAAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAAT
* * *
5476530 TTTTCTTAAAAATAAATTTTCAAAAAAAGTTTTTTTGAGAAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAAATAAATTTT-AAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAAT
* * * * *
5476589 TTTTCTTAAAAACT---TTCT--AAAAAATATTTTTGGAAAAAAATTTAAAATATCAA-
1 TTTTCTTAAAAA-TAAATTTTAAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAAT
* * * ** *
5476642 TTTTCTTTAAAAATAAATTTCAAAAAAAGTTTTTTTTTGAGGAAAGTTGAAAGTATCAAT
1 TTTTC-TTAAAAATAAATTTTAAAAAAAATATTTTTGGGA-AAAAGTTGAAAGTATCAAT
** * *
5476702 TTTTCTCGAAATTAAAGTTTT-CAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAAATAAA-TTTTAAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAAT
* *
5476760 TTTTCTTAAAAATAAATTTTCAAAAAAAGTTTTTTTGAGG-AAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAAATAAATTTT-AAAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAAT
5476819 TTTTC
1 TTTTC
5476824 CTGCATAAAA
Statistics
Matches: 526, Mismatches: 89, Indels: 57
0.78 0.13 0.08
Matches are distributed among these distances:
53 6 0.01
54 35 0.07
56 3 0.01
57 85 0.16
58 159 0.30
59 162 0.31
60 63 0.12
61 13 0.02
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (58 bp):
TTTTCTTAAAAATAAATTTTAAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAAT
Found at i:5476224 original size:58 final size:57
Alignment explanation
Indices: 5476149--5476823 Score: 647
Period size: 58 Copynumber: 11.6 Consensus size: 57
5476139 TAAAAAATAT
* * * *
5476149 ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCCAAAAA
1 ATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTCAAAAAA
* * *
5476207 ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTTAAAAAAA
1 ATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAGTTTTCAAAAAA
* * *
5476266 AAAGTTTTGAGGAAAAAGTTGAAAGTATCAA-TTTTCTTAAAAATAAGTTTTTAAAAAA
1 ATATTTTTG-GG-AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTCAAAAAA
* * * *
5476324 AGATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCTTGAAAATAAACTTTT-TAAAAA
1 ATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAGTTTTCAAAAAA
** * *
5476381 ATATTTTTAGAAAAAAATTGAAAGTATCAA-TTTTCTTTAAAAATAAATTTTCAAAAAA
1 ATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTTC-TTAAAAATAAGTTTTCAAAAAA
* * * * * * *
5476439 GTTTTTTTTTTAGGAAAAGTTAAAAGTATCAATTTTTCTTGAAATTAAAG-TTTCCAAAAA
1 ---ATATTTTTGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAGTTTTCAAAAAA
* *
5476499 ATATTTTTGGGGAAATGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAA
1 ATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTCAAAAAA
* * * *
5476557 AGTTTTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT--AAA-AA-CTTTCTAAAAA
1 A-TATTTTTG-GGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTCAAAAAA
* * * * *
5476612 ATATTTTTGGAAAAAAATTTAAAATATCAA-TTTTCTTTAAAAATAA-ATTTCAAAAAA
1 ATATTTTTGG-GAAAAGTTGAAAGTATCAATTTTTC-TTAAAAATAAGTTTTCAAAAAA
* ** *
5476669 AGTTTTTTTTTGAGG-AAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTTC-AAAAA
1 A---TATTTTTG-GGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAGTTTTCAAAAAA
*
5476729 ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAA
1 ATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTCAAAAAA
*
5476787 AGTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC
1 A-TATTTTTG-GGAAAAGTTGAAAGTATCAATTTTTC
5476824 CTGCATAAAA
Statistics
Matches: 515, Mismatches: 68, Indels: 67
0.79 0.10 0.10
Matches are distributed among these distances:
53 6 0.01
54 25 0.05
55 10 0.02
56 7 0.01
57 107 0.21
58 156 0.30
59 115 0.22
60 71 0.14
61 18 0.03
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (57 bp):
ATATTTTTGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTCAAAAAA
Found at i:5476323 original size:117 final size:115
Alignment explanation
Indices: 5476149--5476823 Score: 848
Period size: 117 Copynumber: 5.8 Consensus size: 115
5476139 TAAAAAATAT
* ** * *
5476149 ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCCAAAAAA-TATTT
1 ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTT-CTTAAAAATAAATTTTCAAAAAAAGTTTTT
* *
5476213 TT-AGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTTAAAAAAA
65 TTGA-GGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAATTTTT--AAAAA
* * * * *
5476266 AAAGTTTTGAGGAAAAAGTTGAAAGTATCAATTTTCTTAAAAATAAGTTTTTAAAAAAAG-ATTT
1 ATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCTTAAAAATAAATTTTCAAAAAAAGTTTTT
5476330 TTGAGGAAAAGTTGAAAGTATCAA-TTTTCTTGAAAATAAACTTTTTAAAAA
65 TTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAA-TTTTTAAAAA
* * *
5476381 ATATTTTTAGAAAAAAATTGAAAGTATCAATTTTCTTTAAAAATAAATTTTC-AAAAAAGTTTTT
1 ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTC-TTAAAAATAAATTTTCAAAAAAAG--TTT
* * * **
5476445 TTTTTAGGAAAAGTTAAAAGTATCAATTTTTCTTGAAATTAAAGTTTCCAAAAA
63 TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAA-TTTTTAAAAA
* *
5476499 ATATTTTTGGGGAAATGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAAGTTTTT
1 ATATTTTTGGGAAAAAGTTGAAAGTATCAA-TTTTCTTAAAAATAAATTTTCAAAAAAAGTTTTT
* * *
5476564 TTGAGAAAAAGTTGAAAGTATCAATTTTTCTT--AAA-AACTTTCTAAAAA
65 TTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAATTTTTAAAAA
* * * *
5476612 ATATTTTTGGAAAAAAATTTAAAATATCAATTTTCTTTAAAAATAAA-TTTCAAAAAAAGTTTTT
1 ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTC-TTAAAAATAAATTTTCAAAAAAAG--TTT
* * *
5476676 TTTTGAGG-AAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTTCAAAAA
63 TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAA-TTTTTAAAAA
5476729 ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAAGTTTTT
1 ATATTTTTGGGAAAAAGTTGAAAGTATCAA-TTTTCTTAAAAATAAATTTTCAAAAAAAGTTTTT
5476794 TTGAGGAAAAGTTGAAAGTATCAATTTTTC
65 TTGAGGAAAAGTTGAAAGTATCAATTTTTC
5476824 CTGCATAAAA
Statistics
Matches: 488, Mismatches: 49, Indels: 42
0.84 0.08 0.07
Matches are distributed among these distances:
112 17 0.03
113 68 0.14
114 43 0.09
115 29 0.06
116 27 0.06
117 185 0.38
118 107 0.22
119 12 0.02
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (115 bp):
ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCTTAAAAATAAATTTTCAAAAAAAGTTTTTT
TGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAATTTTTAAAAA
Found at i:5477969 original size:2 final size:2
Alignment explanation
Indices: 5477962--5478002 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
5477952 GCACCTTATC
*
5477962 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5478002 A
1 A
5478003 ATTACCAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5479779 original size:22 final size:23
Alignment explanation
Indices: 5479736--5479779 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
5479726 TAAAATTTTT
* * *
5479736 TAAAATTATTTTTACTATTTAAC
1 TAAAATTATATTTAATAATTAAC
5479759 TAAAATTA-ATTTAATAATTAA
1 TAAAATTATATTTAATAATTAA
5479780 TTAATTAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAAATTATATTTAATAATTAAC
Found at i:5480417 original size:21 final size:22
Alignment explanation
Indices: 5480370--5480429 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
5480360 CAACTAATTT
5480370 TTTAAATATTTAAATATGTTAAGA
1 TTTAAAT-TTT-AATATGTTAAGA
5480394 TTTAAATTTTAAT-TGTTATA-A
1 TTTAAATTTTAATATGTTA-AGA
*
5480415 TTTTAATTTTAATAT
1 TTTAAATTTTAATAT
5480430 TTTATTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 18 0.55
22 5 0.15
23 3 0.09
24 7 0.21
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
TTTAAATTTTAATATGTTAAGA
Found at i:5481751 original size:17 final size:20
Alignment explanation
Indices: 5481717--5481764 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 20
5481707 GAAATTAATC
5481717 AAATATTATTTATAAATATA
1 AAATATTATTTATAAATATA
*
5481737 AAATATTTTTTAATATAAATATA
1 AAATA-TTATT--TATAAATATA
5481760 AAATA
1 AAATA
5481765 AATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 5 0.21
21 4 0.17
23 15 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATATTATTTATAAATATA
Found at i:5482876 original size:23 final size:22
Alignment explanation
Indices: 5482834--5482878 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
5482824 TAAAAAAATT
* *
5482834 TAAATAAATAAATAAGATTTGA
1 TAAAAAAATAAATAAAATTTGA
5482856 TAAAAAAATAAAATAAAATTTGA
1 TAAAAAAAT-AAATAAAATTTGA
5482879 GTTTTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (22 bp):
TAAAAAAATAAATAAAATTTGA
Found at i:5485958 original size:23 final size:23
Alignment explanation
Indices: 5485932--5485976 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
5485922 AAAAAAATAA
*
5485932 TTATTATAATTATGATTAAAAAT
1 TTATCATAATTATGATTAAAAAT
5485955 TTATCATAATTATGATTAAAAA
1 TTATCATAATTATGATTAAAAA
5485977 AATTTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (23 bp):
TTATCATAATTATGATTAAAAAT
Found at i:5485977 original size:25 final size:25
Alignment explanation
Indices: 5485918--5486006 Score: 94
Period size: 25 Copynumber: 3.6 Consensus size: 25
5485908 ATTTTGATAA
*
5485918 GATTAAAAAAATAATTATTATAATTAT
1 GATTAAAAAAAT--TTATAATAATTAT
*
5485945 GATT--AAAAATTTATCATAATTAT
1 GATTAAAAAAATTTATAATAATTAT
*
5485968 GATTAAAAAAATTTATAAAAATTTAT
1 GATTAAAAAAATTTATAATAA-TTAT
*
5485994 G-TTAAATAAATTT
1 GATTAAAAAAATTT
5486007 TATTAAAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
23 16 0.29
25 30 0.55
26 5 0.09
27 4 0.07
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (25 bp):
GATTAAAAAAATTTATAATAATTAT
Found at i:5486014 original size:26 final size:26
Alignment explanation
Indices: 5485918--5486016 Score: 82
Period size: 25 Copynumber: 3.9 Consensus size: 26
5485908 ATTTTGATAA
* *
5485918 GATTAAAAAAATAATTATTATAA-TTAT
1 GATTAAAAAAAT--TTATAAAAATTTAT
* *
5485945 GATT--AAAAATTTATCATAA-TTAT
1 GATTAAAAAAATTTATAAAAATTTAT
5485968 GATTAAAAAAATTTATAAAAATTTAT
1 GATTAAAAAAATTTATAAAAATTTAT
* *
5485994 G-TTAAATAAATTTTATTAAAATT
1 GATTAAA-AAAATTTATAAAAATT
5486017 AATATTTAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
23 16 0.25
25 24 0.38
26 19 0.30
27 4 0.06
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (26 bp):
GATTAAAAAAATTTATAAAAATTTAT
Found at i:5487136 original size:29 final size:29
Alignment explanation
Indices: 5487103--5487165 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
5487093 TTATCATTTT
* *
5487103 TTTTTAATGTCTTAAAATTATGTTTTAATA
1 TTTTTAATATC-TAAAACTATGTTTTAATA
* * *
5487133 TTTTTAATATCTAAAACTCTTTTTTTATA
1 TTTTTAATATCTAAAACTATGTTTTAATA
5487162 TTTT
1 TTTT
5487166 AAAATTATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.60
Consensus pattern (29 bp):
TTTTTAATATCTAAAACTATGTTTTAATA
Found at i:5492879 original size:21 final size:22
Alignment explanation
Indices: 5492853--5492906 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
5492843 AATATATAAA
5492853 AATAATATTAAT-TAAAAATTT
1 AATAATATTAATATAAAAATTT
*
5492874 AATAATAATT-ATATATAAATTT
1 AATAAT-ATTAATATAAAAATTT
*
5492896 AATGATATTAA
1 AATAATATTAA
5492907 AAATTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATAATATTAATATAAAAATTT
Found at i:5497208 original size:4 final size:4
Alignment explanation
Indices: 5497199--5497246 Score: 96
Period size: 4 Copynumber: 12.0 Consensus size: 4
5497189 TTGCTTTTAC
5497199 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5497247 TATATATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:5502089 original size:2 final size:2
Alignment explanation
Indices: 5502084--5502112 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5502074 AGTATATATA
5502084 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
5502113 ATGAAATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:5509685 original size:29 final size:27
Alignment explanation
Indices: 5509623--5509677 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
5509613 ATGATTGTTC
*
5509623 AAAAATTTAGTAAAATTTGTTAAAAAA
1 AAAAATTTAGTAAAATTTGATAAAAAA
5509650 AGGAAAATTTA-TATAAATTTGATAAAAA
1 A--AAAATTTAGTA-AAATTTGATAAAAA
5509678 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 1 0.04
28 2 0.08
29 21 0.88
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (27 bp):
AAAAATTTAGTAAAATTTGATAAAAAA
Found at i:5514150 original size:16 final size:16
Alignment explanation
Indices: 5514129--5514161 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5514119 TATTATTGAA
*
5514129 AAAATAATTATTTATT
1 AAAATAAATATTTATT
5514145 AAAATAAATATTTATT
1 AAAATAAATATTTATT
5514161 A
1 A
5514162 TTTACTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAATAAATATTTATT
Found at i:5514162 original size:19 final size:18
Alignment explanation
Indices: 5514119--5514163 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
5514109 TATATAATCA
*
5514119 TATTATTGAAAAAATAAT
1 TATTATTAAAAAAATAAT
*
5514137 TATTTATTAAAATAAATATT
1 TA-TTATTAAAA-AAATAAT
5514157 TATTATT
1 TATTATT
5514164 TACTTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 13 0.57
20 8 0.35
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TATTATTAAAAAAATAAT
Found at i:5514518 original size:22 final size:23
Alignment explanation
Indices: 5514471--5514515 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5514461 AAGCAATCGT
5514471 TTTTAAAATATAACATCTAATAA
1 TTTTAAAATATAACATCTAATAA
*
5514494 TTTTAAAATTTAA-ATCTCAATA
1 TTTTAAAATATAACATCT-AATA
5514516 TTTATTATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (23 bp):
TTTTAAAATATAACATCTAATAA
Found at i:5515657 original size:19 final size:21
Alignment explanation
Indices: 5515628--5515674 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
5515618 CAAATGCATA
*
5515628 ATTTCATTTAATTTTATA-TT
1 ATTTCATTTAATTATATACTT
5515648 ATTT-ATTTAATTATATACTT
1 ATTTCATTTAATTATATACTT
5515668 A-TTCATT
1 ATTTCATT
5515675 ACTTTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTCATTTAATTATATACTT
Found at i:5515977 original size:2 final size:2
Alignment explanation
Indices: 5515970--5516011 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
5515960 GCTTCTCTTT
5515970 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5516011 T
1 T
5516012 TACAACGTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5518124 original size:16 final size:15
Alignment explanation
Indices: 5518100--5518129 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5518090 ATTCATACAT
5518100 TATAAAATTTAAATG
1 TATAAAATTTAAATG
5518115 TATAATAATTTAAAT
1 TATAA-AATTTAAAT
5518130 AATTACATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
TATAAAATTTAAATG
Found at i:5518267 original size:13 final size:13
Alignment explanation
Indices: 5518252--5518291 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
5518242 TTTATTGATA
5518252 TTTTAT-TTTTAT
1 TTTTATATTTTAT
5518264 ATTTTATATTTTAT
1 -TTTTATATTTTAT
5518278 TTTTATATTTTAT
1 TTTTATATTTTAT
5518291 T
1 T
5518292 AAAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATATTTTAT
Found at i:5518270 original size:7 final size:7
Alignment explanation
Indices: 5518249--5518290 Score: 70
Period size: 7 Copynumber: 6.3 Consensus size: 7
5518239 TGTTTTATTG
5518249 ATATTTT
1 ATATTTT
5518256 AT-TTTT
1 ATATTTT
5518262 ATATTTT
1 ATATTTT
5518269 ATATTTT
1 ATATTTT
5518276 AT-TTTT
1 ATATTTT
5518282 ATATTTT
1 ATATTTT
5518289 AT
1 AT
5518291 TAAAAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.36
7 21 0.64
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
ATATTTT
Found at i:5518274 original size:20 final size:20
Alignment explanation
Indices: 5518249--5518290 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
5518239 TGTTTTATTG
5518249 ATATTTTATTTTTATATTTT
1 ATATTTTATTTTTATATTTT
5518269 ATATTTTATTTTTATATTTT
1 ATATTTTATTTTTATATTTT
5518289 AT
1 AT
5518291 TAAAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
ATATTTTATTTTTATATTTT
Found at i:5530283 original size:20 final size:20
Alignment explanation
Indices: 5530254--5530536 Score: 170
Period size: 20 Copynumber: 13.9 Consensus size: 20
5530244 GCAAATAGAC
5530254 ATGCAATTAAATATATAATA
1 ATGCAATTAAATATATAATA
* *
5530274 ATGTAATT-AATAATATAAAA
1 ATGCAATTAAAT-ATATAATA
* * *
5530294 CACGTC-ATTAAATATCTAATT
1 -ATG-CAATTAAATATATAATA
* *
5530315 ATGCAATTAACA-ATGTAAAA
1 ATGCAATTAA-ATATATAATA
*
5530335 CATGCAATTAAATATATAAATT
1 -ATGCAATTAAATATAT-AATA
* * *
5530357 ATACAATTAAAAATATAAAA
1 ATGCAATTAAATATATAATA
* * * *
5530377 CATGCAAATATATATATTATC
1 -ATGCAATTAAATATATAATA
*
5530398 ATGCAATTAACA-ATATAAAA
1 ATGCAATTAA-ATATATAATA
* * *
5530418 CATGCAA--ATATATATTATC
1 -ATGCAATTAAATATATAATA
* *
5530437 ATGCAATTAAATATATTATC
1 ATGCAATTAAATATATAATA
5530457 ATGCAATTAACA-ATATAA-A
1 ATGCAATTAA-ATATATAATA
* *
5530476 CATGCAACTAAATATATAATC
1 -ATGCAATTAAATATATAATA
*
5530497 ATGCAATTAACA-ATATAAAA
1 ATGCAATTAA-ATATATAATA
5530517 CATGCAATTAAATATATAAT
1 -ATGCAATTAAATATATAAT
5530537 CATATAATCA
Statistics
Matches: 198, Mismatches: 43, Indels: 43
0.70 0.15 0.15
Matches are distributed among these distances:
18 7 0.04
19 11 0.06
20 99 0.50
21 76 0.38
22 5 0.03
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (20 bp):
ATGCAATTAAATATATAATA
Found at i:5530305 original size:41 final size:41
Alignment explanation
Indices: 5530252--5530514 Score: 220
Period size: 41 Copynumber: 6.5 Consensus size: 41
5530242 ATGCAAATAG
* * *
5530252 ACATGCAATTAAATATATAATAATGTAATTAATAATATAAA
1 ACATGCAATTAAATATATAATTATGCAATTAACAATATAAA
* * *
5530293 ACACGTC-ATTAAATATCTAATTATGCAATTAACAATGTAAA
1 ACATG-CAATTAAATATATAATTATGCAATTAACAATATAAA
* *
5530334 ACATGCAATTAAATATATAAATTATACAATTAAAAATATAAA
1 ACATGCAATTAAATATAT-AATTATGCAATTAACAATATAAA
* * * *
5530376 ACATGCAAATATATATATTATCATGCAATTAACAATATAAA
1 ACATGCAATTAAATATATAATTATGCAATTAACAATATAAA
* * * *
5530417 ACATGCAA--ATATATATTATCATGCAATT-A-AATATATTA
1 ACATGCAATTAAATATATAATTATGCAATTAACAATATA-AA
* ** *
5530455 TCATGCAATTAACA-ATATAAACATGCAACT-A-AATATATAA
1 ACATGCAATTAA-ATATATAATTATGCAATTAACAATATA-AA
*
5530495 TCATGCAATTAACA-ATATAA
1 ACATGCAATTAA-ATATATAA
5530515 AACATGCAAT
Statistics
Matches: 191, Mismatches: 24, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
37 6 0.03
38 9 0.05
39 20 0.10
40 44 0.23
41 75 0.39
42 37 0.19
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (41 bp):
ACATGCAATTAAATATATAATTATGCAATTAACAATATAAA
Found at i:5530402 original size:83 final size:82
Alignment explanation
Indices: 5530252--5530424 Score: 222
Period size: 83 Copynumber: 2.1 Consensus size: 82
5530242 ATGCAAATAG
** * * * *
5530252 ACATGCAATTAAATATATAATAATGTAATTAATAATATAAAACACGTCATTAAATATCTAATTAT
1 ACATGCAATTAAATATATAATAATACAATTAAAAATATAAAACACGTCAATAAATATATAATCAT
*
5530317 GCAATTAACAATGTAAA
66 GCAATTAACAATATAAA
* * * *
5530334 ACATGCAATTAAATATATAAATTATACAATTAAAAATATAAAACATG-CAAATATATATATTATC
1 ACATGCAATTAAATATAT-AATAATACAATTAAAAATATAAAACACGTC-AATAAATATATAATC
5530398 ATGCAATTAACAATATAAA
64 ATGCAATTAACAATATAAA
5530417 ACATGCAA
1 ACATGCAA
5530425 ATATATATTA
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
82 19 0.24
83 59 0.76
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.31
Consensus pattern (82 bp):
ACATGCAATTAAATATATAATAATACAATTAAAAATATAAAACACGTCAATAAATATATAATCAT
GCAATTAACAATATAAA
Found at i:5530457 original size:59 final size:59
Alignment explanation
Indices: 5530253--5530506 Score: 208
Period size: 62 Copynumber: 4.2 Consensus size: 59
5530243 TGCAAATAGA
* * * * * ** *
5530253 CATGCAATTAAATATATAATAATGTAATTAATAATATAAAACACGTCATTAAATATCTAAT
1 CATGCAATTAAATATATTATCATGCAATTAACAATAT-AAACATG-CAACAAATATATAAT
* * * * * * * * *
5530314 TATGCAATTAACA-ATGTAAAACATGCAATTAA-ATATATAAATTATACAATTAAAAATATAAAA
1 CATGCAATTAA-ATATAT-TATCATGCAATTAACA-ATATAAA-CATGCAA-CAAATATAT-AAT
* * * *
5530377 CATGCAAATATATATATTATCATGCAATTAACAATATAAAACATGCAA-ATATATATTAT
1 CATGCAATTAAATATATTATCATGCAATTAACAATAT-AAACATGCAACAAATATATAAT
5530436 CATGCAATTAAATATATTATCATGCAATTAACAATATAAACATGCAACTAAATATATAAT
1 CATGCAATTAAATATATTATCATGCAATTAACAATATAAACATGCAAC-AAATATATAAT
5530496 CATGCAATTAA
1 CATGCAATTAA
5530507 CAATATAAAA
Statistics
Matches: 154, Mismatches: 28, Indels: 23
0.75 0.14 0.11
Matches are distributed among these distances:
58 10 0.06
59 36 0.23
60 26 0.17
61 19 0.12
62 46 0.30
63 17 0.11
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (59 bp):
CATGCAATTAAATATATTATCATGCAATTAACAATATAAACATGCAACAAATATATAAT
Found at i:5530491 original size:99 final size:101
Alignment explanation
Indices: 5530335--5530523 Score: 301
Period size: 99 Copynumber: 1.9 Consensus size: 101
5530325 CAATGTAAAA
* * *
5530335 CATGCAATTAAATATATAAATTATACAATTAAAAATATAAAACATGCAAATATATATATTATCAT
1 CATGCAATTAAATATATAAATCATACAATTAAAAATATAAAACATGCAAATAAATATATAATCAT
5530400 GCAATTAACAATATAAAACATGCAAATATATATTAT
66 GCAATTAACAATATAAAACATGCAAATATATATTAT
* * * *
5530436 CATGCAATTAAATATAT-TATCATGCAATTAACAATAT-AAACATGCAACTAAATATATAATCAT
1 CATGCAATTAAATATATAAATCATACAATTAAAAATATAAAACATGCAAATAAATATATAATCAT
5530499 GCAATTAACAATATAAAACATGCAA
66 GCAATTAACAATATAAAACATGCAA
5530524 TTAAATATAT
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
99 48 0.59
100 16 0.20
101 17 0.21
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (101 bp):
CATGCAATTAAATATATAAATCATACAATTAAAAATATAAAACATGCAAATAAATATATAATCAT
GCAATTAACAATATAAAACATGCAAATATATATTAT
Found at i:5531196 original size:17 final size:17
Alignment explanation
Indices: 5531164--5531195 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5531154 TCCCACATTT
5531164 CTCTTTTTTATTTTTTA
1 CTCTTTTTTATTTTTTA
5531181 CTCTTTTTT-TTTTTT
1 CTCTTTTTTATTTTTT
5531196 TTTTACCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.81
Consensus pattern (17 bp):
CTCTTTTTTATTTTTTA
Found at i:5532994 original size:18 final size:17
Alignment explanation
Indices: 5532971--5533018 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
5532961 ATTATATTAC
*
5532971 ATAATTATATTGTTAAAA
1 ATAATTAT-TTATTAAAA
5532989 ATAATTATTTATT-AAA
1 ATAATTATTTATTAAAA
* *
5533005 ATAAATATTCATTA
1 ATAATTATTTATTA
5533019 TTTATTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 14 0.54
17 4 0.15
18 8 0.31
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
ATAATTATTTATTAAAA
Found at i:5533496 original size:20 final size:20
Alignment explanation
Indices: 5533468--5533516 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
5533458 TAAATTTATA
* *
5533468 ATTTAAATATTATATTAAAT
1 ATTTTAATATCATATTAAAT
5533488 ATTTTAATATCATATTAAAT
1 ATTTTAATATCATATTAAAT
5533508 ATTTTAATA
1 ATTTTAATA
5533517 AATTTAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTTAATATCATATTAAAT
Found at i:5533524 original size:29 final size:26
Alignment explanation
Indices: 5533453--5533524 Score: 65
Period size: 32 Copynumber: 2.6 Consensus size: 26
5533443 TATTACATTA
5533453 TTTAATAAATTT-ATAATTTAAATAT
1 TTTAATAAATTTAATAATTTAAATAT
* *
5533478 TATATTAAATATTTTAATATCATATTAAATAT
1 TTTAAT-AA-A-TTTAATA--AT-TTAAATAT
5533510 TTTAATAAATTTAAT
1 TTTAATAAATTTAAT
5533525 GACCATTCGT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
25 4 0.11
26 2 0.06
27 1 0.03
28 3 0.08
29 9 0.25
30 1 0.03
31 4 0.11
32 12 0.33
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTAATAAATTTAATAATTTAAATAT
Found at i:5533686 original size:2 final size:2
Alignment explanation
Indices: 5533681--5533706 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5533671 TTATGAAAAA
5533681 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
5533707 TCAAAATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.