Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 55 of 187
Found at i:16312815 original size:148 final size:149
Alignment explanation
Indices: 16312287--16312996 Score: 795
Period size: 148 Copynumber: 4.7 Consensus size: 149
16312277 TTATCGTTTT
* * * * **
16312287 TTTTCTTGAAAAATAGAAATTGAAAATACCTCAGCATGATCCGAGTCTCAACTTGCCTCTCGCAT
1 TTTT-TTGAAAAACAGAAATTGAAAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCAT
* * ** * *
16312352 TATGAGTTGATTTTTGAGAAACGGAAATTTAAAAGAAATACCTC-GATATGTGACCCGAGGTTCA
65 TATGAGTTGATTTTTGAAAAACAGAAATTT---A-AAATACCTCAG-CGTGCGACCCGAGGCTCA
*
16312416 ACTCACCTCTGGCAATATGAGTTGA
125 ACTCACCTCTCGCAATATGAGTTGA
* * * *
16312441 TTTTTTTGAAAAGCAGAAATTTAAAAGAAATACATC-GGTATGTGACCCGAGACTCAACTCACCT
1 -TTTTTTGAAAAACAGAAA-TT--GA-AAATACCTCAGG-A--TGACCCGAGGCTCAACTCACCT
* * *
16312505 CTCGCAATATGAGTCGATTTTT-AAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCAAGGCT
58 CTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCT
*
16312569 CAACTTACCTCTCGCAATATGAGTTGA
123 CAACTCACCTCTCGCAATATGAGTTGA
* * * *
16312596 TTTTTTTGAAAAACATAAATTGAAAATACCTCAGGATGACCCAAGGCTCAACTCGCTTCTCGCAT
1 -TTTTTTGAAAAACAGAAATTGAAAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCAT
* * *
16312661 TATGAGTCGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCTGAGGCCCAACTCA
65 TATGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCA
* *
16312726 CCTATCGCAATATGGGTTGA
130 CCTCTCGCAATATGAGTTGA
*
16312746 -TTTTTGAAAAACAGAAATTGAAAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGTATT
1 TTTTTTGAAAAACAGAAATTGAAAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCATT
* * * *
16312810 GTGAGTTGATTTTTGAAAAAAAGAAAATTTAAAAGAAATACCTCGGCGT--GACCCGAGACTCAA
66 ATGAGTTGATTTTTGAAAAACAG-AAATTT---A-AAATACCTCAGCGTGCGACCCGAGGCTCAA
16312873 CTCACCTCTCGCAATATGAGTTGA
126 CTCACCTCTCGCAATATGAGTTGA
* * * *
16312897 TTTTTTTGAAAAACAGCAATTTAAAAATAACTCAGCG-TGACCCGAGGCTCAACTCACCTCTCGT
1 -TTTTTTGAAAAACAG-AAATTGAAAATACCTCAG-GATGACCCGAGGCTCAACTCACCTCTCGC
* *
16312961 ATTATGAGTTGATTTTTGAAAAACAAAAATTGAAAA
63 ATTATGAGTTGATTTTTGAAAAACAGAAATTTAAAA
16312997 ATATAATTCT
Statistics
Matches: 480, Mismatches: 56, Indels: 44
0.83 0.10 0.08
Matches are distributed among these distances:
148 79 0.16
149 48 0.10
150 64 0.13
151 42 0.09
152 4 0.01
153 32 0.07
154 79 0.16
155 69 0.14
156 2 0.00
157 2 0.00
158 9 0.02
159 12 0.03
160 38 0.08
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (149 bp):
TTTTTTGAAAAACAGAAATTGAAAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCATT
ATGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCAC
CTCTCGCAATATGAGTTGA
Found at i:16312835 original size:73 final size:73
Alignment explanation
Indices: 16312292--16312999 Score: 656
Period size: 75 Copynumber: 9.3 Consensus size: 73
16312282 GTTTTTTTTC
* * * * * ** *
16312292 TTGAAAAATAGAAATTGAAAATACCTCAGCATGATCCGAGTCTCAACTTGCCTCTCGCATTATGA
1 TTGAAAAACAGAAATTAAAAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCAATATGA
16312357 GTTGATTT
66 GTTGATTT
* * * * *
16312365 TTGAGAAACGGAAATTTAAAAGAAATACCTC-GATATGTGACCCGAGGTTCAACTCACCTCTGGC
1 TTGAAAAACAGAAA-TT--AA-AAATACCTCAG-GA--TGACCCGAGGCTCAACTCACCTCTCGC
16312429 AATATGAGTTGATTTTT
59 AATATGAGTTGA--TTT
* * *
16312446 TTGAAAAGCAGAAATTTAAAAGAAATACATC-GGTATGTGACCCGAGACTCAACTCACCTCTCGC
1 TTGAAAAACAGAAA-TT--AA-AAATACCTCAGG-A--TGACCCGAGGCTCAACTCACCTCTCGC
*
16312510 AATATGAGTCGATTT
59 AATATGAGTTGATTT
* * *
16312525 TT-AAAAACAGAAATTTAAAATACCTCAGCG-TGCGACCCAAGGCTCAACTTACCTCTCGCAATA
1 TTGAAAAACAGAAATTAAAAATACCTCAG-GAT--GACCCGAGGCTCAACTCACCTCTCGCAATA
16312588 TGAGTTGATTTTT
63 TGAGTTGA--TTT
* * * * * *
16312601 TTGAAAAACATAAATTGAAAATACCTCAGGATGACCCAAGGCTCAACTCGCTTCTCGCATTATGA
1 TTGAAAAACAGAAATTAAAAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCAATATGA
*
16312666 GTCGATTT
66 GTTGATTT
* * * *
16312674 TTGAAAAACAGAAATTTAAAATACCTCAGCG-TGCGACCTGAGGCCCAACTCACCTATCGCAATA
1 TTGAAAAACAGAAATTAAAAATACCTCAG-GAT--GACCCGAGGCTCAACTCACCTCTCGCAATA
*
16312738 TGGGTTGATTT
63 TGAGTTGATTT
* * * *
16312749 TTGAAAAACAGAAATTGAAAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGTATTGTGA
1 TTGAAAAACAGAAATTAAAAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCAATATGA
16312814 GTTGATTT
66 GTTGATTT
* * *
16312822 TTGAAAAAAAGAAAATTTAAAAGAAATACCTC-GGCGTGACCCGAGACTCAACTCACCTCTCGCA
1 TTGAAAAACAG-AAA-TT--AA-AAATACCTCAGG-ATGACCCGAGGCTCAACTCACCTCTCGCA
16312886 ATATGAGTTGATTTTT
60 ATATGAGTTGA--TTT
* * * *
16312902 TTGAAAAACAGCAATTTAAAAATAACTCAGCG-TGACCCGAGGCTCAACTCACCTCTCGTATTAT
1 TTGAAAAACAG-AAATTAAAAATACCTCAG-GATGACCCGAGGCTCAACTCACCTCTCGCAATAT
16312966 GAGTTGATTT
64 GAGTTGATTT
*
16312976 TTGAAAAACAAAAATTGAAAAATA
1 TTGAAAAACAGAAATT-AAAAATA
16313000 TAATTCTTGA
Statistics
Matches: 532, Mismatches: 70, Indels: 65
0.80 0.10 0.10
Matches are distributed among these distances:
72 1 0.00
73 90 0.17
74 69 0.13
75 98 0.18
76 53 0.10
77 43 0.08
78 55 0.10
79 39 0.07
80 15 0.03
81 69 0.13
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (73 bp):
TTGAAAAACAGAAATTAAAAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTT
Found at i:16313870 original size:13 final size:13
Alignment explanation
Indices: 16313854--16313893 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
16313844 CGGGTTTTTA
16313854 TCTTGATTTTTCT
1 TCTTGATTTTTCT
*
16313867 TCTT--TTTTT-A
1 TCTTGATTTTTCT
16313877 TCTTGATTTTTCT
1 TCTTGATTTTTCT
16313890 TCTT
1 TCTT
16313894 TTTTTTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
10 4 0.18
11 5 0.23
12 5 0.23
13 8 0.36
ACGTcount: A:0.07, C:0.15, G:0.05, T:0.72
Consensus pattern (13 bp):
TCTTGATTTTTCT
Found at i:16313878 original size:23 final size:23
Alignment explanation
Indices: 16313848--16313898 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
16313838 CTTTTTCGGG
16313848 TTTTTATCTTGATTTTTCTTCTT
1 TTTTTATCTTGATTTTTCTTCTT
16313871 TTTTTATCTTGATTTTTCTTCTT
1 TTTTTATCTTGATTTTTCTTCTT
16313894 TTTTT
1 TTTTT
16313899 TTACTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.76
Consensus pattern (23 bp):
TTTTTATCTTGATTTTTCTTCTT
Found at i:16313896 original size:1 final size:1
Alignment explanation
Indices: 16313892--16313967 Score: 53
Period size: 1 Copynumber: 76.0 Consensus size: 1
16313882 ATTTTTCTTC
** ** * * * * * *
16313892 TTTTTTTTTACTTTTTTTTTTGCTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTGTTGTTTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
16313957 TCTTTTTTTTT
1 TTTTTTTTTTT
16313968 AGGCATAATA
Statistics
Matches: 55, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.01, C:0.05, G:0.08, T:0.86
Consensus pattern (1 bp):
T
Found at i:16313910 original size:24 final size:22
Alignment explanation
Indices: 16313860--16313967 Score: 87
Period size: 23 Copynumber: 4.8 Consensus size: 22
16313850 TTTATCTTGA
* **
16313860 TTTTTCTTCTTTTTTTATCTTGA
1 TTTTTCTTCTTTTTTT-TTTTTT
16313883 TTTTTCTTCTTTTTTTTTACTTTT
1 TTTTTCTTCTTTTTTTTT--TTTT
*
16313907 TTTTT-TGCTTTTTTGTTTTTTT
1 TTTTTCTTCTTTTTT-TTTTTTT
* * *
16313929 GTTTTT-TTGTTTTTTTGTTGTT
1 -TTTTTCTTCTTTTTTTTTTTTT
16313951 TTTTTC-TCTTTTTTTTT
1 TTTTTCTTCTTTTTTTTT
16313968 AGGCATAATA
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
21 14 0.20
22 10 0.14
23 36 0.51
24 10 0.14
ACGTcount: A:0.03, C:0.08, G:0.06, T:0.82
Consensus pattern (22 bp):
TTTTTCTTCTTTTTTTTTTTTT
Found at i:16313918 original size:8 final size:8
Alignment explanation
Indices: 16313906--16313953 Score: 78
Period size: 8 Copynumber: 5.9 Consensus size: 8
16313896 TTTTTACTTT
16313906 TTTTTTTG
1 TTTTTTTG
*
16313914 CTTTTTTG
1 TTTTTTTG
16313922 TTTTTTTG
1 TTTTTTTG
16313930 TTTTTTTG
1 TTTTTTTG
16313938 TTTTTTTG
1 TTTTTTTG
16313946 TTGTTTTT
1 TT-TTTTT
16313954 TTCTCTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
8 32 0.86
9 5 0.14
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.85
Consensus pattern (8 bp):
TTTTTTTG
Found at i:16319613 original size:21 final size:19
Alignment explanation
Indices: 16319573--16319616 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
16319563 ACAACAACCC
*
16319573 TTTTTTTTGAAAACACGAA
1 TTTTTTTTGAAAACAAGAA
*
16319592 TTTTTTTTTAAAACGCAAGAA
1 TTTTTTTTGAAAA--CAAGAA
16319613 TTTT
1 TTTT
16319617 AGAAACACGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
21 9 0.43
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (19 bp):
TTTTTTTTGAAAACAAGAA
Found at i:16319659 original size:37 final size:36
Alignment explanation
Indices: 16319578--16319672 Score: 95
Period size: 37 Copynumber: 2.6 Consensus size: 36
16319568 AACCCTTTTT
* * *
16319578 TTTGAAAACACG-AATTTTTTTTTAAAACGCAAGAAT
1 TTTG-AAACACGAAATTTTTTTTAAAAACACAAGAAA
16319614 TTTAGAAACACGAAATTTTTTTTAAAAAACACGAA-AAA
1 TTT-GAAACACGAAATTTTTTTT-AAAAACAC-AAGAAA
*
16319652 TTTGAAACATGAGAATTTTTT
1 TTTGAAACACGA-AATTTTTT
16319673 CAAAACACGA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
36 10 0.20
37 19 0.38
38 19 0.38
39 2 0.04
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (36 bp):
TTTGAAACACGAAATTTTTTTTAAAAACACAAGAAA
Found at i:16319711 original size:16 final size:16
Alignment explanation
Indices: 16319690--16319725 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
16319680 CGAATTTTCT
16319690 TTTTG-AAACACGAAAA
1 TTTTGAAAACAC-AAAA
16319706 TTTTGAAAACACAAAA
1 TTTTGAAAACACAAAA
16319722 TTTT
1 TTTT
16319726 ATTTTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.33
Consensus pattern (16 bp):
TTTTGAAAACACAAAA
Found at i:16319737 original size:38 final size:37
Alignment explanation
Indices: 16319669--16319911 Score: 108
Period size: 38 Copynumber: 6.2 Consensus size: 37
16319659 CATGAGAATT
* * *
16319669 TTTTCAAAACACGAATTTTCTTTTTG-AAACACGAAAA
1 TTTTGAAAACACAAAATTT-TTTTTGAAAACACGAAAA
16319706 TTTTGAAAACACAAAATTTTATTTTGAAAACAC-AAAA
1 TTTTGAAAACACAAAATTTT-TTTTGAAAACACGAAAA
* *
16319743 GATTTGATAAATTACGAAACATAAGATTTTTTTTTG-AAACACGGAAA
1 -TTTTG--AAA--AC---ACA-AA-A-TTTTTTTTGAAAACACGAAAA
**
16319790 TTTATG-AAACACGGTCAA---TTTTTGAAAACACGAAAA
1 TTT-TGAAAACAC--AAAATTTTTTTTGAAAACACGAAAA
*** *
16319826 TTTTTGAAAGAC-GGGATTTTTTTTTGAAAACACGAAAA
1 -TTTTGAAA-ACACAAAATTTTTTTTGAAAACACGAAAA
* * *
16319864 TATAT-AAAACACAGAAATTTTTTCTGAAAACAAGAAAA
1 T-TTTGAAAACACA-AAATTTTTTTTGAAAACACGAAAA
16319902 TTTTCGAAAA
1 TTTT-GAAAA
16319912 ACGAGAATGT
Statistics
Matches: 156, Mismatches: 21, Indels: 56
0.67 0.09 0.24
Matches are distributed among these distances:
35 7 0.04
36 15 0.10
37 36 0.23
38 53 0.34
39 7 0.04
40 4 0.03
42 4 0.03
44 2 0.01
45 3 0.02
46 10 0.06
47 11 0.07
48 4 0.03
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.33
Consensus pattern (37 bp):
TTTTGAAAACACAAAATTTTTTTTGAAAACACGAAAA
Found at i:16319815 original size:18 final size:17
Alignment explanation
Indices: 16319773--16319839 Score: 80
Period size: 17 Copynumber: 3.8 Consensus size: 17
16319763 ATAAGATTTT
16319773 TTTTTGAAACACGGAAA
1 TTTTTGAAACACGGAAA
* *
16319790 TTTATGAAACACGGTCAA
1 TTTTTGAAACACGG-AAA
*
16319808 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGGAAA
*
16319826 TTTTTGAAAGACGG
1 TTTTTGAAACACGG
16319840 GATTTTTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
17 19 0.46
18 15 0.37
19 7 0.17
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (17 bp):
TTTTTGAAACACGGAAA
Found at i:16319945 original size:19 final size:18
Alignment explanation
Indices: 16319773--16319961 Score: 102
Period size: 18 Copynumber: 10.3 Consensus size: 18
16319763 ATAAGATTTT
16319773 TTTTTG-AAACACGGAAA
1 TTTTTGAAAACACGGAAA
* *
16319790 TTTATG-AAACACGGTCAA
1 TTTTTGAAAACACGG-AAA
*
16319808 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGGAAA
* **
16319826 TTTTTGAAAGAC-GGGATTTT
1 TTTTTGAAA-ACACGGA--AA
*
16319846 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGGAAA
* * *
16319864 TATAT-AAAACACAGAAA
1 TTTTTGAAAACACGGAAA
* *
16319881 TTTTTTCTGAAAACAAGAAAA
1 --TTTT-TGAAAACACGGAAA
*
16319902 TTTTCGAAAA-AC-GAGAA
1 TTTTTGAAAACACGGA-AA
*
16319919 TGTTTGAAAACACGGGAAA
1 TTTTTGAAAACAC-GGAAA
* * *
16319938 TTTTTGAAAATATGAAAA
1 TTTTTGAAAACACGGAAA
16319956 TTTTTG
1 TTTTTG
16319962 TTACACTAGA
Statistics
Matches: 127, Mismatches: 31, Indels: 27
0.69 0.17 0.15
Matches are distributed among these distances:
16 1 0.01
17 34 0.27
18 40 0.31
19 29 0.23
20 14 0.11
21 9 0.07
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (18 bp):
TTTTTGAAAACACGGAAA
Found at i:16320011 original size:18 final size:18
Alignment explanation
Indices: 16319990--16320057 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
16319980 AACACAAAGA
16319990 TTTTGGAAACATGAGGAT
1 TTTTGGAAACATGAGGAT
* * * *
16320008 TTTTGAAAACACGAAGCT
1 TTTTGGAAACATGAGGAT
*
16320026 TTTT-GAAACATGAGAAT
1 TTTTGGAAACATGAGGAT
*
16320043 TTTTTGAGAACATGA
1 TTTTGGA-AACATGA
16320058 AAACACGAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
17 12 0.31
18 20 0.51
19 7 0.18
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.34
Consensus pattern (18 bp):
TTTTGGAAACATGAGGAT
Found at i:16320017 original size:35 final size:35
Alignment explanation
Indices: 16319969--16320046 Score: 113
Period size: 35 Copynumber: 2.3 Consensus size: 35
16319959 TTGTTACACT
16319969 AGAA-TTTTGAAAACACAAAGATTTTGGAAACATG
1 AGAATTTTTGAAAACACAAAGATTTTGGAAACATG
* * * *
16320003 AGGATTTTTGAAAACACGAAGCTTTTTGAAACATG
1 AGAATTTTTGAAAACACAAAGATTTTGGAAACATG
16320038 AGAATTTTT
1 AGAATTTTT
16320047 TGAGAACATG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
34 3 0.08
35 35 0.92
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (35 bp):
AGAATTTTTGAAAACACAAAGATTTTGGAAACATG
Found at i:16320035 original size:17 final size:18
Alignment explanation
Indices: 16319807--16320033 Score: 92
Period size: 18 Copynumber: 12.6 Consensus size: 18
16319797 AACACGGTCA
*
16319807 ATTTTTGAAAACACGAAA
1 ATTTTTGAAAACACGAAG
** **
16319825 ATTTTTGAAAGACGGGATTT
1 ATTTTTGAAA-ACACGA-AG
* *
16319845 TTTTTTGAAAACACGAAA
1 ATTTTTGAAAACACGAAG
* *
16319863 ATATAT-AAAACACAGAA-
1 ATTTTTGAAAACAC-GAAG
* *
16319880 ATTTTTTCTGAAAACAAGAAA
1 A--TTTT-TGAAAACACGAAG
*
16319901 ATTTTCGAAAA-ACG-AG
1 ATTTTTGAAAACACGAAG
*
16319917 AATGTTTGAAAACACGGGAA-
1 -ATTTTTGAAAACAC--GAAG
* * *
16319937 ATTTTTGAAAATATGAAA
1 ATTTTTGAAAACACGAAG
** *
16319955 ATTTTTG-TTACAC-TAG
1 ATTTTTGAAAACACGAAG
* *
16319971 AATTTTGAAAACACAAAG
1 ATTTTTGAAAACACGAAG
* * *
16319989 A-TTTTGGAAACATGAGG
1 ATTTTTGAAAACACGAAG
16320006 ATTTTTGAAAACACGAAG
1 ATTTTTGAAAACACGAAG
*
16320024 CTTTTTGAAA
1 ATTTTTGAAA
16320034 CATGAGAATT
Statistics
Matches: 151, Mismatches: 41, Indels: 34
0.67 0.18 0.15
Matches are distributed among these distances:
16 8 0.05
17 41 0.27
18 55 0.36
19 25 0.17
20 14 0.09
21 8 0.05
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.31
Consensus pattern (18 bp):
ATTTTTGAAAACACGAAG
Found at i:16320079 original size:44 final size:44
Alignment explanation
Indices: 16320011--16320098 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
16320001 TGAGGATTTT
** * * * *
16320011 TGAAAACACGAAGCTTTTTGAAACATGAGAATTTTTTGAGAACA
1 TGAAAACACGAAAATTTGTCAAACACGAGAATTTTTTGAAAACA
*
16320055 TGAAAACACGAAAATTTGTCAAACACGGGAATTTTTTGAAAACA
1 TGAAAACACGAAAATTTGTCAAACACGAGAATTTTTTGAAAACA
16320099 CGATAACATC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.27
Consensus pattern (44 bp):
TGAAAACACGAAAATTTGTCAAACACGAGAATTTTTTGAAAACA
Found at i:16320196 original size:18 final size:17
Alignment explanation
Indices: 16320173--16320222 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
16320163 AAGTGAAGAT
16320173 TTTTTGAAATACGAGAAA
1 TTTTTGAAATACGA-AAA
*
16320191 TTTTTGAAGATATGAAAA
1 TTTTTGAA-ATACGAAAA
*
16320209 TTTTTGAAACACGA
1 TTTTTGAAATACGA
16320223 TTTTTCTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 4 0.14
18 19 0.68
19 5 0.18
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (17 bp):
TTTTTGAAATACGAAAA
Found at i:16320503 original size:13 final size:13
Alignment explanation
Indices: 16320474--16320553 Score: 76
Period size: 13 Copynumber: 6.2 Consensus size: 13
16320464 GACTTTTAAT
* *
16320474 TTTTTTCTTTTAC
1 TTTTCTCTTTTTC
16320487 -TTTCTCTTTTTC
1 TTTTCTCTTTTTC
16320499 TTTTCTCTTTTTC
1 TTTTCTCTTTTTC
* *
16320512 TTCTCCCTTTTTC
1 TTTTCTCTTTTTC
16320525 TTCTTCT-TTTTTC
1 TT-TTCTCTTTTTC
16320538 -TTTCTTCTTTCTTC
1 TTTTC-TCTTT-TTC
16320552 TT
1 TT
16320554 CTTCGGGCCG
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
11 3 0.05
12 12 0.22
13 34 0.62
14 5 0.09
15 1 0.02
ACGTcount: A:0.01, C:0.25, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTCTCTTTTTC
Found at i:16320717 original size:19 final size:17
Alignment explanation
Indices: 16320693--16320731 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
16320683 TTTCTTGTTT
16320693 TTTTGCTGCTGCGTTTTTG
1 TTTTGCTGCT-C-TTTTTG
*
16320712 TTTTGCTTCTCTTTTTG
1 TTTTGCTGCTCTTTTTG
16320729 TTT
1 TTT
16320732 CAATTTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 1 0.05
19 9 0.47
ACGTcount: A:0.00, C:0.15, G:0.18, T:0.67
Consensus pattern (17 bp):
TTTTGCTGCTCTTTTTG
Found at i:16321214 original size:5 final size:6
Alignment explanation
Indices: 16321197--16321222 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16321187 TAAAATTATT
16321197 ATAAAA ATAAAA ATAAAA ATAAAA AT
1 ATAAAA ATAAAA ATAAAA ATAAAA AT
16321223 GGGCTAAAGC
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:16325839 original size:18 final size:18
Alignment explanation
Indices: 16325816--16325853 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
16325806 AATCGATTTT
*
16325816 AACTTCCTCTTCATTCTC
1 AACTTCCTCTTCATTATC
16325834 AACTTCCTCTTCATTATC
1 AACTTCCTCTTCATTATC
16325852 AA
1 AA
16325854 TCCCAATTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.34, G:0.00, T:0.42
Consensus pattern (18 bp):
AACTTCCTCTTCATTATC
Found at i:16330470 original size:23 final size:23
Alignment explanation
Indices: 16330413--16330471 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
16330403 AAATTAGAAT
16330413 AAAGTTAACATTTACTGTTTAAA
1 AAAGTTAACATTTACTGTTTAAA
** * *
16330436 AAAAATATCATTTACTGTTTAAC
1 AAAGTTAACATTTACTGTTTAAA
16330459 AAAGTTAACATTT
1 AAAGTTAACATTT
16330472 TTAAAGTTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (23 bp):
AAAGTTAACATTTACTGTTTAAA
Found at i:16332634 original size:3 final size:3
Alignment explanation
Indices: 16332626--16332689 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
16332616 AGTTAAAATA
16332626 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16332674 TAT TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TA
16332690 CTTAAAAGTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 58 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:16332718 original size:5 final size:5
Alignment explanation
Indices: 16332710--16332743 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
16332700 AAGTATAAAT
16332710 ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTA
1 ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTA
16332744 TAATATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (5 bp):
ATTAG
Found at i:16332753 original size:15 final size:15
Alignment explanation
Indices: 16332717--16332760 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
16332707 AATATTAGAT
* *
16332717 TAGATTAGATTAGAT
1 TAGATTAGATTATAA
16332732 TAGATTAGATTATAA
1 TAGATTAGATTATAA
* *
16332747 TATATTATATTATA
1 TAGATTAGATTATA
16332761 TTACAAAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.45
Consensus pattern (15 bp):
TAGATTAGATTATAA
Found at i:16333755 original size:25 final size:25
Alignment explanation
Indices: 16333727--16333780 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
16333717 TATTTGATAT
*
16333727 TTAGCACTTCAGTGCTCTCTGATT-A
1 TTAGCACGTCAGTGCTCTCTG-TTCA
16333752 TTAGCACGTCAGTGCTCTCTGTTCA
1 TTAGCACGTCAGTGCTCTCTGTTCA
16333777 TTAG
1 TTAG
16333781 TGCATAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.39
Consensus pattern (25 bp):
TTAGCACGTCAGTGCTCTCTGTTCA
Found at i:16339208 original size:438 final size:437
Alignment explanation
Indices: 16338381--16339694 Score: 1977
Period size: 438 Copynumber: 3.0 Consensus size: 437
16338371 TATGACACCC
* ** ** * *
16338381 TGTATTGGAACCGGGCTTGTTTGTCAACAATCAATACTGAGACAATAATGGTTGGCATGTCTTTT
1 TGTACTGGAACCGGGCTTGCATGTCGGCAATCAATACTGAGACAATAATGGTTGGCGTGTCTTTC
* *
16338446 ACCAATGGCCACAATTACAGATCATTTTTGCATCTAGCTTCTTATGATCTTACATCATACGTTCT
66 ACCAATGGCCACAATTACAGATCATTTTTGCATCTAGCTTCCTATGATCTTACGTCATACGTTCT
* ** * * *
16338511 GCAGTGTATGTATGAGGCTTTTCCAATTTGCTGAATGTCCACATTTGAGTCATTTGCATAAGTGC
131 GCAGTGTATGTATGGGGCCCTTCCAATTTGCTGATTGTCCACATTTGAGTCCTTTGTATAAGTGC
* * * *
16338576 AACACTAACCCACCATTTACACCATTCTTAAGCTCTCCAACACTCCCCAATGTATAATGTCGATG
196 AGCACGAACCCACCATTTACACCATTCTTAAGCTCTCAAACACTCCCCAACGTATAATGTCGATG
* *
16338641 TTGACTTGGTGGCTTTGTAGTCCACAGACACCTACATGCTATACATTTTTATTGCAATAACAAAA
261 TTGACTTGGTGACTTTGTAGTCCACAGACACCTACATGCTATACATTTTTATTGCAATAACACAA
**
16338706 TCCTCCTTGTTCGCGAACTGTTGCCCTATGAACAACTCATCAAAATTTGTATCTTCCATCGAACG
326 TCCTCCTTGTTCGCGAACTGTTGCCCTATGAACAACTCATCAAAATTTGTATCTTCTGTCGAACG
*
16338771 GTGAGCACGCATTATATCTAGCTACTCAGGGAACTCTGGTACATGCGT
391 GTGAGCACGCATTATATCTAG-TACTCAGGGAACTCTGGTGCATGCGT
* *
16338819 TGTACTGGAACCGGGCTTGCATGTCGGTAATCAATACTGAGATAATAATGGTTGGCGTGTCTTTC
1 TGTACTGGAACCGGGCTTGCATGTCGGCAATCAATACTGAGACAATAATGGTTGGCGTGTCTTTC
* * * *
16338884 ACCAGTGGTCACAATTACAGATCATTTTTGCATCTAGCTTCCTATGATCTTATGTCATAAGTTCT
66 ACCAATGGCCACAATTACAGATCATTTTTGCATCTAGCTTCCTATGATCTTACGTCATACGTTCT
* * *
16338949 GTAGTGTATGTATGGGGCCCTTCCAATTTGCTGATTGTCCACATTTAAGTCCTTTGTATAAGCGC
131 GCAGTGTATGTATGGGGCCCTTCCAATTTGCTGATTGTCCACATTTGAGTCCTTTGTATAAGTGC
* * *
16339014 AGCACGAACCCACCATTTACACCATTCTTAAGCTCTCTAACATTCCCTAACGTATAATGTC-AGT
196 AGCACGAACCCACCATTTACACCATTCTTAAGCTCTCAAACACTCCCCAACGTATAATGTCGA-T
* * * * *
16339078 GTTGAGTTAGTGAATTTGTAATCCACAGACACCTACATGCTATACCTTTTTATTGCAATAACACA
260 GTTGACTTGGTGACTTTGTAGTCCACAGACACCTACATGCTATACATTTTTATTGCAATAACACA
* *
16339143 ATTCTCCTTGTTCGCGAATTGTTGCCCTATGAACAACTCATCAAAATTTGTATCTTCTGTCGAAC
325 ATCCTCCTTGTTCGCGAACTGTTGCCCTATGAACAACTCATCAAAATTTGTATCTTCTGTCGAAC
** *
16339208 GGTGAGCACGCATTATATCTAGGTACTCAAAGAACTCTGGTGCATGCAT
390 GGTGAGCACGCATTATATCTA-GTACTCAGGGAACTCTGGTGCATGCGT
* * ** *
16339257 TGTACTGAAACCGGGCTTGCATGTCGGCGATCAATACTGAGACACGAATGGTTGACGTGTCTTTC
1 TGTACTGGAACCGGGCTTGCATGTCGGCAATCAATACTGAGACAATAATGGTTGGCGTGTCTTTC
* * *
16339322 ACCAATGGCCATAGTTGCAGATCA--TTTGCATCTAGCTTCCTATGATCTTACGTCATACGTTCT
66 ACCAATGGCCACAATTACAGATCATTTTTGCATCTAGCTTCCTATGATCTTACGTCATACGTTCT
* *
16339385 GCAGTGTATGTATGGGGCCCTTCCAATTTGCTGATTGTCTATATTTGAGTCCTTTGTATAAGTGC
131 GCAGTGTATGTATGGGGCCCTTCCAATTTGCTGATTGTCCACATTTGAGTCCTTTGTATAAGTGC
16339450 AGCACGAACCCACCATTTACACCATTCTTAAGCTCTCAAACACTCCCCAACGTATAATGTCGATG
196 AGCACGAACCCACCATTTACACCATTCTTAAGCTCTCAAACACTCCCCAACGTATAATGTCGATG
* *
16339515 TTGACTTGGTGACTTTGTAGTCTACAGACGCCTACATGCTATACATTTTTATTGCAATAACACAA
261 TTGACTTGGTGACTTTGTAGTCCACAGACACCTACATGCTATACATTTTTATTGCAATAACACAA
* *
16339580 TCCTCCTTGTTCGTGAACTGTTGCCCTATGAACAACTCATCAAAATATGTATCTTCTGTCGAACG
326 TCCTCCTTGTTCGCGAACTGTTGCCCTATGAACAACTCATCAAAATTTGTATCTTCTGTCGAACG
* * * * * *
16339645 ATAAGCATGCATTATATATAAGTACTCAGGAAACTCTGGTGCATACGT
391 GTGAGCACGCATTATATCT-AGTACTCAGGGAACTCTGGTGCATGCGT
16339693 TG
1 TG
16339695 CATCAAGGTC
Statistics
Matches: 785, Mismatches: 87, Indels: 10
0.89 0.10 0.01
Matches are distributed among these distances:
436 315 0.40
437 3 0.00
438 466 0.59
439 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Consensus pattern (437 bp):
TGTACTGGAACCGGGCTTGCATGTCGGCAATCAATACTGAGACAATAATGGTTGGCGTGTCTTTC
ACCAATGGCCACAATTACAGATCATTTTTGCATCTAGCTTCCTATGATCTTACGTCATACGTTCT
GCAGTGTATGTATGGGGCCCTTCCAATTTGCTGATTGTCCACATTTGAGTCCTTTGTATAAGTGC
AGCACGAACCCACCATTTACACCATTCTTAAGCTCTCAAACACTCCCCAACGTATAATGTCGATG
TTGACTTGGTGACTTTGTAGTCCACAGACACCTACATGCTATACATTTTTATTGCAATAACACAA
TCCTCCTTGTTCGCGAACTGTTGCCCTATGAACAACTCATCAAAATTTGTATCTTCTGTCGAACG
GTGAGCACGCATTATATCTAGTACTCAGGGAACTCTGGTGCATGCGT
Found at i:16350039 original size:2 final size:2
Alignment explanation
Indices: 16350032--16350063 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16350022 AATGTTGCAT
16350032 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
16350064 AGAAGAAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:16364398 original size:12 final size:13
Alignment explanation
Indices: 16364374--16364416 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
16364364 TATTAATAGT
16364374 TTAATAGTTTAATA
1 TTAATA-TTTAATA
16364388 TTAA-ATTTAAT-
1 TTAATATTTAATA
16364399 TTAATATTT-ATA
1 TTAATATTTAATA
16364411 TTAATA
1 TTAATA
16364417 ATATTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.22
12 16 0.59
13 1 0.04
14 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (13 bp):
TTAATATTTAATA
Found at i:16364414 original size:17 final size:17
Alignment explanation
Indices: 16364381--16364433 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
16364371 AGTTTAATAG
*
16364381 TTTAATA-TTAAATTTAA
1 TTTAATATTTATA-TTAA
16364398 TTTAATATTTATATTAA
1 TTTAATATTTATATTAA
16364415 --TAATATTT-TATTAA
1 TTTAATATTTATATTAA
16364429 TTTAA
1 TTTAA
16364434 AATTAAAGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
14 6 0.19
15 8 0.25
16 3 0.09
17 11 0.34
18 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAATATTTATATTAA
Found at i:16364424 original size:23 final size:25
Alignment explanation
Indices: 16364367--16364439 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 25
16364357 CCAGAAATAT
*
16364367 TAATAGTTTAATAGTTTAATATTAA
1 TAATAATTTAATAGTTTAATATTAA
*
16364392 -ATTTAATTTAATA-TTT-ATATTAA
1 TA-ATAATTTAATAGTTTAATATTAA
* * * *
16364415 TAATATTTTATTAATTTAAAATTAA
1 TAATAATTTAATAGTTTAATATTAA
16364440 AGTGATTAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
23 15 0.39
24 8 0.21
25 15 0.39
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (25 bp):
TAATAATTTAATAGTTTAATATTAA
Found at i:16364428 original size:14 final size:15
Alignment explanation
Indices: 16364400--16364429 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16364390 AAATTTAATT
16364400 TAATATTTATATTAA
1 TAATATTTATATTAA
16364415 TAATATTT-TATTAA
1 TAATATTTATATTAA
16364429 T
1 T
16364430 TTAAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATATTTATATTAA
Found at i:16369347 original size:17 final size:19
Alignment explanation
Indices: 16369320--16369361 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
16369310 AAACCTCTAA
16369320 AATAGTAACAA-AATTA-AC
1 AATA-TAACAAGAATTATAC
*
16369338 AATATAACAAGAGTTATAC
1 AATATAACAAGAATTATAC
16369357 AATAT
1 AATAT
16369362 TCAAATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 8 0.38
19 7 0.33
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (19 bp):
AATATAACAAGAATTATAC
Found at i:16381307 original size:40 final size:40
Alignment explanation
Indices: 16381262--16381396 Score: 146
Period size: 40 Copynumber: 3.4 Consensus size: 40
16381252 ACTATGTTTA
* * * *
16381262 GCACTTAGTATGTGATTCGAGATAGCTTCGACTATTTATG
1 GCACTTAGTGTGCGATTCGAGATAGCTTCGGCTATATATG
*
16381302 GCACTTAGTGTGCGATT-GGGAATAGCTTCGGCTATATATG
1 GCACTTAGTGTGCGATTCGAG-ATAGCTTCGGCTATATATG
* ** * *
16381342 ACACTTAGTGTGCGAAACTGAGATAGCTTCGGCTATGTAAG
1 GCACTTAGTGTGCGATTC-GAGATAGCTTCGGCTATATATG
*
16381383 GCACTTAATGTGCG
1 GCACTTAGTGTGCG
16381397 GGATTATAAT
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
39 2 0.03
40 46 0.58
41 29 0.37
42 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (40 bp):
GCACTTAGTGTGCGATTCGAGATAGCTTCGGCTATATATG
Found at i:16382176 original size:24 final size:24
Alignment explanation
Indices: 16382147--16382229 Score: 125
Period size: 23 Copynumber: 3.5 Consensus size: 24
16382137 TTTACATGAT
16382147 AAATGCTGTCCAATTTGATGTATA
1 AAATGCTGTCCAATTTGATGTATA
* *
16382171 AAATGCTGTCCAGTTTGGTGTAT-
1 AAATGCTGTCCAATTTGATGTATA
16382194 AAATGCTGTCCAATTTGATGTATA
1 AAATGCTGTCCAATTTGATGTATA
*
16382218 AAA-GCTATCCAA
1 AAATGCTGTCCAA
16382230 AACAGGGTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
23 29 0.55
24 24 0.45
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (24 bp):
AAATGCTGTCCAATTTGATGTATA
Found at i:16387714 original size:21 final size:23
Alignment explanation
Indices: 16387671--16387714 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
16387661 AAGGATTGAT
16387671 AAATATTGTATAAAAATATAATA
1 AAATATTGTATAAAAATATAATA
*
16387694 AAATATTTTA-AAAAATA-AATA
1 AAATATTGTATAAAAATATAATA
16387715 TTTGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 7 0.35
23 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
AAATATTGTATAAAAATATAATA
Found at i:16387715 original size:16 final size:16
Alignment explanation
Indices: 16387694--16387724 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16387684 AAATATAATA
*
16387694 AAATATTTTAAAAAAT
1 AAATATTTGAAAAAAT
16387710 AAATATTTGAAAAAA
1 AAATATTTGAAAAAA
16387725 AATTAATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATATTTGAAAAAAT
Found at i:16388277 original size:15 final size:15
Alignment explanation
Indices: 16388259--16388300 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
16388249 GAGCAATTTA
16388259 TTTTTTTCTTTTATG
1 TTTTTTTCTTTTATG
* *
16388274 TTTTTTAAC-TTTCTG
1 TTTTTT-TCTTTTATG
16388289 TTTTTTTCTTTT
1 TTTTTTTCTTTT
16388301 TATTTTTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.07, C:0.10, G:0.05, T:0.79
Consensus pattern (15 bp):
TTTTTTTCTTTTATG
Found at i:16389696 original size:2 final size:2
Alignment explanation
Indices: 16389691--16389716 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16389681 ACACACACAC
16389691 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
16389717 GAAAATTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16392725 original size:23 final size:23
Alignment explanation
Indices: 16392698--16392796 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
16392688 AGTGTTATTG
*
16392698 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
16392721 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
16392744 TTCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16392767 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16392790 ATCAGTG
1 ATCAGTG
16392797 TGGCACTTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:16392968 original size:38 final size:37
Alignment explanation
Indices: 16392926--16392998 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
16392916 ATGTGTGGAA
* *
16392926 TTGAATTGAATATTGACTTGAAAA-TGGAAAAGTGAATT
1 TTGAATTGAATAGTGA-TT-AAAAGTGAAAAAGTGAATT
16392964 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
16392999 ATTATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.45, C:0.01, G:0.22, T:0.32
Consensus pattern (37 bp):
TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAATT
Found at i:16394446 original size:25 final size:25
Alignment explanation
Indices: 16394412--16394523 Score: 111
Period size: 25 Copynumber: 4.5 Consensus size: 25
16394402 TACCGATTTA
* * *
16394412 AGCTCTTATGAGCTTACCGATACTC
1 AGCTCGTATGAGCTTACCGTTATTC
*
16394437 AGCTCGTATGAGCTTATCGTTATTC
1 AGCTCGTATGAGCTTACCGTTATTC
* * * *
16394462 AGCTCGAAGGAACTGACCGTTATTC
1 AGCTCGTATGAGCTTACCGTTATTC
* *
16394487 AGCTCGGAGGAGCTTACCGTT-TAT-
1 AGCTCGTATGAGCTTACCGTTAT-TC
16394511 AGCTCGTATGAGC
1 AGCTCGTATGAGC
16394524 GTACATGTAT
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
24 12 0.17
25 60 0.83
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGTTATTC
Found at i:16397409 original size:15 final size:16
Alignment explanation
Indices: 16397376--16397410 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
16397366 AAAATGAAAT
16397376 ATAGGTAAGAAGCACC
1 ATAGGTAAGAAGCACC
*
16397392 ATAGGTAA-AAGTACC
1 ATAGGTAAGAAGCACC
16397407 ATAG
1 ATAG
16397411 AAAACTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.46, C:0.14, G:0.23, T:0.17
Consensus pattern (16 bp):
ATAGGTAAGAAGCACC
Found at i:16398108 original size:50 final size:50
Alignment explanation
Indices: 16398046--16398142 Score: 131
Period size: 50 Copynumber: 1.9 Consensus size: 50
16398036 AAGAAGAAAC
* *
16398046 ATCTCTTTCTAAAATAATCAAGAATTATTAACACAATAAGCTATGATCGA
1 ATCTCTTACTAAAATAATCAAGAATTATTAACACAATAAGCCATGATCGA
* *** *
16398096 ATCTCTTACTAAAATGATCCTTAATTATTAACACAATTAGCCATGAT
1 ATCTCTTACTAAAATAATCAAGAATTATTAACACAATAAGCCATGAT
16398143 TCGACAGGCA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (50 bp):
ATCTCTTACTAAAATAATCAAGAATTATTAACACAATAAGCCATGATCGA
Found at i:16401526 original size:18 final size:18
Alignment explanation
Indices: 16401499--16401541 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
16401489 ATTTTTGTAA
16401499 ATTA-TTTTTGAATATAT
1 ATTATTTTTTGAATATAT
*
16401516 ATTATTTTTTGAATTTAT
1 ATTATTTTTTGAATATAT
16401534 A-TATTTTT
1 ATTATTTTT
16401542 AATTTCAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
ATTATTTTTTGAATATAT
Found at i:16401864 original size:21 final size:21
Alignment explanation
Indices: 16401840--16401881 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
16401830 CGCAAGTAAA
*
16401840 GTTAGGGGGTTGACTAGTATT
1 GTTAGGGCGTTGACTAGTATT
*
16401861 GTTAGGTCGTTGACTAGTATT
1 GTTAGGGCGTTGACTAGTATT
16401882 CTATAAGGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.07, G:0.33, T:0.40
Consensus pattern (21 bp):
GTTAGGGCGTTGACTAGTATT
Found at i:16407771 original size:33 final size:33
Alignment explanation
Indices: 16407707--16407767 Score: 99
Period size: 31 Copynumber: 1.9 Consensus size: 33
16407697 ATATATTTTT
16407707 ATTTTTATTTTTTAATTTTAAAATACTTTTAAA
1 ATTTTTATTTTTTAATTTTAAAATACTTTTAAA
*
16407740 ATTTTTA-TTTTT-ATTTTAAAATAATTTT
1 ATTTTTATTTTTTAATTTTAAAATACTTTT
16407768 TTAATGTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 15 0.56
32 5 0.19
33 7 0.26
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (33 bp):
ATTTTTATTTTTTAATTTTAAAATACTTTTAAA
Found at i:16407778 original size:31 final size:32
Alignment explanation
Indices: 16407693--16407779 Score: 97
Period size: 31 Copynumber: 2.7 Consensus size: 32
16407683 CCGAAATAAT
16407693 AAATATATATTTTT-ATTTTTATTTTTTAATTTTA
1 AAATA-AT-TTTTTAATTTTTA-TTTTTAATTTTA
* **
16407727 AAATACTTTTAAAATTTTTATTTTT-ATTTTA
1 AAATAATTTTTTAATTTTTATTTTTAATTTTA
*
16407758 AAATAATTTTTTAATGTTTATT
1 AAATAATTTTTTAATTTTTATT
16407780 AAAAAATGGG
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
31 24 0.53
32 8 0.18
33 8 0.18
34 5 0.11
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (32 bp):
AAATAATTTTTTAATTTTTATTTTTAATTTTA
Found at i:16409558 original size:125 final size:126
Alignment explanation
Indices: 16409335--16409738 Score: 572
Period size: 125 Copynumber: 3.3 Consensus size: 126
16409325 TTGTTAATTT
* * * *
16409335 AAAGAAGCTCCTACGTGGACGCGTTTTTGCTACAGTAGCTCCTGAAAAAATAAATTCGAATTGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTTGAC
*
16409400 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
66 CTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
* * *
16409461 AAAGAAGCGCCCACGTGGACGCGCTTTTGCTATA-TAGCTCCTGGAAAAATAATTTCGAGTTGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTTGAC
*
16409525 CTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTC
66 CTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
16409586 AAAGAAGCTCCCACGTGGA--CGC----G---C-----CT--TGAAAAAATAATTTCGAGTTGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTTGAC
* *
16409635 CTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATTGTTAGCAAAAGTACTG
66 CTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
* *
16409696 AAAGAAGCTCCCACATGGACGCGTTTTTGCTACAGTAGCTCCT
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCT
16409739 ATTAGGCCTG
Statistics
Matches: 245, Mismatches: 17, Indels: 32
0.83 0.06 0.11
Matches are distributed among these distances:
110 98 0.40
112 4 0.02
116 1 0.00
119 2 0.01
123 3 0.01
124 2 0.01
125 104 0.42
126 31 0.13
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (126 bp):
AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTTGAC
CTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
Found at i:16409700 original size:110 final size:110
Alignment explanation
Indices: 16409505--16409718 Score: 392
Period size: 110 Copynumber: 1.9 Consensus size: 110
16409495 TAGCTCCTGG
*
16409505 AAAAATAATTTCGAGTTGACCTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTT
1 AAAAATAATTTCGAGTTGACCTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATT
*
16409570 GTCAGCAAAAGTACTCAAAGAAGCTCCCACGTGGACGCGCCTTGA
66 GTCAGCAAAAGTACTCAAAGAAGCTCCCACATGGACGCGCCTTGA
16409615 AAAAATAATTTCGAGTTGACCTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATT
1 AAAAATAATTTCGAGTTGACCTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATT
* *
16409680 GTTAGCAAAAGTACTGAAAGAAGCTCCCACATGGACGCG
66 GTCAGCAAAAGTACTCAAAGAAGCTCCCACATGGACGCG
16409719 TTTTTGCTAC
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 100 1.00
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (110 bp):
AAAAATAATTTCGAGTTGACCTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATT
GTCAGCAAAAGTACTCAAAGAAGCTCCCACATGGACGCGCCTTGA
Found at i:16411446 original size:22 final size:22
Alignment explanation
Indices: 16411418--16411459 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
16411408 TTAAGCAATG
16411418 CGTACTAAGCTCTCATGTTTCA
1 CGTACTAAGCTCTCATGTTTCA
16411440 CGTACTAAGCTCTCATGTTT
1 CGTACTAAGCTCTCATGTTT
16411460 GAACAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.38
Consensus pattern (22 bp):
CGTACTAAGCTCTCATGTTTCA
Found at i:16412514 original size:33 final size:33
Alignment explanation
Indices: 16412485--16412575 Score: 111
Period size: 28 Copynumber: 2.9 Consensus size: 33
16412475 TAAAAATATT
*
16412485 AAAGTAAATTACAATTGGTACATAGAAAATGTA
1 AAAGTAAATTACAATTGATACATAGAAAATGTA
* *
16412518 AAAG--AATTTCTATT-ATAC-TA-AAAATGTA
1 AAAGTAAATTACAATTGATACATAGAAAATGTA
*
16412546 AAAGTAAATTACAATTGCTACATAGAAAAT
1 AAAGTAAATTACAATTGATACATAGAAAAT
16412576 CTAATCTATT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
28 12 0.26
29 2 0.04
30 11 0.23
31 11 0.23
32 2 0.04
33 9 0.19
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.30
Consensus pattern (33 bp):
AAAGTAAATTACAATTGATACATAGAAAATGTA
Found at i:16412514 original size:49 final size:50
Alignment explanation
Indices: 16412459--16412594 Score: 130
Period size: 61 Copynumber: 2.5 Consensus size: 50
16412449 CTTATTTAAA
*
16412459 AGAAAATCTAATCTATTAAAAATATT-AAAGTAAATTACAATTGGTACAT
1 AGAAAATCTAATCTATTAAAAATATTAAAAGTAAATTACAATTGCTACAT
* *
16412508 AGAAAATGTAAAAGAATTTCTATTATACTAAAAATGTAAAAGTAAATTACAATTGCTACAT
1 AGAAAATCT-----AA--TCTATTA-A--AAATAT-TAAAAGTAAATTACAATTGCTACAT
*
16412569 AGAAAATCTAATCTATTAAACATATT
1 AGAAAATCTAATCTATTAAAAATATT
16412595 GCCTTATTTA
Statistics
Matches: 69, Mismatches: 6, Indels: 23
0.70 0.06 0.23
Matches are distributed among these distances:
49 8 0.12
50 1 0.01
51 4 0.06
53 1 0.01
54 9 0.13
56 9 0.13
57 1 0.01
59 5 0.07
60 1 0.01
61 30 0.43
ACGTcount: A:0.51, C:0.09, G:0.08, T:0.32
Consensus pattern (50 bp):
AGAAAATCTAATCTATTAAAAATATTAAAAGTAAATTACAATTGCTACAT
Found at i:16412521 original size:61 final size:61
Alignment explanation
Indices: 16412455--16412575 Score: 170
Period size: 61 Copynumber: 2.0 Consensus size: 61
16412445 TTGACTTATT
* * * *
16412455 TAAAAGAAAATCTAATCTATTAAAAATATTAAAGTAAATTACAATTGGTACATAGAAAATG
1 TAAAAGAAAATCTAATATACTAAAAATATAAAAGTAAATTACAATTGCTACATAGAAAATG
** * *
16412516 TAAAAGAATTTCTATTATACTAAAAATGTAAAAGTAAATTACAATTGCTACATAGAAAAT
1 TAAAAGAAAATCTAATATACTAAAAATATAAAAGTAAATTACAATTGCTACATAGAAAAT
16412576 CTAATCTATT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (61 bp):
TAAAAGAAAATCTAATATACTAAAAATATAAAAGTAAATTACAATTGCTACATAGAAAATG
Found at i:16412701 original size:34 final size:34
Alignment explanation
Indices: 16412615--16412706 Score: 96
Period size: 34 Copynumber: 2.6 Consensus size: 34
16412605 AAAGAAAATC
* *
16412615 TATTATATTAAAAATGTAAAAGTAAATTTCTATTT
1 TATTATATTAAAAATATAAAAG-AAATTTATATTT
* * *
16412650 TATTACATGAAAAAATATAGAAG-AATTTATATTT
1 TATTATAT-TAAAAATATAAAAGAAATTTATATTT
16412684 TATTATATTAAATAATATCAAAA
1 TATTATATTAAA-AATAT-AAAA
16412707 ATTGGTAGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
33 3 0.07
34 22 0.48
35 10 0.22
36 11 0.24
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.41
Consensus pattern (34 bp):
TATTATATTAAAAATATAAAAGAAATTTATATTT
Found at i:16412862 original size:20 final size:20
Alignment explanation
Indices: 16412839--16412887 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
16412829 GTGAGGGTTG
16412839 TGGTTGTCCGGCA-GGGATTC
1 TGGTTGTCCGGCAGGGGA-TC
* *
16412859 TGGTTCCTCCGGTAGGGGATC
1 TGGTT-GTCCGGCAGGGGATC
16412880 TGGTTGTC
1 TGGTTGTC
16412888 GGTGTTGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 7 0.29
21 13 0.54
22 4 0.17
ACGTcount: A:0.08, C:0.20, G:0.39, T:0.33
Consensus pattern (20 bp):
TGGTTGTCCGGCAGGGGATC
Found at i:16413791 original size:7 final size:7
Alignment explanation
Indices: 16413779--16413810 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
16413769 TTAGTTATAT
16413779 ATACTAA
1 ATACTAA
16413786 ATACTAA
1 ATACTAA
16413793 ATACTAA
1 ATACTAA
16413800 ATACTAA
1 ATACTAA
16413807 ATAC
1 ATAC
16413811 CAATCGACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACTAA
Found at i:16414969 original size:29 final size:29
Alignment explanation
Indices: 16414932--16414988 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
16414922 TCAAAAAAAT
*
16414932 AAAATTTAAAACTTTTTTAAAAATAATTA
1 AAAAATTAAAACTTTTTTAAAAATAATTA
*
16414961 AAAAATTAAAGCTTTTTTAAAAATAATT
1 AAAAATTAAAACTTTTTTAAAAATAATT
16414989 TGAGAGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (29 bp):
AAAAATTAAAACTTTTTTAAAAATAATTA
Found at i:16415013 original size:22 final size:23
Alignment explanation
Indices: 16414985--16415047 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 23
16414975 TTTTAAAAAT
16414985 AATTTGAGAGGAAT-TT-GAGAAG
1 AATTTGAGAGGAATATTAGAG-AG
16415007 AATTTGAGA-GAATATTAGAGAG
1 AATTTGAGAGGAATATTAGAGAG
*
16415029 AATTTGAGAGAAATGATTA
1 AATTTGAGAGGAAT-ATTA
16415048 AGTTGTGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
21 4 0.11
22 22 0.61
23 6 0.17
24 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.27, T:0.29
Consensus pattern (23 bp):
AATTTGAGAGGAATATTAGAGAG
Found at i:16415037 original size:10 final size:10
Alignment explanation
Indices: 16414985--16415040 Score: 76
Period size: 11 Copynumber: 5.2 Consensus size: 10
16414975 TTTTAAAAAT
16414985 AATTTGAGAGG
1 AATTTGAGA-G
16414996 AATTTGAGAAG
1 AATTTGAG-AG
16415007 AATTTGAGAG
1 AATTTGAGAG
16415017 AATATTAGAGAG
1 AAT-TT-GAGAG
16415029 AATTTGAGAG
1 AATTTGAGAG
16415039 AA
1 AA
16415041 ATGATTAAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
10 12 0.29
11 21 0.50
12 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.27
Consensus pattern (10 bp):
AATTTGAGAG
Found at i:16416774 original size:21 final size:21
Alignment explanation
Indices: 16416750--16416793 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
16416740 TCAATTTATA
16416750 TTTTATTTTATATATAAATATT
1 TTTTA-TTTATATATAAATATT
* *
16416772 TTTTATTTATATTTATATATT
1 TTTTATTTATATATAAATATT
16416793 T
1 T
16416794 GTTCGCTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTATTTATATATAAATATT
Found at i:16417320 original size:87 final size:86
Alignment explanation
Indices: 16416906--16417558 Score: 907
Period size: 87 Copynumber: 7.5 Consensus size: 86
16416896 GAACGACCAA
* * * * *
16416906 ATTT-ATTTTAATACTTGTTTGGAAATAAAATAAAAAATGGAATAAAATTTGTTGAATGACGGAA
1 ATTTAATTTTAATACTCGTTTGGAAATAAAATAAAAAATGGAATAAAATCTGTTGAACGGCGGGA
*
16416970 ATAAATCCCGAAA-TAAATTTT
66 ATAAATCCCGAAACT-GATTTT
* ** ***
16416991 ATTTAATTTTAATACTCGTTTGGAAACAAAATAAAAAATGGAATAAAATCTGTAAAACGGCAACA
1 ATTTAATTTTAATACTCGTTTGGAAATAAAATAAAAAATGGAATAAAATCTGTTGAACGGCGGGA
*
16417056 ATAAATCCCGAAA-TAAATTTT
66 ATAAATCCCGAAACT-GATTTT
* * *
16417077 ATTTAATTTTAATACTCGTTTAGAAACAAAATAAAAAATGGAATAAAATCTATTGAACGGCGGGA
1 ATTTAATTTTAATACTCGTTTGGAAATAAAATAAAAAATGGAATAAAATCTGTTGAACGGCGGGA
* *
16417142 ATAAATCTCAAAACTGATTTTTT
66 ATAAATCCCGAAACTGA--TTTT
* * *
16417165 TTTTAATTTTAATACTCGTTTGGAAATAAAATAAAAAATAGAATAAAATCTTTTGAACGGCGGGA
1 ATTTAATTTTAATACTCGTTTGGAAATAAAATAAAAAATGGAATAAAATCTGTTGAACGGCGGGA
16417230 ATAAATCCCGAAACTGATTTT
66 ATAAATCCCGAAACTGATTTT
* * * *
16417251 ATTTAATTTTAATACTCATTTGGAAATAAAATAAAAAAATAGAATAGAATCTTTTGAACGGCGGG
1 ATTTAATTTTAATACTCGTTTGGAAATAAAAT-AAAAAATGGAATAAAATCTGTTGAACGGCGGG
*
16417316 AATAAATTCCGAAACTGATTTT
65 AATAAATCCCGAAACTGATTTT
16417338 ATTTAATTTTAATACTCGTTTGGAAATAAAATAAAAAAATGGAATAAAATCTGTTGAACGGCGGG
1 ATTTAATTTTAATACTCGTTTGGAAATAAAAT-AAAAAATGGAATAAAATCTGTTGAACGGCGGG
*
16417403 AATAAATCCCGAAACTGATTAT
65 AATAAATCCCGAAACTGATTTT
* * *
16417425 ATTTAATTTTAATACTCGTTTGGAAATAAAATAAAAAAATGAAATAAAATCTGTTGAACGACAGG
1 ATTTAATTTTAATACTCGTTTGGAAATAAAAT-AAAAAATGGAATAAAATCTGTTGAACGGCGGG
* ** *
16417490 AATAAATACTAAAACAGATTTT
65 AATAAATCCCGAAACTGATTTT
*
16417512 ATTTAATTTTAATACTCGTTTGGAAACAAAATAAAAAATGGAATAAA
1 ATTTAATTTTAATACTCGTTTGGAAATAAAATAAAAAATGGAATAAA
16417559 TCTCGAAACA
Statistics
Matches: 516, Mismatches: 47, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
85 4 0.01
86 189 0.37
87 244 0.47
88 79 0.15
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.32
Consensus pattern (86 bp):
ATTTAATTTTAATACTCGTTTGGAAATAAAATAAAAAATGGAATAAAATCTGTTGAACGGCGGGA
ATAAATCCCGAAACTGATTTT
Found at i:16417694 original size:22 final size:22
Alignment explanation
Indices: 16417666--16417707 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16417656 CACGTTAGCG
16417666 AACAAATATATAAATATAAACA
1 AACAAATATATAAATATAAACA
* *
16417688 AACAAATATTTATATATAAA
1 AACAAATATATAAATATAAA
16417708 ATAAAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (22 bp):
AACAAATATATAAATATAAACA
Found at i:16418993 original size:30 final size:31
Alignment explanation
Indices: 16418957--16419014 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
16418947 TCAATTTTTT
*
16418957 AAATTAAAAATTTTAAAAAAAT-TATTTAAC
1 AAATTAAAAATTATAAAAAAATATATTTAAC
*
16418987 AAATTAAAAATTATATAAAAATATATTT
1 AAATTAAAAATTATAAAAAAATATATTT
16419015 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
AAATTAAAAATTATAAAAAAATATATTTAAC
Found at i:16429526 original size:83 final size:83
Alignment explanation
Indices: 16429373--16429526 Score: 227
Period size: 83 Copynumber: 1.9 Consensus size: 83
16429363 AAATTGATTT
* * * * * * *
16429373 TTTTCAATTTAGTCCTCTTATAAATAGAGAAATTATAAATTAATATATAATGAATTTGTACTTTG
1 TTTTCAATTCAATCCTCTTATAAATAAAGAAATTATAAATTAATATATAATAAAATTGTAATTTA
*
16429438 GCCCCCGCAAATAAAACA
66 ACCCCCGCAAATAAAACA
*
16429456 TTTTCAATTCAATCCTCTTATAAATAAAGAAATTATAAATTAATATATAGTAAAATTGTAATTTA
1 TTTTCAATTCAATCCTCTTATAAATAAAGAAATTATAAATTAATATATAATAAAATTGTAATTTA
16429521 ACCCCC
66 ACCCCC
16429527 CATAAAAAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
83 62 1.00
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (83 bp):
TTTTCAATTCAATCCTCTTATAAATAAAGAAATTATAAATTAATATATAATAAAATTGTAATTTA
ACCCCCGCAAATAAAACA
Found at i:16429840 original size:29 final size:29
Alignment explanation
Indices: 16429808--16429863 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
16429798 AAAAACCCAT
16429808 TTTTTTAAAAAATTACCGAAATGGGCCGG
1 TTTTTTAAAAAATTACCGAAATGGGCCGG
** * *
16429837 TTTTTTAATTATTTACCGGAATGGGCC
1 TTTTTTAAAAAATTACCGAAATGGGCC
16429864 ATTTTCCGCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.38
Consensus pattern (29 bp):
TTTTTTAAAAAATTACCGAAATGGGCCGG
Found at i:16430128 original size:10 final size:10
Alignment explanation
Indices: 16430115--16430160 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
16430105 TTCCGTTCAA
16430115 AAATTCTCTC
1 AAATTCTCTC
*
16430125 AAATTCCTTCTA
1 AAATT-C-TCTC
16430137 AAATTCTCTC
1 AAATTCTCTC
16430147 AAA--CTCTC
1 AAATTCTCTC
16430155 AAATTC
1 AAATTC
16430161 CTTCCAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
8 8 0.27
10 12 0.40
11 2 0.07
12 8 0.27
ACGTcount: A:0.35, C:0.28, G:0.00, T:0.37
Consensus pattern (10 bp):
AAATTCTCTC
Found at i:16430149 original size:22 final size:22
Alignment explanation
Indices: 16430079--16430149 Score: 108
Period size: 22 Copynumber: 3.2 Consensus size: 22
16430069 AAATTCAATA
*
16430079 TCAATTTCCTTCAAAAATTCTC
1 TCAAATTCCTTCAAAAATTCTC
16430101 TC-AATTCCGTTCAAAAATTCTC
1 TCAAATTCC-TTCAAAAATTCTC
*
16430123 TCAAATTCCTTCTAAAATTCTC
1 TCAAATTCCTTCAAAAATTCTC
16430145 TCAAA
1 TCAAA
16430150 CTCTCAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.11
22 34 0.76
23 6 0.13
ACGTcount: A:0.34, C:0.27, G:0.01, T:0.38
Consensus pattern (22 bp):
TCAAATTCCTTCAAAAATTCTC
Found at i:16430155 original size:30 final size:30
Alignment explanation
Indices: 16430120--16430178 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
16430110 TTCAAAAATT
* *
16430120 CTCTCAAATTCCTTCTAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
16430150 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
16430179 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:16430170 original size:52 final size:51
Alignment explanation
Indices: 16430098--16430200 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 51
16430088 TTCAAAAATT
* * *
16430098 CTCTCAATTCCGTTCAAAAATTCTCTCAAATTCCTTCTAAAATTCTCTCAAA
1 CTCTCAATTCCGTTCAAAAATCCTCTCAAATTCCTTCAAAAAATCTC-CAAA
* *
16430150 CTCTCAAATTCC-TTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCGTTCAAAAATCCTCTCAAATTCCTTCAAAAAATCTCCAAA
16430201 TCCATATTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
51 4 0.09
52 35 0.78
53 6 0.13
ACGTcount: A:0.34, C:0.31, G:0.01, T:0.34
Consensus pattern (51 bp):
CTCTCAATTCCGTTCAAAAATCCTCTCAAATTCCTTCAAAAAATCTCCAAA
Found at i:16430189 original size:21 final size:22
Alignment explanation
Indices: 16430150--16430191 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16430140 TTCTCTCAAA
16430150 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
16430172 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
16430192 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:16430297 original size:29 final size:29
Alignment explanation
Indices: 16430237--16430297 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
16430227 AATTTCATTA
* *
16430237 TTTTAAGAAAATTTTAAAATTTTTTATTT
1 TTTTAAGAAAATTTTAAAATTTTTAATAT
16430266 TTTTAA-AATAATTTTAAAATTTTTAATAT
1 TTTTAAGAA-AATTTTAAAATTTTTAATAT
16430295 TTT
1 TTT
16430298 CAACAATGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTTAAGAAAATTTTAAAATTTTTAATAT
Found at i:16430417 original size:14 final size:15
Alignment explanation
Indices: 16430388--16430421 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
16430378 AAATTTTAAA
16430388 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
16430403 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
16430417 TTTTA
1 TTTTA
16430422 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:16444930 original size:23 final size:23
Alignment explanation
Indices: 16444906--16444986 Score: 65
Period size: 24 Copynumber: 3.3 Consensus size: 23
16444896 AAAATAACAG
16444906 AAGAAAAGAAGGAAAAGAGAAAGA
1 AAGAAAAGAAGGAAAAGA-AAAGA
* *
16444930 AAGAAATAG-AGAGAAGAGAAATAACA
1 AAGAAA-AGAAG-GAAAAG-AA-AAGA
*
16444956 GAAGAAAAGAAGGAGAAGACAAAGA
1 -AAGAAAAGAAGGAAAAGA-AAAGA
16444981 AAGAAA
1 AAGAAA
16444987 TAGGGAGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
24 14 0.31
25 12 0.27
26 11 0.24
27 8 0.18
ACGTcount: A:0.68, C:0.02, G:0.27, T:0.02
Consensus pattern (23 bp):
AAGAAAAGAAGGAAAAGAAAAGA
Found at i:16444980 original size:51 final size:51
Alignment explanation
Indices: 16444897--16444995 Score: 171
Period size: 51 Copynumber: 1.9 Consensus size: 51
16444887 TTTAGAAAAA
*
16444897 AAATAACAGAAGAAAAGAAGGAAAAGAGAAAGAAAGAAATAGAGAGAAGAG
1 AAATAACAGAAGAAAAGAAGGAAAAGACAAAGAAAGAAATAGAGAGAAGAG
* *
16444948 AAATAACAGAAGAAAAGAAGGAGAAGACAAAGAAAGAAATAGGGAGAA
1 AAATAACAGAAGAAAAGAAGGAAAAGACAAAGAAAGAAATAGAGAGAA
16444996 AAAAATGTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.66, C:0.03, G:0.27, T:0.04
Consensus pattern (51 bp):
AAATAACAGAAGAAAAGAAGGAAAAGACAAAGAAAGAAATAGAGAGAAGAG
Found at i:16444993 original size:23 final size:23
Alignment explanation
Indices: 16444920--16444995 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 23
16444910 AAAGAAGGAA
*
16444920 AAGAGAAAGAAAGAAATAGAGAG
1 AAGAGAAAGAAAGAAATAGGGAG
* *
16444943 AAGAGAAATAACAGAAGAAAAGAAGGAG
1 AAGAGAAAGAA-AG-A-AATAG--GGAG
*
16444971 AAGACAAAGAAAGAAATAGGGAG
1 AAGAGAAAGAAAGAAATAGGGAG
16444994 AA
1 AA
16444996 AAAAATGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
23 16 0.38
24 2 0.05
25 5 0.12
26 5 0.12
27 2 0.05
28 12 0.29
ACGTcount: A:0.64, C:0.03, G:0.29, T:0.04
Consensus pattern (23 bp):
AAGAGAAAGAAAGAAATAGGGAG
Found at i:16447424 original size:5 final size:5
Alignment explanation
Indices: 16447414--16447447 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
16447404 AATGCATTAA
16447414 TAATT TAATT TAATT TAATT TAATT TAATT TAAT
1 TAATT TAATT TAATT TAATT TAATT TAATT TAAT
16447448 GTTACCAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TAATT
Found at i:16448643 original size:18 final size:19
Alignment explanation
Indices: 16448611--16448648 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
16448601 TCTCCCAAAA
16448611 TAAATATAATAAATTAATT
1 TAAATATAATAAATTAATT
*
16448630 TAAAT-TAATTAATTAATT
1 TAAATATAATAAATTAATT
16448648 T
1 T
16448649 TCCAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAATATAATAAATTAATT
Found at i:16448657 original size:16 final size:16
Alignment explanation
Indices: 16448636--16448666 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16448626 AATTTAAATT
*
16448636 AATTAATTAATTTTCC
1 AATTAAATAATTTTCC
16448652 AATTAAATAATTTTC
1 AATTAAATAATTTTC
16448667 TCAACTCGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTAAATAATTTTCC
Found at i:16448806 original size:18 final size:19
Alignment explanation
Indices: 16448762--16448806 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
16448752 CCACTATGAC
*
16448762 TAATTAA-TTTAATTCTAT
1 TAATTAATTTTAATTCAAT
16448780 T-ATTGAATTTTAATT-AAT
1 TAATT-AATTTTAATTCAAT
16448798 TAATTAATT
1 TAATTAATT
16448807 AATAATTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 3 0.13
18 10 0.43
19 10 0.43
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TAATTAATTTTAATTCAAT
Found at i:16452884 original size:13 final size:14
Alignment explanation
Indices: 16452860--16452890 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
16452850 AAACATATAT
16452860 AATAAAGTTATAAA
1 AATAAAGTTATAAA
16452874 AATAAAG-TATAAA
1 AATAAAGTTATAAA
16452887 AATA
1 AATA
16452891 TGTATAGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (14 bp):
AATAAAGTTATAAA
Found at i:16453167 original size:26 final size:26
Alignment explanation
Indices: 16453138--16453191 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
16453128 TATATAAAAC
16453138 TAAGAATAT-AAAATAATAATAAAATA
1 TAAG-ATATGAAAATAATAATAAAATA
* * *
16453164 TAAGATATGTATATATTAATAAAATA
1 TAAGATATGAAAATAATAATAAAATA
16453190 TA
1 TA
16453192 TATATATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (26 bp):
TAAGATATGAAAATAATAATAAAATA
Found at i:16462061 original size:13 final size:13
Alignment explanation
Indices: 16462043--16462121 Score: 71
Period size: 13 Copynumber: 6.5 Consensus size: 13
16462033 TAGATTTTTC
*
16462043 CTAAATATTATTA
1 CTAAATATTATCA
*
16462056 CTAAATA--AT-T
1 CTAAATATTATCA
*
16462066 CTAGATATTATCA
1 CTAAATATTATCA
16462079 CTAAATATTATCA
1 CTAAATATTATCA
*
16462092 CTAAATA--AT-T
1 CTAAATATTATCA
*
16462102 CTAATTATTATCA
1 CTAAATATTATCA
16462115 CTAAATA
1 CTAAATA
16462122 ATTCAAAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
10 12 0.23
11 4 0.08
12 4 0.08
13 32 0.62
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.41
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:16462084 original size:36 final size:36
Alignment explanation
Indices: 16462043--16462121 Score: 133
Period size: 36 Copynumber: 2.2 Consensus size: 36
16462033 TAGATTTTTC
*
16462043 CTAAATATTATTACTAAATAATTCTAGA-TATTATCA
1 CTAAATATTATCACTAAATAATTCTA-ATTATTATCA
16462079 CTAAATATTATCACTAAATAATTCTAATTATTATCA
1 CTAAATATTATCACTAAATAATTCTAATTATTATCA
16462115 CTAAATA
1 CTAAATA
16462122 ATTCAAAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
35 1 0.02
36 40 0.98
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.41
Consensus pattern (36 bp):
CTAAATATTATCACTAAATAATTCTAATTATTATCA
Found at i:16462105 original size:23 final size:23
Alignment explanation
Indices: 16462079--16462130 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
16462069 GATATTATCA
16462079 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
16462102 CTAATTATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
16462125 CAAAAT
1 CTAAAT
16462131 TTAAAAATCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.38
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:16473851 original size:39 final size:38
Alignment explanation
Indices: 16473773--16473851 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 38
16473763 CTTGGAAGAG
* * *
16473773 AATATGTAGTGTATTAAATAATTATTATGATACGCAAA
1 AATATATAGTGTATTAAATAATTATTATAATAAGCAAA
*
16473811 AATATATAGTGTATTAATATCAA-TATTATAATAAGTAAA
1 AATATATAGTGTATTAA-AT-AATTATTATAATAAGCAAA
16473850 AA
1 AA
16473852 GCTTATATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
38 16 0.46
39 17 0.49
40 2 0.06
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (38 bp):
AATATATAGTGTATTAAATAATTATTATAATAAGCAAA
Found at i:16480995 original size:20 final size:19
Alignment explanation
Indices: 16480966--16481026 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
16480956 TTTTTTGAAA
16480966 TTTTGAATTTTTAAATTTC
1 TTTTGAATTTTTAAATTTC
* *
16480985 TTTTAGAATTTATATATATT-
1 TTTT-GAATTTTTAAAT-TTC
* *
16481005 TTTTGTATTTTT-ACTTTC
1 TTTTGAATTTTTAAATTTC
16481023 TTTT
1 TTTT
16481027 ATAATTTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
17 2 0.06
18 5 0.15
19 10 0.30
20 14 0.42
21 2 0.06
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTGAATTTTTAAATTTC
Found at i:16485607 original size:16 final size:16
Alignment explanation
Indices: 16485586--16485619 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
16485576 ATCAAATTAA
*
16485586 TTTTAATTAATTAATT
1 TTTTAATTAAATAATT
16485602 TTTTAATTAAATAATT
1 TTTTAATTAAATAATT
16485618 TT
1 TT
16485620 CTCAACTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTAATTAAATAATT
Found at i:16486250 original size:24 final size:21
Alignment explanation
Indices: 16486199--16486254 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
16486189 TTTTGCTAGT
**
16486199 TTTTGTTGTTGTTTGATGTTA
1 TTTTGTTGTTGTTTGATGCCA
16486220 TTTTGTTGTTGTTTGATGCCA
1 TTTTGTTGTTGTTTGATGCCA
*
16486241 TTTTGATGTTGTTT
1 TTTTGTTGTTGTTT
16486255 TGTTTCCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.09, C:0.04, G:0.23, T:0.64
Consensus pattern (21 bp):
TTTTGTTGTTGTTTGATGCCA
Found at i:16488407 original size:27 final size:27
Alignment explanation
Indices: 16488377--16488435 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
16488367 GTAATCACAA
* *
16488377 GGTAGTCTACCGGGATAGTAAACACGG
1 GGTAGTCTACCAGGATAATAAACACGG
* **
16488404 GGTAGTTTGTCAGGATAATAAACACGG
1 GGTAGTCTACCAGGATAATAAACACGG
16488431 GGTAG
1 GGTAG
16488436 CTCGTCAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.22
Consensus pattern (27 bp):
GGTAGTCTACCAGGATAATAAACACGG
Found at i:16488442 original size:27 final size:27
Alignment explanation
Indices: 16488389--16488442 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
16488379 TAGTCTACCG
* * *
16488389 GGATAGTAAACACGGGGTAGTTTGTCA
1 GGATAATAAACACGGGGTAGCTCGTCA
16488416 GGATAATAAACACGGGGTAGCTCGTCA
1 GGATAATAAACACGGGGTAGCTCGTCA
16488443 AGACATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.22
Consensus pattern (27 bp):
GGATAATAAACACGGGGTAGCTCGTCA
Found at i:16488452 original size:27 final size:27
Alignment explanation
Indices: 16488395--16488454 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
16488385 ACCGGGATAG
* * * *
16488395 TAAACACGGGGTAGTTTGTCAGGATAA
1 TAAACACGGGGTAGCTCGTCAAGACAA
*
16488422 TAAACACGGGGTAGCTCGTCAAGACAT
1 TAAACACGGGGTAGCTCGTCAAGACAA
16488449 TAAACA
1 TAAACA
16488455 TTAATTTACA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.22
Consensus pattern (27 bp):
TAAACACGGGGTAGCTCGTCAAGACAA
Found at i:16490594 original size:28 final size:28
Alignment explanation
Indices: 16490552--16490613 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
16490542 ATTTTCCTCT
* *
16490552 ACTCTCATCATAGCAGTCGTTCTCCTTC
1 ACTCTCTTCACAGCAGTCGTTCTCCTTC
16490580 ACTCTCTTCACAGCAGTCGTTCTCCTTC
1 ACTCTCTTCACAGCAGTCGTTCTCCTTC
16490608 -CTCTCT
1 ACTCTCT
16490614 GTCCATCAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 6 0.19
28 26 0.81
ACGTcount: A:0.15, C:0.39, G:0.10, T:0.37
Consensus pattern (28 bp):
ACTCTCTTCACAGCAGTCGTTCTCCTTC
Found at i:16491202 original size:2 final size:2
Alignment explanation
Indices: 16491195--16491234 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
16491185 TTTATTTAGC
16491195 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16491235 CAGAAATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16493942 original size:46 final size:45
Alignment explanation
Indices: 16493836--16494161 Score: 245
Period size: 37 Copynumber: 7.6 Consensus size: 45
16493826 CATATGACCT
*
16493836 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
16493879 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
16493925 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
* *
16493962 CTTATCACTTTGTCTCTTAATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
* *
16493999 CTTATCACTTTGTCTCTTAATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
** * * *
16494036 CTTATCACTTTGTTTCTTGATCAGATATTGTTTCTTGATCAGATAAGTGTAGCCA
1 CTTATCACTTTGTCACTTGATCAGATA-AG-----TG-T-AGCTAAG-CTA-CCA
*
16494091 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAACTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
16494137 CTTATCACTTTGTCACTTGATCAGA
1 CTTATCACTTTGTCACTTGATCAGA
16494162 AGTACTCAAA
Statistics
Matches: 244, Mismatches: 16, Indels: 43
0.81 0.05 0.14
Matches are distributed among these distances:
37 98 0.40
40 2 0.01
42 1 0.00
43 9 0.04
44 6 0.02
45 22 0.09
46 63 0.26
47 5 0.02
48 4 0.02
49 3 0.01
50 1 0.00
54 2 0.01
55 28 0.11
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:16494068 original size:18 final size:18
Alignment explanation
Indices: 16494045--16494080 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
16494035 ACTTATCACT
16494045 TTGTTTCTTGATCAGATA
1 TTGTTTCTTGATCAGATA
16494063 TTGTTTCTTGATCAGATA
1 TTGTTTCTTGATCAGATA
16494081 AGTGTAGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (18 bp):
TTGTTTCTTGATCAGATA
Found at i:16494102 original size:55 final size:55
Alignment explanation
Indices: 16494008--16494117 Score: 175
Period size: 55 Copynumber: 2.0 Consensus size: 55
16493998 ACTTATCACT
**
16494008 TTGTCTCTTAATCAGATAAGTGTAACCACTTATCACTTTGTTTCTTGATCAGATA
1 TTGTCTCTTAATCAGATAAGTGTAACCACTTATCACTTTGTCACTTGATCAGATA
* * *
16494063 TTGTTTCTTGATCAGATAAGTGTAGCCACTTATCACTTTGTCACTTGATCAGATA
1 TTGTCTCTTAATCAGATAAGTGTAACCACTTATCACTTTGTCACTTGATCAGATA
16494118 AGTGTAGCTA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (55 bp):
TTGTCTCTTAATCAGATAAGTGTAACCACTTATCACTTTGTCACTTGATCAGATA
Found at i:16495979 original size:21 final size:21
Alignment explanation
Indices: 16495954--16495993 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16495944 GCCTAAGATG
*
16495954 TGAATTGGATTGAATTGAGTA
1 TGAATTGGATTAAATTGAGTA
*
16495975 TGAATTGTATTAAATTGAG
1 TGAATTGGATTAAATTGAG
16495994 CTAAATTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (21 bp):
TGAATTGGATTAAATTGAGTA
Found at i:16496163 original size:21 final size:21
Alignment explanation
Indices: 16496122--16496163 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
16496112 TAAATTATGT
*
16496122 ATGTTTATATGTTTAAATTTA
1 ATGTTTATATGTTGAAATTTA
*
16496143 ATGTTGTATATG-TGAATTTTA
1 ATGTT-TATATGTTGAAATTTA
16496164 TGAATGCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (21 bp):
ATGTTTATATGTTGAAATTTA
Found at i:16496682 original size:23 final size:23
Alignment explanation
Indices: 16496656--16496726 Score: 56
Period size: 25 Copynumber: 2.9 Consensus size: 23
16496646 TAATTATGAC
16496656 TCTTATGAGCTTCCCGTTATACA
1 TCTTATGAGCTTCCCGTTATACA
*
16496679 TCTTGGATAAGCTTCCC-TT-TACA
1 TCTT--ATGAGCTTCCCGTTATACA
*
16496702 TGGCTCATATGAGCTTTCCGTTATA
1 T--CT--TATGAGCTTCCCGTTATA
16496727 TGGCTCGAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
23 9 0.24
24 2 0.05
25 21 0.57
26 2 0.05
27 3 0.08
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (23 bp):
TCTTATGAGCTTCCCGTTATACA
Found at i:16496759 original size:27 final size:25
Alignment explanation
Indices: 16496712--16496780 Score: 61
Period size: 27 Copynumber: 2.7 Consensus size: 25
16496702 TGGCTCATAT
* *
16496712 GAGCTTTCCGTTATATGGCTCGAGAG
1 GAGCTTCCCGATATATGGCTCGA-AG
*
16496738 AGAGCTTCCCGATA-ATGTGCTCTAAG
1 -GAGCTTCCCGATATATG-GCTCGAAG
16496764 GAGCTCTCCCGA-ATATG
1 GAGCT-TCCCGATATATG
16496781 AATTGACGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
25 6 0.17
26 14 0.39
27 16 0.44
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (25 bp):
GAGCTTCCCGATATATGGCTCGAAG
Found at i:16500277 original size:23 final size:25
Alignment explanation
Indices: 16500243--16500296 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
16500233 GAAAAGGACT
16500243 AAAT-TGAAAAG-T-TGAAATAATA
1 AAATATGAAAAGTTATGAAATAATA
* *
16500265 AAATATGATAAGTTAATTAAATAATA
1 AAATATGAAAAGTT-ATGAAATAATA
16500291 AAATAT
1 AAATAT
16500297 CATCTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 4 0.15
23 6 0.23
24 1 0.04
26 15 0.58
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (25 bp):
AAATATGAAAAGTTATGAAATAATA
Found at i:16501133 original size:17 final size:17
Alignment explanation
Indices: 16501113--16501145 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16501103 GTTGTGGTCA
16501113 TGCTTATGTTGCGGACT
1 TGCTTATGTTGCGGACT
*
16501130 TGCTTATGTTGTGGAC
1 TGCTTATGTTGCGGAC
16501146 ACACCATAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.15, G:0.30, T:0.42
Consensus pattern (17 bp):
TGCTTATGTTGCGGACT
Found at i:16501529 original size:25 final size:25
Alignment explanation
Indices: 16501391--16501532 Score: 94
Period size: 25 Copynumber: 5.8 Consensus size: 25
16501381 GACTATCTGA
* *
16501391 AGCTTCCCGTTA-ATGGCTCTTC-GG
1 AGCTTCCCGTTATATGGCTC-ACATG
* *
16501415 AGCTACCCGTTAT-TGGCTTACATG
1 AGCTTCCCGTTATATGGCTCACATG
* ** * **
16501439 AGCTTCTCAAT-TATGGATCTTATG
1 AGCTTCCCGTTATATGGCTCACATG
* * ** *
16501463 AGCTTCCCGTTATATAGCCCGGATA
1 AGCTTCCCGTTATATGGCTCACATG
* *
16501488 AGCTTCCCTTTACATGGCTCACATG
1 AGCTTCCCGTTATATGGCTCACATG
16501513 AGCTTCCCGTTATATGGCTC
1 AGCTTCCCGTTATATGGCTC
16501533 GAGAGAGGGC
Statistics
Matches: 84, Mismatches: 30, Indels: 7
0.69 0.25 0.06
Matches are distributed among these distances:
23 2 0.02
24 39 0.46
25 43 0.51
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.34
Consensus pattern (25 bp):
AGCTTCCCGTTATATGGCTCACATG
Found at i:16508820 original size:3 final size:3
Alignment explanation
Indices: 16508812--16508836 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16508802 TTTCAACCTT
16508812 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
16508837 CTTTTCATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:16516460 original size:13 final size:13
Alignment explanation
Indices: 16516442--16516515 Score: 103
Period size: 13 Copynumber: 5.7 Consensus size: 13
16516432 AGTTTTTCAT
*
16516442 TGCTTTTGATAAG
1 TGCTTTTGAGAAG
16516455 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
* * *
16516468 TGCTGTGGAAAAG
1 TGCTTTTGAGAAG
16516481 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
16516494 TGCTTTTGAGGAG
1 TGCTTTTGAGAAG
16516507 TGCTTTTGA
1 TGCTTTTGA
16516516 AAAATTTGAG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 53 1.00
ACGTcount: A:0.22, C:0.08, G:0.31, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:16521957 original size:21 final size:23
Alignment explanation
Indices: 16521933--16521975 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16521923 TTATTAGGGA
16521933 CAAAATAC-CA-AAAAAAGGGGG
1 CAAAATACACATAAAAAAGGGGG
*
16521954 CAAATTACACATAAAAAAGGGG
1 CAAAATACACATAAAAAAGGGG
16521976 TATTTATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 2 0.11
23 10 0.53
ACGTcount: A:0.56, C:0.14, G:0.21, T:0.09
Consensus pattern (23 bp):
CAAAATACACATAAAAAAGGGGG
Found at i:16523141 original size:13 final size:13
Alignment explanation
Indices: 16523125--16523158 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
16523115 AAAAAATTAT
16523125 TTTTAAAAAAAAA
1 TTTTAAAAAAAAA
16523138 TTTT--AAAAAAA
1 TTTTAAAAAAAAA
16523149 TTTTAAAAAA
1 TTTTAAAAAA
16523159 TAAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.58
13 8 0.42
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TTTTAAAAAAAAA
Found at i:16523159 original size:10 final size:11
Alignment explanation
Indices: 16523131--16523158 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
16523121 TTATTTTTAA
16523131 AAAAAAATTTT
1 AAAAAAATTTT
16523142 AAAAAAATTTT
1 AAAAAAATTTT
16523153 AAAAAA
1 AAAAAA
16523159 TAAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAAAAATTTT
Found at i:16525096 original size:22 final size:20
Alignment explanation
Indices: 16525058--16525097 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
16525048 TGATAATCTA
16525058 GATTTTAGAGAGATTTAAGT
1 GATTTTAGAGAGATTTAAGT
*
16525078 GATTTATAGATGATATTTAA
1 GATTT-TAGA-GAGATTTAA
16525098 AGAGAGATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 4 0.24
22 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.42
Consensus pattern (20 bp):
GATTTTAGAGAGATTTAAGT
Found at i:16541089 original size:2 final size:2
Alignment explanation
Indices: 16541082--16541117 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
16541072 AACCATTTTC
16541082 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16541118 ATCACTTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16542548 original size:2 final size:2
Alignment explanation
Indices: 16542541--16542662 Score: 244
Period size: 2 Copynumber: 61.0 Consensus size: 2
16542531 NNNNNNNNNN
16542541 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
16542583 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
16542625 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
16542663 TATTGCCACT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 120 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:16544167 original size:13 final size:13
Alignment explanation
Indices: 16544149--16544173 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16544139 TCAAACGATC
16544149 AAATTTTCACACG
1 AAATTTTCACACG
16544162 AAATTTTCACAC
1 AAATTTTCACAC
16544174 ATATAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:16545870 original size:22 final size:22
Alignment explanation
Indices: 16545845--16545897 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
16545835 TTTTTTAAAT
* *
16545845 AATAATTACTCTAATT-AAGTGA
1 AATAATTAAT-TAATTAAAATGA
* *
16545867 AATATTTAATTGATTAAAATGA
1 AATAATTAATTAATTAAAATGA
16545889 AATAATTAA
1 AATAATTAA
16545898 ATGGGTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.38
Consensus pattern (22 bp):
AATAATTAATTAATTAAAATGA
Found at i:16549728 original size:15 final size:15
Alignment explanation
Indices: 16549708--16549759 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
16549698 ACTACAAAAC
16549708 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
16549723 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
16549742 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
16549757 ATT
1 ATT
16549760 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:16549806 original size:15 final size:16
Alignment explanation
Indices: 16549786--16549819 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
16549776 ATATGTGAAG
*
16549786 AATATTATTTAAA-AA
1 AATATTATTAAAATAA
16549801 AATATTATTAAAATAA
1 AATATTATTAAAATAA
16549817 AAT
1 AAT
16549820 TGAAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATTATTAAAATAA
Found at i:16552085 original size:13 final size:13
Alignment explanation
Indices: 16552067--16552145 Score: 80
Period size: 13 Copynumber: 6.5 Consensus size: 13
16552057 AATTTTGACT
16552067 TATTTAGTGATAA
1 TATTTAGTGATAA
*
16552080 TATTTA--GA-AT
1 TATTTAGTGATAA
16552090 TATTTAGTGATAA
1 TATTTAGTGATAA
*
16552103 TATTTAATGATAA
1 TATTTAGTGATAA
*
16552116 TATTTA--GA-AT
1 TATTTAGTGATAA
*
16552126 TATTTAATGATAA
1 TATTTAGTGATAA
16552139 TATTTAG
1 TATTTAG
16552146 AAAAATCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
10 14 0.26
11 4 0.07
12 4 0.07
13 32 0.59
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:16552114 original size:36 final size:36
Alignment explanation
Indices: 16552067--16552144 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
16552057 AATTTTGACT
* *
16552067 TATTTAGTGATAATATTTAGAATTATTTAGTGATAA
1 TATTTAATGATAATATTTAGAATTATTTAATGATAA
16552103 TATTTAATGATAATATTTAGAATTATTTAATGATAA
1 TATTTAATGATAATATTTAGAATTATTTAATGATAA
16552139 TATTTA
1 TATTTA
16552145 GAAAAATCTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (36 bp):
TATTTAATGATAATATTTAGAATTATTTAATGATAA
Found at i:16552129 original size:23 final size:23
Alignment explanation
Indices: 16552103--16552147 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
16552093 TTAGTGATAA
16552103 TATTTAATGATAATATTTAGAAT
1 TATTTAATGATAATATTTAGAAT
16552126 TATTTAATGATAATATTTAGAA
1 TATTTAATGATAATATTTAGAA
16552148 AAATCTAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (23 bp):
TATTTAATGATAATATTTAGAAT
Done.