Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, 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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 8 of 32
Found at i:3987912 original size:6 final size:6
Alignment explanation
Indices: 3987874--3987946 Score: 74
Period size: 6 Copynumber: 11.7 Consensus size: 6
3987864 AACCAGCAAC
* * * * *
3987874 AAGAAG AAGAGG AGGAGG AGGAGG AGGAGG AAGAAGAAG AAGAAG AAGAGG
1 AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAG-AG--G AAGAGG AAGAGG
3987925 AAGAGG AAGAGG AAGAGG AAGA
1 AAGAGG AAGAGG AAGAGG AAGA
3987947 TGAGCATGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
6 52 0.88
7 2 0.03
8 1 0.02
9 4 0.07
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
AAGAGG
Found at i:3989518 original size:14 final size:14
Alignment explanation
Indices: 3989501--3989555 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
3989491 TAATATTATA
3989501 ATTAAAATAAAAAT
1 ATTAAAATAAAAAT
3989515 ATTAAAAT-AAAAT
1 ATTAAAATAAAAAT
* *
3989528 ATGTAATATAAGAAT
1 AT-TAAAATAAAAAT
*
3989543 A--AAAATTAAAAT
1 ATTAAAATAAAAAT
3989555 A
1 A
3989556 AAATAAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 9 0.26
13 7 0.21
14 13 0.38
15 5 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (14 bp):
ATTAAAATAAAAAT
Found at i:3989661 original size:28 final size:26
Alignment explanation
Indices: 3989607--3990245 Score: 151
Period size: 30 Copynumber: 23.0 Consensus size: 26
3989597 AACAAATAAA
*
3989607 ATAAAATATATAATATAAAA-AATATATT
1 ATAAAA-ATA-AATA-AAAATAAAATATT
3989635 A-AAAAATGAAAATAAAATATAAAATATT
1 ATAAAAAT--AAATAAAA-ATAAAATATT
*
3989663 ATAATAATAAATAAAAATAAAATATAT
1 ATAAAAATAAATAAAAATAAAATAT-T
* * **
3989690 GACATTAAAAATATATTTAAAATATGATATTAT
1 ---A-TAAAAATA-AATAAAAATAAAATA-T-T
3989723 ATAAAAATTAATAATAAAAATATAAATA-T
1 ATAAAAA-T-A-AATAAAAATA-AAATATT
*
3989752 ATTAAAAAT--A-AAATATAAAATATT
1 A-TAAAAATAAATAAAAATAAAATATT
3989776 ATAAAAATAAAT-AAAATAAAATATAT
1 ATAAAAATAAATAAAAATAAAATAT-T
* * **
3989802 GACATTAAAAATATATTTAAAATATGATATTAT
1 ---A-TAAAAATA-AATAAAAATAAAATA-T-T
*
3989835 ATAAAAATTAGTAATATAAATATAAATA-T
1 ATAAAAA-TA--AATAAAAATA-AAATATT
*
3989864 ATTAAAAAT--A-AAATATAAAATATT
1 A-TAAAAATAAATAAAAATAAAATATT
*
3989888 ATAATAATAAAT-AAAATAAAATATAT
1 ATAAAAATAAATAAAAATAAAATAT-T
** * *
3989914 GACATTAAAATATATTTAAGAAATGATAT-TAT
1 ---A-TAAAA-ATAAATAA-AAATAAAATAT-T
3989946 ATAAAAATTAATAATAAAAATATAAATA-T
1 ATAAAAA-T-A-AATAAAAATA-AAATATT
* *
3989975 ATTAAAAATAAA-ATATAT-AAA-ATT
1 A-TAAAAATAAATAAAAATAAAATATT
*
3989999 ATAATAATAAATAAAAATAAAATATATGAT
1 ATAAAAATAAATAAAAAT-AAA-ATAT--T
* * **
3990029 ATTAAAAATATATTTAAAATATGATATTAT
1 A-TAAAAATA-AATAAAAATAAAATA-T-T
*
3990059 ATAAAAATTAATAATAAAATATAAATA-T
1 ATAAAAATAAAT-A-AAAATA-AAATATT
* *
3990087 ATTAAAAATAAAATATAAATATAATA--
1 A-TAAAAAT-AAATAAAAATAAAATATT
** *
3990113 ATAATAAATAAAATAAAATATATGACATT
1 ATAA-AAAT-AAATAAAA-ATAAAATATT
** * *
3990142 A-AAAATATATTTAAAAATGATAT-TAT
1 ATAAAA-ATAAATAAAAATAAAATAT-T
3990168 ATAAAAATTAATAATAAAAATATAAATA-T
1 ATAAAAA-T-A-AATAAAAATA-AAATATT
*
3990197 ATTAAAAAT--A-AAATATAAAATATT
1 A-TAAAAATAAATAAAAATAAAATATT
*
3990221 ATAATAATAAATAAAAATAAAATAT
1 ATAAAAATAAATAAAAATAAAATAT
3990246 ATGATATTAA
Statistics
Matches: 460, Mismatches: 68, Indels: 168
0.66 0.10 0.24
Matches are distributed among these distances:
23 44 0.10
24 32 0.07
25 32 0.07
26 53 0.12
27 45 0.10
28 33 0.07
29 60 0.13
30 68 0.15
31 43 0.09
32 37 0.08
33 13 0.03
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (26 bp):
ATAAAAATAAATAAAAATAAAATATT
Found at i:3989679 original size:39 final size:38
Alignment explanation
Indices: 3989600--3990262 Score: 156
Period size: 38 Copynumber: 17.9 Consensus size: 38
3989590 TAGGTAAAAC
* *
3989600 AAATAAAATAAAATATATAATATAAAAAATATATTAAA
1 AAATAAAATAAAATATAAAATATAAAAAATATAATAAA
*
3989638 AAATGAAAATAAAATATAAAATATTATAATAATA-AAT-AA
1 AAAT-AAAATAAAATATAAAATA-TA-AAAAATATAATAAA
* * **
3989677 AAATAAAAT---ATATGACAT-T-AAAAATAT-ATTTA
1 AAATAAAATAAAATATAAAATATAAAAAATATAATAAA
** ** * *
3989709 AAATATGATATTATATAAAA-ATTAATAATA-AA-AATA
1 AAATAAAATAAAATATAAAATATAAAAAATATAATAA-A
* * *
3989745 TAAATATATTAAAA-ATAAAATATAAAATATTATAA-AAA
1 -AAATAAAATAAAATATAAAATATAAAA-AATATAATAAA
** * * **
3989783 TAAATAAAATAAAATATATGACATTAAAAATAT-ATTTA
1 -AAATAAAATAAAATATAAAATATAAAAAATATAATAAA
** ** * ** *
3989821 AAATATGATATTATATAAAA-ATTAGTAATATAA-ATAT
1 AAATAAAATAAAATATAAAATATAAAAAATATAATA-AA
* * * *
3989858 AAATATATTAAAA-ATAAAATATAAAATATTATAATAAT
1 AAATAAAATAAAATATAAAATATAAAA-AATATAATAAA
* * * *
3989896 AAATAAAATAAAATATATGACAT-TAAAATATAT-TTAAG
1 AAATAAAATAAAATATA--AAATATAAAAAATATAATAAA
* * * * *
3989934 AAATGATATTATATA-AAAAT-TAATAATAA-A-AAT-AT
1 AAATAAAATAAAATATAAAATATAA-AA-AATATAATAAA
* * * *
3989969 AAATATATTAAAA-ATAAAATATATAAAATTATAATAAT
1 AAATAAAATAAAATATAAAATATA-AAAAATATAATAAA
** * **
3990007 AAATAAAAATAAAATATATGATATTAAAAATAT-ATTTA
1 AAAT-AAAATAAAATATAAAATATAAAAAATATAATAAA
** ** * * * *
3990045 AAATATGATATTATATAAAA-ATTAATAATAAAAT-AT
1 AAATAAAATAAAATATAAAATATAAAAAATATAATAAA
* * * *
3990081 AAATATATTAAAA-ATAAAATAT-AAATATAATAATAAT
1 AAATAAAATAAAATATAAAATATAAAAAAT-ATAATAAA
** * * * *
3990118 AAATAAAATAAAATATATGACATTAAAAATATATTTAA
1 AAATAAAATAAAATATAAAATATAAAAAATATAATAAA
* * * * *
3990156 AAATGATATTATATA-AAAAT-TAATAATAA-A-AAT-AT
1 AAATAAAATAAAATATAAAATATAA-AA-AATATAATAAA
* * * *
3990191 AAATATATTAAAA-ATAAAATATAAAATATTATAATAAT
1 AAATAAAATAAAATATAAAATATAAAA-AATATAATAAA
** *
3990229 AAATAAAAATAAAATATATGATATTAAAAATATA
1 AAAT-AAAATAAAATATAAAATATAAAAAATATA
3990263 TTTAAGAAAT
Statistics
Matches: 444, Mismatches: 129, Indels: 103
0.66 0.19 0.15
Matches are distributed among these distances:
31 8 0.02
32 8 0.02
33 1 0.00
34 2 0.00
35 61 0.14
36 70 0.16
37 80 0.18
38 105 0.24
39 74 0.17
40 26 0.06
41 9 0.02
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (38 bp):
AAATAAAATAAAATATAAAATATAAAAAATATAATAAA
Found at i:3989684 original size:33 final size:32
Alignment explanation
Indices: 3989604--3989688 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 32
3989594 TAAAACAAAT
* *
3989604 AAAATAAAATATATAATATAAAAAATATATTAA
1 AAAATAAAA-ATAAAATATAAAAAATATAATAA
* *
3989637 AAAATGAAAATAAAATATAAAATATTATAATAA
1 AAAATAAAAATAAAATATAAAA-AATATAATAA
*
3989670 TAAATAAAAATAAAATATA
1 AAAATAAAAATAAAATATA
3989689 TGACATTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 12 0.27
33 33 0.73
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (32 bp):
AAAATAAAAATAAAATATAAAAAATATAATAA
Found at i:3989753 original size:48 final size:48
Alignment explanation
Indices: 3989698--3990206 Score: 156
Period size: 48 Copynumber: 10.3 Consensus size: 48
3989688 ATGACATTAA
*
3989698 AAATATATTTAAAATATGATATTATATAAAAATTAATAATAAAAATAT
1 AAATATATTAAAAATATGATATTATATAAAAATTAATAATAAAAATAT
** *
3989746 AAATATATTAAAAATAAAATATAAAATATTATAAAAATAAATAAAATAAAATATATGACATT
1 AAATATATTAAAAATATGATAT----TA-TATAAAAATTAAT--AAT-AAA-A-AT---A-T
* * *
3989808 AAAAATATATTTAAAATATGATATTATATAAAAATTAGTAATATAAATAT
1 --AAATATATTAAAAATATGATATTATATAAAAATTAATAATAAAAATAT
*
3989858 AAATATATTAAAAATA--A-A--ATATAAAATATTATAATAATAAATAAAAT
1 AAATATATTAAAAATATGATATTATATAAAA-A-T-TAATAATAAA-AATAT
* * *
3989905 AAAATATATGACATTAAA-AT-ATATT-TA-AGAAATGATATTATATAAAAAT-T
1 -AAATATATTA-A--AAATATGATATTATATAAAAAT--TAATA-ATAAAAATAT
* * *
3989955 -AATA-A-TAAAAATAT-A-AATATATTAAAAATAAAATATATAAAATTAT
1 AAATATATTAAAAATATGATATTATA-TAAAAAT-TAATA-ATAAAAATAT
* ** * *
3990001 -AATAATAAATAAAAATAAAATATATGATATTAAAAA-T-ATATTTAAAATAT
1 AAAT-AT-ATTAAAAATATGATAT-T-ATA-TAAAAATTAATAATAAAAATAT
* * ** *
3990051 -GATATTATATAAAAATTAATAATAAAATATAAATATATTAAAAAT-AAAATAT
1 AAATA-TAT-TAAAAA-T-ATGATATTATATAAA-A-ATTAATAATAAAAATAT
* * * * * * * *
3990103 AAATATAATAATAATA--A-ATAAAAT-AAAA-T-AT-ATGACATTAA
1 AAATATATTAAAAATATGATATTATATAAAAATTAATAATAAAAATAT
*
3990144 AAATATATTTAAAA-ATGATATTATATAAAAATTAATAATAAAAATAT
1 AAATATATTAAAAATATGATATTATATAAAAATTAATAATAAAAATAT
3990191 AAATATATTAAAAATA
1 AAATATATTAAAAATA
3990207 AAATATAAAA
Statistics
Matches: 344, Mismatches: 56, Indels: 122
0.66 0.11 0.23
Matches are distributed among these distances:
40 3 0.01
41 16 0.05
42 2 0.01
43 19 0.06
44 11 0.03
45 18 0.05
46 26 0.08
47 26 0.08
48 48 0.14
49 9 0.03
50 33 0.10
51 24 0.07
52 27 0.08
53 21 0.06
54 12 0.03
55 4 0.01
56 5 0.01
57 4 0.01
58 2 0.01
59 11 0.03
60 2 0.01
61 1 0.00
62 1 0.00
64 19 0.06
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (48 bp):
AAATATATTAAAAATATGATATTATATAAAAATTAATAATAAAAATAT
Found at i:3989765 original size:64 final size:62
Alignment explanation
Indices: 3989667--3989886 Score: 206
Period size: 60 Copynumber: 3.7 Consensus size: 62
3989657 AATATTATAA
* *
3989667 TAATAAATAAAAATA-AAATATATGACATTAAA-AATATATTTAAAATATGATATTATATAAAAA
1 TAAT-AATAAAAATATAAATATATTA-A--AAATAAAATATTTAAAATATGATATTATATAAAAA
3989730 T
62 T
*
3989731 TAATAATAAAAATATAAATATATTAAAAATAAAATA--TAAAATAT--TA-TA-A-AAATAAA
1 TAATAATAAAAATATAAATATATTAAAAATAAAATATTTAAAATATGATATTATATAAA-AAT
*
3989787 TAA-AAT-AAAATAT--ATGACATTAAAAAT---ATATTTAAAATATGATATTATATAAAAAT
1 TAATAATAAAAATATAAAT-ATATTAAAAATAAAATATTTAAAATATGATATTATATAAAAAT
* *
3989843 TAGTAATATAAATATAAATATATTAAAAATAAAATA--TAAAATAT
1 TAATAATAAAAATATAAATATATTAAAAATAAAATATTTAAAATAT
3989887 TATAATAATA
Statistics
Matches: 130, Mismatches: 8, Indels: 40
0.73 0.04 0.22
Matches are distributed among these distances:
50 3 0.02
52 10 0.08
53 10 0.08
54 9 0.07
55 8 0.06
56 11 0.08
57 8 0.06
58 8 0.06
59 10 0.08
60 18 0.14
61 3 0.02
62 8 0.06
63 11 0.08
64 13 0.10
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (62 bp):
TAATAATAAAAATATAAATATATTAAAAATAAAATATTTAAAATATGATATTATATAAAAAT
Found at i:3989824 original size:112 final size:112
Alignment explanation
Indices: 3989643--3990316 Score: 1182
Period size: 112 Copynumber: 6.0 Consensus size: 112
3989633 TTAAAAAATG
3989643 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
3989708 AAAATATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
66 AAAA-ATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
*
3989756 AAAATAAAATATAAAATATTATAAAAATAAAT-AAAATAAAATATATGACATTAAAAATATATTT
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
* *
3989820 AAAATATGATATTATATAAAAATTAGTAATATAAATATAAATATATTA
66 AAAA-ATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
3989868 AAAATAAAATATAAAATATTATAATAATAAAT-AAAATAAAATATATGACATT-AAAATATATTT
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
3989931 AAGAAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
66 AA-AAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
*
3989979 AAAATAAAATATATAAA-ATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATT
1 AAAATAAAATATA-AAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATT
3990043 TAAAATATGATATTATATAAAAATTAATAAT-AAAATATAAATATATTA
65 TAAAA-ATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
*
3990091 AAAATAAAATAT-AAATATAATAATAATAAAT-AAAATAAAATATATGACATTAAAAATATATTT
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
3990154 AAAAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
66 AAAAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
*
3990201 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTT
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
3990266 AAGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTA
66 AA-AAATGATATTATATAAAAATTAATAAT-AAAAATATAAATATATTA
3990315 AA
1 AA
3990317 CTTATATTTT
Statistics
Matches: 539, Mismatches: 11, Indels: 21
0.94 0.02 0.04
Matches are distributed among these distances:
109 25 0.05
110 67 0.12
111 114 0.21
112 217 0.40
113 96 0.18
114 20 0.04
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.34
Consensus pattern (112 bp):
AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
AAAAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
Found at i:3989857 original size:21 final size:21
Alignment explanation
Indices: 3989833--3990239 Score: 101
Period size: 22 Copynumber: 19.5 Consensus size: 21
3989823 ATATGATATT
3989833 ATATAAAA-ATTAGTAATATAA
1 ATATAAAATATTA-TAATATAA
*
3989854 ATATAAATATATTA-AAAATAAA
1 ATATAAA-ATATTATAATAT-AA
3989876 ATATAAAATATTATAATAATAA
1 ATATAAAATATTATAAT-ATAA
3989898 ATAAAATAAAATA-TATGACAT-TAA
1 AT---ATAAAATATTAT-A-ATATAA
* * *
3989922 A-AT-ATAT-TTAAGAAATGATATT
1 ATATAAAATATT-A-TAAT-ATA-A
*
3989944 ATATAAAA-ATTAATAATAAAA
1 ATATAAAATATT-ATAATATAA
*
3989965 ATATAAATATATTA-AAAATAAA
1 ATATAAA-ATATTATAATAT-AA
3989987 ATATATAAA-ATTATAATAATAA
1 ATATA-AAATATTATAAT-ATAA
*
3990009 ATA-AAAATA--A-AATATATG
1 ATATAAAATATTATAATATA-A
*
3990027 ATATTAAAA-A-TAT-ATTTAA
1 ATA-TAAAATATTATAATATAA
** *
3990046 A-ATATGATATTAT-ATAAAA
1 ATATAAAATATTATAATATAA
3990065 AT-TAATAATA--A-AATATAA
1 ATATAA-AATATTATAATATAA
* *
3990083 ATATATTAAA-AATAAAATATAA
1 ATATA--AAATATTATAATATAA
3990105 ATATAATAATA--ATAA-ATAA
1 ATATAA-AATATTATAATATAA
3990124 A-ATAAAATA-TATGACAT-TAA
1 ATATAAAATATTAT-A-ATATAA
* * * *
3990144 AAAT-ATAT-TTAAAAATGATATT
1 ATATAAAATATT-ATAAT-ATA-A
*
3990166 ATATAAAA-ATTAATAATAAAA
1 ATATAAAATATT-ATAATATAA
*
3990187 ATATAAATATATTA-AAAATAAA
1 ATATAAA-ATATTATAATAT-AA
3990209 ATATAAAATATTATAATAATAA
1 ATATAAAATATTATAAT-ATAA
3990231 ATA-AAAATA
1 ATATAAAATA
3990240 AAATATATGA
Statistics
Matches: 291, Mismatches: 34, Indels: 122
0.65 0.08 0.27
Matches are distributed among these distances:
17 10 0.03
18 22 0.08
19 30 0.10
20 35 0.12
21 66 0.23
22 72 0.25
23 32 0.11
24 13 0.04
25 9 0.03
26 2 0.01
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
ATATAAAATATTATAATATAA
Found at i:3989929 original size:63 final size:65
Alignment explanation
Indices: 3989858--3990309 Score: 217
Period size: 68 Copynumber: 6.8 Consensus size: 65
3989848 ATATAAATAT
*
3989858 AAATATATTAA-AAATAAAATATAAAATATT-ATAATAATAAATAAAATAAAATATATGACATTA
1 AAATATATTAAGAAATAAAATATAAAATATTAATAATAATAAATAAAATAAAATATATGATATTA
* * *
3989921 AAATATATTTAAGAAATGATATTATATAAAA-ATTAATAATAAAAATATAAATATATTAAAAATA
1 AAATATA-TTAAGAAAT-A-A-AATATAAAATATTAATAATAATAA-ATAAA-ATA--AAATATA
**
3989985 AAATATATA
58 TGATAT-TA
* * * * * * *
3989994 AAATTATAATAATAAATAAAA-ATAAAATATATGATATTAA-AAATATATTTAAA-ATATGATAT
1 AAA-TATATTAAGAAATAAAATATAAAATAT-TAATAATAATAAATAAAATAAAATATATGATAT
3990056 TA
64 TA
* * *
3990058 TATAA-AAATTAA-TAATAAAATATAAATATATTAAAAATAA-AATATAAATATAATAATA-AT-
1 -A-AATATATTAAGAAATAAAATATAAA-ATATTAATAATAATAA-ATAAA-ATAA-AATATATG
*
3990118 A-AATA
60 ATATTA
* * * * * *
3990123 AAATAAAATATATGACATTAAAA-AT-ATAT-TTAAAAATGATATTATATAAAAATTAATAATA-
1 AAAT-ATAT-TAAGA-AATAAAATATAAAATATTAATAAT-A-A-TAAAT-AAAA-TAA-AATAT
**
3990184 AAAATA-T-
57 ATGATATTA
3990191 AAATATATTAA-AAATAAAATATAAAATATT-ATAATAATAAATAAAAATAAAATATATGATATT
1 AAATATATTAAGAAATAAAATATAAAATATTAATAATAATAAAT-AAAATAAAATATATGATATT
3990254 AA
65 -A
* *
3990256 AAATATATTTAAGAAATGATATTATATAAAA-ATTAATAATAAAAAATATAAATA
1 AAATATA-TTAAGAAAT-A-A-AATATAAAATATTAATAATAATAAATA-AAATA
3990310 TATTAAACTT
Statistics
Matches: 298, Mismatches: 42, Indels: 91
0.69 0.10 0.21
Matches are distributed among these distances:
61 4 0.01
62 7 0.02
63 26 0.09
64 40 0.13
65 41 0.14
66 26 0.09
67 22 0.07
68 43 0.14
69 22 0.07
70 33 0.11
71 8 0.03
72 10 0.03
73 12 0.04
74 4 0.01
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (65 bp):
AAATATATTAAGAAATAAAATATAAAATATTAATAATAATAAATAAAATAAAATATATGATATTA
Found at i:3990018 original size:24 final size:24
Alignment explanation
Indices: 3989954--3990021 Score: 70
Period size: 26 Copynumber: 2.8 Consensus size: 24
3989944 ATATAAAAAT
*
3989954 TAAT-AATAAAAATATAAA-TATAT
1 TAATAAATAAAAATA-AAATTATAA
3989977 TAA-AAATAAAATATATAAAATTATAA
1 TAATAAAT-AAA-A-ATAAAATTATAA
3990003 TAATAAATAAAAATAAAAT
1 TAATAAATAAAAATAAAAT
3990022 ATATGATATT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
23 6 0.16
24 10 0.26
25 5 0.13
26 13 0.34
27 4 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (24 bp):
TAATAAATAAAAATAAAATTATAA
Found at i:3990079 original size:5 final size:5
Alignment explanation
Indices: 3990071--3990132 Score: 54
Period size: 5 Copynumber: 11.8 Consensus size: 5
3990061 AAAAATTAAT
* * *
3990071 AATAA AATATA AATAT ATTAAA AATAA AATATA AATAT AATAA TAAT-A
1 AATAA AATA-A AATAA AAT-AA AATAA AATA-A AATAA AATAA -AATAA
3990119 AATAA AATAA AATA
1 AATAA AATAA AATA
3990133 TATGACATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
4 3 0.07
5 27 0.59
6 16 0.35
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (5 bp):
AATAA
Found at i:3990201 original size:23 final size:23
Alignment explanation
Indices: 3989944--3990040 Score: 94
Period size: 21 Copynumber: 4.2 Consensus size: 23
3989934 AAATGATATT
3989944 ATATAAA-A-ATTAATAATAAAA
1 ATATAAATATATTAATAATAAAA
*
3989965 ATATAAATATATTAAAAATAAAA
1 ATATAAATATATTAATAATAAAA
*
3989988 TATATAAAATTATAATAATAAATAAAA
1 -ATAT-AAA-TATATTAAT-AATAAAA
* *
3990015 ATA-AAATATA-TGATATTAAAA
1 ATATAAATATATTAATAATAAAA
3990036 ATATA
1 ATATA
3990041 TTTAAAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
21 16 0.25
22 5 0.08
23 16 0.25
24 7 0.11
25 3 0.05
26 10 0.16
27 7 0.11
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (23 bp):
ATATAAATATATTAATAATAAAA
Found at i:3990206 original size:23 final size:23
Alignment explanation
Indices: 3990166--3990247 Score: 82
Period size: 23 Copynumber: 3.5 Consensus size: 23
3990156 AAATGATATT
*
3990166 ATATAAA-A-ATTAATAATAAAA
1 ATATAAATATATTAAAAATAAAA
3990187 ATATAAATATATTAAAAAT-AAA
1 ATATAAATATATTAAAAATAAAA
3990209 ATATAAAATATTATAATAATAAATAAAA
1 ATAT-AAATA-TAT--TAA-AAATAAAA
3990237 ATA-AAATATAT
1 ATATAAATATAT
3990248 GATATTAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
21 7 0.13
22 8 0.15
23 13 0.25
24 3 0.06
25 3 0.06
26 8 0.15
27 4 0.08
28 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
ATATAAATATATTAAAAATAAAA
Found at i:3990224 original size:222 final size:223
Alignment explanation
Indices: 3989643--3990316 Score: 1205
Period size: 222 Copynumber: 3.0 Consensus size: 223
3989633 TTAAAAAATG
3989643 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
1 AAAATAAAATATAAAATATTATAATAATAAAT-AAAATAAAATATATGACATTAAAAATATATTT
3989708 AAAATATGATATTATATAAAAATTAATAATAAAAATATAAATATATTAAAAATAAAATATAAAAT
65 AAAA-ATGATATTATATAAAAATTAATAATAAAAATATAAATATATTAAAAATAAAATATAAAAT
* *
3989773 ATTATAAAAATAAAT-AAAATAAAATATATGACATTAAAAATATATTTAAAATATGATATTATAT
129 ATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAAATATGATATTATAT
*
3989837 AAAAATTAGTAATATAAATATAAATATATTA
194 AAAAATTAATAATA-AAATATAAATATATTA
3989868 AAAATAAAATATAAAATATTATAATAATAAATAAAATAAAATATATGACATT-AAAATATATTTA
1 AAAATAAAATATAAAATATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTA
3989932 AGAAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTAAAAATAAAATATATAAA-
66 A-AAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTAAAAATAAAATATA-AAAT
3989996 ATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAAATATGATATTATAT
129 ATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAAATATGATATTATAT
3990061 AAAAATTAATAATAAAATATAAATATATTA
194 AAAAATTAATAATAAAATATAAATATATTA
*
3990091 AAAATAAAATAT-AAATATAATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTA
1 AAAATAAAATATAAAATATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTA
3990155 AAAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTAAAAATAAAATATAAAATAT
66 AAAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTAAAAATAAAATATAAAATAT
3990220 TATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAA-ATGATATTATATA
131 TATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAA-AATATGATATTATATA
3990284 AAAATTAATAATAAAAAATATAAATATATTA
195 AAAATTAATAAT--AAAATATAAATATATTA
3990315 AA
1 AA
3990317 CTTATATTTT
Statistics
Matches: 437, Mismatches: 4, Indels: 17
0.95 0.01 0.04
Matches are distributed among these distances:
221 3 0.01
222 171 0.39
223 126 0.29
224 105 0.24
225 32 0.07
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.34
Consensus pattern (223 bp):
AAAATAAAATATAAAATATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTA
AAAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTAAAAATAAAATATAAAATAT
TATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAAATATGATATTATATAA
AAATTAATAATAAAATATAAATATATTA
Found at i:3990486 original size:15 final size:15
Alignment explanation
Indices: 3990466--3990519 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
3990456 TTTTCCCTGT
*
3990466 AATCACATTGCTTGC
1 AATCACATTACTTGC
3990481 AATCACATTACTTGC
1 AATCACATTACTTGC
* *
3990496 AATCACATTACCTGT
1 AATCACATTACTTGC
3990511 AATCACATT
1 AATCACATT
3990520 GCATTGTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (15 bp):
AATCACATTACTTGC
Found at i:3998817 original size:2 final size:2
Alignment explanation
Indices: 3998810--3998838 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3998800 GCTTGTTTTC
3998810 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3998839 TCAAGTGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3999428 original size:7 final size:7
Alignment explanation
Indices: 3999416--3999441 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3999406 GCTGACACTT
3999416 AATTTAA
1 AATTTAA
3999423 AATTTAA
1 AATTTAA
3999430 AATTTAA
1 AATTTAA
3999437 AATTT
1 AATTT
3999442 TTTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
AATTTAA
Found at i:4000852 original size:12 final size:12
Alignment explanation
Indices: 4000820--4000853 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4000810 AACCAGAGAG
*
4000820 CCAAAACCAAAA
1 CCAAAACCCAAA
4000832 CCAAAACCCAAA
1 CCAAAACCCAAA
*
4000844 CCCAAACCCA
1 CCAAAACCCA
4000854 GAATTAGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.44, G:0.00, T:0.00
Consensus pattern (12 bp):
CCAAAACCCAAA
Found at i:4005638 original size:3 final size:3
Alignment explanation
Indices: 4005630--4005657 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4005620 CTTTTGATGC
4005630 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4005658 AAAGATCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4012291 original size:3 final size:3
Alignment explanation
Indices: 4012283--4012314 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
4012273 ACAAAGGTAC
*
4012283 TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4012315 TTGGTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4014831 original size:14 final size:14
Alignment explanation
Indices: 4014812--4014844 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
4014802 TATATATATT
4014812 ATTAATAAAATTAA
1 ATTAATAAAATTAA
*
4014826 ATTAATAAATTTAA
1 ATTAATAAAATTAA
4014840 ATTAA
1 ATTAA
4014845 ACCATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATTAATAAAATTAA
Found at i:4020572 original size:21 final size:21
Alignment explanation
Indices: 4020546--4020599 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
4020536 TTCTCTCCTC
*
4020546 TTTTTTTAAAAACATGTATTT
1 TTTTTTTAAAAAAATGTATTT
*
4020567 TTTTTTTAAAAAAATTTATTT
1 TTTTTTTAAAAAAATGTATTT
* *
4020588 TTGTTTCAAAAA
1 TTTTTTTAAAAA
4020600 TATCCTCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTTTTAAAAAAATGTATTT
Found at i:4020869 original size:14 final size:14
Alignment explanation
Indices: 4020837--4020881 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 14
4020827 CAAACAATTT
4020837 ATTTATAAAAA-AA
1 ATTTATAAAAATAA
*
4020850 ACTTATAAAAATAA
1 ATTTATAAAAATAA
*
4020864 ATTTAT-TAAATAA
1 ATTTATAAAAATAA
4020877 ATTTA
1 ATTTA
4020882 ACTTAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 21 0.75
14 7 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTTATAAAAATAA
Found at i:4026600 original size:9 final size:8
Alignment explanation
Indices: 4026573--4026609 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
4026563 ACTCCATCTG
4026573 ATTTTAAA
1 ATTTTAAA
4026581 ATTTTAAA
1 ATTTTAAA
4026589 ATTTTAAA
1 ATTTTAAA
*
4026597 AATTTAACA
1 ATTTTAA-A
4026606 ATTT
1 ATTT
4026610 CTCATTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 22 0.85
9 4 0.15
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (8 bp):
ATTTTAAA
Found at i:4056820 original size:51 final size:51
Alignment explanation
Indices: 4056763--4056870 Score: 207
Period size: 51 Copynumber: 2.1 Consensus size: 51
4056753 ATAGGCACAA
4056763 ATTCAAATATGAAAACTCAAAACGAATTAAAGATATATTCAGCATTAACTT
1 ATTCAAATATGAAAACTCAAAACGAATTAAAGATATATTCAGCATTAACTT
4056814 ATTCAAATATGAAAACTCAAAACGAATTAAAGATATATTCAGCATTAACTT
1 ATTCAAATATGAAAACTCAAAACGAATTAAAGATATATTCAGCATTAACTT
*
4056865 ACTCAA
1 ATTCAA
4056871 GGCTGTCTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (51 bp):
ATTCAAATATGAAAACTCAAAACGAATTAAAGATATATTCAGCATTAACTT
Found at i:4067435 original size:21 final size:21
Alignment explanation
Indices: 4067409--4067458 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
4067399 CATGCACATA
4067409 TCAGCCACAATATACTACCTG
1 TCAGCCACAATATACTACCTG
* *
4067430 TTAGCCACAATATGCTACCTG
1 TCAGCCACAATATACTACCTG
4067451 TCAGCCAC
1 TCAGCCAC
4067459 CACTGGCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.34, G:0.12, T:0.24
Consensus pattern (21 bp):
TCAGCCACAATATACTACCTG
Found at i:4071757 original size:50 final size:49
Alignment explanation
Indices: 4071675--4071776 Score: 170
Period size: 50 Copynumber: 2.1 Consensus size: 49
4071665 ATTGTCTCAA
4071675 AGTCTGAACCATTTAAACCAAATTCCTCTTCTTGAACCTTCCAAGAAAG
1 AGTCTGAACCATTTAAACCAAATTCCTCTTCTTGAACCTTCCAAGAAAG
*
4071724 AGTCATGAACCATTTAAACC-AATTCCCTTTTCTTGAACCTTCCAAGAAAG
1 AGTC-TGAACCATTTAAACCAAATT-CCTCTTCTTGAACCTTCCAAGAAAG
4071774 AGT
1 AGT
4071777 AATATAGTGT
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
49 8 0.16
50 42 0.84
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.29
Consensus pattern (49 bp):
AGTCTGAACCATTTAAACCAAATTCCTCTTCTTGAACCTTCCAAGAAAG
Found at i:4079036 original size:30 final size:30
Alignment explanation
Indices: 4078986--4079051 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 30
4078976 AAAATCTATT
*
4078986 ATTATTAATATAAATTTTAAATATATTATATAA
1 ATTATTAATAT--ATTTTAAATATATT-TACAA
4079019 ATTATTAATAT-TTTTAAATATATTTACAA
1 ATTATTAATATATTTTAAATATATTTACAA
4079048 ATTA
1 ATTA
4079052 ATTTCATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 8 0.25
30 13 0.41
33 11 0.34
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (30 bp):
ATTATTAATATATTTTAAATATATTTACAA
Found at i:4080113 original size:14 final size:15
Alignment explanation
Indices: 4080079--4080128 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
4080069 AATAAATATT
*
4080079 TTTATAATTATGAATA
1 TTTATAATTATTAA-A
4080095 TTTAT-ATT-TTAAGA
1 TTTATAATTATTAA-A
4080109 TTTATAATTATTAAA
1 TTTATAATTATTAAA
4080124 TTTAT
1 TTTAT
4080129 TTATTGATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 9 0.30
15 12 0.40
16 9 0.30
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (15 bp):
TTTATAATTATTAAA
Found at i:4087907 original size:2 final size:2
Alignment explanation
Indices: 4087900--4087931 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4087890 CTTTCTTTCC
4087900 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
4087932 TTGTATGTTG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4092896 original size:16 final size:17
Alignment explanation
Indices: 4092875--4092908 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4092865 CCCTCTTATC
*
4092875 TTTCCTTTATTC-TAAT
1 TTTCCTTAATTCTTAAT
4092891 TTTCCTTAATTCTTAAT
1 TTTCCTTAATTCTTAAT
4092908 T
1 T
4092909 AATTACCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTCCTTAATTCTTAAT
Found at i:4106475 original size:2 final size:2
Alignment explanation
Indices: 4106468--4106506 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
4106458 CTTCAAAATC
4106468 CT CT CT CT CT CT CT CT CT CT C- 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 CT
4106507 ACTTTGATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:4106492 original size:21 final size:21
Alignment explanation
Indices: 4106466--4106506 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
4106456 AACTTCAAAA
4106466 TCCTCTCTCTCTCTCTCTCTC
1 TCCTCTCTCTCTCTCTCTCTC
4106487 TCCTCTCTCTCTCTCTCTCT
1 TCCTCTCTCTCTCTCTCTCT
4106507 ACTTTGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (21 bp):
TCCTCTCTCTCTCTCTCTCTC
Found at i:4115421 original size:14 final size:15
Alignment explanation
Indices: 4115393--4115427 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4115383 AATCTATTTT
4115393 TTTATATTTTAAAAA
1 TTTATATTTTAAAAA
* *
4115408 TTTATTTTTTAAAAT
1 TTTATATTTTAAAAA
4115423 TTTAT
1 TTTAT
4115428 GAAATATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATATTTTAAAAA
Found at i:4126341 original size:2 final size:2
Alignment explanation
Indices: 4126329--4126357 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4126319 TTCCCTCCAC
4126329 AT AT A- 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
4126358 TTCTGTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4146243 original size:81 final size:83
Alignment explanation
Indices: 4146100--4146265 Score: 255
Period size: 81 Copynumber: 2.0 Consensus size: 83
4146090 GAACAACTTG
* *
4146100 ACTCTGAAAAAAATAAGAGATAATCAAATATATATATATAATTTAAATAAATGAAGAATACAACC
1 ACTCTGAAAAAAATAAGAGATAATCAAATATATATATATAATTAAAATAAAAGAAGAATACAACC
* *
4146165 AGCGGACGGCCGGGATGT
66 AGCAGACGGCCGGGAGGT
* *
4146183 ACTCTGAAAAAAATATGAGATAATCAGATATATATA-A-AATTAAAATAAAAGAAGAATACAACC
1 ACTCTGAAAAAAATAAGAGATAATCAAATATATATATATAATTAAAATAAAAGAAGAATACAACC
*
4146246 AGCAGACGGCTGGGAGGT
66 AGCAGACGGCCGGGAGGT
4146264 AC
1 AC
4146266 GAGCCTGTGC
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
81 41 0.54
82 1 0.01
83 34 0.45
ACGTcount: A:0.49, C:0.12, G:0.17, T:0.21
Consensus pattern (83 bp):
ACTCTGAAAAAAATAAGAGATAATCAAATATATATATATAATTAAAATAAAAGAAGAATACAACC
AGCAGACGGCCGGGAGGT
Found at i:4152660 original size:1 final size:1
Alignment explanation
Indices: 4152654--4152703 Score: 82
Period size: 1 Copynumber: 50.0 Consensus size: 1
4152644 GTCAAAAGAA
* *
4152654 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGGGGGGAGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
4152704 TAATGAACGA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.04, C:0.00, G:0.96, T:0.00
Consensus pattern (1 bp):
G
Found at i:4156248 original size:15 final size:15
Alignment explanation
Indices: 4156228--4156259 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4156218 TAATGTTATA
4156228 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
4156243 ATTAAAATAAAATAT
1 ATTAAAATAAAAAAT
4156258 AT
1 AT
4156260 AATATAAGAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:4156320 original size:54 final size:50
Alignment explanation
Indices: 4156227--4156356 Score: 140
Period size: 54 Copynumber: 2.5 Consensus size: 50
4156217 GTAATGTTAT
* * *
4156227 AATTAAAAT--AAAAAATATTAAAATAAAATATATAATATAAG-AATCAGA
1 AATTAAAATAAAAAAAATATAAAAATAAAATATATAATATAAGTAA-AAAA
4156275 AATTAAAATAAAACAAAATATAAAAATTAAAATTTATATAATATAAGTAAAAAA
1 AATTAAAATAAAA-AAAATATAAAAA-TAAAA--TATATAATATAAGTAAAAAA
4156329 AATTAAAATAAAATATATAATATAAAAA
1 AATTAAAATAAAA-A-A-AATATAAAAA
4156357 ATTATATTAA
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
48 9 0.13
50 2 0.03
51 11 0.16
52 5 0.07
54 29 0.42
55 3 0.04
56 10 0.14
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (50 bp):
AATTAAAATAAAAAAAATATAAAAATAAAATATATAATATAAGTAAAAAA
Found at i:4156353 original size:14 final size:13
Alignment explanation
Indices: 4156326--4156402 Score: 50
Period size: 14 Copynumber: 5.7 Consensus size: 13
4156316 TATAAGTAAA
*
4156326 AAAAAT-TAAAAT
1 AAAAATATAATAT
4156338 AAAATATATAATAT
1 AAAA-ATATAATAT
*
4156352 AAAAA-ATTATATT
1 AAAAATATAATA-T
* *
4156365 AAAAAAATGAAAAT
1 AAAAATAT-AATAT
*
4156379 AAAATATATGATATT
1 AAAA-ATATAATA-T
4156394 AAAAATATA
1 AAAAATATA
4156403 TCTAAGAGAT
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
12 9 0.18
13 9 0.18
14 22 0.44
15 10 0.20
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
AAAAATATAATAT
Found at i:4156357 original size:30 final size:33
Alignment explanation
Indices: 4156282--4156357 Score: 84
Period size: 33 Copynumber: 2.2 Consensus size: 33
4156272 AGAAATTAAA
4156282 ATAAAACAAAATATAAAAATTAAAATTTATATAAT
1 ATAAAA-AAAATATAAAAATTAAAA-TTATATAAT
* *
4156317 ATAAGTAAAAAAAATTAAAA-TAAAA-TATATAAT
1 ATAA--AAAAAATATAAAAATTAAAATTATATAAT
4156350 ATAAAAAA
1 ATAAAAAA
4156358 TTATATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
31 4 0.11
33 12 0.32
35 9 0.24
36 10 0.27
37 2 0.05
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (33 bp):
ATAAAAAAAATATAAAAATTAAAATTATATAAT
Found at i:4156369 original size:41 final size:40
Alignment explanation
Indices: 4156324--4156403 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 40
4156314 AATATAAGTA
*
4156324 AAAAAAATTAAAATAAAATATATAATATAAAAAATTATATT
1 AAAAAAATGAAAATAAAATATATAATATAAAAAA-TATATT
* *
4156365 AAAAAAATGAAAATAAAATATATGATATTAAAAATATAT
1 AAAAAAATGAAAATAAAATATATAATATAAAAAATATAT
4156404 CTAAGAGATA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 5 0.14
41 31 0.86
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (40 bp):
AAAAAAATGAAAATAAAATATATAATATAAAAAATATATT
Found at i:4156370 original size:29 final size:29
Alignment explanation
Indices: 4156338--4156403 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
4156328 AAATTAAAAT
*
4156338 AAAATATATAATATAAAA-A-ATTATATTA
1 AAAATATATAA-ATAAAATATATGATATTA
*
4156366 AAAAAATGA-AAATAAAATATATGATATTA
1 AAAATAT-ATAAATAAAATATATGATATTA
4156395 AAAATATAT
1 AAAATATAT
4156404 CTAAGAGATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
27 6 0.19
28 10 0.32
29 15 0.48
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (29 bp):
AAAATATATAAATAAAATATATGATATTA
Found at i:4172334 original size:2 final size:2
Alignment explanation
Indices: 4172329--4172358 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4172319 GCGCGGGGTG
*
4172329 GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4172359 TAGAAAGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4175209 original size:16 final size:16
Alignment explanation
Indices: 4175190--4175220 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4175180 TGATTCTATT
*
4175190 AAATTATGTTATAATC
1 AAATTATGATATAATC
4175206 AAATTATGATATAAT
1 AAATTATGATATAAT
4175221 TATGTTAGAT
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:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (16 bp):
AAATTATGATATAATC
Found at i:4175558 original size:16 final size:16
Alignment explanation
Indices: 4175537--4175570 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
4175527 CTTTGTACAT
*
4175537 GTATGAGAATAGGAAA
1 GTATGAAAATAGGAAA
4175553 GTATGAAAATAGGAAA
1 GTATGAAAATAGGAAA
4175569 GT
1 GT
4175571 TTGCACAAGA
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:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (16 bp):
GTATGAAAATAGGAAA
Found at i:4178928 original size:23 final size:23
Alignment explanation
Indices: 4178902--4178948 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
4178892 CATGCTAATA
*
4178902 GAATTTTAATTTATAATAAATGT
1 GAATTTTAATTCATAATAAATGT
* *
4178925 GAATTTTGATTCATAATGAATGT
1 GAATTTTAATTCATAATAAATGT
4178948 G
1 G
4178949 CACTCTTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.45
Consensus pattern (23 bp):
GAATTTTAATTCATAATAAATGT
Found at i:4180651 original size:24 final size:23
Alignment explanation
Indices: 4180614--4180660 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
4180604 ATAATTTATG
4180614 AATTATAATTATAAAATATATTC
1 AATTATAATTATAAAATATATTC
*
4180637 AATTATTACTTATAAAATATATTC
1 AATTA-TAATTATAAAATATATTC
4180661 CCCATTCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTATAATTATAAAATATATTC
Found at i:4184340 original size:2 final size:2
Alignment explanation
Indices: 4184333--4184362 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4184323 CTGATTCAAG
4184333 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
4184363 TAAATTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4190819 original size:16 final size:16
Alignment explanation
Indices: 4190789--4190841 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
4190779 AGTTATACGG
* *
4190789 ATTTAAATCAATTTAA
1 ATTTAGATCATTTTAA
* *
4190805 ATTTTGATTATTTTAA
1 ATTTAGATCATTTTAA
4190821 ATTTAGATCATTTTAA
1 ATTTAGATCATTTTAA
*
4190837 GTTTA
1 ATTTA
4190842 AGTTAGATGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.53
Consensus pattern (16 bp):
ATTTAGATCATTTTAA
Found at i:4191268 original size:141 final size:143
Alignment explanation
Indices: 4190941--4191341 Score: 592
Period size: 141 Copynumber: 2.8 Consensus size: 143
4190931 TTATAGTTGG
* * *
4190941 ATAATTTCACTTGACCTATTACTGTTCTTTAAAATTTCGTATACGACTTTAAAATTTTGTTGAAT
1 ATAATTTCACTTGACCTATTAATGTTCTTTAAAATTTCGTACATGACTTTAAAATTTTGTTGAAT
* *
4191006 TATCTACGAAGATAATTCATTTTAATTTCTATATTAATAGTGTGTAAGACTTATAAGGATAATTT
66 TATCTACGAAGATAATTCATTTTAATTTCTATATTAATAATGTGTAAGACTTACAAGGATAATTT
4191071 CATTGAATTATCA
131 CATTGAATTATCA
* * * * * *
4191084 ATAATTTCACTTGGCCTATTAATGTTATTTAAAATTTCATACATGATTTTAAAATTTCGTTAAAT
1 ATAATTTCACTTGACCTATTAATGTTCTTTAAAATTTCGTACATGACTTTAAAATTTTGTTGAAT
* * **
4191149 TATCTATGAAGATAATTCATTTTAA-TTCTATATTAATAATGTGTAAGACTTGCATTGATAA-TT
66 TATCTACGAAGATAATTCATTTTAATTTCTATATTAATAATGTGTAAGACTTACAAGGATAATTT
*
4191212 CCTTGAATTATCA
131 CATTGAATTATCA
* **
4191225 ATAATTTCACTTGACCTATTAATGTTCTTTAAAGTTTCGTACATGACTCCAAAATTTTGTTGAAT
1 ATAATTTCACTTGACCTATTAATGTTCTTTAAAATTTCGTACATGACTTTAAAATTTTGTTGAAT
* *
4191290 TATCTACGAAAATAATT-ATTTTAATTTCTATATTAATAATATGTAAGACTTA
66 TATCTACGAAGATAATTCATTTTAATTTCTATATTAATAATGTGTAAGACTTA
4191342 TATACGGATA
Statistics
Matches: 228, Mismatches: 29, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
140 7 0.03
141 110 0.48
142 31 0.14
143 80 0.35
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.44
Consensus pattern (143 bp):
ATAATTTCACTTGACCTATTAATGTTCTTTAAAATTTCGTACATGACTTTAAAATTTTGTTGAAT
TATCTACGAAGATAATTCATTTTAATTTCTATATTAATAATGTGTAAGACTTACAAGGATAATTT
CATTGAATTATCA
Found at i:4203195 original size:2 final size:2
Alignment explanation
Indices: 4203188--4203212 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4203178 GAATTTCATC
4203188 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4203213 GCTCATAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4206794 original size:30 final size:30
Alignment explanation
Indices: 4206758--4206821 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
4206748 AATTAAATTC
*
4206758 TTATACTTTCATTTTGAATCATATAAGTTT
1 TTATACTTTCATTTTGAATCAAATAAGTTT
* * *
4206788 TTATACTTTTATTTTTAATTAAATAAGTTT
1 TTATACTTTCATTTTGAATCAAATAAGTTT
4206818 TTAT
1 TTAT
4206822 TACTAATGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.06, G:0.05, T:0.58
Consensus pattern (30 bp):
TTATACTTTCATTTTGAATCAAATAAGTTT
Found at i:4207666 original size:17 final size:17
Alignment explanation
Indices: 4207636--4207673 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
4207626 ACGCTCTCAA
4207636 TCTCTTCCCTTCTTCTC
1 TCTCTTCCCTTCTTCTC
4207653 TCTCTGTCCC-TCTTCTC
1 TCTCT-TCCCTTCTTCTC
4207670 TCTC
1 TCTC
4207674 CACACCGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (17 bp):
TCTCTTCCCTTCTTCTC
Found at i:4207974 original size:39 final size:38
Alignment explanation
Indices: 4207909--4207982 Score: 94
Period size: 39 Copynumber: 1.9 Consensus size: 38
4207899 TCGTCTGTGG
* *
4207909 AAAATGCAATTGGGTTTTCGAATTTAGAGGTGAAAAGTA
1 AAAATGCAAATGGGTTTTCGAATTTAG-GGGGAAAAGTA
* * *
4207948 AAAATTCAAATGGGTTTTCTAGTTTAGGGGGAAAA
1 AAAATGCAAATGGGTTTTCGAATTTAGGGGGAAAA
4207983 AAAGAAGATC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 7 0.23
39 23 0.77
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (38 bp):
AAAATGCAAATGGGTTTTCGAATTTAGGGGGAAAAGTA
Found at i:4209618 original size:23 final size:25
Alignment explanation
Indices: 4209592--4209638 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
4209582 ACTCTCCATT
4209592 TTCC-AAAA-ACCCTACGATTCCTA
1 TTCCAAAAATACCCTACGATTCCTA
4209615 TTCCATAAAATACCCTACGATTCC
1 TTCCA-AAAATACCCTACGATTCC
4209639 CGGAAAACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
25 4 0.19
26 13 0.62
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.28
Consensus pattern (25 bp):
TTCCAAAAATACCCTACGATTCCTA
Found at i:4219637 original size:12 final size:12
Alignment explanation
Indices: 4219599--4219644 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
4219589 TTTATGCTAC
4219599 TATTTTTGCTTGA
1 TATTTTTGCTT-A
*
4219612 -ACTTTTGCTT-
1 TATTTTTGCTTA
4219622 TATTTTTGCTTA
1 TATTTTTGCTTA
4219634 TATTGTTTGCT
1 TATT-TTTGCT
4219645 CTCTTGAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 9 0.32
12 13 0.46
13 6 0.21
ACGTcount: A:0.13, C:0.11, G:0.13, T:0.63
Consensus pattern (12 bp):
TATTTTTGCTTA
Found at i:4226541 original size:28 final size:29
Alignment explanation
Indices: 4226503--4226557 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
4226493 TTATTAAAAA
4226503 ATTTAAATAAATTTTTAT-TTTTTATTAT
1 ATTTAAATAAATTTTTATATTTTTATTAT
*
4226531 ATTTAATTAAATTTTTATATTTTTATT
1 ATTTAAATAAATTTTTATATTTTTATT
4226558 TTAAGTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
ATTTAAATAAATTTTTATATTTTTATTAT
Found at i:4233320 original size:2 final size:2
Alignment explanation
Indices: 4233313--4233344 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4233303 CTTACCTTTA
4233313 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
4233345 CCATTTTATT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4233764 original size:20 final size:19
Alignment explanation
Indices: 4233728--4233770 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
4233718 AAGTAATGAG
*
4233728 TTTTCTTTGTTTTTATTTAC
1 TTTTCTTTGTTTATATTT-C
4233748 TTTTCCTTT-TTTATATTTC
1 TTTT-CTTTGTTTATATTTC
4233767 TTTT
1 TTTT
4233771 GCATATTCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 12 0.57
21 4 0.19
ACGTcount: A:0.09, C:0.12, G:0.02, T:0.77
Consensus pattern (19 bp):
TTTTCTTTGTTTATATTTC
Found at i:4244244 original size:13 final size:13
Alignment explanation
Indices: 4244226--4244250 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4244216 TTTAAATAAC
4244226 AAAATAAATAAAA
1 AAAATAAATAAAA
4244239 AAAATAAATAAA
1 AAAATAAATAAA
4244251 CAAGTCCTCT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAATAAATAAAA
Found at i:4251606 original size:24 final size:25
Alignment explanation
Indices: 4251525--4251608 Score: 95
Period size: 22 Copynumber: 3.4 Consensus size: 25
4251515 TTATTCGATT
4251525 TTTAAATATTAATAATCTATAATTTAA
1 TTTAAATATTAATAAT-T-TAATTTAA
* *
4251552 TTGAAATATTAATCA-TTAATTT--
1 TTTAAATATTAATAATTTAATTTAA
*
4251574 TTTAAATATTAAT-ATTTTATTTAA
1 TTTAAATATTAATAATTTAATTTAA
4251598 TTTAAATATTA
1 TTTAAATATTA
4251609 TTAGGATTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
21 1 0.02
22 18 0.36
24 17 0.34
25 1 0.02
27 13 0.26
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (25 bp):
TTTAAATATTAATAATTTAATTTAA
Found at i:4251634 original size:108 final size:104
Alignment explanation
Indices: 4251511--4251809 Score: 348
Period size: 106 Copynumber: 2.8 Consensus size: 104
4251501 TATATGATTA
** * * * * **
4251511 TTTTTTATTCGATTTTTAAATATTAATAATCTATAATTTAATTGAAATATTAATCATTAATTTTT
1 TTTTTTATTTTATTTTTAAATATTAATAAT-TATAATTTATTTAAAATATTAATAATTGATAATT
4251576 TAAATATTAATATTTTATT-TAATTTAAATATTATTAGGAT
65 TAAATATTAATATTTTATTATAATTTAAATATTATTAGG-T
*
4251616 TAAATTTTTATTTTATTTTTAAATATTAATAATTAATACTTTATTTAAAATATTAATAATTGATA
1 T---TTTTTATTTTATTTTTAAATATTAATAATT-ATAATTTATTTAAAATATTAATAATTGATA
* * * *
4251681 ATTTAATTATTAATATTTTATATATAATTTAACTGTTATTATGT
62 ATTTAAATATTAATATTTTAT-TATAATTTAAATATTATTAGGT
* * ** * *
4251725 TTATTTATTTTATTTTCAAATAGAAATAATTTATAATTTATTTTAAATATTAATAATTGATCATT
1 TTTTTTATTTTATTTTTAAATATTAATAA-TTATAATTTATTTAAAATATTAATAATTGATAATT
4251790 TAAATATTAATATTTTATTA
65 TAAATATTAATATTTTATTA
4251810 GAAGTTAGAA
Statistics
Matches: 166, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
105 3 0.02
106 71 0.43
107 3 0.02
108 70 0.42
109 3 0.02
110 16 0.10
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (104 bp):
TTTTTTATTTTATTTTTAAATATTAATAATTATAATTTATTTAAAATATTAATAATTGATAATTT
AAATATTAATATTTTATTATAATTTAAATATTATTAGGT
Found at i:4251673 original size:27 final size:28
Alignment explanation
Indices: 4251627--4251685 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
4251617 AAATTTTTAT
* *
4251627 TTTATTTTTAAATATTAATAATTAATAC
1 TTTATTTTAAAATATTAATAATTAATAA
*
4251655 TTTA-TTTAAAATATTAATAATTGATAA
1 TTTATTTTAAAATATTAATAATTAATAA
4251682 TTTA
1 TTTA
4251686 ATTATTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (28 bp):
TTTATTTTAAAATATTAATAATTAATAA
Found at i:4251768 original size:28 final size:27
Alignment explanation
Indices: 4251733--4251791 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
4251723 GTTTATTTAT
*
4251733 TTTATTTTCAAATAGAAATAATTTATAA
1 TTTATTTT-AAATAGAAATAATTGATAA
** *
4251761 TTTATTTTAAATATTAATAATTGATCA
1 TTTATTTTAAATAGAAATAATTGATAA
4251788 TTTA
1 TTTA
4251792 AATATTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.51
Consensus pattern (27 bp):
TTTATTTTAAATAGAAATAATTGATAA
Found at i:4265492 original size:27 final size:27
Alignment explanation
Indices: 4265462--4265772 Score: 98
Period size: 27 Copynumber: 10.9 Consensus size: 27
4265452 TAAATAGTCC
4265462 ATTATTAATATTTAAAATAAATTATAA
1 ATTATTAATATTTAAAATAAATTATAA
**
4265489 ATTATTAATATTTAAAAAATAAAAAAATAA
1 ATTATTAATATTT--AAAAT-AAATTATAA
*** * *
4265519 ATTAAGCATA-ATAACATTTAAATTATAA
1 ATTATTAATATTTAA-A-ATAAATTATAA
* * *
4265547 A-TA-AAATA-CTAATAATTAAATTATCA
1 ATTATTAATATTTAA-AA-TAAATTATAA
* * *
4265573 ATTAGTCATATTTTAAATAAATTATAA
1 ATTATTAATATTTAAAATAAATTATAA
* *
4265600 ATTATTAATA-TTAAAATTTAATTAAATA
1 ATTATTAATATTTAAAA-TAAATTATA-A
* ***
4265628 ATCATAATAATATTTCCCTTATAAA-TA-AA
1 AT--TATTAATATTT--AAAATAAATTATAA
* *
4265657 A-TATTAATATTTTAAAATGTTAATGATTAA
1 ATTATTAATA-TTTAAAA--TAAATTA-TAA
* * *
4265687 GTTATAAATAAGATGTTAATAATTAAATTATCA
1 ATTAT---TAATAT-TTAA-AA-TAAATTATAA
* * *
4265720 ATTATTAATGTTTTAAATAAATTATCA
1 ATTATTAATATTTAAAATAAATTATAA
4265747 ATTATTAATATTTAAAAATTAAATTA
1 ATTATTAATATTT-AAAA-TAAATTA
4265773 AATTAAATTA
Statistics
Matches: 206, Mismatches: 48, Indels: 58
0.66 0.15 0.19
Matches are distributed among these distances:
25 1 0.00
26 29 0.14
27 71 0.34
28 23 0.11
29 21 0.10
30 28 0.14
31 7 0.03
32 3 0.01
33 8 0.04
34 13 0.06
35 2 0.01
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (27 bp):
ATTATTAATATTTAAAATAAATTATAA
Found at i:4265707 original size:147 final size:156
Alignment explanation
Indices: 4265539--4265901 Score: 467
Period size: 147 Copynumber: 2.4 Consensus size: 156
4265529 ATAACATTTA
** * *
4265539 AATTATAAATAAAATACTAATAATTAAATTATCAATTAGTCATATTTTAAATAAATTATAAATTA
1 AATTATAAATAAAATGTTAATAATTAAATTATCAATTATTAATATTTTAAATAAATTATAAATTA
** *
4265604 TTAATA-TT-AAAA-T-TT-AATTAAA-T-A-A-TCATAATAATATTTCCCTTATAAATAAAATA
66 TTAATATTTAAAAATTATTAAATTAAATTAATAGTCATAATAATATTTCAATTATAAACAAAATA
*
4265660 TTAATATTTT-AAAATGTTAATGATT
131 TTAATATTTTAAAAATATTAATGATT
* * *
4265685 AAGTTATAAATAAGATGTTAATAATTAAATTATCAATTATTAATGTTTTAAATAAATTATCAATT
1 AA-TTATAAATAAAATGTTAATAATTAAATTATCAATTATTAATATTTTAAATAAATTATAAATT
4265750 ATTAATATTTAAAAATTAAATTAAATTAAATTAAATAGTCATAATAATATTTCAATTATAAACAA
65 ATTAATATTTAAAAATT--ATTAAATTAAATT-AATAGTCATAATAATATTTCAATTATAAACAA
4265815 AATATTAATATTTTAAAAATATTAATGATT
127 AATATTAATATTTTAAAAATATTAATGATT
* * * *
4265845 ACATTATAAATAAAATGTTAATAACTAAATGATCTATTATTAATATTTAAAAATAAA
1 A-ATTATAAATAAAATGTTAATAATTAAATTATCAATTATTAATATTT-TAAATAAA
4265902 ATAAAATAAA
Statistics
Matches: 184, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
146 2 0.01
147 62 0.34
148 2 0.01
149 4 0.02
150 1 0.01
153 2 0.01
154 7 0.04
155 1 0.01
157 1 0.01
158 1 0.01
159 38 0.21
160 55 0.30
161 8 0.04
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (156 bp):
AATTATAAATAAAATGTTAATAATTAAATTATCAATTATTAATATTTTAAATAAATTATAAATTA
TTAATATTTAAAAATTATTAAATTAAATTAATAGTCATAATAATATTTCAATTATAAACAAAATA
TTAATATTTTAAAAATATTAATGATT
Found at i:4265839 original size:127 final size:121
Alignment explanation
Indices: 4265708--4266150 Score: 394
Period size: 127 Copynumber: 3.6 Consensus size: 121
4265698 GATGTTAATA
* * *
4265708 ATTAA-ATTATCAATTAT-TAATGTTTTAAATAAATTATCAATTATTAATATTTAAAAATTAAAT
1 ATTAAGATTA-CAATTATATAATATTTTAAATAAATGATCAATTATTAATATTTAAAAA-TAAAA
* * *
4265771 TAAATTAAATTAAATAGTCATAATAATATTTCAATTATAAACAAAATATTAATATTTTAAAAAT
64 TAAAATAAA--AAATA-TCATAATAATATTT-AAAT-TAAATAAAATATTAATATTTT-AAAAT
* * *
4265835 ATTAATGATTAC-ATTATAAATAAAATGTTAATAACTAAATGATCTATTATTAATATTTAAAAAT
1 ATTAA-GATTACAATTAT--ATAATAT-TT--TAAATAAATGATCAATTATTAATATTTAAAAAT
* *
4265899 AAAATAAAATAAAAAGTAATCATAATAATATTTAAATTAAATTAAATATTAATATTTTAAAAT
60 AAAATAAAATAAAAAAT-ATCATAATAATATTTAAATTAAATAAAATATTAATATTTTAAAAT
* * * *
4265962 ATTAATGATTA-AATTATAAATAAAATATTAATATTTTAATGATCTATTATTAATATTTAAAAAT
1 ATTAA-GATTACAATTAT--ATAATATTTTAA-A--TAAATGATCAATTATTAATATTTAAAAAT
* *
4266026 AAAATAAAAGAAAAAA-ATCATAGTAATATTTAAATTAAATAAAATATTAATATTTT---A-
60 AAAATAAAATAAAAAATATCATAATAATATTTAAATTAAATAAAATATTAATATTTTAAAAT
* * *
4266083 ATT---A-T-CAATTAT-TAATATTTTTAATAAATTATCATTTATTAATATTTAAAAAATAAAAT
1 ATTAAGATTACAATTATATAATATTTTAAATAAATGATCAATTATTAATATTT-AAAAATAAAAT
4266142 AAATATAAA
65 AAA-ATAAA
4266151 TATTTATATA
Statistics
Matches: 274, Mismatches: 26, Indels: 47
0.79 0.07 0.14
Matches are distributed among these distances:
110 19 0.07
111 14 0.05
112 5 0.02
113 8 0.03
116 7 0.03
117 1 0.00
121 3 0.01
122 1 0.00
124 3 0.01
125 38 0.14
126 1 0.00
127 82 0.30
128 20 0.07
129 7 0.03
130 21 0.08
131 3 0.01
132 12 0.04
133 29 0.11
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (121 bp):
ATTAAGATTACAATTATATAATATTTTAAATAAATGATCAATTATTAATATTTAAAAATAAAATA
AAATAAAAAATATCATAATAATATTTAAATTAAATAAAATATTAATATTTTAAAAT
Found at i:4265940 original size:160 final size:156
Alignment explanation
Indices: 4265536--4265946 Score: 412
Period size: 160 Copynumber: 2.6 Consensus size: 156
4265526 ATAATAACAT
* ** * * * * *
4265536 TTAAATTATAAATAAAATACTAATAATTAAATTATCAATTAGTCATATTTTAAATAAAT-T---A
1 TTAAGTTATAAATAAAATGTTAATAACTAAATGATCAATTATTAATATTTAAAATAAATATAAAA
* * ** *
4265597 T--AAAT-TAT--TAATATTAAAATTTAATTAAATAATCATAATAATATTTCCCTTATAAATAAA
66 TAAAAATATATAATAATATTTAAATTAAATTAAATAATCATAATAATATTTCAATTATAAACAAA
*
4265657 ATATTAATATTTTAAAATGTTAATGA
131 ATATTAATATTTTAAAATATTAATGA
* * * * * *
4265683 TTAAGTTATAAATAAGATGTTAATAATTAAATTATCAATTATTAATGTTTTAAATAAATTATCAA
1 TTAAGTTATAAATAAAATGTTAATAACTAAATGATCAATTATTAATATTTAAAATAAA-TATAAA
* ** * * * *
4265748 TTATTAATATTTAAAAATTAAATTAAATTAAATTAAATAGTCATAATAATATTTCAATTATAAAC
65 ATAAAAATATATAATAA-T-ATTTAAATTAAATTAAATAATCATAATAATATTTCAATTATAAAC
4265813 AAAATATTAATATTTTAAAAATATTAATGA
128 AAAATATTAATATTTT-AAAATATTAATGA
*
4265843 TTACA-TTATAAATAAAATGTTAATAACTAAATGATCTATTATTAATATTTAAAAATAAA-ATAA
1 TTA-AGTTATAAATAAAATGTTAATAACTAAATGATCAATTATTAATATTT-AAAATAAATATAA
4265906 AATAAAAAGTAATCATAATAATATTTAAATTAAATTAAATA
64 AATAAAAA-T-AT-ATAATAATATTTAAATTAAATTAAATA
4265947 TTAATATTTT
Statistics
Matches: 214, Mismatches: 32, Indels: 23
0.80 0.12 0.09
Matches are distributed among these distances:
147 51 0.24
148 1 0.00
149 1 0.00
152 1 0.00
154 3 0.01
155 2 0.01
157 2 0.01
158 1 0.00
159 62 0.29
160 74 0.35
161 11 0.05
162 5 0.02
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.41
Consensus pattern (156 bp):
TTAAGTTATAAATAAAATGTTAATAACTAAATGATCAATTATTAATATTTAAAATAAATATAAAA
TAAAAATATATAATAATATTTAAATTAAATTAAATAATCATAATAATATTTCAATTATAAACAAA
ATATTAATATTTTAAAATATTAATGA
Found at i:4266080 original size:24 final size:22
Alignment explanation
Indices: 4266049--4266102 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
4266039 AAAATCATAG
4266049 TAATATTTAAATTAAATAAAATAT
1 TAATATTTAAATT--ATAAAATAT
* * *
4266073 TAATATTTTAATTATCAATTAT
1 TAATATTTAAATTATAAAATAT
4266095 TAATATTT
1 TAATATTT
4266103 TTAATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 15 0.56
24 12 0.44
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATATTTAAATTATAAAATAT
Found at i:4269089 original size:21 final size:21
Alignment explanation
Indices: 4269064--4269105 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4269054 TTTTCATTCA
4269064 AAATTTAGCATGACCTATCTC
1 AAATTTAGCATGACCTATCTC
4269085 AAATTTAGCATGACCTATCTC
1 AAATTTAGCATGACCTATCTC
4269106 TTTTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (21 bp):
AAATTTAGCATGACCTATCTC
Found at i:4269116 original size:2 final size:2
Alignment explanation
Indices: 4269109--4269135 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4269099 CTATCTCTTT
4269109 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4269136 CAAGGCATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4283387 original size:2 final size:2
Alignment explanation
Indices: 4283380--4283409 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4283370 ATCGATTGTT
4283380 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4283410 CATAAAGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4295793 original size:20 final size:18
Alignment explanation
Indices: 4295756--4295794 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
4295746 TTATTAACGC
*
4295756 AATGATAATATTTGATTT
1 AATGATAATATTAGATTT
4295774 AATGATAATATATAGAATTT
1 AATGATAATAT-TAG-ATTT
4295794 A
1 A
4295795 TTTATTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 2 0.11
20 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (18 bp):
AATGATAATATTAGATTT
Found at i:4297437 original size:2 final size:2
Alignment explanation
Indices: 4297430--4297458 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4297420 TGGTTGAGAA
4297430 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 A
4297459 GTCAGATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4302891 original size:12 final size:12
Alignment explanation
Indices: 4302874--4302899 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4302864 AAATTTTATA
4302874 AATTTTTTAATT
1 AATTTTTTAATT
4302886 AATTTTTTAATT
1 AATTTTTTAATT
4302898 AA
1 AA
4302900 AAAAGAGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
AATTTTTTAATT
Found at i:4302988 original size:24 final size:21
Alignment explanation
Indices: 4302944--4302992 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
4302934 TTATTTTCTT
* *
4302944 TTTTTAAAAAATATAATAATAA
1 TTTTTAAAAAATAAAAAAAT-A
4302966 TTTTTAAAATTAATAAAAAAATA
1 TTTTTAAAA--AATAAAAAAATA
4302989 TTTT
1 TTTT
4302993 AATATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 9 0.39
23 5 0.22
24 9 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTTTAAAAAATAAAAAAATA
Found at i:4303192 original size:45 final size:45
Alignment explanation
Indices: 4303128--4303216 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
4303118 AAATGATGTC
* *
4303128 ACACATTATATATACTAGAAATGAATTAATGCTTATGACTCTTGA
1 ACACATTATACATACTAGAAATGAATTAATGCTTATAACTCTTGA
4303173 ACACATTATACATACTAGAAATGAATTAATGCTTATAACTCTTG
1 ACACATTATACATACTAGAAATGAATTAATGCTTATAACTCTTG
4303217 CGTGATTCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (45 bp):
ACACATTATACATACTAGAAATGAATTAATGCTTATAACTCTTGA
Found at i:4305022 original size:16 final size:17
Alignment explanation
Indices: 4304997--4305039 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
4304987 TTATTTTGTT
4304997 TTAATGTTATAAAAATTA
1 TTAAT-TTATAAAAATTA
4305015 -TAATTTAT-AAAATTA
1 TTAATTTATAAAAATTA
4305030 TTAA-TTATAA
1 TTAATTTATAA
4305040 TATATATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 11 0.48
16 8 0.35
17 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TTAATTTATAAAAATTA
Found at i:4310698 original size:29 final size:28
Alignment explanation
Indices: 4310657--4310724 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 28
4310647 AAAATTATAC
*
4310657 TAAATTTTTATTTTT-TATTATATTTAA
1 TAAATTTTTATTTTTATATTATATTAAA
*
4310684 TCAAATTTTATATTTTTATTTTATATTAAA
1 T-AAATTTT-TATTTTTATATTATATTAAA
4310714 TAAATTTTTAT
1 TAAATTTTTAT
4310725 AATTAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 1 0.03
28 10 0.28
29 14 0.39
30 11 0.31
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (28 bp):
TAAATTTTTATTTTTATATTATATTAAA
Found at i:4310723 original size:30 final size:28
Alignment explanation
Indices: 4310657--4310725 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 28
4310647 AAAATTATAC
*
4310657 TAAATTTTTAT-TTTTTATTATATTTAA
1 TAAATTTTTATATTTTTATTATATTAAA
4310684 TCAAA-TTTTATATTTTTATTTTATATTAAA
1 T-AAATTTTTATATTTTTA--TTATATTAAA
4310714 TAAATTTTTATA
1 TAAATTTTTATA
4310726 ATTAATAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
27 7 0.19
28 9 0.25
29 3 0.08
30 17 0.47
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (28 bp):
TAAATTTTTATATTTTTATTATATTAAA
Found at i:4312538 original size:2 final size:2
Alignment explanation
Indices: 4312533--4312577 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
4312523 AAACATGTCT
* *
4312533 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4312575 TA T
1 TA T
4312578 GTTTGTGTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4318399 original size:14 final size:14
Alignment explanation
Indices: 4318380--4318411 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
4318370 TTCTCCAATT
4318380 TCATCTTCTTCTTC
1 TCATCTTCTTCTTC
4318394 TCATCTTCTTCTTC
1 TCATCTTCTTCTTC
4318408 -CATC
1 TCATC
4318412 AAAATTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.09, C:0.38, G:0.00, T:0.53
Consensus pattern (14 bp):
TCATCTTCTTCTTC
Found at i:4319843 original size:31 final size:31
Alignment explanation
Indices: 4319808--4319888 Score: 137
Period size: 31 Copynumber: 2.6 Consensus size: 31
4319798 TCAATCCAAA
4319808 CTATCAATTCGAAAATTTAAACCGACCTAAC
1 CTATCAATTCGAAAATTTAAACCGACCTAAC
* *
4319839 CTATCAATTCGAAAATTGAAACCTACCTAAC
1 CTATCAATTCGAAAATTTAAACCGACCTAAC
4319870 CTATCAATTCG-AAATTTAA
1 CTATCAATTCGAAAATTTAA
4319889 GTCTTAGATT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 7 0.15
31 40 0.85
ACGTcount: A:0.42, C:0.23, G:0.06, T:0.28
Consensus pattern (31 bp):
CTATCAATTCGAAAATTTAAACCGACCTAAC
Found at i:4324324 original size:2 final size:2
Alignment explanation
Indices: 4324317--4324351 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
4324307 CCTTAAGGTT
4324317 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4324352 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4324356 original size:2 final size:2
Alignment explanation
Indices: 4324351--4324380 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4324341 ATATATATAT
4324351 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4324381 TATATATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4329413 original size:12 final size:12
Alignment explanation
Indices: 4329396--4329423 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
4329386 AAGCTCATGC
4329396 ATTTTCTATATT
1 ATTTTCTATATT
4329408 ATTTTCTATATT
1 ATTTTCTATATT
4329420 ATTT
1 ATTT
4329424 GTGAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTTCTATATT
Found at i:4336580 original size:28 final size:28
Alignment explanation
Indices: 4336547--4336602 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
4336537 ATTATCCTCA
*
4336547 TGCCTAAAGAATAGAGTTCGAATCCCCC
1 TGCCTAAAGAACAGAGTTCGAATCCCCC
* *
4336575 TGCCTAAAGAACAGGGTTTGAATCCCCC
1 TGCCTAAAGAACAGAGTTCGAATCCCCC
4336603 CTCCTCTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (28 bp):
TGCCTAAAGAACAGAGTTCGAATCCCCC
Found at i:4342772 original size:21 final size:21
Alignment explanation
Indices: 4342726--4342773 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
4342716 TAATGATCTC
*
4342726 TAATAGTTTTTTTTATATATA
1 TAATATTTTTTTTTATATATA
* *
4342747 AAATATTTTTTTTTCA-ATTTA
1 TAATATTTTTTTTT-ATATATA
4342768 TAATAT
1 TAATAT
4342774 CCACTTATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TAATATTTTTTTTTATATATA
Found at i:4345500 original size:562 final size:562
Alignment explanation
Indices: 4344437--4345553 Score: 2198
Period size: 562 Copynumber: 2.0 Consensus size: 562
4344427 TTCTTATTTG
*
4344437 TATTTGGGTTTAGAAACCATAAACCCATATTTGATAAAATTCTCTAAAGAGTTATTGATACATTA
1 TATTTGGGTTTAAAAACCATAAACCCATATTTGATAAAATTCTCTAAAGAGTTATTGATACATTA
4344502 TTTGTCTTCATACCTTTTATATTATTGACACGTTAGATATTTCACATTTATTGTTATAAGTAAAA
66 TTTGTCTTCATACCTTTTATATTATTGACACGTTAGATATTTCACATTTATTGTTATAAGTAAAA
4344567 CTTAGAGAAATAAAAATATTTTATTTTATTTTATTTACTAGTTCACATAGTAGTTATAAAAGTTG
131 CTTAGAGAAATAAAAATATTTTATTTTATTTTATTTACTAGTTCACATAGTAGTTATAAAAGTTG
4344632 GCAGAAAGCTAGAACGAAACAAGACGTTGAGCATGGGGCGAAGTGCAACATGGCACTGTACGAAT
196 GCAGAAAGCTAGAACGAAACAAGACGTTGAGCATGGGGCGAAGTGCAACATGGCACTGTACGAAT
4344697 GAGAAACTCGGCTTAATAGGGGTAGAGCCAGGTTTGGCAGGGCTCTGAGCTAGAGTTGGATTTAA
261 GAGAAACTCGGCTTAATAGGGGTAGAGCCAGGTTTGGCAGGGCTCTGAGCTAGAGTTGGATTTAA
*
4344762 ATAATCATTAATAGCACTAATATTAATGAACCAGATTGGCTAACGTTTGCAGCTATAACTGTGAG
326 ATAATCATTAATAGCACTAATATTAATGAACCAGATTGGCTAACGTTTGCAACTATAACTGTGAG
4344827 CACAAATTGCAAAATCATAGGTAGTCAGAAACGTATGAAAGAATAGATTAGAATTCAAGAAAAAT
391 CACAAATTGCAAAATCATAGGTAGTCAGAAACGTATGAAAGAATAGATTAGAATTCAAGAAAAAT
4344892 GGAGTTAGATTTCTTAAGGTTGATTGTAGCAGTAATTCTAGGAACATCTGTTCTCCTATCTGAAT
456 GGAGTTAGATTTCTTAAGGTTGATTGTAGCAGTAATTCTAGGAACATCTGTTCTCCTATCTGAAT
4344957 TCCTTAAGAATGTGTTTAAAATATTGTACAATTTTAAACCCA
521 TCCTTAAGAATGTGTTTAAAATATTGTACAATTTTAAACCCA
4344999 TATTTGGGTTTAAAAACCATAAACCCATATTTGATAAAATTCTCTAAAGAGTTATTGATACATTA
1 TATTTGGGTTTAAAAACCATAAACCCATATTTGATAAAATTCTCTAAAGAGTTATTGATACATTA
* *
4345064 TTTGTCTTCGTACTTTTTATATTATTGACACGTTAGATATTTCACATTTATTGTTATAAGTAAAA
66 TTTGTCTTCATACCTTTTATATTATTGACACGTTAGATATTTCACATTTATTGTTATAAGTAAAA
4345129 CTTAGAGAAATAAAAATATTTTATTTTATTTTATTTACTAGTTCACATAGTAGTTATAAAAGTTG
131 CTTAGAGAAATAAAAATATTTTATTTTATTTTATTTACTAGTTCACATAGTAGTTATAAAAGTTG
4345194 GCAGAAAGCTAGAACGAAACAAGACGTTGAGCATGGGGCGAAGTGCAACATGGCACTGTACGAAT
196 GCAGAAAGCTAGAACGAAACAAGACGTTGAGCATGGGGCGAAGTGCAACATGGCACTGTACGAAT
4345259 GAGAAACTCGGCTTAATAGGGGTAGAGCCAGGTTTGGCAGGGCTCTGAGCTAGAGTTGGATTTAA
261 GAGAAACTCGGCTTAATAGGGGTAGAGCCAGGTTTGGCAGGGCTCTGAGCTAGAGTTGGATTTAA
4345324 ATAATCATTAATAGCACTAATATTAATGAACCAGATTGGCTAACGTTTGCAACTATAACTGTGAG
326 ATAATCATTAATAGCACTAATATTAATGAACCAGATTGGCTAACGTTTGCAACTATAACTGTGAG
4345389 CACAAATTGCAAAATCATAGGTAGTCAGAAACGTATGAAAGAATAGATTAGAATTCAAGAAAAAT
391 CACAAATTGCAAAATCATAGGTAGTCAGAAACGTATGAAAGAATAGATTAGAATTCAAGAAAAAT
4345454 GGAGTTAGATTTCTTAAGGTTGATTGTAGCAGTAATTCTAGGAACATCTGTTCTCCTATCTGAAT
456 GGAGTTAGATTTCTTAAGGTTGATTGTAGCAGTAATTCTAGGAACATCTGTTCTCCTATCTGAAT
4345519 TCCTTAAGAATGTGTTTAAAATATTGTACAATTTT
521 TCCTTAAGAATGTGTTTAAAATATTGTACAATTTT
4345554 GTAAGTTTTC
Statistics
Matches: 551, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
562 551 1.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.33
Consensus pattern (562 bp):
TATTTGGGTTTAAAAACCATAAACCCATATTTGATAAAATTCTCTAAAGAGTTATTGATACATTA
TTTGTCTTCATACCTTTTATATTATTGACACGTTAGATATTTCACATTTATTGTTATAAGTAAAA
CTTAGAGAAATAAAAATATTTTATTTTATTTTATTTACTAGTTCACATAGTAGTTATAAAAGTTG
GCAGAAAGCTAGAACGAAACAAGACGTTGAGCATGGGGCGAAGTGCAACATGGCACTGTACGAAT
GAGAAACTCGGCTTAATAGGGGTAGAGCCAGGTTTGGCAGGGCTCTGAGCTAGAGTTGGATTTAA
ATAATCATTAATAGCACTAATATTAATGAACCAGATTGGCTAACGTTTGCAACTATAACTGTGAG
CACAAATTGCAAAATCATAGGTAGTCAGAAACGTATGAAAGAATAGATTAGAATTCAAGAAAAAT
GGAGTTAGATTTCTTAAGGTTGATTGTAGCAGTAATTCTAGGAACATCTGTTCTCCTATCTGAAT
TCCTTAAGAATGTGTTTAAAATATTGTACAATTTTAAACCCA
Found at i:4352267 original size:26 final size:26
Alignment explanation
Indices: 4352213--4352267 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
4352203 TATTTATATT
*
4352213 AATTATTAAATAAAAATTAATTTAAA
1 AATTATTAAATAAAAATTAATATAAA
* *
4352239 AATTATTAAATATACA-TAATATAATA
1 AATTATTAAATAAAAATTAATATAA-A
4352265 AAT
1 AAT
4352268 AAATGATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
AATTATTAAATAAAAATTAATATAAA
Found at i:4353406 original size:19 final size:18
Alignment explanation
Indices: 4353382--4353421 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
4353372 TCTTTTTCAA
*
4353382 TATAAACAATTAAATTATC
1 TATAAAAAATT-AATTATC
*
4353401 TATAAAAAATTTATTATC
1 TATAAAAAATTAATTATC
4353419 TAT
1 TAT
4353422 TTTGTTTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (18 bp):
TATAAAAAATTAATTATC
Found at i:4356095 original size:3 final size:3
Alignment explanation
Indices: 4356087--4356111 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4356077 GTGAGTCTGG
4356087 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
4356112 ATGACAGCTT
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:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:4368045 original size:19 final size:19
Alignment explanation
Indices: 4368023--4368060 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4368013 GTTGTTTTTG
4368023 GGTCTTTGTTTAGTTTCTA
1 GGTCTTTGTTTAGTTTCTA
4368042 GGTCTTTGTTTAGTTTCTA
1 GGTCTTTGTTTAGTTTCTA
4368061 AACCCTCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.21, T:0.58
Consensus pattern (19 bp):
GGTCTTTGTTTAGTTTCTA
Found at i:4375181 original size:49 final size:49
Alignment explanation
Indices: 4375127--4375228 Score: 204
Period size: 49 Copynumber: 2.1 Consensus size: 49
4375117 TCAATTAGTT
4375127 TAACAATTACAACTATAAATCAAATTTATTAACGTTTTAAGAATAAATG
1 TAACAATTACAACTATAAATCAAATTTATTAACGTTTTAAGAATAAATG
4375176 TAACAATTACAACTATAAATCAAATTTATTAACGTTTTAAGAATAAATG
1 TAACAATTACAACTATAAATCAAATTTATTAACGTTTTAAGAATAAATG
4375225 TAAC
1 TAAC
4375229 GTTTGAATTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (49 bp):
TAACAATTACAACTATAAATCAAATTTATTAACGTTTTAAGAATAAATG
Found at i:4375585 original size:26 final size:24
Alignment explanation
Indices: 4375544--4375591 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
4375534 ATTTTTATAT
*
4375544 TTTATTAAAATAGTAAATTTAATC
1 TTTATTAAAATAGTAAAATTAATC
*
4375568 TTTATATAATAATTGTAAAATTAA
1 TTTAT-TAA-AATAGTAAAATTAA
4375592 ATCGTATGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 3 0.15
26 12 0.60
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
TTTATTAAAATAGTAAAATTAATC
Found at i:4378802 original size:3 final size:3
Alignment explanation
Indices: 4378794--4378848 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
4378784 GCAAGAGAAG
* * * *
4378794 AGC AGC AGC AGC AGC -GA AGC AGC AGA AGCC AGA AAC AGC AGC AGC
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AG-C AGC AGC AGC AGC AGC
4378839 AGC AGC AGC A
1 AGC AGC AGC A
4378849 ACTCTCTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 1 0.02
3 39 0.93
4 2 0.05
ACGTcount: A:0.40, C:0.29, G:0.31, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:4393070 original size:7 final size:7
Alignment explanation
Indices: 4393058--4393083 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4393048 GCATTAAACA
4393058 CAACTCC
1 CAACTCC
4393065 CAACTCC
1 CAACTCC
4393072 CAACTCC
1 CAACTCC
4393079 CAACT
1 CAACT
4393084 TACAACTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.54, G:0.00, T:0.15
Consensus pattern (7 bp):
CAACTCC
Found at i:4393089 original size:14 final size:14
Alignment explanation
Indices: 4393056--4393090 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
4393046 GAGCATTAAA
4393056 CACAACTCCCAACT
1 CACAACTCCCAACT
*
4393070 CCCAACTCCCAACT
1 CACAACTCCCAACT
*
4393084 TACAACT
1 CACAACT
4393091 TAATCTCGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.49, G:0.00, T:0.17
Consensus pattern (14 bp):
CACAACTCCCAACT
Found at i:4414533 original size:15 final size:15
Alignment explanation
Indices: 4414509--4414538 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4414499 AAATGCAGTC
*
4414509 TTTAATTTAAAAAAT
1 TTTAACTTAAAAAAT
4414524 TTTAACTTAAAAAAT
1 TTTAACTTAAAAAAT
4414539 AAAACTTAAA
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:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTAACTTAAAAAAT
Found at i:4426860 original size:26 final size:26
Alignment explanation
Indices: 4426829--4426918 Score: 69
Period size: 26 Copynumber: 3.4 Consensus size: 26
4426819 AGTAATAATA
4426829 ATATTTTTTTCAACATGACATGTAAC
1 ATATTTTTTTCAACATGACATGTAAC
* * *
4426855 ATATTTTTGTATATAACGTATAACA-ATAA-
1 ATATTTTT-T-T-CAAC--ATGACATGTAAC
* *
4426884 TTTTTTTTTTCAACATGACATGTAAC
1 ATATTTTTTTCAACATGACATGTAAC
4426910 A-ATTTTTTT
1 ATATTTTTTT
4426919 TAATCATGGT
Statistics
Matches: 47, Mismatches: 10, Indels: 15
0.65 0.14 0.21
Matches are distributed among these distances:
24 5 0.11
25 10 0.21
26 11 0.23
27 2 0.04
28 2 0.04
29 9 0.19
30 3 0.06
31 5 0.11
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (26 bp):
ATATTTTTTTCAACATGACATGTAAC
Found at i:4427045 original size:111 final size:110
Alignment explanation
Indices: 4426930--4427132 Score: 298
Period size: 110 Copynumber: 1.8 Consensus size: 110
4426920 AATCATGGTG
* * * * *
4426930 TATAACATATTTTTATATATGATGTATAATAATAATATTTTTTTAATATGACGTATAACATGTTT
1 TATAACATATTTTTATACATAATGTATAATAATAATA-TTTTTTAACATGACATATAACATATTT
* *
4426995 TTATACGTAGTATATAATAATAATATATATATTTTTAATAATGACA
65 TTATACATAGTATATAACAATAATATATATATTTTTAATAATGACA
* *
4427041 TATAACATGTTTTTATACATAATGTATAATAATAATATTTTTTAACATGACATATAATATATTTT
1 TATAACATATTTTTATACATAATGTATAATAATAATATTTTTTAACATGACATATAACATATTTT
* *
4427106 TATATATAGTATGTAACAATAATATAT
66 TATACATAGTATATAACAATAATATAT
4427133 TTTTGTAACA
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
110 47 0.58
111 34 0.42
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.46
Consensus pattern (110 bp):
TATAACATATTTTTATACATAATGTATAATAATAATATTTTTTAACATGACATATAACATATTTT
TATACATAGTATATAACAATAATATATATATTTTTAATAATGACA
Found at i:4427052 original size:58 final size:55
Alignment explanation
Indices: 4426930--4427136 Score: 239
Period size: 58 Copynumber: 3.8 Consensus size: 55
4426920 AATCATGGTG
* * *
4426930 TATAACATATTTTTATATAT-G-ATGT-ATAATAATAATATTTTTTTAATATGACG
1 TATAACATGTTTTTATACATAGTATGTAATAATAATAATA-TTTTTTAATATGACA
* *
4426983 TATAACATGTTTTTATACGTAGTATATAATAATAATATATATATTTTTAATAATGACA
1 TATAACATGTTTTTATACATAGTATGTAATAATAATA-ATAT-TTTTTAAT-ATGACA
*
4427041 TATAACATGTTTTTATACATA--ATGT-ATAATAATAATATTTTTTAACATGACA
1 TATAACATGTTTTTATACATAGTATGTAATAATAATAATATTTTTTAATATGACA
* * * *
4427093 TATAATATATTTTTATATATAGTATGTAACAATAAT-ATATTTTT
1 TATAACATGTTTTTATACATAGTATGTAATAATAATAATATTTTT
4427137 GTAACACAAT
Statistics
Matches: 133, Mismatches: 12, Indels: 17
0.82 0.07 0.10
Matches are distributed among these distances:
52 24 0.18
53 24 0.18
54 17 0.13
55 19 0.14
56 13 0.10
57 11 0.08
58 25 0.19
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (55 bp):
TATAACATGTTTTTATACATAGTATGTAATAATAATAATATTTTTTAATATGACA
Found at i:4429205 original size:2 final size:2
Alignment explanation
Indices: 4429198--4429222 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4429188 TAACTTAATC
4429198 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
4429223 CACTTCATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:4444885 original size:16 final size:17
Alignment explanation
Indices: 4444850--4444893 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
4444840 AAGTAATGTT
4444850 ATAATTAAAATAATAATA
1 ATAATT-AAATAATAATA
*
4444868 ATAATTAAA-AATATTA
1 ATAATTAAATAATAATA
*
4444884 ATATTTAAAT
1 ATAATTAAAT
4444894 TATTAACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 14 0.61
17 3 0.13
18 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAATTAAATAATAATA
Found at i:4452391 original size:2 final size:2
Alignment explanation
Indices: 4452343--4452375 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4452333 TTAGTTTCGA
*
4452343 AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4452376 AGATGGAGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4469703 original size:12 final size:12
Alignment explanation
Indices: 4469669--4469713 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
4469659 ATCTATAAAT
*
4469669 ATATTGCAAAAA
1 ATATTACAAAAA
4469681 ATA-TACAAAAA
1 ATATTACAAAAA
*
4469692 ATATTACTAAAA
1 ATATTACAAAAA
*
4469704 ATATTTCAAA
1 ATATTACAAA
4469714 TGCACATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.29
Consensus pattern (12 bp):
ATATTACAAAAA
Found at i:4485656 original size:2 final size:2
Alignment explanation
Indices: 4485649--4485697 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
4485639 GAGTGCAATG
* *
4485649 TA TA TA TA TA TG TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4485691 TA TA TA T
1 TA TA TA T
4485698 TGCTGTTGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4487835 original size:12 final size:12
Alignment explanation
Indices: 4487818--4487843 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4487808 ATATTTTGTG
4487818 TGTATATATATA
1 TGTATATATATA
4487830 TGTATATATATA
1 TGTATATATATA
4487842 TG
1 TG
4487844 AAATACGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (12 bp):
TGTATATATATA
Found at i:4489195 original size:2 final size:2
Alignment explanation
Indices: 4489188--4489212 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4489178 ACAATCAATG
4489188 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4489213 ATAAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4489628 original size:3 final size:3
Alignment explanation
Indices: 4489620--4489645 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4489610 TGAGTGTTAG
4489620 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
4489646 GGTGGGCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4491106 original size:27 final size:27
Alignment explanation
Indices: 4491076--4491131 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
4491066 ATAGATTGTG
* * *
4491076 TTTGATTCTTTATATAGGTAGTTTAGA
1 TTTGAGTCCTTATATAGGTAGTATAGA
*
4491103 TTTGAGTCCTTATATGGGTAGTATAGA
1 TTTGAGTCCTTATATAGGTAGTATAGA
4491130 TT
1 TT
4491132 CAAGCTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.05, G:0.21, T:0.48
Consensus pattern (27 bp):
TTTGAGTCCTTATATAGGTAGTATAGA
Found at i:4495398 original size:2 final size:2
Alignment explanation
Indices: 4495391--4495416 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4495381 ATCGCAATGC
4495391 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
4495417 GATTCCCAAT
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):
TA
Found at i:4502470 original size:124 final size:125
Alignment explanation
Indices: 4502249--4502497 Score: 464
Period size: 124 Copynumber: 2.0 Consensus size: 125
4502239 TTAGCACAAA
4502249 ACCATAAGCTATGGTATTTAAACCTAAATCCTAGGTAGAAGGAAAGATAAGGAACACTCTGAATG
1 ACCATAAGCTATGGTATTTAAACCTAAATCCTAGGTAGAAGGAAAGATAAGGAACACTCTGAATG
*
4502314 TTAAATCTGAAAATTTTATTTCACCACAAAATCTTTAGTCTTGATTACAATCTATTAAAC
66 TTAAATCTGAAAACTTTATTTCACCACAAAATCTTTAGTCTTGATTACAATCTATTAAAC
*
4502374 ACCATAAGCTATGGTGTTTAAACCTAAATCCTAGGTAGAAGG-AAGATAAGGAACACTCTGAATG
1 ACCATAAGCTATGGTATTTAAACCTAAATCCTAGGTAGAAGGAAAGATAAGGAACACTCTGAATG
*
4502438 TTAAATCTGAAAACTTTATTTCACCACAAAATCTTTAGTCTTGATTGCAATCTATTAAAC
66 TTAAATCTGAAAACTTTATTTCACCACAAAATCTTTAGTCTTGATTACAATCTATTAAAC
4502498 TTTGTCTCCG
Statistics
Matches: 121, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
124 80 0.66
125 41 0.34
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (125 bp):
ACCATAAGCTATGGTATTTAAACCTAAATCCTAGGTAGAAGGAAAGATAAGGAACACTCTGAATG
TTAAATCTGAAAACTTTATTTCACCACAAAATCTTTAGTCTTGATTACAATCTATTAAAC
Found at i:4508959 original size:3 final size:3
Alignment explanation
Indices: 4508944--4508973 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
4508934 TTCCGCCTCT
*
4508944 TTC TTC CTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
4508974 GTCTGCGTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:4508985 original size:3 final size:3
Alignment explanation
Indices: 4508979--4509013 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
4508969 TCTTCGTCTG
*
4508979 CGT CGT CGT CGT CGT CGT CGT CGT CGT CGA CGT CG
1 CGT CGT CGT CGT CGT CGT CGT CGT CGT CGT CGT CG
4509014 ACGAAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.34, G:0.34, T:0.29
Consensus pattern (3 bp):
CGT
Found at i:4510892 original size:17 final size:18
Alignment explanation
Indices: 4510870--4510906 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
4510860 ACTGTTTGAG
*
4510870 AAATAAAAATA-ATTTTT
1 AAATAAAAAAATATTTTT
4510887 AAATAAAAAAATATTTTT
1 AAATAAAAAAATATTTTT
4510905 AA
1 AA
4510907 GGTCATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATAAAAAAATATTTTT
Found at i:4525081 original size:66 final size:64
Alignment explanation
Indices: 4524924--4525108 Score: 203
Period size: 66 Copynumber: 2.8 Consensus size: 64
4524914 ATTATTATTC
* * * *
4524924 TTTTAATATCTATAAGACGTTCTTTAACGTGCTCTTACATGATAAGCATC-TTCTCTCATATTGA
1 TTTT-ATATCTATAAGTCGTTATTTAACGTGCTCTTCCATGACAAGCA-CATTCTCTCATATTGA
4524988 G
64 G
* * * *
4524989 TTTTATATCCCATAAGTTGTTATTTAATGTGCTCTTCCATGACAAACACATTCTCTCATAATTGA
1 TTTTATAT-CTATAAGTCGTTATTTAACGTGCTCTTCCATGACAAGCACATTCTCTCAT-ATTGA
4525054 G
64 G
* * *
4525055 TTTTATATCTAATAAGTCATTTTTTAACGTTCT-TTCCCATGACAAGCACATTCT
1 TTTTATATCT-ATAAGTCGTTATTTAACGTGCTCTT-CCATGACAAGCACATTCT
4525109 TCTATGATTG
Statistics
Matches: 100, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
64 5 0.05
65 47 0.47
66 48 0.48
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.42
Consensus pattern (64 bp):
TTTTATATCTATAAGTCGTTATTTAACGTGCTCTTCCATGACAAGCACATTCTCTCATATTGAG
Found at i:4547817 original size:45 final size:45
Alignment explanation
Indices: 4547742--4547841 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 45
4547732 GGTAAAAGGG
* * * *
4547742 CAGGCCCATTCATCCGTGGGGATGGAAGATTGGGCATTGGTGGAA
1 CAGGACCATTCATCCGTGGAGAAGGAAGATTAGGCATTGGTGGAA
* * *
4547787 CAGGACCATTCATTCGTGGAGAAGGGAGATTAGGCATTGGTGGTA
1 CAGGACCATTCATCCGTGGAGAAGGAAGATTAGGCATTGGTGGAA
4547832 CAGGACCATT
1 CAGGACCATT
4547842 TACTCCTCTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.25, C:0.17, G:0.35, T:0.23
Consensus pattern (45 bp):
CAGGACCATTCATCCGTGGAGAAGGAAGATTAGGCATTGGTGGAA
Done.