Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 178 of 190
Found at i:29881770 original size:12 final size:13
Alignment explanation
Indices: 29881743--29881775 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
29881733 GAAAGTGAGA
29881743 GAAATGTGAGCATG
1 GAAATG-GAGCATG
29881757 GAAATGGA-CATG
1 GAAATGGAGCATG
29881769 GAAATGG
1 GAAATGG
29881776 GATTTGGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 2 0.11
14 6 0.32
ACGTcount: A:0.39, C:0.06, G:0.36, T:0.18
Consensus pattern (13 bp):
GAAATGGAGCATG
Found at i:29883837 original size:33 final size:32
Alignment explanation
Indices: 29883796--29883859 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
29883786 ACATATTTTT
* *
29883796 AAATTTAATAATTCGTATATTTATATTATATA
1 AAATTTAATAATTCATATATTTATATAATATA
* *
29883828 AAATATTAATAATTTATTTATTTATATAATAT
1 AAAT-TTAATAATTCATATATTTATATAATAT
29883860 TTTATATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (32 bp):
AAATTTAATAATTCATATATTTATATAATATA
Found at i:29888947 original size:3 final size:3
Alignment explanation
Indices: 29888939--29888979 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
29888929 CAGAAAAGAC
29888939 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
29888980 CTCTTCGCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:29897906 original size:59 final size:59
Alignment explanation
Indices: 29897826--29897943 Score: 209
Period size: 59 Copynumber: 2.0 Consensus size: 59
29897816 GCTTCCTGTT
29897826 CCGACGGAAAGAATCAATGCATTTCAAGAATCGACTGTACACCTGGAACAAGCAGATTA
1 CCGACGGAAAGAATCAATGCATTTCAAGAATCGACTGTACACCTGGAACAAGCAGATTA
* * *
29897885 CCGATGGAAAGAATCAGTGCATTTCAAGAATCGACTGTATACCTGGAACAAGCAGATTA
1 CCGACGGAAAGAATCAATGCATTTCAAGAATCGACTGTACACCTGGAACAAGCAGATTA
29897944 AAAAAAATTC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.20
Consensus pattern (59 bp):
CCGACGGAAAGAATCAATGCATTTCAAGAATCGACTGTACACCTGGAACAAGCAGATTA
Found at i:29909908 original size:34 final size:34
Alignment explanation
Indices: 29909870--29909959 Score: 110
Period size: 34 Copynumber: 2.6 Consensus size: 34
29909860 AAACACTTAA
*
29909870 TTTTACATATAGAAATACTTATAAAAAT-ATTTAC
1 TTTTACATATAGAAATACTTA-AAAAATAAATTAC
* * *
29909904 TTTTACATATAAAAATACTTCAAAACATAAATTAG
1 TTTTACATATAGAAATACTT-AAAAAATAAATTAC
*
29909939 TCTTACATATAGAAATACTTA
1 TTTTACATATAGAAATACTTA
29909960 CTTTTACATA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
34 25 0.52
35 23 0.48
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (34 bp):
TTTTACATATAGAAATACTTAAAAAATAAATTAC
Found at i:29915092 original size:22 final size:23
Alignment explanation
Indices: 29915038--29915092 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
29915028 TTTTTTTTTT
* *
29915038 TTAAATTTGAGTTTTAGATCAGA
1 TTAAATTTGAGTTTTAAATCAAA
29915061 TTAAATTTGAGTTTTAAAT-AAA
1 TTAAATTTGAGTTTTAAATCAAA
*
29915083 TTTAATTTGA
1 TTAAATTTGA
29915093 TCTGATCTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 11 0.38
23 18 0.62
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (23 bp):
TTAAATTTGAGTTTTAAATCAAA
Found at i:29915160 original size:16 final size:15
Alignment explanation
Indices: 29915136--29915192 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
29915126 AATTAATTTT
29915136 ATATATTTATATAATA
1 ATAT-TTTATATAATA
* * *
29915152 ATATTTTTAAATATTT
1 ATA-TTTTATATAATA
*
29915168 ATATTTAATA-AATA
1 ATATTTTATATAATA
29915182 ATATTTTATAT
1 ATATTTTATAT
29915193 TTTAAAAAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
14 11 0.35
15 5 0.16
16 14 0.45
17 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATATTTTATATAATA
Found at i:29915202 original size:22 final size:21
Alignment explanation
Indices: 29915161--29915212 Score: 79
Period size: 22 Copynumber: 2.5 Consensus size: 21
29915151 AATATTTTTA
*
29915161 AATA-TTTATATTTAATAAAT
1 AATATTTTATATTTAAAAAAT
29915181 AATATTTTATATTTTAAAAAAT
1 AATATTTTATA-TTTAAAAAAT
29915203 AATATTTTAT
1 AATATTTTAT
29915213 TAATTTCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 4 0.14
21 6 0.21
22 19 0.66
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATATTTTATATTTAAAAAAT
Found at i:29919341 original size:26 final size:26
Alignment explanation
Indices: 29919311--29919360 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
29919301 CCTGTACAGC
29919311 TGAAACTGAAAGCAATGGTACAAAGT
1 TGAAACTGAAAGCAATGGTACAAAGT
29919337 TGAAACTGAAAGCAATGGTACAAA
1 TGAAACTGAAAGCAATGGTACAAA
29919361 ATTCTTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.48, C:0.12, G:0.22, T:0.18
Consensus pattern (26 bp):
TGAAACTGAAAGCAATGGTACAAAGT
Found at i:29923712 original size:4 final size:4
Alignment explanation
Indices: 29923703--29923727 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
29923693 CTAACAATCT
29923703 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
29923728 CATTGGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:29928732 original size:27 final size:27
Alignment explanation
Indices: 29928688--29928747 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
29928678 AAGATATTTT
29928688 TATAAATAAAAATATTTATAAAT-ATA
1 TATAAATAAAAATATTTATAAATAATA
* *
29928714 TATAAATTAAATATGTTTATAAATAATA
1 TATAAA-TAAAAATATTTATAAATAATA
*
29928742 AATAAA
1 TATAAA
29928748 ATATAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 6 0.21
27 15 0.52
28 8 0.28
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
TATAAATAAAAATATTTATAAATAATA
Found at i:29928767 original size:43 final size:43
Alignment explanation
Indices: 29928681--29928877 Score: 104
Period size: 43 Copynumber: 4.5 Consensus size: 43
29928671 AAATGATAAG
* ** *
29928681 ATATTTTTATAAATAAAAATATTTATAAATATATATAAATTAA
1 ATATGTTTATAAATAAAAATAAATATAAATATAAATAAATTAA
*
29928724 ATATGTTTATAAATAATAAATAAA-ATATAAT-TAAATAATTTAA
1 ATATGTTTATAAATAA-AAATAAATATA-AATATAAATAAATTAA
* * * * *
29928767 ATATATTAATCATAAATTAACAT-AA-ATAAATACAAAT-GATATAA
1 ATATGTT--T-ATAAATAAAAATAAATATAAATATAAATAAAT-TAA
* * * * *
29928811 AT-TAATTT-TAAATAAAATTAAAATAAAAAATAAAAATAATTTAA
1 ATAT-GTTTATAAATAAAAAT-AAAT-ATAAATATAAATAAATTAA
29928855 TTATAT-TTTATAAATAAAAATAA
1 --ATATGTTTATAAATAAAAATAA
29928878 TAAACAAATA
Statistics
Matches: 118, Mismatches: 19, Indels: 32
0.70 0.11 0.19
Matches are distributed among these distances:
40 8 0.07
42 3 0.03
43 39 0.33
44 38 0.32
45 10 0.08
46 19 0.16
47 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (43 bp):
ATATGTTTATAAATAAAAATAAATATAAATATAAATAAATTAA
Found at i:29928781 original size:20 final size:19
Alignment explanation
Indices: 29928738--29928798 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
29928728 GTTTATAAAT
*
29928738 AATAAATAAAATATAATTA
1 AATAAATTAAATATAATTA
*
29928757 AATAATTTAAATAT-ATTA
1 AATAAATTAAATATAATTA
29928775 ATCATAAATTAACATA-AA-TA
1 A--ATAAATTAA-ATATAATTA
29928795 AATA
1 AATA
29928799 CAAATGATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
18 8 0.23
19 12 0.34
20 11 0.31
21 4 0.11
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
AATAAATTAAATATAATTA
Found at i:29928792 original size:10 final size:9
Alignment explanation
Indices: 29928738--29928798 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
29928728 GTTTATAAAT
*
29928738 AATAAATAA
1 AATAAATTA
29928747 AATATAATTA
1 AATA-AATTA
*
29928757 AATAATTTA
1 AATAAATTA
*
29928766 AATATATTA
1 AATAAATTA
29928775 ATCATAAATTA
1 A--ATAAATTA
29928786 ACATAAA-TA
1 A-ATAAATTA
29928795 AATA
1 AATA
29928799 CAAATGATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
8 3 0.07
9 19 0.43
10 14 0.32
11 8 0.18
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (9 bp):
AATAAATTA
Found at i:29928826 original size:44 final size:44
Alignment explanation
Indices: 29928780--29928889 Score: 109
Period size: 45 Copynumber: 2.5 Consensus size: 44
29928770 TATTAATCAT
* * *
29928780 AAATTAACATAAATAAATACAAATGATATAAATTA-ATTTTAAATA
1 AAATTAAAATAAA-AAATAAAAATAAT-TAAATTATATTTTAAATA
*
29928825 AAATTAAAATAAAAAATAAAAATAATTTAATTATATTTTATAAATA
1 AAATTAAAATAAAAAATAAAAATAATTAAATTATA-TTT-TAAATA
*
29928871 AAA--ATAATAAACAAATAAA
1 AAATTAAAATAAA-AAATAAA
29928890 CAAATAAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
43 6 0.11
44 19 0.34
45 22 0.39
46 9 0.16
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.32
Consensus pattern (44 bp):
AAATTAAAATAAAAAATAAAAATAATTAAATTATATTTTAAATA
Found at i:29931966 original size:29 final size:30
Alignment explanation
Indices: 29931934--29931996 Score: 119
Period size: 29 Copynumber: 2.1 Consensus size: 30
29931924 TTTAATTTTT
29931934 TAAATAAATTTTTATATTTTTA-TTATATC
1 TAAATAAATTTTTATATTTTTATTTATATC
29931963 TAAATAAATTTTTATATTTTTATTTATATC
1 TAAATAAATTTTTATATTTTTATTTATATC
29931993 TAAA
1 TAAA
29931997 AAAGTTCTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 22 0.67
30 11 0.33
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (30 bp):
TAAATAAATTTTTATATTTTTATTTATATC
Found at i:29932009 original size:28 final size:29
Alignment explanation
Indices: 29931934--29932009 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
29931924 TTTAATTTTT
* *
29931934 TAAATAAATTTTTATATTTTTATTATATC
1 TAAATAAAGTTCTATATTTTTATTATATC
* *
29931963 TAAATAAATTTTTATATTTTTATTTATATC
1 TAAATAAAGTTCTATATTTTTA-TTATATC
29931993 TAAA-AAAGTTCT-TATTT
1 TAAATAAAGTTCTATATTT
29932010 CAAATGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
28 5 0.11
29 28 0.64
30 11 0.25
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (29 bp):
TAAATAAAGTTCTATATTTTTATTATATC
Found at i:29932095 original size:53 final size:51
Alignment explanation
Indices: 29932029--29932155 Score: 145
Period size: 53 Copynumber: 2.5 Consensus size: 51
29932019 AAATATATAT
* * * *
29932029 TAAAAGTTTATTTAAATATAAATTTAATAATTTATTTATATACAATTAAAA-A
1 TAAAATTTTATTTAAATATAAATTTAAAAAGTTATTGA-ATACAA-TAAAATA
**
29932081 TAAAAATTTTATTTAAATATAAA-TTAAAAAGTTATTGAATGTAATAAAATA
1 T-AAAATTTTATTTAAATATAAATTTAAAAAGTTATTGAATACAATAAAATA
29932132 TAAAATTTTATTT-AAT-TAAATTTA
1 TAAAATTTTATTTAAATATAAATTTA
29932156 TAAATTCATA
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
48 4 0.06
49 6 0.09
50 17 0.26
51 6 0.09
52 13 0.20
53 20 0.30
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (51 bp):
TAAAATTTTATTTAAATATAAATTTAAAAAGTTATTGAATACAATAAAATA
Found at i:29932103 original size:25 final size:24
Alignment explanation
Indices: 29932029--29932146 Score: 67
Period size: 24 Copynumber: 4.6 Consensus size: 24
29932019 AAATATATAT
* **
29932029 TAAAAGTTTATTTAAATATAAATT
1 TAAAAATTTATTTAAATATAAAAA
* *
29932053 TAATAATTTATTTATATACAATTAAAAA
1 TAAAAATTTATTTA-A-A-TA-TAAAAA
*
29932081 TAAAAATTTTATTTAAATAT-AAAT
1 TAAAAA-TTTATTTAAATATAAAAA
* * *
29932105 TAAAAAGTTATTGAATGTAATAAAATA
1 TAAAAATTTATTTAA-AT-ATAAAA-A
*
29932132 TAAAATTTTATTTAA
1 TAAAAATTTATTTAA
29932147 TTAAATTTAT
Statistics
Matches: 70, Mismatches: 15, Indels: 15
0.70 0.15 0.15
Matches are distributed among these distances:
23 7 0.10
24 22 0.31
25 4 0.06
26 5 0.07
27 14 0.20
28 10 0.14
29 8 0.11
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (24 bp):
TAAAAATTTATTTAAATATAAAAA
Found at i:29932109 original size:23 final size:23
Alignment explanation
Indices: 29932019--29932153 Score: 76
Period size: 23 Copynumber: 5.5 Consensus size: 23
29932009 TCAAATGAAA
* *
29932019 AAATATATATTAAAAGTTTATTT
1 AAATATAAATTAAAATTTTATTT
*
29932042 AAATATAAATTTAATAATTTATTTATAT
1 AAATATAAA-TTAA-AA--T-TTTATTT
* *
29932070 ACAATTAAAAATAAAAATTTTATTT
1 A-AA-TATAAATTAAAATTTTATTT
** *
29932095 AAATATAAATTAAAAAGTTATTG
1 AAATATAAATTAAAATTTTATTT
*
29932118 AATGTAATAAAATATAAAATTTTATTT
1 AA-AT-AT-AAAT-TAAAATTTTATTT
29932145 -AAT-TAAATT
1 AAATATAAATT
29932154 TATAAATTCA
Statistics
Matches: 85, Mismatches: 16, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
21 1 0.01
22 4 0.05
23 26 0.31
24 7 0.08
25 12 0.14
26 6 0.07
27 10 0.12
28 9 0.11
29 5 0.06
30 5 0.06
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (23 bp):
AAATATAAATTAAAATTTTATTT
Found at i:29932110 original size:24 final size:23
Alignment explanation
Indices: 29932019--29932116 Score: 79
Period size: 24 Copynumber: 4.0 Consensus size: 23
29932009 TCAAATGAAA
* *
29932019 AAATATATATTAAAAGTTTATTT
1 AAATATAAATTAAAAATTTATTT
*
29932042 AAATATAAATTTAATAATTTATTT
1 AAATATAAA-TTAAAAATTTATTT
* *
29932066 ATATACAATTAAAAATAAAAATTTTATTT
1 A-A-A-TA-T-AAATTAAAAA-TTTATTT
*
29932095 AAATATAAATTAAAAAGTTATT
1 AAATATAAATTAAAAATTTATT
29932117 GAATGTAATA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
23 13 0.22
24 22 0.37
25 2 0.03
26 2 0.03
27 2 0.03
28 7 0.12
29 11 0.19
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (23 bp):
AAATATAAATTAAAAATTTATTT
Found at i:29932421 original size:19 final size:19
Alignment explanation
Indices: 29932384--29932427 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
29932374 AAATCATGTC
**
29932384 ATTTTT-TATATTTTTATT
1 ATTTTTATATATTTGAATT
29932402 ATTTTTATATATTTGAATT
1 ATTTTTATATATTTGAATT
*
29932421 ATATTTA
1 ATTTTTA
29932428 AAATTATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTTTTATATATTTGAATT
Found at i:29938054 original size:2 final size:2
Alignment explanation
Indices: 29938047--29938083 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
29938037 GTTTGCATCC
29938047 CT CT CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
29938084 GTGACATAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:29938924 original size:2 final size:2
Alignment explanation
Indices: 29938917--29938955 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
29938907 AGTACTACTG
* *
29938917 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29938956 CACTCATCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29938940 original size:16 final size:16
Alignment explanation
Indices: 29938919--29938955 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
29938909 TACTACTGTA
29938919 TATATATATATATATG
1 TATATATATATATATG
29938935 TATATATATATATATG
1 TATATATATATATATG
29938951 TATAT
1 TATAT
29938956 CACTCATCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (16 bp):
TATATATATATATATG
Found at i:29939226 original size:21 final size:21
Alignment explanation
Indices: 29939186--29939226 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
29939176 TATATTGGTG
* *
29939186 TTAAAATTATTTATATTATAT
1 TTAAAATTATATATAATATAT
*
29939207 TTAAAATTATATCTAATATA
1 TTAAAATTATATATAATATA
29939227 AAATAGACAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAAAATTATATATAATATAT
Found at i:29940624 original size:20 final size:20
Alignment explanation
Indices: 29940599--29940642 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
29940589 GGCTCTTACT
*
29940599 GATCCTGTGCGCTTCTAGAA
1 GATCCTGTGCACTTCTAGAA
29940619 GATCCTGTGCACTTCTAGAA
1 GATCCTGTGCACTTCTAGAA
29940639 GATC
1 GATC
29940643 TCGGGCACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (20 bp):
GATCCTGTGCACTTCTAGAA
Found at i:29940650 original size:20 final size:20
Alignment explanation
Indices: 29940599--29940652 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
29940589 GGCTCTTACT
* *
29940599 GATCCTGTGCGCTTCTAGAA
1 GATCCTGGGCACTTCTAGAA
*
29940619 GATCCTGTGCACTTCTAGAA
1 GATCCTGGGCACTTCTAGAA
29940639 GAT-CTCGGGCACTT
1 GATCCT-GGGCACTT
29940653 TCATTTTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (20 bp):
GATCCTGGGCACTTCTAGAA
Found at i:29952561 original size:19 final size:19
Alignment explanation
Indices: 29952537--29952578 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
29952527 AATATAATTG
29952537 AAAATTTTAA-AAAATTATA
1 AAAATTTTAATAAAATTA-A
29952556 AAAATTTTAATAAAATTAA
1 AAAATTTTAATAAAATTAA
29952575 AAAA
1 AAAA
29952579 AATAATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTTTAATAAAATTAA
Found at i:29957696 original size:6 final size:6
Alignment explanation
Indices: 29957649--29957683 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
29957639 CGTCTCATTT
*
29957649 ATGATA ATGATA ATGATA ATGATA ATGACA ATGAT
1 ATGATA ATGATA ATGATA ATGATA ATGATA ATGAT
29957684 GTCGATGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.31
Consensus pattern (6 bp):
ATGATA
Found at i:29966991 original size:21 final size:20
Alignment explanation
Indices: 29966966--29967004 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
29966956 AGATTAAAAT
29966966 AAAATAATTTATTTATTAATC
1 AAAATAATTT-TTTATTAATC
* *
29966987 AAAATTATTTTTTCTTAA
1 AAAATAATTTTTTATTAA
29967005 AGTTTATACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
AAAATAATTTTTTATTAATC
Found at i:29970915 original size:23 final size:23
Alignment explanation
Indices: 29970889--29970958 Score: 140
Period size: 23 Copynumber: 3.0 Consensus size: 23
29970879 TTCCTCCATT
29970889 AAAGTAAGTCAAATGGGAGAAAA
1 AAAGTAAGTCAAATGGGAGAAAA
29970912 AAAGTAAGTCAAATGGGAGAAAA
1 AAAGTAAGTCAAATGGGAGAAAA
29970935 AAAGTAAGTCAAATGGGAGAAAA
1 AAAGTAAGTCAAATGGGAGAAAA
29970958 A
1 A
29970959 GAAAGCCTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.57, C:0.04, G:0.26, T:0.13
Consensus pattern (23 bp):
AAAGTAAGTCAAATGGGAGAAAA
Found at i:29981067 original size:25 final size:23
Alignment explanation
Indices: 29981024--29981069 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
29981014 TATCTATTTG
*
29981024 TATATATATTTTTTAAAAATTCT
1 TATATATATTTTTAAAAAATTCT
29981047 TATATATATTTATTAATAAAATT
1 TATATATATTT-TTAA-AAAATT
29981070 ATAATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 3 0.15
25 6 0.30
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TATATATATTTTTAAAAAATTCT
Found at i:29981424 original size:21 final size:21
Alignment explanation
Indices: 29981372--29981427 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
29981362 CTTTTAATAA
* *
29981372 AAAAATAATAATAATAAAATT
1 AAAATTAATAATGATAAAATT
*
29981393 AATTATT-ATAATGATAAAATT
1 AA-AATTAATAATGATAAAATT
29981414 AAAATTAATAATGA
1 AAAATTAATAATGA
29981428 GATATGAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.10
21 24 0.83
22 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (21 bp):
AAAATTAATAATGATAAAATT
Found at i:29982462 original size:15 final size:15
Alignment explanation
Indices: 29982442--29982470 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29982432 CCCAGTAAAT
29982442 AGCCAAAACAAGATA
1 AGCCAAAACAAGATA
29982457 AGCCAAAACAAGAT
1 AGCCAAAACAAGAT
29982471 TGCTAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.21, G:0.14, T:0.07
Consensus pattern (15 bp):
AGCCAAAACAAGATA
Found at i:29982718 original size:62 final size:62
Alignment explanation
Indices: 29982641--29982767 Score: 220
Period size: 62 Copynumber: 2.0 Consensus size: 62
29982631 TAATGAATTT
*
29982641 TTTATAACTATTAAATCT-TTAAAAGTAATTATTAAAAAATTAAATTACGTATTAACCCTTTA
1 TTTATAACTATTAAAT-TGTTAAAAGTAATTATTAAAAAATTAAATTACATATTAACCCTTTA
*
29982703 TTTATAACTATTAAATTGTTAAAAGTAATTATTAAAAAATTAAATTGCATATTAACCCTTTA
1 TTTATAACTATTAAATTGTTAAAAGTAATTATTAAAAAATTAAATTACATATTAACCCTTTA
29982765 TTT
1 TTT
29982768 TTCTTCTTAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
61 1 0.02
62 61 0.98
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (62 bp):
TTTATAACTATTAAATTGTTAAAAGTAATTATTAAAAAATTAAATTACATATTAACCCTTTA
Found at i:29987500 original size:15 final size:15
Alignment explanation
Indices: 29987480--29987530 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
29987470 AATATACCTC
*
29987480 TCTTTTCCTTTCCTT
1 TCTTTTCCTTTCTTT
*
29987495 TCTTTTCTTTTCTTT
1 TCTTTTCCTTTCTTT
29987510 TC-TTTCCTTTCTTTT
1 TCTTTTCCTTTC-TTT
29987525 TCTTTT
1 TCTTTT
29987531 TCTCTTTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 8 0.26
15 20 0.65
16 3 0.10
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (15 bp):
TCTTTTCCTTTCTTT
Found at i:29987530 original size:5 final size:5
Alignment explanation
Indices: 29987480--29987530 Score: 59
Period size: 5 Copynumber: 10.2 Consensus size: 5
29987470 AATATACCTC
* * *
29987480 TCTTT TCCTT TCCTT TCTTT TCTTT TCTTT TC-TT TCCTT TCTTTT TCTTT
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TC-TTT TCTTT
29987530 T
1 T
29987531 TCTCTTTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
4 4 0.10
5 33 0.80
6 4 0.10
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (5 bp):
TCTTT
Found at i:29988207 original size:18 final size:18
Alignment explanation
Indices: 29988179--29988224 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
29988169 TAGTAGATTT
* *
29988179 AATAATTTAAAATATAAT
1 AATAATATAAAATATAAA
*
29988197 ATTAATATAAAATATAAA
1 AATAATATAAAATATAAA
29988215 AATAATATAA
1 AATAATATAA
29988225 TTTAAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATAATATAAAATATAAA
Found at i:29992640 original size:30 final size:28
Alignment explanation
Indices: 29992582--29992640 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 28
29992572 CTCACTCCTG
*
29992582 TATATATAAAAATATAATTTTTATTATT
1 TATATATAAAAATATAATTTTTAATATT
29992610 TATATATTAATAAA-ATAATTATTTAATATT
1 TATATA-TAA-AAATATAATT-TTTAATATT
29992640 T
1 T
29992641 TAATTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 6 0.22
29 9 0.33
30 12 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TATATATAAAAATATAATTTTTAATATT
Found at i:29994659 original size:6 final size:6
Alignment explanation
Indices: 29994648--29994674 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
29994638 TTTTAGAAGC
29994648 CATAAA CATAAA CATAAA CATAAA CAT
1 CATAAA CATAAA CATAAA CATAAA CAT
29994675 GTCAATCACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.19, G:0.00, T:0.19
Consensus pattern (6 bp):
CATAAA
Found at i:30008777 original size:32 final size:32
Alignment explanation
Indices: 30008741--30008806 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 32
30008731 TATAACACAT
*
30008741 AATTTTTATATAAAATATAATATAAATAAATA
1 AATTTTAATATAAAATATAATATAAATAAATA
*** * *
30008773 AATTTTAATATTTTATATTATATAAATATATA
1 AATTTTAATATAAAATATAATATAAATAAATA
30008805 AA
1 AA
30008807 ATTGTCATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
AATTTTAATATAAAATATAATATAAATAAATA
Found at i:30009995 original size:22 final size:23
Alignment explanation
Indices: 30009970--30010020 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
30009960 TATCACAAAT
*
30009970 AATA-AAATATTTTTTTTGTTTA
1 AATATAAATATTTTTTTGGTTTA
**
30009992 AATATATTTATTTTTTTGGTTTA
1 AATATAAATATTTTTTTGGTTTA
30010015 AATATA
1 AATATA
30010021 TTATTATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (23 bp):
AATATAAATATTTTTTTGGTTTA
Found at i:30010025 original size:22 final size:23
Alignment explanation
Indices: 30009977--30010022 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
30009967 AATAATAAAA
*
30009977 TATTTTTTTTGTTTAAATATATT
1 TATTTTTTTGGTTTAAATATATT
30010000 TATTTTTTTGGTTTAAATATATT
1 TATTTTTTTGGTTTAAATATATT
30010023 ATTATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (23 bp):
TATTTTTTTGGTTTAAATATATT
Found at i:30010037 original size:23 final size:23
Alignment explanation
Indices: 30009977--30010038 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
30009967 AATAATAAAA
* *
30009977 TATTTTTTTTGTTTAAATATATT
1 TATTTTATTAGTTTAAATATATT
* *
30010000 TATTTTTTTGGTTTAAATATA-T
1 TATTTTATTAGTTTAAATATATT
*
30010022 TATTATTATTATTTTAA
1 TATT-TTATTAGTTTAA
30010039 TTTCATTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 5 0.15
23 29 0.85
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (23 bp):
TATTTTATTAGTTTAAATATATT
Found at i:30012220 original size:15 final size:15
Alignment explanation
Indices: 30012196--30012227 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
30012186 ATCATTTGGG
*
30012196 TTTTGTTTTTTTTTT
1 TTTTGGTTTTTTTTT
30012211 TTTTGGTTTTTTTTT
1 TTTTGGTTTTTTTTT
30012226 TT
1 TT
30012228 CGCATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (15 bp):
TTTTGGTTTTTTTTT
Found at i:30012221 original size:16 final size:15
Alignment explanation
Indices: 30012196--30012227 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
30012186 ATCATTTGGG
30012196 TTTTGTTTTTTTTTT
1 TTTTGTTTTTTTTTT
30012211 TTTTGGTTTTTTTTTT
1 TTTT-GTTTTTTTTTT
30012227 T
1 T
30012228 CGCATTGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (15 bp):
TTTTGTTTTTTTTTT
Found at i:30014028 original size:27 final size:27
Alignment explanation
Indices: 30013988--30014056 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
30013978 ATGATAAATA
*
30013988 AATAATATTT-TAAATACTATATCA-ATT
1 AATAA-ATTTATAAATA-AATATCACATT
30014015 AATAAATTTATAAATTAAATATCACATT
1 AATAAATTTATAAA-TAAATATCACATT
*
30014043 AAAAAATTTA-AAAT
1 AATAAATTTATAAAT
30014057 TTAGATATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
26 5 0.14
27 18 0.49
28 14 0.38
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (27 bp):
AATAAATTTATAAATAAATATCACATT
Found at i:30014073 original size:28 final size:28
Alignment explanation
Indices: 30014006--30014057 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
30013996 TTTAAATACT
*
30014006 ATATCA-ATTAATAAATTTATAAATTAA
1 ATATCACATTAAAAAATTTATAAATTAA
30014033 ATATCACATTAAAAAATTTA-AAATT
1 ATATCACATTAAAAAATTTATAAATT
30014058 TAGATATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (28 bp):
ATATCACATTAAAAAATTTATAAATTAA
Found at i:30018292 original size:19 final size:19
Alignment explanation
Indices: 30018268--30018306 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
30018258 ATTCCAACAA
30018268 TACCATTATGAAGAAGTAC
1 TACCATTATGAAGAAGTAC
30018287 TACCATTATGAAGAAGTAC
1 TACCATTATGAAGAAGTAC
30018306 T
1 T
30018307 CCAAATAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (19 bp):
TACCATTATGAAGAAGTAC
Found at i:30019399 original size:27 final size:31
Alignment explanation
Indices: 30019369--30019431 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
30019359 TTCAATAAAT
30019369 TAATTTT-ATTT-TTATA-T-TTTAATTAGA
1 TAATTTTGATTTATTATATTATTTAATTAGA
* *
30019396 TAATTTTGATTTATTTTATTATTTAATTAGT
1 TAATTTTGATTTATTATATTATTTAATTAGA
30019427 TAATT
1 TAATT
30019432 GACTAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 7 0.23
28 4 0.13
29 4 0.13
30 1 0.03
31 14 0.47
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (31 bp):
TAATTTTGATTTATTATATTATTTAATTAGA
Found at i:30023698 original size:30 final size:29
Alignment explanation
Indices: 30023647--30023711 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
30023637 GATATCAAAA
30023647 TAATAAAAAATAATACAATTTAA-AAATT
1 TAATAAAAAATAATACAATTTAATAAATT
*
30023675 TAATAAAAATTATATATCAATTTAATAAATT
1 TAATAAAAAATA-ATA-CAATTTAATAAATT
30023706 T-ATAAA
1 TAATAAA
30023712 TATTTTTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
28 11 0.33
29 3 0.09
30 13 0.39
31 6 0.18
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (29 bp):
TAATAAAAAATAATACAATTTAATAAATT
Found at i:30031871 original size:4 final size:4
Alignment explanation
Indices: 30031862--30031899 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
30031852 AAAAATATAC
30031862 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
30031900 ATGAATGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:30045472 original size:15 final size:16
Alignment explanation
Indices: 30045460--30045493 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
30045450 TTTTAAAAAG
30045460 CAAAAAAAAAAAAATTC
1 CAAAAAAAAAAAAA-TC
30045477 CAAAAAAAAAAGAAATC
1 CAAAAAAAAAA-AAATC
30045494 AGAGCCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.76, C:0.12, G:0.03, T:0.09
Consensus pattern (16 bp):
CAAAAAAAAAAAAATC
Found at i:30046540 original size:13 final size:13
Alignment explanation
Indices: 30046495--30046540 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
30046485 ATTTGTTAAA
30046495 ATTATTTTAAATGT
1 ATTATTTTAAAT-T
* *
30046509 ATGATTTTTAATT
1 ATTATTTTAAATT
30046522 ATTTATTTTAAATT
1 A-TTATTTTAAATT
30046536 ATTAT
1 ATTAT
30046541 GTATAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 6 0.22
14 21 0.78
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (13 bp):
ATTATTTTAAATT
Found at i:30046552 original size:28 final size:28
Alignment explanation
Indices: 30046496--30046553 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
30046486 TTTGTTAAAA
* *
30046496 TTATTTTAAATGTATGATTTTTAATTAT
1 TTATTTTAAATGTATGATGTATAATTAT
*
30046524 TTATTTTAAAT-TATTATGTATAATATAT
1 TTATTTTAAATGTATGATGTATAAT-TAT
30046552 TT
1 TT
30046554 TATTCTTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (28 bp):
TTATTTTAAATGTATGATGTATAATTAT
Found at i:30057669 original size:333 final size:333
Alignment explanation
Indices: 30057057--30059974 Score: 3779
Period size: 333 Copynumber: 8.8 Consensus size: 333
30057047 ATTTGCTAGA
* * * * * *
30057057 AACAGACGA-CTTCAAAATTTTCCCAGTAAATATTTTGGGAATTATTAAAAGCATGTTT-TACTA
1 AACAGAC-ACCTTCAAAATTTTCTCACTAAATATTTTGAGAATTATTAAAGGCGT-TTTCTACTG
* * * * * * *
30057120 TAAAATGCTTTTTATTTACCACTACACATATTGTAACACTATTATTGAATGCGTATATTTAAGAT
64 TAAAATACCTTCTATATACCGCTACACATATTGTAACACTGTTATTGAAGGCGTATATTTAAGAT
* * * * *
30057185 AGACGCCTTTAATAA-TTCTTATCATAGTTTGTATATAATTATTAAAGGCAATTTCAGATAATAA
129 AGACGCCTTTAATAATTTC-TATCACAGTTTGTATATAATTACTGAAGGCGATTTCAGATAACAA
* * * *
30057249 CACCTTCAATAATTTTTCTAATAAAAGTTTTCAGGATTATTAAAGACGTCTTTTATTATAAGCTG
193 CGCCTTCAATAATTTTTCTAATAAAAGTTTTCAAGATTATTAAAGGCGTCTTTTATTATAAGCCG
* ** *
30057314 CCTTCGATATACCACGATGGTAATTGAAGGCGAGTATTAGAAAATGCACTTTCAATTACTGAAGG
258 CCTTCGATATACCACGATGGTAATCGAAGGCGTTTATTAGAAAATGCACCTTCAATTACTGAAGG
* **
30057379 CATTTACTAAT
323 CGTTTGTTAAT
* **
30057390 AACAGACACCTTCAAAATTTTCTCAGTAAATATTTTG-GAAATTATTAAAGGTATTTTCTACTGT
1 AACAGACACCTTCAAAATTTTCTCACTAAATATTTTGAG-AATTATTAAAGGCGTTTTCTACTGT
* * * * * * * *
30057454 ATAATGCCTTTTACATACTGCTACACATATTGTAACATTGTTATTGAAGGTGAATATTTAAGATA
65 AAAATACCTTCTATATACCGCTACACATATTGTAACACTGTTATTGAAGGCGTATATTTAAGATA
* * * *
30057519 GACGTCTTTAATAATTTCTATCACAGTTTGTATATAATTACTGAAGGTGATTTCAGATAATAACA
130 GACGCCTTTAATAATTTCTATCACAGTTTGTATATAATTACTGAAGGCGATTTCAGATAACAACG
* *
30057584 CCTTCAATAATTTTTTTAATAAAAGTTTTCAAGATTATTAAAGGCATCTTTTATTATAAGCCGCC
195 CCTTCAATAATTTTTCTAATAAAAGTTTTCAAGATTATTAAAGGCGTCTTTTATTATAAGCCGCC
* *** *
30057649 TTCGATATACCACAATGGTAATCGAAGGCGTTTATTAGAAAATGTGTCTTCAATTACTGAAGGTG
260 TTCGATATACCACGATGGTAATCGAAGGCGTTTATTAGAAAATGCACCTTCAATTACTGAAGGCG
30057714 TTTGTTAAT
325 TTTGTTAAT
30057723 AAC--ACACCTTCAAAATTTT-TCCACTAAATATTTTGAGAATTATTAAAGGCGTCTTT-TACTG
1 AACAGACACCTTCAAAATTTTCT-CACTAAATATTTTGAGAATTATTAAAGGCGT-TTTCTACTG
* * *
30057784 TAAATTACCTTTTATATACCGCTATACATATTGTAACACTGTTATTGAAGGCGTATATTTAAGAT
64 TAAAATACCTTCTATATACCGCTACACATATTGTAACACTGTTATTGAAGGCGTATATTTAAGAT
* * ** * *
30057849 AAACGCTTTTAATAATTTCTATCACAGTTTGTATATAATTACTGAAGATGATTTTAGATAACAAT
129 AGACGCCTTTAATAATTTCTATCACAGTTTGTATATAATTACTGAAGGCGATTTCAGATAACAAC
* * * *
30057914 GCATTCAATAATTTTTCTAATAAAAGTTCTT-AGGATTATTAAATGCGTCTTTTATTATAAGTCG
194 GCCTTCAATAATTTTTCTAATAAAAGTT-TTCAAGATTATTAAAGGCGTCTTTTATTATAAGCCG
* * *
30057978 CCTTCAATATACCACGATGGTAATCGAAGGCGTTTATTAGAAAATGCACCTTCAATTATTAAAGG
258 CCTTCGATATACCACGATGGTAATCGAAGGCGTTTATTAGAAAATGCACCTTCAATTACTGAAGG
*
30058043 CGTTCGTTAAT
323 CGTTTGTTAAT
* * *
30058054 AACAGACGCCTTCAAAATTTTTTCACTAAATATTTT-AGGAATTATTAAAGGCGTCTTCTACTGT
1 AACAGACACCTTCAAAATTTTCTCACTAAATATTTTGA-GAATTATTAAAGGCGTTTTCTACTGT
* * *
30058118 AAAATATCTTCTATATACCGCTACACATATTGTAACACTGTTATTAAAGACGTATATTTAAGATA
65 AAAATACCTTCTATATACCGCTACACATATTGTAACACTGTTATTGAAGGCGTATATTTAAGATA
* * * * * * *
30058183 GACACCTTTAATAATTCCTATCATAGTTTGTATATAATTATTGAAAGCGATTTTAGATAACAATG
130 GACGCCTTTAATAATTTCTATCACAGTTTGTATATAATTACTGAAGGCGATTTCAGATAACAACG
* * * * *
30058248 CCTTTAATAATTTTTCTAATAGAAGTTTTTAGGATTATTAAATGCGTCTTTTATTATAAGCCGCC
195 CCTTCAATAATTTTTCTAATAAAAGTTTTCAAGATTATTAAAGGCGTCTTTTATTATAAGCCGCC
* * * ** * *
30058313 TTTGATATACCACGATGGTAATCGAAAGCGTTTATTAGAAAAGGTGCCGTCAATTACTAAAGGCG
260 TTCGATATACCACGATGGTAATCGAAGGCGTTTATTAGAAAATGCACCTTCAATTACTGAAGGCG
30058378 TTTGTTAAT
325 TTTGTTAAT
* * * * * *
30058387 AATAGACACCTTTAAAATTTTTTCACTAAATATTTTGAGAATTATTAAATGCATCTTCTACTGTA
1 AACAGACACCTTCAAAATTTTCTCACTAAATATTTTGAGAATTATTAAAGGCGTTTTCTACTGTA
* * * * *
30058452 AAATACCTTCTATATACCTCTACAGATATTGTAACACTGTTATTGAAGACGTATATTTAATAAAG
66 AAATACCTTCTATATACCGCTACACATATTGTAACACTGTTATTGAAGGCGTATATTTAAGATAG
* * *
30058517 ACGCCTTTAATAATTTTTATCACAGTTTGTATATAATTACTAAAGGCGATTTCAGATAACAACGT
131 ACGCCTTTAATAATTTCTATCACAGTTTGTATATAATTACTGAAGGCGATTTCAGATAACAACGC
* *
30058582 CTTCAATAATTTTTCTAATAAAAGTTTT-AAGGATTATTAAAGGCATCTTTTATTATAAACCGCC
196 CTTCAATAATTTTTCTAATAAAAGTTTTCAA-GATTATTAAAGGCGTCTTTTATTATAAGCCGCC
* * ** *
30058646 TTCGATATACCACGATGGTAATTGAAGGCATTTATTAGAAAATGTGCCTTTAATTACTGAAGGCG
260 TTCGATATACCACGATGGTAATCGAAGGCGTTTATTAGAAAATGCACCTTCAATTACTGAAGGCG
30058711 TTTGTTAAT
325 TTTGTTAAT
* * * * *
30058720 AACAGACGA-CTTTAAAATTTTCTCACTAAATATTTTAAAAATTATTAAAGGTGTCTTT-TATTG
1 AACAGAC-ACCTTCAAAATTTTCTCACTAAATATTTTGAGAATTATTAAAGGCGT-TTTCTACTG
* * * * *
30058783 TAAAATGCCTTCTATATATCGCTATACATATTATAATACTGTTATTGAAGGCGTATATTTAAGAT
64 TAAAATACCTTCTATATACCGCTACACATATTGTAACACTGTTATTGAAGGCGTATATTTAAGAT
* * * *
30058848 AGACGCCTTTAATAATTCCTATTACAGTTTGTATATAATTATTGAAGGCGATTTTAGATAACAAC
129 AGACGCCTTTAATAATTTCTATCACAGTTTGTATATAATTACTGAAGGCGATTTCAGATAACAAC
* * *
30058913 GCCTTTAATAATTTTTCTAATAAAAGTTTTCAAGATTATTAAAGGCATCTTTTATTATAAGTCGC
194 GCCTTCAATAATTTTTCTAATAAAAGTTTTCAAGATTATTAAAGGCGTCTTTTATTATAAGCCGC
* * *
30058978 CTTCGATATACCACGACGGTAATCGAAGGCGTTTATTAGAAAAGGCGCCTTCAATTACTGAAGGC
259 CTTCGATATACCACGATGGTAATCGAAGGCGTTTATTAGAAAATGCACCTTCAATTACTGAAGGC
30059043 GTTTGTTAAT
324 GTTTGTTAAT
* * * * * **
30059053 AATAGACGCTTTTAAAAATTTT-TTACTAAATATTTTGAGAATTATTAAAGGCGTAATCTACTGT
1 AACAGACAC-CTTCAAAATTTTCTCACTAAATATTTTGAGAATTATTAAAGGCGTTTTCTACTGT
* ** * *
30059117 AAAATGCCTTCTATATACCATTACACATATTGTAACATTATTATTGAAGGCGTATATTTAAGATA
65 AAAATACCTTCTATATACCGCTACACATATTGTAACACTGTTATTGAAGGCGTATATTTAAGATA
* * * * * *
30059182 GACACTTTTAATAATTCCTACCATAGTTTGTATATAATTACTGAAGGCGATTTCAGATAACAATG
130 GACGCCTTTAATAATTTCTATCACAGTTTGTATATAATTACTGAAGGCGATTTCAGATAACAACG
* * *
30059247 CCTTTAATAATTTTT-TCAATAAAAGTTTTCAAGATTATTAAAGGCATCTTTTATTATAAGCTGC
195 CCTTCAATAATTTTTCT-AATAAAAGTTTTCAAGATTATTAAAGGCGTCTTTTATTATAAGCCGC
* * * *
30059311 CTTCGATATACTACGATGGTAATCAAAAGTGTTTATTAGAAAA-GACACCTTCAATTACTGAAGG
259 CTTCGATATACCACGATGGTAATCGAAGGCGTTTATTAGAAAATG-CACCTTCAATTACTGAAGG
*
30059375 TGTTTGTTAAT
323 CGTTTGTTAAT
* * **
30059386 AACAGACGCCTTCAAAATTTTCTCATTAAATATTTTGAGAATTATTAAAGATGTTTTCTACTGTA
1 AACAGACACCTTCAAAATTTTCTCACTAAATATTTTGAGAATTATTAAAGGCGTTTTCTACTGTA
*
30059451 AAATACCTTCTATATACCACTACACATATTGTAACACTGTTATTGAAGGCGTATATTTAAGATAG
66 AAATACCTTCTATATACCGCTACACATATTGTAACACTGTTATTGAAGGCGTATATTTAAGATAG
* * * *
30059516 ACGCCTTTAATAATTAT-TATCATAGTTTGTATATAATTACTGAAGGCGATTTTAGCTAACAACA
131 ACGCCTTTAATAATT-TCTATCACAGTTTGTATATAATTACTGAAGGCGATTTCAGATAACAACG
* * * *
30059580 TCTTCAATAATTTCTCTAATAAAAGTTTTCAAGATTATTAAAGACGTCTTTTATTAAAAGCCGCC
195 CCTTCAATAATTTTTCTAATAAAAGTTTTCAAGATTATTAAAGGCGTCTTTTATTATAAGCCGCC
* * * * *
30059645 TTCGATATACTACGATGGTAATCGAAGACGTTTATTAGAAAAGGCACCTTCAATTACTAAAGGCA
260 TTCGATATACCACGATGGTAATCGAAGGCGTTTATTAGAAAATGCACCTTCAATTACTGAAGGCG
30059710 TTTGTTAAT
325 TTTGTTAAT
* * * *
30059719 AACAGACGCCTTCAAAATTTTCTTACTAAATATTTTGAGAATTATTAAAGGCATCTTCTACTGTA
1 AACAGACACCTTCAAAATTTTCTCACTAAATATTTTGAGAATTATTAAAGGCGTTTTCTACTGTA
* * * * * *
30059784 AAATACATTTTATATACCGTTACATATATTGTAACACTGTTATTGAAGGCGTACATTTAAGATAA
66 AAATACCTTCTATATACCGCTACACATATTGTAACACTGTTATTGAAGGCGTATATTTAAGATAG
* * *
30059849 ACGCCTTTAATAATTTCTATCACTGTTTGTATATAATTACTTAAGGTGATTTCAGATAACAACGC
131 ACGCCTTTAATAATTTCTATCACAGTTTGTATATAATTACTGAAGGCGATTTCAGATAACAACGC
* * * * * *
30059914 CTTTAAT-ATTTTCTCAAAAAAAAATTTT--GGATTATTAAAGGGGTCTTTTATTATAAGCCGC
196 CTTCAATAATTTT-TCTAATAAAAGTTTTCAAGATTATTAAAGGCGTCTTTTATTATAAGCCGC
30059975 ATTTAATAAT
Statistics
Matches: 2281, Mismatches: 274, Indels: 62
0.87 0.10 0.02
Matches are distributed among these distances:
330 1 0.00
331 314 0.14
332 35 0.02
333 1909 0.84
334 22 0.01
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (333 bp):
AACAGACACCTTCAAAATTTTCTCACTAAATATTTTGAGAATTATTAAAGGCGTTTTCTACTGTA
AAATACCTTCTATATACCGCTACACATATTGTAACACTGTTATTGAAGGCGTATATTTAAGATAG
ACGCCTTTAATAATTTCTATCACAGTTTGTATATAATTACTGAAGGCGATTTCAGATAACAACGC
CTTCAATAATTTTTCTAATAAAAGTTTTCAAGATTATTAAAGGCGTCTTTTATTATAAGCCGCCT
TCGATATACCACGATGGTAATCGAAGGCGTTTATTAGAAAATGCACCTTCAATTACTGAAGGCGT
TTGTTAAT
Found at i:30082607 original size:45 final size:43
Alignment explanation
Indices: 30082561--30082697 Score: 204
Period size: 45 Copynumber: 3.1 Consensus size: 43
30082551 TGGAGCTGGT
* * *
30082561 GGTGGGGATTGTAC-TGGTGGTGGTGGTGAATAAACTGGTGGA
1 GGTGGGGACTGTACGTGGTGGTGGTGGTGAGTAAGCTGGTGGA
30082603 GGTGGGGACTGTACAGGTGGTGGTGGTGGTGAGTAAGCTGGTGGA
1 GGTGGGGACTGTAC--GTGGTGGTGGTGGTGAGTAAGCTGGTGGA
30082648 GGTGGGGACTGTACAGGTGGTGGTGGTGGTGAGTAAGCTGGTGGA
1 GGTGGGGACTGTAC--GTGGTGGTGGTGGTGAGTAAGCTGGTGGA
30082693 GGTGG
1 GGTGG
30082698 AGAGTGGACG
Statistics
Matches: 89, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
42 13 0.15
45 76 0.85
ACGTcount: A:0.16, C:0.06, G:0.53, T:0.26
Consensus pattern (43 bp):
GGTGGGGACTGTACGTGGTGGTGGTGGTGAGTAAGCTGGTGGA
Found at i:30082712 original size:45 final size:45
Alignment explanation
Indices: 30082575--30082697 Score: 228
Period size: 45 Copynumber: 2.7 Consensus size: 45
30082565 GGGATTGTAC
* *
30082575 TGGTGGTGGTGGTGAATAAACTGGTGGAGGTGGGGACTGTACAGG
1 TGGTGGTGGTGGTGAGTAAGCTGGTGGAGGTGGGGACTGTACAGG
30082620 TGGTGGTGGTGGTGAGTAAGCTGGTGGAGGTGGGGACTGTACAGG
1 TGGTGGTGGTGGTGAGTAAGCTGGTGGAGGTGGGGACTGTACAGG
30082665 TGGTGGTGGTGGTGAGTAAGCTGGTGGAGGTGG
1 TGGTGGTGGTGGTGAGTAAGCTGGTGGAGGTGG
30082698 AGAGTGGACG
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.16, C:0.06, G:0.53, T:0.25
Consensus pattern (45 bp):
TGGTGGTGGTGGTGAGTAAGCTGGTGGAGGTGGGGACTGTACAGG
Found at i:30082766 original size:21 final size:21
Alignment explanation
Indices: 30082557--30082867 Score: 191
Period size: 21 Copynumber: 14.3 Consensus size: 21
30082547 GAGTTGGAGC
*
30082557 TGGTGGTGGGGA-TTGTACTGG
1 TGGTGGTGGGGAGTAG-ACTGG
* * *
30082578 TGGTGGTGGTGAATAAACTGG
1 TGGTGGTGGGGAGTAGACTGG
* * *
30082599 TGGAGGTGGGGACTGTACAGGTGG
1 TGGTGGTGGGGA--GTAGA-CTGG
*
30082623 TGGTGGTGGTGAGTA-AGCTGG
1 TGGTGGTGGGGAGTAGA-CTGG
* * *
30082644 TGGAGGTGGGGACTGTACAGGTGG
1 TGGTGGTGGGGA--GTAGA-CTGG
*
30082668 TGGTGGTGGTGAGTA-AGCTGG
1 TGGTGGTGGGGAGTAGA-CTGG
* * * *
30082689 TGGAGGTGGAGAGTGGACGGG
1 TGGTGGTGGGGAGTAGACTGG
* *
30082710 TGGCGGAGGGGAGTAGACTGG
1 TGGTGGTGGGGAGTAGACTGG
*
30082731 TGGTGG-AGGGAGTAGACTGG
1 TGGTGGTGGGGAGTAGACTGG
30082751 TGGTGGTGGGGAGTAGACGGGTGG
1 TGGTGGTGGGGAGTAGAC---TGG
* * * *
30082775 AGGTGGCGGGGGTGAGTGGACGGG
1 TGGT-G-GTGGG-GAGTAGACTGG
*
30082799 TGGGGGTGGGGAGTAGACTGG
1 TGGTGGTGGGGAGTAGACTGG
*
30082820 TGGTGGTGGGGAATAGACTGG
1 TGGTGGTGGGGAGTAGACTGG
* * *
30082841 TGGAGGTGGAGA-TTGAACTGG
1 TGGTGGTGGGGAGTAG-ACTGG
30082862 TGGTGG
1 TGGTGG
30082868 AGGTGAGCGA
Statistics
Matches: 230, Mismatches: 44, Indels: 32
0.75 0.14 0.10
Matches are distributed among these distances:
20 21 0.09
21 140 0.61
22 12 0.05
23 7 0.03
24 38 0.17
25 1 0.00
26 4 0.02
27 7 0.03
ACGTcount: A:0.16, C:0.06, G:0.56, T:0.22
Consensus pattern (21 bp):
TGGTGGTGGGGAGTAGACTGG
Found at i:30082825 original size:69 final size:68
Alignment explanation
Indices: 30082708--30082849 Score: 205
Period size: 69 Copynumber: 2.1 Consensus size: 68
30082698 AGAGTGGACG
* * *
30082708 GGTGGCGGAGGGGAGTAGACTGGTGGTGGAGGGAGTAGACTGGTGGTGGTGGGGAGTAGACGGGT
1 GGTGGCGGAGGGGAGTAGACGGGTGGGGGAGGGAGTAGACTGGTGGTGGTGGGGAATAGACGGGT
30082773 GGA
66 GGA
* * *
30082776 GGTGGCGG-GGGTGAGTGGACGGGTGGGGGTGGGGAGTAGACTGGTGGTGGTGGGGAATAGACTG
1 GGTGGCGGAGGG-GAGTAGACGGGTGGGGG-AGGGAGTAGACTGGTGGTGGTGGGGAATAGACGG
30082840 GTGGA
64 GTGGA
30082845 GGTGG
1 GGTGG
30082850 AGATTGAACT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
67 3 0.05
68 22 0.33
69 41 0.62
ACGTcount: A:0.15, C:0.06, G:0.61, T:0.18
Consensus pattern (68 bp):
GGTGGCGGAGGGGAGTAGACGGGTGGGGGAGGGAGTAGACTGGTGGTGGTGGGGAATAGACGGGT
GGA
Found at i:30085629 original size:18 final size:19
Alignment explanation
Indices: 30085606--30085652 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
30085596 TTTTTATAAT
30085606 TTTATATTTAAATTAAA-A
1 TTTATATTTAAATTAAATA
*
30085624 TTTATATTCAAATTAAATA
1 TTTATATTTAAATTAAATA
30085643 TTTATATTTA
1 TTTATATTTA
30085653 TTATTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTATATTTAAATTAAATA
Found at i:30092514 original size:11 final size:11
Alignment explanation
Indices: 30092494--30092524 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
30092484 GATAATAGAT
30092494 TATAAAAATAA
1 TATAAAAATAA
*
30092505 TATGAAAATAA
1 TATAAAAATAA
30092516 TATAAAAAT
1 TATAAAAAT
30092525 TAAAGAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
TATAAAAATAA
Found at i:30092847 original size:1 final size:1
Alignment explanation
Indices: 30092841--30092866 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
30092831 TCAAGTTGAG
30092841 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
30092867 AAGGTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:30099555 original size:2 final size:2
Alignment explanation
Indices: 30099548--30099580 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
30099538 TTATTAATTA
30099548 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30099581 ACAATGGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30104158 original size:14 final size:15
Alignment explanation
Indices: 30104132--30104161 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
30104122 CAAAAAAACC
30104132 AATAATATTATAAAA
1 AATAATATTATAAAA
30104147 AATAAT-TTATAAAA
1 AATAATATTATAAAA
30104161 A
1 A
30104162 CTTAATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAATATTATAAAA
Found at i:30115199 original size:62 final size:61
Alignment explanation
Indices: 30115125--30115250 Score: 189
Period size: 62 Copynumber: 2.0 Consensus size: 61
30115115 AGAAATTGCA
* * * *
30115125 TTTTAAAGAAAATTGATACTTTCAACTTTTTCCTAAAAATATATATTTTTTTGAAATTTTAT
1 TTTTAAAAAAAATTGATACTTTCAACTTTTTCCTAAAAACATAT-GTTTTTGGAAATTTTAT
* *
30115187 TTTTAAAAAAAATTGATATTTTCAACTTTTTCCTAAAAACATATGTTTTTGGAATTTTTAT
1 TTTTAAAAAAAATTGATACTTTCAACTTTTTCCTAAAAACATATGTTTTTGGAAATTTTAT
30115248 TTT
1 TTT
30115251 AGGAAAATCA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
61 17 0.29
62 41 0.71
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.51
Consensus pattern (61 bp):
TTTTAAAAAAAATTGATACTTTCAACTTTTTCCTAAAAACATATGTTTTTGGAAATTTTAT
Found at i:30115281 original size:3 final size:3
Alignment explanation
Indices: 30115275--30115333 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
30115265 AAAAAGAAAA
* *
30115275 AAT AAT AA- AAT AA- AAT AAA AAT AA- AATT AAGG AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AA-T AAT AAT AAT AAT
30115319 AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT A
30115334 TATCAAAGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
2 8 0.17
3 34 0.74
4 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:30116026 original size:4 final size:4
Alignment explanation
Indices: 30116019--30116163 Score: 86
Period size: 4 Copynumber: 36.2 Consensus size: 4
30116009 ATAGATAATT
* * * *
30116019 AATA AATA AATA AATA TATT AATA GATA AAT- AATA AA-A AATTTT AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AA--TA AATA
* * * * *
30116067 GATA AAT- AATA AAAA ATATA AATA AATA TATT AATA GATA AAT- AATA
1 AATA AATA AATA AATA A-ATA AATA AATA AATA AATA AATA AATA AATA
* * *
30116114 AA-A AATTTT AATA GATA AAT- AATA AAAA ATATA AATA AATA AATA AATA
1 AATA AA--TA AATA AATA AATA AATA AATA A-ATA AATA AATA AATA AATA
30116163 A
1 A
30116164 TAATGATAAT
Statistics
Matches: 105, Mismatches: 24, Indels: 24
0.69 0.16 0.16
Matches are distributed among these distances:
3 18 0.17
4 77 0.73
5 6 0.06
6 4 0.04
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (4 bp):
AATA
Found at i:30116080 original size:24 final size:24
Alignment explanation
Indices: 30115989--30116083 Score: 100
Period size: 24 Copynumber: 3.6 Consensus size: 24
30115979 AAAGTAAAAA
*
30115989 AAATAGATAAAAAAATATTAATAGAT
1 AAATA-AT-AAAAAATTTTAATAGAT
30116015 AATTAATAAATAAATAAATATATTAATAGAT
1 -A--AAT-AATAAA-AAAT-T-TTAATAGAT
30116046 AAATAATAAAAAATTTTAATAGAT
1 AAATAATAAAAAATTTTAATAGAT
30116070 AAATAATAAAAAAT
1 AAATAATAAAAAAT
30116084 ATAAATAAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 15
0.79 0.01 0.19
Matches are distributed among these distances:
24 23 0.38
25 1 0.02
26 4 0.07
27 7 0.11
28 6 0.10
29 9 0.15
30 2 0.03
31 9 0.15
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (24 bp):
AAATAATAAAAAATTTTAATAGAT
Found at i:30116108 original size:36 final size:36
Alignment explanation
Indices: 30116046--30116162 Score: 122
Period size: 36 Copynumber: 3.4 Consensus size: 36
30116036 ATTAATAGAT
30116046 AAATAATAAA-AAAT-T-TTAATAGATAAATAATAAA
1 AAAT-ATAAATAAATATATTAATAGATAAATAATAAA
30116080 AAATATAAATAAATATATTAATAGATAAATAATAAA
1 AAATATAAATAAATATATTAATAGATAAATAATAAA
* * * * *
30116116 AAATTTTAATAGATA-AATAATA-AAAAAT-ATAAA
1 AAATATAAATAAATATATTAATAGATAAATAATAAA
*
30116149 TAA-ATAAATAAATA
1 AAATATAAATAAATA
30116163 ATAATGATAA
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
32 8 0.11
33 12 0.17
34 13 0.18
35 7 0.10
36 31 0.44
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (36 bp):
AAATATAAATAAATATATTAATAGATAAATAATAAA
Found at i:30116108 original size:60 final size:60
Alignment explanation
Indices: 30116024--30116154 Score: 262
Period size: 60 Copynumber: 2.2 Consensus size: 60
30116014 TAATTAATAA
30116024 ATAAATAAATATATTAATAGATAAATAATAAAAAATTTTAATAGATAAATAATAAAAAAT
1 ATAAATAAATATATTAATAGATAAATAATAAAAAATTTTAATAGATAAATAATAAAAAAT
30116084 ATAAATAAATATATTAATAGATAAATAATAAAAAATTTTAATAGATAAATAATAAAAAAT
1 ATAAATAAATATATTAATAGATAAATAATAAAAAATTTTAATAGATAAATAATAAAAAAT
30116144 ATAAATAAATA
1 ATAAATAAATA
30116155 AATAAATAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 71 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (60 bp):
ATAAATAAATATATTAATAGATAAATAATAAAAAATTTTAATAGATAAATAATAAAAAAT
Found at i:30116111 original size:24 final size:24
Alignment explanation
Indices: 30116094--30116159 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 24
30116084 ATAAATAAAT
30116094 ATATTAATAGATAAATAATAAAAA
1 ATATTAATAGATAAATAATAAAAA
*
30116118 ATTTTAATAGATAAATAATAAAAA
1 ATATTAATAGATAAATAATAAAAA
* *
30116142 ATATAAATAAATAAATAA
1 ATATTAATAGATAAATAA
30116160 ATAATAATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (24 bp):
ATATTAATAGATAAATAATAAAAA
Found at i:30116135 original size:84 final size:88
Alignment explanation
Indices: 30115975--30116160 Score: 242
Period size: 84 Copynumber: 2.1 Consensus size: 88
30115965 ATCAAGATAA
30115975 AGATAAAGTAAAAAAAATAGATAAAAAAATATTAATAGATAATTAATAAATAAATAAATATATTA
1 AGATAAA-TAAAAAAAATA-ATAAAAAAATATTAATAGATAA-TAATAAATAAATAAATATATTA
* *
30116040 ATAGATAAATAATAAAAAATTTTAAT
63 ATAGATAAATAATAAAAAATATAAAT
30116066 AGATAAATAATAAAAAAT-ATAAATAAATATATTAATAGAT-A-AAT-AATAAA-AAAT-T-TTA
1 AGATAAATAA-AAAAAATAATAAA-AAA-ATATTAATAGATAATAATAAATAAATAAATATATTA
30116124 ATAGATAAATAATAAAAAATATAAAT
63 ATAGATAAATAATAAAAAATATAAAT
*
30116150 AAATAAATAAA
1 AGATAAATAAA
30116161 TAATAATGAT
Statistics
Matches: 89, Mismatches: 3, Indels: 14
0.84 0.03 0.13
Matches are distributed among these distances:
83 1 0.01
84 36 0.40
85 1 0.01
86 4 0.04
87 6 0.07
88 3 0.03
89 5 0.06
90 7 0.08
91 26 0.29
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (88 bp):
AGATAAATAAAAAAAATAATAAAAAAATATTAATAGATAATAATAAATAAATAAATATATTAATA
GATAAATAATAAAAAATATAAAT
Found at i:30116139 original size:91 final size:90
Alignment explanation
Indices: 30115975--30116144 Score: 213
Period size: 91 Copynumber: 1.9 Consensus size: 90
30115965 ATCAAGATAA
* * *
30115975 AGATAAAGTAAAAAAAATAGATAAAAAAATATTAATAGATAATTAATAAATAAATAAATATATTA
1 AGATAAAGTAAAAAAAATA-ATAAAAAAATATTAATAGATAAATAATAAATAAATAAATAGATAA
*
30116040 ATAGATAAATAATAAAAAATTTTAAT
65 ATAGATAAAAAATAAAAAATTTTAAT
*
30116066 AGATAAA-TAATAAAAAAT-ATAAATAAATATATTAATAGATAAATAATAAA-AAATTTTAATAG
1 AGATAAAGTAA-AAAAAATAATAAA-AAA-ATATTAATAGATAAATAATAAATAAA--TAAATAG
30116128 ATAAATA-ATAAAAAATA
61 ATAAATAGATAAAAAATA
30116145 TAAATAAATA
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
89 5 0.07
90 9 0.13
91 44 0.64
92 11 0.16
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (90 bp):
AGATAAAGTAAAAAAAATAATAAAAAAATATTAATAGATAAATAATAAATAAATAAATAGATAAA
TAGATAAAAAATAAAAAATTTTAAT
Found at i:30116174 original size:24 final size:24
Alignment explanation
Indices: 30115989--30116172 Score: 86
Period size: 24 Copynumber: 7.1 Consensus size: 24
30115979 AAAGTAAAAA
*
30115989 AAATAGATAAAAAAATATTAATAGAT
1 AAATA-AT-AAAAAATAATAATAGAT
30116015 AATTAATAAATAAATAAATATATTAATAGAT
1 -A--AAT-AATAAA-AAATA-A-TAATAGAT
**
30116046 AAATAATAAAAAATTTTAATAGAT
1 AAATAATAAAAAATAATAATAGAT
*
30116070 AAATAATAAAAAAT-ATAAATAAAT
1 AAATAATAAAAAATAAT-AATAGAT
* * * *
30116094 ATATTAATAGATAAATAATAAAAAATTT
1 A-AATAATA-AAAAATAATAATAGA--T
* * * *
30116122 TAATAGATAAATAATAA-AAAATAT
1 AAATA-ATAAAAAATAATAATAGAT
30116146 AAATAAATAAATAAATAATAAT-GAT
1 AAAT-AATAAA-AAATAATAATAGAT
30116171 AA
1 AA
30116173 TACAAATACA
Statistics
Matches: 124, Mismatches: 17, Indels: 34
0.71 0.10 0.19
Matches are distributed among these distances:
23 1 0.01
24 38 0.31
25 16 0.13
26 21 0.17
27 18 0.15
28 10 0.08
29 10 0.08
30 2 0.02
31 8 0.06
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (24 bp):
AAATAATAAAAAATAATAATAGAT
Found at i:30116479 original size:44 final size:44
Alignment explanation
Indices: 30116426--30116661 Score: 251
Period size: 44 Copynumber: 5.4 Consensus size: 44
30116416 CTTCTCAAAG
* *
30116426 CAGAGGCTCAACAACTTAAAAAAAATAAACATAGCTCTTCTAAT
1 CAGAGGCTCAACGACTTAAAAAAAATAAACATAGCTCATCTAAT
* *** * * * *
30116470 CAGAAGCTCAACGACTTTGGAAAAACAAATAAAGCTCATCTAAA
1 CAGAGGCTCAACGACTTAAAAAAAATAAACATAGCTCATCTAAT
* * * * * * *
30116514 CAGAGGCTTAATGAATTTGAAAAAAAT-AA-ATTGCTCCTCTAAA
1 CAGAGGCTCAACG-ACTTAAAAAAAATAAACATAGCTCATCTAAT
* *
30116557 CAGAGGCTCAATGACTTAAAAAAAATAAACACAGCTCATCTAAT
1 CAGAGGCTCAACGACTTAAAAAAAATAAACATAGCTCATCTAAT
* *
30116601 CAGAGGCTCAACGACTTAAAAAAAATAAACATTGTTCATCTAAT
1 CAGAGGCTCAACGACTTAAAAAAAATAAACATAGCTCATCTAAT
*
30116645 CAAAGGCTCAACGACTT
1 CAGAGGCTCAACGACTT
30116662 TGGAAAAAAT
Statistics
Matches: 156, Mismatches: 33, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
42 11 0.07
43 25 0.16
44 112 0.72
45 8 0.05
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (44 bp):
CAGAGGCTCAACGACTTAAAAAAAATAAACATAGCTCATCTAAT
Found at i:30116555 original size:43 final size:42
Alignment explanation
Indices: 30116426--30116693 Score: 234
Period size: 44 Copynumber: 6.1 Consensus size: 42
30116416 CTTCTCAAAG
* * * *
30116426 CAGAGGCTCAACAACTTAAAAAAAATAAACATAGCTCTTCTAAT
1 CAGAGGCTCAACGACTTAAAAAAAAT-AA-ATTGCTCATCTAAA
*
30116470 CAGAAGCTCAACGACTTTGGAAAAACAAATAAA--GCTCATCTAAA
1 CAGAGGCTCAACGAC-TT--AAAAA-AAATAAATTGCTCATCTAAA
* * * * *
30116514 CAGAGGCTTAATGAATTTGAAAAAAATAAATTGCTCCTCTAAA
1 CAGAGGCTCAACG-ACTTAAAAAAAATAAATTGCTCATCTAAA
* ** *
30116557 CAGAGGCTCAATGACTTAAAAAAAATAAACACAGCTCATCTAAT
1 CAGAGGCTCAACGACTTAAAAAAAAT-AA-ATTGCTCATCTAAA
* *
30116601 CAGAGGCTCAACGACTTAAAAAAAATAAACATTGTTCATCTAAT
1 CAGAGGCTCAACGACTTAAAAAAAAT-AA-ATTGCTCATCTAAA
* ** *
30116645 CAAAGGCTCAACGACTTTGGAAAAAATAAATTGCTCCTCTAAA
1 CAGAGGCTCAACGAC-TTAAAAAAAATAAATTGCTCATCTAAA
30116688 CAGAGG
1 CAGAGG
30116694 TAGCACAACT
Statistics
Matches: 186, Mismatches: 28, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
41 7 0.04
42 15 0.08
43 40 0.22
44 100 0.54
45 12 0.06
46 1 0.01
47 7 0.04
48 4 0.02
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (42 bp):
CAGAGGCTCAACGACTTAAAAAAAATAAATTGCTCATCTAAA
Found at i:30116573 original size:87 final size:87
Alignment explanation
Indices: 30116426--30116693 Score: 283
Period size: 87 Copynumber: 3.1 Consensus size: 87
30116416 CTTCTCAAAG
* * * *
30116426 CAGAGGCTCAACAACTTAAAAAAAATAAACATAGCTCTTCTAATCAGAAGCTCAACGACTTTGGA
1 CAGAGGCTCAACGACTTAAAAAAAATAAACATTGCTCATCTAATCAGAGGCTCAACGACTTTGGA
30116491 AAAACAAATAAAGCTCATCTAAA
66 AAAA-AAATAAAGCTCATCTAAA
* * * * * * * ***
30116514 CAGAGGCTTAATGAATTTGAAAAAAAT-AA-ATTGCTCCTCTAAACAGAGGCTCAATGACTTAAA
1 CAGAGGCTCAACG-ACTTAAAAAAAATAAACATTGCTCATCTAATCAGAGGCTCAACGACTTTGG
* * *
30116577 AAAAATAAACACAGCTCATCTAAT
65 AAAAA-AAATAAAGCTCATCTAAA
* *
30116601 CAGAGGCTCAACGACTTAAAAAAAATAAACATTGTTCATCTAATCAAAGGCTCAACGACTTTGG-
1 CAGAGGCTCAACGACTTAAAAAAAATAAACATTGCTCATCTAATCAGAGGCTCAACGACTTTGGA
*
30116665 -AAAAAATAAATTGCTCCTCTAAA
66 AAAAAAATAAA--GCTCATCTAAA
30116688 CAGAGG
1 CAGAGG
30116694 TAGCACAACT
Statistics
Matches: 142, Mismatches: 33, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
85 5 0.04
86 14 0.10
87 74 0.52
88 38 0.27
89 11 0.08
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (87 bp):
CAGAGGCTCAACGACTTAAAAAAAATAAACATTGCTCATCTAATCAGAGGCTCAACGACTTTGGA
AAAAAAATAAAGCTCATCTAAA
Found at i:30116603 original size:131 final size:131
Alignment explanation
Indices: 30116426--30116693 Score: 365
Period size: 131 Copynumber: 2.0 Consensus size: 131
30116416 CTTCTCAAAG
* * ***
30116426 CAGAGGCTCAACAACTTAAAAAAAATAAACATAGCTCTTCTAATCAGAAGCTCAACGACTTTGGA
1 CAGAGGCTCAACAACTTAAAAAAAATAAACACAGCTCATCTAATCAGAAGCTCAACGACTTAAAA
* * * *
30116491 AAAACAAATAAAGCTCATCTAAACAGAGGCTTAATGAATTTGAAAAAAATAAATTGCTCCTCTAA
66 AAAACAAACAAAGCTCATCTAAACAAAGGCTCAACGAATTTGAAAAAAATAAATTGCTCCTCTAA
30116556 A
131 A
** *
30116557 CAGAGGCTCAATGACTTAAAAAAAATAAACACAGCTCATCTAATCAGAGGCTCAACGACTTAAAA
1 CAGAGGCTCAACAACTTAAAAAAAATAAACACAGCTCATCTAATCAGAAGCTCAACGACTTAAAA
* ** * * * *
30116622 AAAATAAACATTGTTCATCTAATCAAAGGCTCAACGACTTTGGAAAAAATAAATTGCTCCTCTAA
66 AAAACAAACAAAGCTCATCTAAACAAAGGCTCAACGAATTTGAAAAAAATAAATTGCTCCTCTAA
30116687 A
131 A
30116688 CAGAGG
1 CAGAGG
30116694 TAGCACAACT
Statistics
Matches: 118, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
131 118 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (131 bp):
CAGAGGCTCAACAACTTAAAAAAAATAAACACAGCTCATCTAATCAGAAGCTCAACGACTTAAAA
AAAACAAACAAAGCTCATCTAAACAAAGGCTCAACGAATTTGAAAAAAATAAATTGCTCCTCTAA
A
Found at i:30117175 original size:20 final size:20
Alignment explanation
Indices: 30117146--30117184 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30117136 CGCATCCAAA
*
30117146 AGTTCAAAGATTCTCATTCT
1 AGTTCAAAGATTCACATTCT
*
30117166 AGTTCGAAGATTCACATTC
1 AGTTCAAAGATTCACATTC
30117185 AACAAACCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
AGTTCAAAGATTCACATTCT
Found at i:30117246 original size:25 final size:24
Alignment explanation
Indices: 30117210--30117296 Score: 90
Period size: 25 Copynumber: 3.7 Consensus size: 24
30117200 TTCACACCTC
30117210 AAAGATTCTCATTTAAAAACATCTT
1 AAAGATTCTCATTTAAAAA-ATCTT
* * *
30117235 AAAGATTTTCATTT---AAGTCTC
1 AAAGATTCTCATTTAAAAAATCTT
*
30117256 AAAGATTCTCATTTGAAAATATCTT
1 AAAGATTCTCATTT-AAAAAATCTT
*
30117281 AAAGATTCTTATTTAA
1 AAAGATTCTCATTTAA
30117297 GACCTAAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
21 16 0.32
22 2 0.04
24 2 0.04
25 30 0.60
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (24 bp):
AAAGATTCTCATTTAAAAAATCTT
Found at i:30117316 original size:46 final size:47
Alignment explanation
Indices: 30117205--30117317 Score: 160
Period size: 46 Copynumber: 2.4 Consensus size: 47
30117195 AGGGTTTCAC
*
30117205 ACCTCAAAGATTCTCATTTAAAAACATCTTAAAGATTTTCATTTAAG
1 ACCTCAAAGATTCTCATTTGAAAACATCTTAAAGATTTTCATTTAAG
* *
30117252 -TCTCAAAGATTCTCATTTGAAAATATCTTAAAGATTCTT-ATTTAAG
1 ACCTCAAAGATTCTCATTTGAAAACATCTTAAAGATT-TTCATTTAAG
*
30117298 ACCT-AAATATTCTCATTTGA
1 ACCTCAAAGATTCTCATTTGA
30117318 TGACTTTTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
46 55 0.93
47 4 0.07
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (47 bp):
ACCTCAAAGATTCTCATTTGAAAACATCTTAAAGATTTTCATTTAAG
Found at i:30117760 original size:23 final size:23
Alignment explanation
Indices: 30117717--30117760 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
30117707 TTGGAGCAAG
*
30117717 TTTCATCAACTGATCATCATTAT
1 TTTCATCAACTGATCACCATTAT
*
30117740 TTTCATC-ACTTAGTCACCATT
1 TTTCATCAACTGA-TCACCATT
30117761 CTCAACACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.27, C:0.25, G:0.05, T:0.43
Consensus pattern (23 bp):
TTTCATCAACTGATCACCATTAT
Found at i:30118535 original size:19 final size:18
Alignment explanation
Indices: 30118513--30118577 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 18
30118503 TTCTTTCATC
30118513 TTTTTTTTTTATTTTTTTA
1 TTTTTTTTTT-TTTTTTTA
*
30118532 TTTTTTTTTTTCATTTTTCA
1 TTTTTTTTTTT--TTTTTTA
**
30118552 TTTTTTCTTTCCTTTTTTA
1 TTTTTT-TTTTTTTTTTTA
30118571 TTTTTTT
1 TTTTTTT
30118578 CATCCTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 2 0.05
19 22 0.56
20 12 0.31
21 3 0.08
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTTTTTTTTTTTTTA
Found at i:30118536 original size:20 final size:19
Alignment explanation
Indices: 30118513--30118577 Score: 76
Period size: 20 Copynumber: 3.3 Consensus size: 19
30118503 TTCTTTCATC
30118513 TTTTTTTTTTATTTTTTTAT
1 TTTTTTTTTTA-TTTTTTAT
*
30118533 TTTTTTTTTTCATTTTTCAT
1 TTTTTTTTTT-ATTTTTTAT
* **
30118553 TTTTTCTTTCCTTTTTTAT
1 TTTTTTTTTTATTTTTTAT
30118572 TTTTTT
1 TTTTTT
30118578 CATCCTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 12 0.32
20 25 0.66
21 1 0.03
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTTTTTTTTATTTTTTAT
Found at i:30118548 original size:8 final size:8
Alignment explanation
Indices: 30118485--30118558 Score: 54
Period size: 7 Copynumber: 9.9 Consensus size: 8
30118475 TTCTTTTTTT
30118485 TTTTTTCA
1 TTTTTTCA
30118493 TCTTTTTCCA
1 T-TTTTT-CA
*
30118503 TTCTTTCA
1 TTTTTTCA
*
30118511 TCTTTT--
1 TTTTTTCA
30118517 TTTTTT-A
1 TTTTTTCA
*
30118524 TTTTTTTA
1 TTTTTTCA
30118532 -TTTTT--
1 TTTTTTCA
30118537 TTTTTTCA
1 TTTTTTCA
30118545 -TTTTTCA
1 TTTTTTCA
30118552 TTTTTTC
1 TTTTTTC
30118559 TTTCCTTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
6 10 0.19
7 18 0.33
8 14 0.26
9 9 0.17
10 3 0.06
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTCA
Found at i:30118568 original size:30 final size:29
Alignment explanation
Indices: 30118477--30118591 Score: 82
Period size: 28 Copynumber: 4.0 Consensus size: 29
30118467 TTGAGTATTT
*
30118477 CTTTTTT-TTTTTTTCATCTTTTTCCATT-
1 CTTTTTTATTTTTTTCATCTTTTT-CTTTC
* * *
30118505 CTTTCATCTT-TTTTTTTTATTTTTTTATTT-
1 CTTT--T-TTATTTTTTTCATCTTTTTCTTTC
30118535 -TTTTTT-TTCATTTTTCAT-TTTTTCTTTC
1 CTTTTTTATT--TTTTTCATCTTTTTCTTTC
30118563 CTTTTTTATTTTTTTCATCCTTTTTCTTT
1 CTTTTTTATTTTTTTCAT-CTTTTTCTTT
30118592 TTCCTCATAT
Statistics
Matches: 71, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
26 4 0.06
27 9 0.13
28 19 0.27
29 9 0.13
30 14 0.20
31 16 0.23
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (29 bp):
CTTTTTTATTTTTTTCATCTTTTTCTTTC
Found at i:30118578 original size:20 final size:20
Alignment explanation
Indices: 30118525--30118587 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 20
30118515 TTTTTTTTAT
* *
30118525 TTTTTTATTTTTTTTTTTCA
1 TTTTTTATTTTTTTCTTTCC
*
30118545 TTTTTCA-TTTTTTCTTTCC
1 TTTTTTATTTTTTTCTTTCC
*
30118564 TTTTTTATTTTTTTC-ATCC
1 TTTTTTATTTTTTTCTTTCC
30118583 TTTTT
1 TTTTT
30118588 CTTTTTCCTC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
19 24 0.65
20 13 0.35
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTATTTTTTTCTTTCC
Found at i:30118593 original size:19 final size:15
Alignment explanation
Indices: 30118474--30118578 Score: 59
Period size: 17 Copynumber: 6.3 Consensus size: 15
30118464 AACTTGAGTA
30118474 TTTCTTTTTTTTTTT
1 TTTCTTTTTTTTTTT
*
30118489 TTCATCTTTTTCCATTCTTT
1 TT--TCTTTTT---TTTTTT
**
30118509 CATCTTTTTTTTTTAT
1 TTTCTTTTTTTTTT-T
30118525 TTT-TTTATTTTTTTT
1 TTTCTTT-TTTTTTTT
30118540 TTTCATTTTTCATTTTTT
1 TTTC-TTTTT--TTTTTT
*
30118558 CTTTCCTTTTTTATTTT
1 -TTT-CTTTTTTTTTTT
30118575 TTTC
1 TTTC
30118579 ATCCTTTTTC
Statistics
Matches: 70, Mismatches: 7, Indels: 26
0.68 0.07 0.25
Matches are distributed among these distances:
15 14 0.20
16 14 0.20
17 15 0.21
18 13 0.19
19 8 0.11
20 6 0.09
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCTTTTTTTTTTT
Found at i:30121461 original size:15 final size:15
Alignment explanation
Indices: 30121441--30121470 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30121431 TTTAAATATG
*
30121441 ATGAATGAGAATGCA
1 ATGAATGAAAATGCA
30121456 ATGAATGAAAATGCA
1 ATGAATGAAAATGCA
30121471 TGTATGCAAA
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:0.50, C:0.07, G:0.23, T:0.20
Consensus pattern (15 bp):
ATGAATGAAAATGCA
Found at i:30124312 original size:88 final size:90
Alignment explanation
Indices: 30124159--30124335 Score: 247
Period size: 88 Copynumber: 2.0 Consensus size: 90
30124149 CGTCAAACCA
* *
30124159 TCATAATGTCTAGATCTAGGGATCCATTGCTAGACATTGACTTTAGGAGTCGCCACCATCTTTTT
1 TCATAACGTCTAGATCTAGGGATCCATTGCTAGACATTGACTTTAGGAGTCGCCACAATCTTTTT
30124224 TGT-T-TAGGTGCGATTGGCCACCTG
66 T-TATCTAGGTGCGATTGGCCACCTG
* *
30124248 TCATAACGTCTAGATC-CGGTATCCATTGCTAGACATT-ATCTTTAGGAGTCGCCACAAATC-TT
1 TCATAACGTCTAGATCTAGGGATCCATTGCTAGACATTGA-CTTTAGGAGTCGCCAC-AATCTTT
*
30124310 TTTTATCTAGGTGCGATTGGTCACCT
64 TTTTATCTAGGTGCGATTGGCCACCT
30124336 AAGGAATCTG
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
87 2 0.03
88 41 0.52
89 36 0.46
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (90 bp):
TCATAACGTCTAGATCTAGGGATCCATTGCTAGACATTGACTTTAGGAGTCGCCACAATCTTTTT
TTATCTAGGTGCGATTGGCCACCTG
Found at i:30124325 original size:89 final size:89
Alignment explanation
Indices: 30124159--30124335 Score: 259
Period size: 89 Copynumber: 2.0 Consensus size: 89
30124149 CGTCAAACCA
* *
30124159 TCATAATGTCTAGATCTAGGGATCCATTGCTAGACATTGACTTTAGGAGTCGCCACCATCTTTTT
1 TCATAACGTCTAGATCTAGGGATCCATTGCTAGACATTGACTTTAGGAGTCGCCACAATCTTTTT
* *
30124224 TGTTTAGGTGCGATTGGCCACCTG
66 TATCTAGGTGCGATTGGCCACCTG
* *
30124248 TCATAACGTCTAGATC-CGGTATCCATTGCTAGACATT-ATCTTTAGGAGTCGCCACAAATCTTT
1 TCATAACGTCTAGATCTAGGGATCCATTGCTAGACATTGA-CTTTAGGAGTCGCCAC-AATCTTT
*
30124311 TTTATCTAGGTGCGATTGGTCACCT
64 TTTATCTAGGTGCGATTGGCCACCT
30124336 AAGGAATCTG
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
87 1 0.01
88 35 0.44
89 43 0.54
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (89 bp):
TCATAACGTCTAGATCTAGGGATCCATTGCTAGACATTGACTTTAGGAGTCGCCACAATCTTTTT
TATCTAGGTGCGATTGGCCACCTG
Found at i:30124929 original size:16 final size:17
Alignment explanation
Indices: 30124910--30124942 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
30124900 TTCTCAAAAA
*
30124910 TATTTTTTAA-AAAATT
1 TATTTTTAAAGAAAATT
30124926 TATTTTTAAAGAAAATT
1 TATTTTTAAAGAAAATT
30124943 AATACTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TATTTTTAAAGAAAATT
Found at i:30124941 original size:115 final size:113
Alignment explanation
Indices: 30124815--30125149 Score: 415
Period size: 115 Copynumber: 2.9 Consensus size: 113
30124805 TTTTTTTTTG
* * *
30124815 TTTAAGGAAAATTGGTACTTTCAACTTTTTTTCAAAATATTTTTCT-GAAACTTTAATTTCAAGA
1 TTTAAGGAAAATTGATACTTTCAACTTTTTTTCAAAATATTTTT-TAAAAACTTTATTTTCAAGA
* *
30124879 AAGATTGATAGTTTCAACTTTTTCTCAAAAATATTTTTTAAAAAATTTATT
65 AA-ATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAAAAAA-TTATT
* * *
30124930 TTTAAAGAAAATTAATACTTTCAA-TTTTTTCTCAAAAATATTTTTTAAAAATTTTATTTTCAAG
1 TTTAAGGAAAATTGATACTTTCAACTTTTTT-TC-AAAATATTTTTTAAAAACTTTATTTTCAA-
* * * *
30124994 GAAAATAGATACTTTTACCTTTTCCTCAAAAATATTTTTTAGAAAATTATT
63 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAAAAAATTATT
* * *
30125045 TTCAAGGAAAATTGATACTTTTAACTTTTTCTTGAAAATATTTTTTAAAAAAC-TTATTTTCAAG
1 TTTAAGGAAAATTGATACTTTCAACTTTTT-TTCAAAATATTTTTT-AAAAACTTTATTTTCAAG
*
30125109 AAAAATTGATACTTTCAACTTTTCCTAAAAAATATATTTTT
64 -AAAATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTT
30125150 TTGGAATTTT
Statistics
Matches: 189, Mismatches: 22, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
114 7 0.04
115 101 0.53
116 76 0.40
117 5 0.03
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.46
Consensus pattern (113 bp):
TTTAAGGAAAATTGATACTTTCAACTTTTTTTCAAAATATTTTTTAAAAACTTTATTTTCAAGAA
AATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAAAAAATTATT
Found at i:30125172 original size:58 final size:57
Alignment explanation
Indices: 30124821--30125149 Score: 385
Period size: 58 Copynumber: 5.7 Consensus size: 57
30124811 TTTGTTTAAG
* * * * *
30124821 GAAAATTGGTACTTTCAACTTTTTTTC-AAAATATTTTTCT-GAAACTTTAATTTCAA
1 GAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTT-TAAAAAATTTATTTTCAA
* *
30124877 GAAAGATTGATAGTTTCAACTTTTTCTCAAAAATATTTTTTAAAAAATTTATTTTTAAA
1 GAAA-ATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAAATTTA-TTTTCAA
* * *
30124936 GAAAATTAATACTTTCAATTTTTTCTCAAAAATATTTTTTAAAAATTTTATTTTCAA
1 GAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAAATTTATTTTCAA
* * * * *
30124993 GGAAAATAGATACTTTTACCTTTTCCTCAAAAATATTTTTTAGAAAA-TTATTTTCAA
1 -GAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAAATTTATTTTCAA
* ** *
30125050 GGAAAATTGATACTTTTAACTTTTTCTTGAAAATATTTTTTAAAAAACTTATTTTCAA
1 -GAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAAATTTATTTTCAA
* *
30125108 GAAAAATTGATACTTTCAACTTTTCCTAAAAAATATATTTTT
1 G-AAAATTGATACTTTCAACTTTTTCTCAAAAATAT-TTTTT
30125150 TTGGAATTTT
Statistics
Matches: 235, Mismatches: 30, Indels: 13
0.85 0.11 0.05
Matches are distributed among these distances:
56 4 0.02
57 79 0.34
58 138 0.59
59 14 0.06
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.46
Consensus pattern (57 bp):
GAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAAATTTATTTTCAA
Found at i:30125262 original size:21 final size:22
Alignment explanation
Indices: 30125231--30125271 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
30125221 TTCCTAATCT
30125231 AAATCAATAATAATAATAAAAG
1 AAATCAATAATAATAATAAAAG
30125253 AAAT-AATAATAATAATAAA
1 AAATCAATAATAATAATAAA
30125272 TAAGAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
AAATCAATAATAATAATAAAAG
Found at i:30126361 original size:45 final size:44
Alignment explanation
Indices: 30126309--30126689 Score: 346
Period size: 44 Copynumber: 8.7 Consensus size: 44
30126299 TTGATTAAGT
* *
30126309 TCCTCTAAGCAGAGGCTTAACGACTTTGAAAAAAATAAACAAAGT
1 TCCTCTAAACAGAGGCTTAACGACTTTG-AAAAAATAAACAAAGC
* * *
30126354 TCTTCTAATA-AGAGGCTT-ACCACTTTG-GAAAAT-AACTAAAGC
1 TCCTCTAA-ACAGAGGCTTAACGACTTTGAAAAAATAAAC-AAAGC
* * *
30126396 TCCTCTAATA-AGAGGCTTAATGACTTTG-GAAAATAAATAAAGC
1 TCCTCTAA-ACAGAGGCTTAACGACTTTGAAAAAATAAACAAAGC
* * * *
30126439 TCTTCTAATCAGAGGCTCAACGACTTTGGAAAAATAAACAAAGC
1 TCCTCTAAACAGAGGCTTAACGACTTTGAAAAAATAAACAAAGC
* * ** * * *
30126483 TTCTTTAAGTAGAGGCTCAATGATTTTGAAAAAATAAACAAAGC
1 TCCTCTAAACAGAGGCTTAACGACTTTGAAAAAATAAACAAAGC
* * *
30126527 TCCTTTAAACAGAGGTTTAACGACTTTGAAAAAATAAATAAAGC
1 TCCTCTAAACAGAGGCTTAACGACTTTGAAAAAATAAACAAAGC
* * * * * *
30126571 TCCTCTAAATAGAGGCTCAATGACTTTTAGTAAAATAAATAAAGC
1 TCCTCTAAACAGAGGCTTAACGACTTTGA-AAAAATAAACAAAGC
* * * *
30126616 TCCTCTAAGCAGAGGCTCAATGACTTTTG-AAAAATAAATAAAGC
1 TCCTCTAAACAGAGGCTTAACGAC-TTTGAAAAAATAAACAAAGC
*
30126660 TCCTCTAAATAGAGG-TTCAACGACTTTGAA
1 TCCTCTAAACAGAGGCTT-AACGACTTTGAA
30126690 TGACAATCAT
Statistics
Matches: 280, Mismatches: 46, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
41 3 0.01
42 26 0.09
43 46 0.16
44 151 0.54
45 51 0.18
46 3 0.01
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (44 bp):
TCCTCTAAACAGAGGCTTAACGACTTTGAAAAAATAAACAAAGC
Found at i:30126549 original size:88 final size:89
Alignment explanation
Indices: 30126309--30126689 Score: 395
Period size: 88 Copynumber: 4.3 Consensus size: 89
30126299 TTGATTAAGT
** * * *
30126309 TCCTCTAAGCAGAGGCTTAACGACTTTGAAAAAAATAAACAAAG-TTCTTCTAATA-AGAGGCT-
1 TCCTCTAAATAGAGGCTCAATGACTTTG-AAAAAATAAACAAAGCTCCTTCTAA-ACAGAGGCTC
* *
30126371 TACCACTTTGG-AAAAT-AACTAAAGC
64 AACGACTTTGGAAAAATAAAC-AAAGC
* * * *
30126396 TCCTCT-AATAAGAGGCTTAATGACTTTG-GAAAATAAATAAAGCT-CTTCTAATCAGAGGCTCA
1 TCCTCTAAAT-AGAGGCTCAATGACTTTGAAAAAATAAACAAAGCTCCTTCTAAACAGAGGCTCA
30126458 ACGACTTTGGAAAAATAAACAAAGC
65 ACGACTTTGGAAAAATAAACAAAGC
* * * * * *
30126483 TTCTTTAAGTAGAGGCTCAATGATTTTGAAAAAATAAACAAAGCTCCTT-TAAACAGAGGTTTAA
1 TCCTCTAAATAGAGGCTCAATGACTTTGAAAAAATAAACAAAGCTCCTTCTAAACAGAGGCTCAA
* *
30126547 CGACTTTGAAAAAATAAATAAAGC
66 CGACTTTGGAAAAATAAACAAAGC
* * * *
30126571 TCCTCTAAATAGAGGCTCAATGACTTTTAGTAAAATAAATAAAGCTCC-TCTAAGCAGAGGCTCA
1 TCCTCTAAATAGAGGCTCAATGACTTTGA-AAAAATAAACAAAGCTCCTTCTAAACAGAGGCTCA
* * *
30126635 ATGACTTTTGAAAAATAAATAAAGC
65 ACGACTTTGGAAAAATAAACAAAGC
* *
30126660 TCCTCTAAATAGAGGTTCAACGACTTTGAA
1 TCCTCTAAATAGAGGCTCAATGACTTTGAA
30126690 TGACAATCAT
Statistics
Matches: 246, Mismatches: 37, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
85 26 0.11
86 11 0.04
87 53 0.22
88 78 0.32
89 78 0.32
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (89 bp):
TCCTCTAAATAGAGGCTCAATGACTTTGAAAAAATAAACAAAGCTCCTTCTAAACAGAGGCTCAA
CGACTTTGGAAAAATAAACAAAGC
Found at i:30126642 original size:89 final size:87
Alignment explanation
Indices: 30126339--30126686 Score: 382
Period size: 89 Copynumber: 4.0 Consensus size: 87
30126329 CGACTTTGAA
* * * * * * *
30126339 AAAAATAAACAAAGTTCTTCTAATA-AGAGGCT-TACCACTTTGGAAAATAACTAAAGCTCCTCT
1 AAAAATAAATAAAGCTCCTCTAA-ACAGAGGCTCAACGACTTTGAAAAATAAATAAAGCTCCTCT
*
30126402 -AATAAGAGGCTTAATGAC-TTTG
65 AAAT-AGAGGCTCAATGACTTTTG
* * * * * *
30126424 GAAAATAAATAAAGCTCTTCTAATCAGAGGCTCAACGACTTTGGAAAAATAAACAAAGCTTCTTT
1 AAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACGACTTT-GAAAAATAAATAAAGCTCCTCT
*
30126489 AAGTAGAGGCTCAATGA-TTTTG
65 AAATAGAGGCTCAATGACTTTTG
* * * *
30126511 AAAAAATAAACAAAGCTCCTTTAAACAGAGGTTTAACGACTTTGAAAAAATAAATAAAGCTCCTC
1 -AAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACGACTTTG-AAAAATAAATAAAGCTCCTC
30126576 TAAATAGAGGCTCAATGACTTTTAG
64 TAAATAGAGGCTCAATGACTTTT-G
* * *
30126601 TAAAATAAATAAAGCTCCTCTAAGCAGAGGCTCAATGACTTTTGAAAAATAAATAAAGCTCCTCT
1 AAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACGAC-TTTGAAAAATAAATAAAGCTCCTCT
* *
30126666 AAATAGAGGTTCAACGACTTT
65 AAATAGAGGCTCAATGACTTT
30126687 GAATGACAAT
Statistics
Matches: 220, Mismatches: 33, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
85 27 0.12
86 7 0.03
87 34 0.15
88 71 0.32
89 76 0.35
90 5 0.02
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (87 bp):
AAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATAAAGCTCCTCTA
AATAGAGGCTCAATGACTTTTG
Found at i:30127707 original size:21 final size:21
Alignment explanation
Indices: 30127682--30127739 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
30127672 TTTTATTCCC
* *
30127682 TTTTTCTTTTTTTTTCTTTTCA
1 TTTTT-TTATTTTTTCATTTCA
30127704 TTTTTTTATTTTTTCATTTCA
1 TTTTTTTATTTTTTCATTTCA
30127725 TTTTTTTCATTTTTT
1 TTTTTTT-ATTTTTT
30127740 TAAGCATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.09, C:0.10, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTTTATTTTTTCATTTCA
Found at i:30134990 original size:15 final size:15
Alignment explanation
Indices: 30134969--30135003 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
30134959 TTACTTTGTT
*
30134969 AAATGTATTGAATGA
1 AAATGTAATGAATGA
*
30134984 GAATGTAATGAATGA
1 AAATGTAATGAATGA
30134999 AAATG
1 AAATG
30135004 CATACATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.29
Consensus pattern (15 bp):
AAATGTAATGAATGA
Found at i:30138370 original size:58 final size:57
Alignment explanation
Indices: 30138247--30138577 Score: 409
Period size: 58 Copynumber: 5.8 Consensus size: 57
30138237 TTTTTTGTTT
* * * * *
30138247 AAGGAAAATTGGTAC-TTCTAACTTTT-TTCCAAAATATTTTTCTGAAATTTTATTTTC
1 AAGGAAAATTGATACTTTC-AACTTTTCCTCAAAAATATTTTT-TAAAAATTTATTTTC
* * * *
30138304 GAGAAAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTTAAAAATTTATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTAAAAATTTATTTTC
*
30138362 AAGGAAAATTGAAACTTTCAACTTTTCCTCAAAAATATTTTTTAAAAATTTTATTTTC
1 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAAAAA-TTTATTTTC
* * * *
30138420 AAAGAAAATAT-ATACTTTTACCTTTTCCTAAAAAATATTTTTTAGAAAA-TTATTTTC
1 AAGGAAAAT-TGATACTTTCAACTTTTCCTCAAAAATATTTTTTA-AAAATTTATTTTC
* * * *
30138477 AAGAAAAATTGATACTTTCAACTTTTTCTCGAAAATATTTTTTAGAAAACTTATTTTC
1 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTA-AAAATTTATTTTC
30138535 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
1 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
30138578 TTAGAATTTT
Statistics
Matches: 239, Mismatches: 27, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
56 1 0.00
57 78 0.33
58 150 0.63
59 10 0.04
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (57 bp):
AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAAAAATTTATTTTC
Found at i:30138492 original size:173 final size:173
Alignment explanation
Indices: 30138277--30138600 Score: 496
Period size: 173 Copynumber: 1.9 Consensus size: 173
30138267 ACTTTTTTCC
* *
30138277 AAAATATTTTTCTGAAATTTTATTTTCGAGAAAAATTGATACTTTCAAC-TTTTCTTCAAAAATA
1 AAAATATTTTTCTGAAATATTATTTTCAAGAAAAATTGATACTTTCAACTTTTTC-TCAAAAATA
* *
30138341 TTTTTTTA-AAAATTTATTTTTAAGGAAAATTGAAACTTTCAACTTTTCCTCAAAAATA-TTTTT
65 -TTTTTTAGAAAACTTATTTTCAAGGAAAATTGAAACTTTCAACTTTTCCTCAAAAATATTTTTT
30138404 TAAAAATTTTATTTTCAAAGAAAATATATACTTTTACCTTTTCCTAA
129 TAAAAATTTTATTTT--AAGAAAATATATACTTTTACCTTTTCCTAA
*
30138451 AAAATATTTTT-TAGAAA-ATTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCGAAAATA
1 AAAATATTTTTCT-GAAATATTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATA
*
30138514 TTTTTTAGAAAACTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
65 TTTTTTAGAAAACTTATTTTCAAGGAAAATTGAAACTTTCAACTTTTCCTCAAAAATATTTTTTT
* *
30138579 TAGAATTTTATTTTAAGAAAAT
130 AAAAATTTTATTTTAAGAAAAT
30138601 CATTTTTAAA
Statistics
Matches: 138, Mismatches: 8, Indels: 10
0.88 0.05 0.06
Matches are distributed among these distances:
172 15 0.11
173 85 0.62
174 38 0.28
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (173 bp):
AAAATATTTTTCTGAAATATTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATAT
TTTTTAGAAAACTTATTTTCAAGGAAAATTGAAACTTTCAACTTTTCCTCAAAAATATTTTTTTA
AAAATTTTATTTTAAGAAAATATATACTTTTACCTTTTCCTAA
Found at i:30138600 original size:115 final size:116
Alignment explanation
Indices: 30138244--30138600 Score: 435
Period size: 115 Copynumber: 3.1 Consensus size: 116
30138234 TTTTTTTTTG
* * * *
30138244 TTTAAGGAAAATTGGTAC-TTCTAACTTTTT-TCCAAAATATTTTTCT-GAAATTTTATTTTCGA
1 TTTAAGGAAAATTGATACTTTC-AACTTTTTCTCAAAAATATTTTT-TAGAAAATTTATTTTCAA
* * *
30138306 GAAAAATTGATACTTTCAACTTTTCTTCAAAAATA-TTTTTTTAAAAATTTATT
64 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTAGAAATTTA-T
* * *
30138359 TTTAAGGAAAATTGAAACTTTCAACTTTTCCTCAAAAATATTTTTTA-AAAATTTTATTTTCAAA
1 TTTAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAA-TTTATTTTCAAG
* * * *
30138423 GAAAATAT-ATACTTTTACCTTTTCCT-AAAAA-ATATTTTTTAGAAAATTAT
65 GAAAAT-TGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTAGAAATTTAT
* * *
30138473 TTTCAAGAAAAATTGATACTTTCAACTTTTTCTCGAAAATATTTTTTAGAAAACTTATTTTCAAG
1 TTT-AAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAATTTATTTTCAAG
*
30138538 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTAGAATTTTAT
65 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTAGAAATTTAT
30138590 TTTAA-GAAAAT
1 TTTAAGGAAAAT
30138601 CATTTTTAAA
Statistics
Matches: 205, Mismatches: 26, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
114 6 0.03
115 122 0.60
116 57 0.28
117 20 0.10
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (116 bp):
TTTAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAATTTATTTTCAAGG
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTAGAAATTTAT
Found at i:30138634 original size:11 final size:11
Alignment explanation
Indices: 30138609--30138642 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
30138599 ATCATTTTTA
*
30138609 AAAAATTAAAT
1 AAAAATAAAAT
30138620 -AAAATAAAAT
1 AAAAATAAAAT
30138630 AAAAATAAAAT
1 AAAAATAAAAT
30138641 AA
1 AA
30138643 GGAATACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:30138680 original size:4 final size:4
Alignment explanation
Indices: 30138673--30138728 Score: 70
Period size: 4 Copynumber: 15.5 Consensus size: 4
30138663 TCAATCAATC
30138673 AATA AAT- AAT- AAT- AAT- AAT- AAT- AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
30138715 AATA AATA AATA AA
1 AATA AATA AATA AA
30138729 CCTTTGGAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 18 0.35
4 33 0.65
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:30139999 original size:18 final size:18
Alignment explanation
Indices: 30139978--30140015 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
30139968 AAAATTCAAG
30139978 AAAA-AAAAGAAAAAAAAT
1 AAAATAAAA-AAAAAAAAT
*
30139996 AAAATAAAAAAAAAGAAT
1 AAAATAAAAAAAAAAAAT
30140014 AA
1 AA
30140016 TGATTCAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.87, C:0.00, G:0.05, T:0.08
Consensus pattern (18 bp):
AAAATAAAAAAAAAAAAT
Found at i:30140004 original size:23 final size:23
Alignment explanation
Indices: 30139964--30140008 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
30139954 TTTAATATTT
**
30139964 AAAAAAAATTCAAGAAAAAAAAG
1 AAAAAAAATAAAAGAAAAAAAAG
*
30139987 AAAAAAAATAAAATAAAAAAAA
1 AAAAAAAATAAAAGAAAAAAAA
30140009 AGAATAATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.84, C:0.02, G:0.04, T:0.09
Consensus pattern (23 bp):
AAAAAAAATAAAAGAAAAAAAAG
Found at i:30140014 original size:13 final size:13
Alignment explanation
Indices: 30139978--30140015 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
30139968 AAAATTCAAG
30139978 AAAAAAAAGAA-A
1 AAAAAAAAGAATA
*
30139990 AAAAATAA-AATA
1 AAAAAAAAGAATA
30140002 AAAAAAAAGAATA
1 AAAAAAAAGAATA
30140015 A
1 A
30140016 TGATTCAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.87, C:0.00, G:0.05, T:0.08
Consensus pattern (13 bp):
AAAAAAAAGAATA
Found at i:30140356 original size:3 final size:3
Alignment explanation
Indices: 30140350--30140389 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
30140340 TAAAAAAAGA
*
30140350 AAT AAT AAT AAT AAT AATT AAGG AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA-T AA-T AAT AAT AAT AAT AAT AA
30140390 ATCAAAGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
3 28 0.85
4 5 0.15
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:30140412 original size:6 final size:6
Alignment explanation
Indices: 30140401--30140426 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
30140391 TCAAAGAAAA
30140401 AAAATT AAAATT AAAATT AAAATT AA
1 AAAATT AAAATT AAAATT AAAATT AA
30140427 GGAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:30140441 original size:20 final size:20
Alignment explanation
Indices: 30140353--30140441 Score: 50
Period size: 20 Copynumber: 4.7 Consensus size: 20
30140343 AAAAAGAAAT
30140353 AATAAT-AATAATAATTAAGG
1 AATAATAAATAA-AATTAAGG
* **
30140373 AATAAT-AATAATAATAAATC
1 AATAATAAATAA-AATTAAGG
30140393 AA-AGA-AAA-AAAATTAA--
1 AATA-ATAAATAAAATTAAGG
*
30140409 AATTAA-AATTAAAATTAAGG
1 AA-TAATAAATAAAATTAAGG
30140429 AATAATAAATAAA
1 AATAATAAATAAA
30140442 TAAATAAATC
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
16 2 0.04
17 3 0.05
18 14 0.25
19 6 0.11
20 30 0.55
ACGTcount: A:0.67, C:0.01, G:0.06, T:0.26
Consensus pattern (20 bp):
AATAATAAATAAAATTAAGG
Found at i:30140764 original size:16 final size:17
Alignment explanation
Indices: 30140735--30140766 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30140725 ACCTTCATCC
30140735 TTTTCTCTTCCCTTTTT
1 TTTTCTCTTCCCTTTTT
30140752 TTTTCTCTT-CCTTTT
1 TTTTCTCTTCCCTTTT
30140767 CTCTAAAAGA
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTCTCTTCCCTTTTT
Found at i:30141221 original size:4 final size:4
Alignment explanation
Indices: 30141178--30141310 Score: 94
Period size: 4 Copynumber: 33.8 Consensus size: 4
30141168 TCAAGAAAAG
* * * * *
30141178 ATAA AGTAA A-AA ATAT ATAA ATAT ATAT ATTA ATAG ATAA AT-A ATAA
1 ATAA A-TAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * * * * *
30141225 ATAA ATAA ATAT ATTA ATAG ATAA AT-A ATAA ATAA ATAT ATTA ATAG
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * *
30141272 ATAA AT-A ATAAA ATAT ATAT ATTA ATAA ATAA ATAA ATA
1 ATAA ATAA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA ATA
30141311 CAAATACAAA
Statistics
Matches: 99, Mismatches: 24, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
3 12 0.12
4 80 0.81
5 7 0.07
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (4 bp):
ATAA
Found at i:30141231 original size:31 final size:31
Alignment explanation
Indices: 30141184--30141307 Score: 163
Period size: 31 Copynumber: 4.2 Consensus size: 31
30141174 AAAGATAAAG
* *
30141184 TAAAAAATATATAAATATATATATTAATAGA
1 TAAATAATAAATAAATATATATATTAATAGA
*
30141215 TAAATAATAAATAAATAAATATATTAATAGA
1 TAAATAATAAATAAATATATATATTAATAGA
30141246 TAAATAATAAAT--A-A-ATATATTAATAGA
1 TAAATAATAAATAAATATATATATTAATAGA
*
30141273 TAAATAAT--A-AAATATATATATTAATAAA
1 TAAATAATAAATAAATATATATATTAATAGA
30141301 TAAATAA
1 TAAATAA
30141308 ATACAAATAC
Statistics
Matches: 85, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
25 1 0.01
26 1 0.01
27 22 0.26
28 20 0.24
29 1 0.01
31 40 0.47
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (31 bp):
TAAATAATAAATAAATATATATATTAATAGA
Found at i:30141484 original size:33 final size:33
Alignment explanation
Indices: 30141447--30141512 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
30141437 AATGATGACT
30141447 AAGTCTCTAAGATGACAATATCTCCTACGCAAG
1 AAGTCTCTAAGATGACAATATCTCCTACGCAAG
30141480 AAGTCTCTAAGATGACAATATCTCCTACGCAAG
1 AAGTCTCTAAGATGACAATATCTCCTACGCAAG
30141513 TAAACACCGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (33 bp):
AAGTCTCTAAGATGACAATATCTCCTACGCAAG
Found at i:30144092 original size:62 final size:62
Alignment explanation
Indices: 30144024--30144151 Score: 247
Period size: 62 Copynumber: 2.1 Consensus size: 62
30144014 ATGATTAATT
*
30144024 TTAGCCATTAAGTATTAGGTAAGAATTAGTCTTAGCATTTAAAATGTTGTTAGTTGGTATAG
1 TTAGCCATTAAGTATTAGGTAAGAATTAGTCATAGCATTTAAAATGTTGTTAGTTGGTATAG
30144086 TTAGCCATTAAGTATTAGGTAAGAATTAGTCATAGCATTTAAAATGTTGTTAGTTGGTATAG
1 TTAGCCATTAAGTATTAGGTAAGAATTAGTCATAGCATTTAAAATGTTGTTAGTTGGTATAG
30144148 TTAG
1 TTAG
30144152 TAAGTAATGT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (62 bp):
TTAGCCATTAAGTATTAGGTAAGAATTAGTCATAGCATTTAAAATGTTGTTAGTTGGTATAG
Found at i:30147691 original size:22 final size:20
Alignment explanation
Indices: 30147639--30147693 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
30147629 CAAGCAATTC
*
30147639 TATTTTTTTTTGTATTTTTT
1 TATTTTTTTTAGTATTTTTT
*
30147659 TAGGTTCTTTTTAGTATTTTGTT
1 TA--TTTTTTTTAGTATTTT-TT
30147682 TATTTATTTTTA
1 TATTT-TTTTTA
30147694 TGTGTTTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 2 0.07
21 2 0.07
22 20 0.71
23 4 0.14
ACGTcount: A:0.15, C:0.02, G:0.09, T:0.75
Consensus pattern (20 bp):
TATTTTTTTTAGTATTTTTT
Found at i:30148207 original size:51 final size:51
Alignment explanation
Indices: 30148152--30148289 Score: 127
Period size: 52 Copynumber: 2.7 Consensus size: 51
30148142 CAATGGTGGG
30148152 AAAATTTAGAAATTTCAAAAAAAAAATTTTTTTAATTAACCTAAATAGTAA
1 AAAATTTAGAAATTTCAAAAAAAAAATTTTTTTAATTAACCTAAATAGTAA
* *** * * * ** * * *
30148203 AAAATTTAGAGATAAAAAAATAAAAAAATTTTCTAAATAGGCTCAATGGTGA
1 AAAATTTAGAAATTTCAAAA-AAAAAATTTTTTTAATTAACCTAAATAGTAA
* *
30148255 AAAGTTTAGAAA-TTC-AAAAAAAAATATTTTTAATT
1 AAAATTTAGAAATTTCAAAAAAAAAATTTTTTTAATT
30148290 TGGCTCAAAT
Statistics
Matches: 65, Mismatches: 21, Indels: 4
0.72 0.23 0.04
Matches are distributed among these distances:
49 13 0.20
50 3 0.05
51 16 0.25
52 33 0.51
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (51 bp):
AAAATTTAGAAATTTCAAAAAAAAAATTTTTTTAATTAACCTAAATAGTAA
Done.