Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 71 of 208
Found at i:20806734 original size:24 final size:26
Alignment explanation
Indices: 20806668--20806735 Score: 104
Period size: 24 Copynumber: 2.6 Consensus size: 26
20806658 AAAAATAAAA
20806668 ATTTACCAAAATATTATAACTTTTTTTT
1 ATTTACCAAAATA-TATAAC-TTTTTTT
20806696 ATTTACCAAAATATAT-A-TTTTTTT
1 ATTTACCAAAATATATAACTTTTTTT
20806720 ATTTACCAAAATATAT
1 ATTTACCAAAATATAT
20806736 CAGAAAAACC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
24 23 0.57
26 1 0.03
27 3 0.08
28 13 0.32
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTTACCAAAATATATAACTTTTTTT
Found at i:20806875 original size:4 final size:4
Alignment explanation
Indices: 20806866--20807007 Score: 109
Period size: 4 Copynumber: 35.0 Consensus size: 4
20806856 GTGGTGGGGG
*
20806866 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA G-AA -AAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA GAAA
* * *
20806914 GAAG GAAA GAAAA GGAAA G-GA GAAGA GAAA AAAA GAAA GAAA G-AA G-AA
1 GAAA GAAA G-AAA -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA
*
20806962 G-AA GAAAA GGAAAA GAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAA
1 GAAA G-AAA -G-AAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
20807008 ACGAAAGGAG
Statistics
Matches: 115, Mismatches: 10, Indels: 26
0.76 0.07 0.17
Matches are distributed among these distances:
3 18 0.16
4 69 0.60
5 21 0.18
6 7 0.06
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:20806905 original size:18 final size:19
Alignment explanation
Indices: 20806865--20807031 Score: 125
Period size: 18 Copynumber: 8.6 Consensus size: 19
20806855 GGTGGTGGGG
20806865 GGAAAGAAAGAAA-GA-AA
1 GGAAAGAAAGAAAGGAGAA
20806882 -GAAAGAAAGAAAGGAG-A
1 GGAAAGAAAGAAAGGAGAA
*
20806899 GGAAAGAAAGAAA-AAGAA
1 GGAAAGAAAGAAAGGAGAA
20806917 GGAAAGAAAAGGAAAGGAGAA
1 GGAAAG-AAA-GAAAGGAGAA
* *
20806938 GAGAAAAAAAGAAAGAAAGAA
1 G-GAAAGAAAGAAAG-GAGAA
* *
20806959 GAAGAAGAAAAGGAAAAGAGAA
1 GGA-AAG-AAA-GAAAGGAGAA
*
20806981 -GAAA-AAAGAAAGAAAGAA
1 GGAAAGAAAGAAAG-GAGAA
20806999 GGAAAGAAAACGAAAGGAGAA
1 GGAAAG-AAA-GAAAGGAGAA
20807020 GAGAAA-AAAGAA
1 G-GAAAGAAAGAA
20807032 GAAGAAGAAG
Statistics
Matches: 120, Mismatches: 12, Indels: 34
0.72 0.07 0.20
Matches are distributed among these distances:
16 12 0.10
17 9 0.08
18 26 0.22
19 10 0.08
20 15 0.12
21 24 0.20
22 20 0.17
23 4 0.03
ACGTcount: A:0.69, C:0.01, G:0.30, T:0.00
Consensus pattern (19 bp):
GGAAAGAAAGAAAGGAGAA
Found at i:20806949 original size:44 final size:43
Alignment explanation
Indices: 20806901--20807041 Score: 188
Period size: 40 Copynumber: 3.4 Consensus size: 43
20806891 AAAGGAGAGG
20806901 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAA
1 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAG-AAA
*
20806945 AAAGAAAGAAAGAAGAA-G-AAGAAAAGGAAAAGAG-A-AGAAA
1 AAAGAAAGAAA-AAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAA
*
20806985 AAAGAAAG--AAAGAAGGAAAGAAAACGAAAGGAGAAGAGAAA
1 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAA
*
20807026 AAAG-AAGAAGAAGAAG
1 AAAGAAAGAAAAAGAAG
20807042 AGGGAAGAAG
Statistics
Matches: 86, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
37 5 0.06
38 2 0.02
39 14 0.16
40 15 0.17
41 11 0.13
42 7 0.08
43 15 0.17
44 12 0.14
45 5 0.06
ACGTcount: A:0.70, C:0.01, G:0.29, T:0.00
Consensus pattern (43 bp):
AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAA
Found at i:20806992 original size:70 final size:70
Alignment explanation
Indices: 20806873--20807069 Score: 173
Period size: 73 Copynumber: 2.8 Consensus size: 70
20806863 GGGGAAAGAA
* *
20806873 AGAAAGAAAGAAAG-A-AAGAAAGGAGAGG-AAAGA-AAGAAAAAGAAGGAAAGAAAAGGAAAGG
1 AGAAAGAAAGAAAGAAGAAG-AAGAAAAGGAAAAGAGAAG-AAAA-AA-GAAAGAAAAGGAAA-G
20806934 AGAAGA-GAAA-
61 A-AA-ACGAAAG
20806944 A-AAAGAAAGAAAGAAGAAGAAGAAAAGGAAAAGAGAAGAAAAAAGAAAGAAAGAAGGAAAGAAA
1 AGAAAGAAAGAAAGAAGAAGAAGAAAAGGAAAAGAGAAGAAAAAAGAAAG-AA-AAGGAAAGAAA
20807008 ACGAAAGG
64 ACGAAA-G
*
20807016 AGAAGAGAAA-AAAGAAGAAGAAGAAGAGGGAAGAAG-GAA-AAAAAAGAAA-AAAAG
1 AGAA-AGAAAGAAAGAAGAAGAAGAA-AAGGAA-AAGAGAAGAAAAAAGAAAGAAAAG
20807070 TAATTTTATT
Statistics
Matches: 110, Mismatches: 3, Indels: 27
0.79 0.02 0.19
Matches are distributed among these distances:
69 1 0.01
70 26 0.24
71 17 0.15
72 20 0.18
73 30 0.27
74 13 0.12
75 3 0.03
ACGTcount: A:0.70, C:0.01, G:0.30, T:0.00
Consensus pattern (70 bp):
AGAAAGAAAGAAAGAAGAAGAAGAAAAGGAAAAGAGAAGAAAAAAGAAAGAAAAGGAAAGAAAAC
GAAAG
Found at i:20807050 original size:44 final size:45
Alignment explanation
Indices: 20806906--20807047 Score: 160
Period size: 43 Copynumber: 3.3 Consensus size: 45
20806896 AGAGGAAAGA
*
20806906 AAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAG-AAAAA-AAG
1 AAGAAGAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAGAAG
*
20806949 AAAGAAAGAAGAA-G-AAGAAAAGGAAAAGAG-A-AGAAAAAAG-A-
1 -AAG-AAGAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAGAAG
*
20806990 AAG-A-AAGAAGGAAAGAAAACGAAAGGAGAAGAGAAAAAAGAAG
1 AAGAAGAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAGAAG
*
20807033 AAGAAGAAGAGGGAA
1 AAGAAGAAGAAGGAA
20807048 GAAGGAAAAA
Statistics
Matches: 82, Mismatches: 5, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
37 5 0.06
38 2 0.02
39 14 0.17
40 4 0.05
41 11 0.13
42 8 0.10
43 18 0.22
44 5 0.06
45 15 0.18
ACGTcount: A:0.69, C:0.01, G:0.30, T:0.00
Consensus pattern (45 bp):
AAGAAGAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAGAAG
Found at i:20807068 original size:82 final size:83
Alignment explanation
Indices: 20806901--20807067 Score: 245
Period size: 82 Copynumber: 2.0 Consensus size: 83
20806891 AAAGGAGAGG
*
20806901 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAG
1 AAAGAAAG-AAAAGAAGGAAAGAAAACGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAG
*
20806966 AAAAGGAAAAGAGAAGAAA
65 AAAAGGAAAAAAGAAGAAA
*
20806985 AAAGAAAG-AAAGAAGGAAAGAAAACGAAAGGAGAAGAG-AAAAAAG-AAG-AAGAAGAAGAGGG
1 AAAGAAAGAAAAGAAGGAAAGAAAACGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGA-AG
20807046 AAGAAGGAAAAAA-AAGAAA
65 AA-AAGGAAAAAAGAAGAAA
20807065 AAA
1 AAA
20807068 AGTAATTTTA
Statistics
Matches: 78, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
79 10 0.13
80 15 0.19
81 16 0.21
82 29 0.37
84 8 0.10
ACGTcount: A:0.71, C:0.01, G:0.29, T:0.00
Consensus pattern (83 bp):
AAAGAAAGAAAAGAAGGAAAGAAAACGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAGA
AAAGGAAAAAAGAAGAAA
Found at i:20808939 original size:19 final size:18
Alignment explanation
Indices: 20808915--20808982 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 18
20808905 GTCAATCGTT
20808915 CTTTTTTTT-ATTCCTCCTC
1 CTTTTTTTTGATT-CT-CTC
20808934 CTTTTTTATTGATTCTCTC
1 CTTTTTT-TTGATTCTCTC
20808953 CTTTTTTTTTATTGATTCTCTC
1 C---TTTTTT-TTGATTCTCTC
20808975 CTTTTTTT
1 CTTTTTTT
20808983 ACAATGAAGG
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
18 1 0.02
19 17 0.39
20 4 0.09
21 3 0.07
22 19 0.43
ACGTcount: A:0.07, C:0.22, G:0.03, T:0.68
Consensus pattern (18 bp):
CTTTTTTTTGATTCTCTC
Found at i:20808960 original size:22 final size:22
Alignment explanation
Indices: 20808935--20808982 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
20808925 TTCCTCCTCC
20808935 TTTTTTATTGATTCTCTCCTTT
1 TTTTTTATTGATTCTCTCCTTT
20808957 TTTTTTATTGATTCTCTCCTTT
1 TTTTTTATTGATTCTCTCCTTT
20808979 TTTT
1 TTTT
20808983 ACAATGAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (22 bp):
TTTTTTATTGATTCTCTCCTTT
Found at i:20809118 original size:23 final size:24
Alignment explanation
Indices: 20809088--20809176 Score: 102
Period size: 21 Copynumber: 4.0 Consensus size: 24
20809078 AAATTAAATC
*
20809088 TCTAAGATTACA-AAATCATATCT
1 TCTAAGATTACATATATCATATCT
*
20809111 TCTAAGATTATATATATCATA---
1 TCTAAGATTACATATATCATATCT
20809132 TCTAAGATTACATATATCATA---
1 TCTAAGATTACATATATCATATCT
*
20809153 TCTAAGATTGCATATATCATATCT
1 TCTAAGATTACATATATCATATCT
20809177 AAGATTGCAT
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
21 40 0.69
23 11 0.19
24 7 0.12
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.39
Consensus pattern (24 bp):
TCTAAGATTACATATATCATATCT
Found at i:20809137 original size:21 final size:21
Alignment explanation
Indices: 20809111--20809207 Score: 144
Period size: 21 Copynumber: 4.7 Consensus size: 21
20809101 AATCATATCT
**
20809111 TCTAAGATTATATATATCATA
1 TCTAAGATTGCATATATCATA
*
20809132 TCTAAGATTACATATATCATA
1 TCTAAGATTGCATATATCATA
20809153 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
20809174 TCTAAGATTGCATATA--ATA
1 TCTAAGATTGCATATATCATA
*
20809193 TCTAAGATTGTATAT
1 TCTAAGATTGCATAT
20809208 CCTCGAAAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
19 17 0.23
21 56 0.77
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:20809168 original size:42 final size:42
Alignment explanation
Indices: 20809088--20809207 Score: 156
Period size: 42 Copynumber: 2.9 Consensus size: 42
20809078 AAATTAAATC
* *
20809088 TCTAAGATTACA-AAATCATATCTTCTAAGATTATATATATCATA
1 TCTAAGATTACATATATCATA---TCTAAGATTGTATATATCATA
*
20809132 TCTAAGATTACATATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTACATATATCATATCTAAGATTGTATATATCATA
*
20809174 TCTAAGATTGCATATA--ATATCTAAGATTGTATAT
1 TCTAAGATTACATATATCATATCTAAGATTGTATAT
20809208 CCTCGAAAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
40 17 0.24
42 34 0.49
44 12 0.17
45 7 0.10
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.39
Consensus pattern (42 bp):
TCTAAGATTACATATATCATATCTAAGATTGTATATATCATA
Found at i:20814547 original size:18 final size:18
Alignment explanation
Indices: 20814524--20814561 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20814514 ATCCCAATGA
**
20814524 TCGCCGGCTTCTTCTTCT
1 TCGCCGGCACCTTCTTCT
20814542 TCGCCGGCACCTTCTTCT
1 TCGCCGGCACCTTCTTCT
20814560 TC
1 TC
20814562 ACCACCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.03, C:0.42, G:0.16, T:0.39
Consensus pattern (18 bp):
TCGCCGGCACCTTCTTCT
Found at i:20815141 original size:12 final size:12
Alignment explanation
Indices: 20815121--20815150 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
20815111 AAAAAAATTT
*
20815121 ATACTCAAAATA
1 ATACACAAAATA
20815133 ATACACAAAATA
1 ATACACAAAATA
20815145 ATACAC
1 ATACAC
20815151 CCTTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (12 bp):
ATACACAAAATA
Found at i:20815178 original size:36 final size:34
Alignment explanation
Indices: 20815133--20815243 Score: 89
Period size: 26 Copynumber: 3.4 Consensus size: 34
20815123 ACTCAAAATA
*
20815133 ATACACAAAATAATACACCCTTAAATTATTAATTTT
1 ATACTCAAAATAATACA--CTTAAATTATTAATTTT
20815169 ATACTCAAAATAAT--A-TT--A--A-TAATTTT
1 ATACTCAAAATAATACACTTAAATTATTAATTTT
*
20815195 ATACTCAAAATAATACATACTAAAATTATTAA-TTT
1 ATACTCAAAATAATAC--ACTTAAATTATTAATTTT
*
20815230 -TACTAAAAATAATA
1 ATACTCAAAATAATA
20815244 ACTAACTAAC
Statistics
Matches: 62, Mismatches: 3, Indels: 22
0.71 0.03 0.25
Matches are distributed among these distances:
26 21 0.34
27 1 0.02
29 1 0.02
30 1 0.02
31 3 0.05
33 1 0.02
34 14 0.23
35 4 0.06
36 16 0.26
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (34 bp):
ATACTCAAAATAATACACTTAAATTATTAATTTT
Found at i:20815191 original size:26 final size:26
Alignment explanation
Indices: 20815157--20815209 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
20815147 ACACCCTTAA
*
20815157 ATTATTAATTTTATACTCAAAATAAT
1 ATTAATAATTTTATACTCAAAATAAT
20815183 ATTAATAATTTTATACTCAAAATAAT
1 ATTAATAATTTTATACTCAAAATAAT
20815209 A
1 A
20815210 CATACTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (26 bp):
ATTAATAATTTTATACTCAAAATAAT
Found at i:20815407 original size:3 final size:3
Alignment explanation
Indices: 20815399--20815445 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
20815389 TCTTAATACT
20815399 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
20815446 TAATAATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:20815450 original size:3 final size:3
Alignment explanation
Indices: 20815444--20815490 Score: 76
Period size: 3 Copynumber: 15.3 Consensus size: 3
20815434 CAACAACAAC
*
20815444 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
20815490 A
1 A
20815491 CTATTATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20815560 original size:19 final size:21
Alignment explanation
Indices: 20815536--20815574 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
20815526 ATTAAAACAA
*
20815536 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
20815555 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
20815575 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:20815617 original size:11 final size:11
Alignment explanation
Indices: 20815601--20815638 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
20815591 AAAGATACCT
*
20815601 TCTTTTTTTCC
1 TCTTTTTCTCC
20815612 TCTTTTTCT-C
1 TCTTTTTCTCC
*
20815622 TCTTTTTCTCT
1 TCTTTTTCTCC
20815633 TCTTTT
1 TCTTTT
20815639 CCGCAACAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
TCTTTTTCTCC
Found at i:20815639 original size:10 final size:10
Alignment explanation
Indices: 20815605--20815638 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
20815595 ATACCTTCTT
20815605 TTTTTC-CTC
1 TTTTTCTCTC
20815614 TTTTTCTCTC
1 TTTTTCTCTC
20815624 TTTTTCTCTTC
1 TTTTTCTC-TC
20815635 TTTT
1 TTTT
20815639 CCGCAACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 6 0.26
10 11 0.48
11 6 0.26
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTCTCTC
Found at i:20815767 original size:27 final size:27
Alignment explanation
Indices: 20815737--20815821 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
20815727 CCAATTAGTA
20815737 TGGCACCATTGGTGCCGCCAATGGCAT
1 TGGCACCATTGGTGCCGCCAATGGCAT
**
20815764 TGGCACCATTGGTGCCGCCAATGGTTT
1 TGGCACCATTGGTGCCGCCAATGGCAT
* **
20815791 TGGCACCTTTGGTGCCGCCAATCCCAT
1 TGGCACCATTGGTGCCGCCAATGGCAT
20815818 TGGC
1 TGGC
20815822 GTGACCAGTA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.15, C:0.31, G:0.28, T:0.26
Consensus pattern (27 bp):
TGGCACCATTGGTGCCGCCAATGGCAT
Found at i:20815896 original size:19 final size:19
Alignment explanation
Indices: 20815874--20815912 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
20815864 TTTTTGATAT
*
20815874 ATTTTGATAAATAAAAAAA
1 ATTTCGATAAATAAAAAAA
*
20815893 ATTTCGGTAAATAAAAAAA
1 ATTTCGATAAATAAAAAAA
20815912 A
1 A
20815913 GTTAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.28
Consensus pattern (19 bp):
ATTTCGATAAATAAAAAAA
Found at i:20818536 original size:9 final size:9
Alignment explanation
Indices: 20818519--20818555 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
20818509 TAAGTTTTCG
20818519 AATTCGAAT
1 AATTCGAAT
*
20818528 AACTCGAAT
1 AATTCGAAT
20818537 AATTCGAAT
1 AATTCGAAT
20818546 AATTCGAAT
1 AATTCGAAT
20818555 A
1 A
20818556 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:20823565 original size:18 final size:18
Alignment explanation
Indices: 20823526--20823566 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
20823516 ATGTTTATAT
* * *
20823526 TAGAATGCTTGAAGGATT
1 TAGAATGCTGGAAGCATA
20823544 TAGAATGCTGGAAGCATA
1 TAGAATGCTGGAAGCATA
20823562 TAGAA
1 TAGAA
20823567 ATTTTGAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.27, T:0.27
Consensus pattern (18 bp):
TAGAATGCTGGAAGCATA
Found at i:20832505 original size:23 final size:22
Alignment explanation
Indices: 20832462--20832505 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
20832452 TTGTAAGTCG
20832462 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
20832485 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
20832506 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:20832614 original size:45 final size:45
Alignment explanation
Indices: 20832550--20832643 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
20832540 AACAGATACT
* *
20832550 CGGTGGATTCAACACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
* *
20832595 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
20832640 CGGT
1 CGGT
20832644 TCACATAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:20832707 original size:51 final size:50
Alignment explanation
Indices: 20832640--20832835 Score: 223
Period size: 51 Copynumber: 3.9 Consensus size: 50
20832630 CAATGATGTT
* * *
20832640 CGGTTCACATAGTAGCCTACACATAGTACTACACATGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACCA-TACCATC
* * * * *
20832691 CGATACACGTAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATT
1 CGGTACACGTAGTAGCCTACACATAGTACTACACACGTGA-CCATACCATC
* * * * * *
20832742 CGGTACGCATAGTAGCCTGCACATAGTAATACACATGTGACC-TATCATTC
1 CGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACCATACCA-TC
*
20832792 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACCAT
20832836 CACTTTCACT
Statistics
Matches: 119, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
49 2 0.02
50 40 0.34
51 75 0.63
52 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.24
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACCATACCATC
Found at i:20832855 original size:101 final size:101
Alignment explanation
Indices: 20832645--20832831 Score: 277
Period size: 101 Copynumber: 1.8 Consensus size: 101
20832635 ATGTTCGGTT
*
20832645 CACATAGTAGCCTACACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTA
1 CACATAGTAGCCTACACATAGTAATACACATGTGACCA-TACCATCCGATACACGTAGTAGCCTA
* *
20832710 CACATAGTACTACACACGTGATCGAAACTATTCGGTA
65 CACATAGTACTACACACGTGATCCAAACTATTCCGTA
* * * * *
20832747 CGCATAGTAGCCTGCACATAGTAATACACATGTGACC-TATCATTCCGGTACACGTAGTAGCCTG
1 CACATAGTAGCCTACACATAGTAATACACATGTGACCATACCA-TCCGATACACGTAGTAGCCTA
20832811 CACATAGTACTACACACGTGA
65 CACATAGTACTACACACGTGA
20832832 CCATCACTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
100 4 0.05
101 40 0.51
102 34 0.44
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.24
Consensus pattern (101 bp):
CACATAGTAGCCTACACATAGTAATACACATGTGACCATACCATCCGATACACGTAGTAGCCTAC
ACATAGTACTACACACGTGATCCAAACTATTCCGTA
Found at i:20836503 original size:42 final size:42
Alignment explanation
Indices: 20836443--20836526 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
20836433 TAACCTAATT
* * * *
20836443 GGGAAAATAATTCCCTTATTCTAGTAAACTACTAGAAGATAA
1 GGGAAAATAATTACCTTATTATAATAAACTACTAAAAGATAA
*
20836485 GGGAAAATAATTATCTTATTATAATAAACTACTAAAAGATAA
1 GGGAAAATAATTACCTTATTATAATAAACTACTAAAAGATAA
20836527 AATAAAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.30
Consensus pattern (42 bp):
GGGAAAATAATTACCTTATTATAATAAACTACTAAAAGATAA
Found at i:20836588 original size:19 final size:19
Alignment explanation
Indices: 20836564--20836609 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
20836554 TGATTTATTC
20836564 TAAGATTTATCTA-CATAAA
1 TAAGATTTATCTATC-TAAA
20836583 TAAGATTTATCTATCTAAA
1 TAAGATTTATCTATCTAAA
20836602 TAA-ATTTA
1 TAAGATTTA
20836610 AAATATATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.19
19 20 0.77
20 1 0.04
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (19 bp):
TAAGATTTATCTATCTAAA
Found at i:20837530 original size:15 final size:15
Alignment explanation
Indices: 20837510--20837540 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20837500 AAGAAAGTAT
20837510 TTCAAAGGACCTAAG
1 TTCAAAGGACCTAAG
20837525 TTCAAAGGACCTAAG
1 TTCAAAGGACCTAAG
20837540 T
1 T
20837541 CTTTAATCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (15 bp):
TTCAAAGGACCTAAG
Found at i:20841178 original size:42 final size:42
Alignment explanation
Indices: 20841118--20841201 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
20841108 TAACCTAATT
*
20841118 GGGAAAATAATTCCCTTATTCTAGTAAACTACTAAAAGATAA
1 GGGAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAA
*
20841160 GGGAAAATAATTCTCTTATTCTAATAAACTACTAAAAGATAA
1 GGGAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAA
20841202 AATAAAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (42 bp):
GGGAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAA
Found at i:20841209 original size:42 final size:42
Alignment explanation
Indices: 20841120--20841215 Score: 138
Period size: 42 Copynumber: 2.3 Consensus size: 42
20841110 ACCTAATTGG
* * **
20841120 GAAAATAATTCCCTTATTCTAGTAAACTACTAAAAGATAAGG
1 GAAAATAATTCTCTTATTCTAATAAACTACTAAAAGATAAAA
20841162 GAAAATAATTCTCTTATTCTAATAAACTACTAAAAGATAAAA
1 GAAAATAATTCTCTTATTCTAATAAACTACTAAAAGATAAAA
* *
20841204 TAAAATATTTCT
1 GAAAATAATTCT
20841216 AGAATATATC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.32
Consensus pattern (42 bp):
GAAAATAATTCTCTTATTCTAATAAACTACTAAAAGATAAAA
Found at i:20855110 original size:37 final size:37
Alignment explanation
Indices: 20855060--20855138 Score: 140
Period size: 37 Copynumber: 2.1 Consensus size: 37
20855050 TTGAGGCTAA
*
20855060 AATTTCTTTTAGGGGGTAGAGTTGTAACGCCTTGAAT
1 AATTTCTTTTAGGGGGTAGAGTTGTAACGCCCTGAAT
*
20855097 AATTTCTTTTAGGGGGTAGAGTTGTAATGCCCTGAAT
1 AATTTCTTTTAGGGGGTAGAGTTGTAACGCCCTGAAT
20855134 AATTT
1 AATTT
20855139 AATTTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.39
Consensus pattern (37 bp):
AATTTCTTTTAGGGGGTAGAGTTGTAACGCCCTGAAT
Found at i:20858635 original size:25 final size:26
Alignment explanation
Indices: 20858569--20858660 Score: 91
Period size: 26 Copynumber: 3.6 Consensus size: 26
20858559 CTTATGAGTG
* * *
20858569 TCCCGATATATGGCTCTTCGTGAGCT
1 TCCCGTTACATGGCTCTTTGTGAGCT
* *
20858595 TCCTGATTA-AAGGCTCTTTGTGAGCT
1 TCCCG-TTACATGGCTCTTTGTGAGCT
*
20858621 TCCCGTTA-ATGGCTCTCTG-GAGCT
1 TCCCGTTACATGGCTCTTTGTGAGCT
*
20858645 TCTCGTTACATGGCTC
1 TCCCGTTACATGGCTC
20858661 ACATGAGCTT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
24 12 0.21
25 19 0.34
26 23 0.41
27 2 0.04
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.36
Consensus pattern (26 bp):
TCCCGTTACATGGCTCTTTGTGAGCT
Found at i:20858651 original size:24 final size:25
Alignment explanation
Indices: 20858569--20858685 Score: 96
Period size: 25 Copynumber: 4.6 Consensus size: 25
20858559 CTTATGAGTG
*
20858569 TCCCGATATATGGCTCT-TCGTGAGCT
1 TCCCGTTA-ATGGCTCTCT-GTGAGCT
* * *
20858595 TCCTGATTAAAGGCTCTTTGTGAGCT
1 TCCCG-TTAATGGCTCTCTGTGAGCT
20858621 TCCCGTTAATGGCTCTCTG-GAGCT
1 TCCCGTTAATGGCTCTCTGTGAGCT
* * *
20858645 TCTCGTTACATGGCTCAC-ATGAGCT
1 TCCCGTTA-ATGGCTCTCTGTGAGCT
*
20858670 TCCCATTAAATGGCTC
1 TCCCGTT-AATGGCTC
20858686 GAGAGAGAGA
Statistics
Matches: 75, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
24 12 0.16
25 37 0.49
26 23 0.31
27 3 0.04
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.34
Consensus pattern (25 bp):
TCCCGTTAATGGCTCTCTGTGAGCT
Found at i:20864202 original size:26 final size:26
Alignment explanation
Indices: 20864173--20864224 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
20864163 TTGTGATTAT
20864173 ATTTATTTTATAATATTGTAAGGTAA
1 ATTTATTTTATAATATTGTAAGGTAA
20864199 ATTTATTTTATAATATTGTAAGGTAA
1 ATTTATTTTATAATATTGTAAGGTAA
20864225 GTATTCTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (26 bp):
ATTTATTTTATAATATTGTAAGGTAA
Found at i:20868505 original size:20 final size:20
Alignment explanation
Indices: 20868482--20868522 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20868472 TCCTTAATTA
20868482 TACATAAATTTAATTTTATT
1 TACATAAATTTAATTTTATT
** *
20868502 TACATATTTTTTATTTTATT
1 TACATAAATTTAATTTTATT
20868522 T
1 T
20868523 TTGGCTTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (20 bp):
TACATAAATTTAATTTTATT
Found at i:20868665 original size:18 final size:19
Alignment explanation
Indices: 20868642--20868678 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
20868632 AAATGTTAAA
*
20868642 AATTAAATTTAT-TATAAT
1 AATTAAAATTATGTATAAT
20868660 AATTAAAATTATGTATAAT
1 AATTAAAATTATGTATAAT
20868679 TGATGAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
AATTAAAATTATGTATAAT
Found at i:20872078 original size:43 final size:41
Alignment explanation
Indices: 20872025--20872334 Score: 376
Period size: 43 Copynumber: 7.3 Consensus size: 41
20872015 ACGTCGCTAA
*
20872025 CTTTTGCGGCGCTTACAGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGAAAAAACGCCGCTAAAGATCATGTT
*
20872068 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCAAAAGATCATGTT
1 CTTTAGCGGCGCTTA-G-AAAAAACGCCGCTAAAGATCATGTT
* *
20872111 CTTTAGCGGCGCTTAGAAAAAAAGCCGCAAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAACGCCGCTAAAGATCATGTT
20872152 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-G-AAAAAACGCCGCTAAAGATCATGTT
20872195 CTTTAGCGGCGCTTAGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAACGCCGCTAAAGATCATGTT
* * *
20872236 CTTTAGCGGGGCTTTAGAAGAAAACGCCTCTAAA-AGTAATGTT
1 CTTTAGCGGCGC-TTAGAA-AAAACGCCGCTAAAGA-TCATGTT
* * *
20872279 CTATAGCGGCGCTT-GTTCAAAAATGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTAG--AAAAAACGCCGCTAAAGA-TCA-TGTT
*
20872321 TTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
20872335 GTTTCACAAA
Statistics
Matches: 242, Mismatches: 15, Indels: 21
0.87 0.05 0.08
Matches are distributed among these distances:
41 78 0.32
42 44 0.18
43 120 0.50
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25
Consensus pattern (41 bp):
CTTTAGCGGCGCTTAGAAAAAACGCCGCTAAAGATCATGTT
Found at i:20872144 original size:84 final size:84
Alignment explanation
Indices: 20872025--20872334 Score: 396
Period size: 84 Copynumber: 3.7 Consensus size: 84
20872015 ACGTCGCTAA
* *
20872025 CTTTTGCGGCGCTTACAGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAA
1 CTTTAGCGGCGCTT--AGAAAAAACGCCGCAAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAA
20872090 AACGCCGCAAAAGATCATGTT
64 AACGCCGCAAAAGATCATGTT
*
20872111 CTTTAGCGGCGCTTAGAAAAAAAGCCGCAAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAAA
1 CTTTAGCGGCGCTTAGAAAAAACGCCGCAAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAAA
*
20872176 CGCCGCTAAAGATCATGTT
66 CGCCGCAAAAGATCATGTT
* * *
20872195 CTTTAGCGGCGCTTAGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGGGCTTTA-GAAGAAA
1 CTTTAGCGGCGCTTAGAAAAAACGCCGCAAAAGATCATGTTCTTTAGCGGCGC-TTAGGAAAAAA
* *
20872259 ACGCCTCTAAAAG-TAATGTT
65 ACGCCGC-AAAAGATCATGTT
* * * *
20872279 CTATAGCGGCGCTT-GTTCAAAAATGCCGCTAAAAG-T-AGTGTTTTTTAGCGGCGCTT
1 CTTTAGCGGCGCTTAG--AAAAAACGCCGC-AAAAGATCA-TGTTCTTTAGCGGCGCTT
20872335 GTTTCACAAA
Statistics
Matches: 201, Mismatches: 17, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
83 1 0.00
84 151 0.75
85 32 0.16
86 17 0.08
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25
Consensus pattern (84 bp):
CTTTAGCGGCGCTTAGAAAAAACGCCGCAAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAAA
CGCCGCAAAAGATCATGTT
Found at i:20872775 original size:12 final size:12
Alignment explanation
Indices: 20872758--20872797 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
20872748 TTTTGAACCT
*
20872758 CTGCTTCTATCG
1 CTGCTTCTCTCG
20872770 CTGCTTCTCTCG
1 CTGCTTCTCTCG
20872782 CTGCTTCTCTCG
1 CTGCTTCTCTCG
20872794 CTGC
1 CTGC
20872798 GGCATCTGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.03, C:0.40, G:0.17, T:0.40
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:20878536 original size:9 final size:9
Alignment explanation
Indices: 20878519--20878760 Score: 148
Period size: 9 Copynumber: 27.8 Consensus size: 9
20878509 TATGTATTAA
*
20878519 GTAAATTAT
1 GTAAGTTAT
20878528 GTAAGTTAT
1 GTAAGTTAT
*
20878537 GTACGTGTA-
1 GTAAGT-TAT
20878546 -TAAGTTAT
1 GTAAGTTAT
* *
20878554 TTAAGTTTT
1 GTAAGTTAT
*
20878563 GT-A-TTAA
1 GTAAGTTAT
**
20878570 GTAAACTAT
1 GTAAGTTAT
*
20878579 GTAAGTTGT
1 GTAAGTTAT
20878588 GT-A-TTAT
1 GTAAGTTAT
*
20878595 GTAACTTAT
1 GTAAGTTAT
20878604 GTAAGTTAT
1 GTAAGTTAT
** *
20878613 CAAAGTAAT
1 GTAAGTTAT
*
20878622 GTATGTTAT
1 GTAAGTTAT
20878631 GTAAG-T-T
1 GTAAGTTAT
20878638 GTAAGTTAT
1 GTAAGTTAT
*
20878647 -TATGTATTAT
1 GTAAG--TTAT
* * *
20878657 ATAACTTCT
1 GTAAGTTAT
20878666 GTAAGTTAT
1 GTAAGTTAT
*
20878675 GTAAGTTGT
1 GTAAGTTAT
*
20878684 GTAAGCTAT
1 GTAAGTTAT
* *
20878693 TTCAGTTAT
1 GTAAGTTAT
20878702 GTAAGCTT-T
1 GTAAG-TTAT
20878711 GT-A-TTAT
1 GTAAGTTAT
20878718 GTAAGTTAT
1 GTAAGTTAT
*
20878727 GTAGGTTAT
1 GTAAGTTAT
*
20878736 GTAAGTTGT
1 GTAAGTTAT
*
20878745 GTAAATTAT
1 GTAAGTTAT
20878754 GTAAGTT
1 GTAAGTT
20878761 CTTGTACATA
Statistics
Matches: 174, Mismatches: 43, Indels: 32
0.70 0.17 0.13
Matches are distributed among these distances:
6 2 0.01
7 20 0.11
8 15 0.09
9 127 0.73
10 8 0.05
11 2 0.01
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:20878536 original size:25 final size:25
Alignment explanation
Indices: 20878508--20878612 Score: 106
Period size: 25 Copynumber: 4.2 Consensus size: 25
20878498 TAATATATAT
20878508 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
* *
20878533 TTATGTACGTGT-A-TAAGTTATTTAAG
1 TTATGTA--T-TAAGTAAATTATGTAAG
* *
20878559 TTTTGTATTAAGTAAACTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
* * *
20878584 TTGTGTATTATGTAACTTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
20878609 TTAT
1 TTAT
20878613 CAAAGTAATG
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
23 1 0.02
24 2 0.03
25 41 0.64
26 17 0.27
27 2 0.03
28 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (25 bp):
TTATGTATTAAGTAAATTATGTAAG
Found at i:20878722 original size:34 final size:35
Alignment explanation
Indices: 20878665--20878758 Score: 95
Period size: 34 Copynumber: 2.7 Consensus size: 35
20878655 ATATAACTTC
* * *
20878665 TGTAAGTTATGTAAGTTGTGTAAGCTATTTCA-GTTA
1 TGTAAGTTGTGTAA-TTATGTAAGCTATGT-AGGTTA
*
20878701 TGTAAGCTT-TGT-ATTATGTAAGTTATGTAGGTTA
1 TGTAAG-TTGTGTAATTATGTAAGCTATGTAGGTTA
20878735 TGTAAGTTGTGTAAATTATGTAAG
1 TGTAAGTTGTGT-AATTATGTAAG
20878759 TTCTTGTACA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
33 3 0.06
34 25 0.50
35 1 0.02
36 19 0.38
37 2 0.04
ACGTcount: A:0.29, C:0.03, G:0.23, T:0.45
Consensus pattern (35 bp):
TGTAAGTTGTGTAATTATGTAAGCTATGTAGGTTA
Found at i:20878974 original size:53 final size:53
Alignment explanation
Indices: 20878905--20879040 Score: 218
Period size: 53 Copynumber: 2.6 Consensus size: 53
20878895 TTTATAGCGG
*
20878905 GTAATGTATTTAAGTAACATACTTAAGTAAAAAATTTAACCAAATTTTAGTAA
1 GTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTAA
* * * *
20878958 TTAATGTATCTGAGTAACATATTTAAGTAAAAAATTTAACGAAATTTTAGTAA
1 GTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTAA
*
20879011 GTAATGTATTTAAGTAACTTATTTAAGTAA
1 GTAATGTATTTAAGTAACATATTTAAGTAA
20879041 TATATTCAAG
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 74 1.00
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (53 bp):
GTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTAA
Found at i:20879026 original size:13 final size:13
Alignment explanation
Indices: 20879008--20879059 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
20878998 GAAATTTTAG
*
20879008 TAAGTAATGTATT
1 TAAGTAATATATT
20879021 TAAGTAACT-TATT
1 TAAGTAA-TATATT
20879034 TAAGTAATATATT
1 TAAGTAATATATT
*
20879047 CAAGTAATATATT
1 TAAGTAATATATT
20879060 AAGAGTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
12 1 0.03
13 34 0.94
14 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:20879241 original size:53 final size:54
Alignment explanation
Indices: 20879172--20879283 Score: 172
Period size: 53 Copynumber: 2.1 Consensus size: 54
20879162 TTTATAGCGG
* *
20879172 GTAATGTATTTAAGTAACATATTTAAGTAAAAAAATTAACCAAATTTTAGTAAT
1 GTAATGTATCTAAGTAACATATTTAAGTAAAAAAATTAACCAAATTTAAGTAAT
* * *
20879226 -TAATGTATCTGAGTAACATATTTAAGTAAAAAATTTAACGAAATTTAAGTAAT
1 GTAATGTATCTAAGTAACATATTTAAGTAAAAAAATTAACCAAATTTAAGTAAT
20879279 GTAAT
1 GTAAT
20879284 ATATAAATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
53 48 0.92
54 4 0.08
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (54 bp):
GTAATGTATCTAAGTAACATATTTAAGTAAAAAAATTAACCAAATTTAAGTAAT
Found at i:20879889 original size:21 final size:21
Alignment explanation
Indices: 20879772--20879887 Score: 160
Period size: 21 Copynumber: 5.4 Consensus size: 21
20879762 CACTTCATTC
20879772 AACAGAAAATAGCAAAACAGAA
1 AACAGAAAATAG-AAAACAGAA
*
20879794 AACATAAAATAGAAAACAGAA
1 AACAGAAAATAGAAAACAGAA
* *
20879815 AACATAAAATAGAAAATAGAA
1 AACAGAAAATAGAAAACAGAA
*
20879836 AACAGAAAAATATAAAACAGAA
1 AACAG-AAAATAGAAAACAGAA
* *
20879858 AACAAAAAACAGAAAACAGAA
1 AACAGAAAATAGAAAACAGAA
20879879 AACAGAAAA
1 AACAGAAAA
20879888 CAAAAAATAA
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
21 55 0.65
22 29 0.35
ACGTcount: A:0.72, C:0.10, G:0.10, T:0.07
Consensus pattern (21 bp):
AACAGAAAATAGAAAACAGAA
Found at i:20879894 original size:7 final size:7
Alignment explanation
Indices: 20879772--20879893 Score: 138
Period size: 7 Copynumber: 17.3 Consensus size: 7
20879762 CACTTCATTC
20879772 AACAGAA
1 AACAGAA
*
20879779 AATAGCAA
1 AACAG-AA
20879787 AACAGAA
1 AACAGAA
*
20879794 AACATAA
1 AACAGAA
*
20879801 AATAGAA
1 AACAGAA
20879808 AACAGAA
1 AACAGAA
*
20879815 AACATAA
1 AACAGAA
*
20879822 AATAGAA
1 AACAGAA
*
20879829 AATAGAA
1 AACAGAA
20879836 AACAGAAA
1 AACAG-AA
* *
20879844 AATATAA
1 AACAGAA
20879851 AACAGAA
1 AACAGAA
*
20879858 AACAAAA
1 AACAGAA
20879865 AACAGAA
1 AACAGAA
20879872 AACAGAA
1 AACAGAA
20879879 AACAGAA
1 AACAGAA
20879886 AACA-AA
1 AACAGAA
20879892 AA
1 AA
20879894 ATAAAGAAAC
Statistics
Matches: 97, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
6 4 0.04
7 82 0.85
8 11 0.11
ACGTcount: A:0.73, C:0.11, G:0.10, T:0.07
Consensus pattern (7 bp):
AACAGAA
Found at i:20879940 original size:18 final size:19
Alignment explanation
Indices: 20879898--20879941 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
20879888 CAAAAAATAA
*
20879898 AGAAACATAAAAATGGTAC
1 AGAAACATAAAAATGCTAC
* *
20879917 AGAAACAT-AACATGCTAG
1 AGAAACATAAAAATGCTAC
20879935 AGAAACA
1 AGAAACA
20879942 GAAATTTCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.57, C:0.14, G:0.16, T:0.14
Consensus pattern (19 bp):
AGAAACATAAAAATGCTAC
Found at i:20881856 original size:47 final size:47
Alignment explanation
Indices: 20881768--20881859 Score: 121
Period size: 47 Copynumber: 2.0 Consensus size: 47
20881758 GTTAATTTCG
* **
20881768 GTAATATTTAAAAAAATTAGATAAAATTATCAATCTCAGTTTTTTAA
1 GTAATATTTAAAAAAATTAGATAAAAATAAAAATCTCAGTTTTTTAA
* * * *
20881815 GTAATATTTATAAAAATTAGGTAAAAATAAAAATTTTAGTTTTTT
1 GTAATATTTAAAAAAATTAGATAAAAATAAAAATCTCAGTTTTTT
20881860 TATTTCTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 38 1.00
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (47 bp):
GTAATATTTAAAAAAATTAGATAAAAATAAAAATCTCAGTTTTTTAA
Found at i:20881870 original size:19 final size:19
Alignment explanation
Indices: 20881847--20881896 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
20881837 AAAAATAAAA
20881847 ATTTTAGTTTTTTTA-TTTC
1 ATTTTA-TTTTTTTATTTTC
*
20881866 -TTTTTTATTTTTTATTTTC
1 ATTTTAT-TTTTTTATTTTC
20881885 ATTTTATTTTTT
1 ATTTTATTTTTT
20881897 GTAATTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 1 0.04
18 11 0.42
19 9 0.35
20 5 0.19
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.80
Consensus pattern (19 bp):
ATTTTATTTTTTTATTTTC
Found at i:20882197 original size:7 final size:7
Alignment explanation
Indices: 20882185--20882220 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
20882175 ATAACCCAAT
20882185 CCCTAAC
1 CCCTAAC
20882192 CCCTAAC
1 CCCTAAC
20882199 CCCTAAC
1 CCCTAAC
20882206 CCCTAAC
1 CCCTAAC
*
20882213 CCTTAAC
1 CCCTAAC
20882220 C
1 C
20882221 TTTAACCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.28, C:0.56, G:0.00, T:0.17
Consensus pattern (7 bp):
CCCTAAC
Found at i:20882225 original size:7 final size:7
Alignment explanation
Indices: 20882209--20882267 Score: 55
Period size: 7 Copynumber: 8.4 Consensus size: 7
20882199 CCCTAACCCC
*
20882209 TAACCCT
1 TAACCTT
20882216 TAACCTT
1 TAACCTT
20882223 TAACCTT
1 TAACCTT
20882230 TAACCTT
1 TAACCTT
* *
20882237 AAACCCT
1 TAACCTT
**
20882244 TAACCCA
1 TAACCTT
* *
20882251 TGACCTC
1 TAACCTT
20882258 TAACCTT
1 TAACCTT
20882265 TAA
1 TAA
20882268 TCCCTAACCC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.32, C:0.34, G:0.02, T:0.32
Consensus pattern (7 bp):
TAACCTT
Found at i:20882226 original size:14 final size:14
Alignment explanation
Indices: 20882195--20882248 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
20882185 CCCTAACCCC
* **
20882195 TAACCCCTAACCCC
1 TAACCCTTAACCTT
20882209 TAACCCTTAACCTT
1 TAACCCTTAACCTT
*
20882223 TAACCTTTAACCTT
1 TAACCCTTAACCTT
*
20882237 AAACCCTTAACC
1 TAACCCTTAACC
20882249 CATGACCTCT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.31, C:0.41, G:0.00, T:0.28
Consensus pattern (14 bp):
TAACCCTTAACCTT
Found at i:20882226 original size:21 final size:21
Alignment explanation
Indices: 20882185--20882286 Score: 73
Period size: 21 Copynumber: 4.8 Consensus size: 21
20882175 ATAACCCAAT
* **
20882185 CCCTAACCCCTAACCCCTAAC
1 CCCTAACCCTTAACCTTTAAC
20882206 CCCTAACCCTTAACCTTTAAC
1 CCCTAACCCTTAACCTTTAAC
** *
20882227 CTTTAA-CCTTAAACCCTTAAC
1 CCCTAACCCTT-AACCTTTAAC
* * *
20882248 CCATGA-CCTCTAACCTTTAAT
1 CCCTAACCCT-TAACCTTTAAC
*
20882269 CCCTAACCCCTAAACCTT
1 CCCTAA-CCCTTAACCTT
20882287 ATTTAATATA
Statistics
Matches: 63, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
20 4 0.06
21 49 0.78
22 7 0.11
23 3 0.05
ACGTcount: A:0.29, C:0.43, G:0.01, T:0.26
Consensus pattern (21 bp):
CCCTAACCCTTAACCTTTAAC
Found at i:20882256 original size:28 final size:29
Alignment explanation
Indices: 20882188--20882277 Score: 78
Period size: 28 Copynumber: 3.2 Consensus size: 29
20882178 ACCCAATCCC
* * **
20882188 TAACCCCTAACCCCTAACCCCT-AACCCT
1 TAACCCATAACCTCTAACCTTTAAACCCT
** *
20882216 TAACCTTTAACCTTTAACC-TTAAACCCT
1 TAACCCATAACCTCTAACCTTTAAACCCT
* *
20882244 TAACCCATGACCTCTAACCTTTAATCCC-
1 TAACCCATAACCTCTAACCTTTAAACCCT
20882272 TAACCC
1 TAACCC
20882278 CTAAACCTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
27 1 0.02
28 42 0.84
29 7 0.14
ACGTcount: A:0.30, C:0.42, G:0.01, T:0.27
Consensus pattern (29 bp):
TAACCCATAACCTCTAACCTTTAAACCCT
Found at i:20882391 original size:7 final size:7
Alignment explanation
Indices: 20882381--20882431 Score: 61
Period size: 7 Copynumber: 7.6 Consensus size: 7
20882371 CTCTTAACAT
20882381 CTAACCC
1 CTAACCC
20882388 CTAA--C
1 CTAACCC
*
20882393 TTAACCC
1 CTAACCC
20882400 CTAACCC
1 CTAACCC
*
20882407 TTAACCC
1 CTAACCC
*
20882414 ATAACCC
1 CTAACCC
20882421 CTAACCC
1 CTAACCC
20882428 CTAA
1 CTAA
20882432 TCTATAAACC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
5 4 0.11
7 33 0.89
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.20
Consensus pattern (7 bp):
CTAACCC
Found at i:20882397 original size:19 final size:19
Alignment explanation
Indices: 20882373--20882431 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 19
20882363 ATCCCTAACT
*
20882373 CTTAACATCTAACCCCTAA
1 CTTAACACCTAACCCCTAA
* *
20882392 CTTAACCCCTAACCCTTAA
1 CTTAACACCTAACCCCTAA
* *
20882411 CCCATAACCCCTAACCCCTAA
1 --CTTAACACCTAACCCCTAA
20882432 TCTATAAACC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.34, C:0.44, G:0.00, T:0.22
Consensus pattern (19 bp):
CTTAACACCTAACCCCTAA
Found at i:20882438 original size:21 final size:20
Alignment explanation
Indices: 20882381--20882438 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
20882371 CTCTTAACAT
20882381 CTAACCCCTAACT-TAACCC
1 CTAACCCCTAACTATAACCC
* *
20882400 CTAACCCTTAACCCATAACCC
1 CTAACCCCTAA-CTATAACCC
20882421 CTAACCCCTAATCTATAA
1 CTAACCCCTAA-CTATAA
20882439 ACCTTAAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 10 0.31
20 1 0.03
21 21 0.66
ACGTcount: A:0.34, C:0.43, G:0.00, T:0.22
Consensus pattern (20 bp):
CTAACCCCTAACTATAACCC
Found at i:20883536 original size:75 final size:75
Alignment explanation
Indices: 20883377--20883542 Score: 185
Period size: 75 Copynumber: 2.2 Consensus size: 75
20883367 GGCGTTTTTT
* * * * * *
20883377 AATAAGCGCCACTAACACTAATCTACCTCAAGACCAAACGGTGCATTTTGGTTAAGATATTTGTG
1 AATAAACGCCACTAATACTAATATACCTCAAAACCAAACGCTGCATTTTGGTTAAGATATTTGCG
*
20883442 GCGTTTTATC
66 GCGTCTTATC
* * * *
20883452 -GTAATACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTG
1 AATAA-ACGCCACTAATACTAATATACCTCAAAACCAAACGCTGCATTTTGGTTAAGATA-TTTG
20883516 CGGCG-CTTA-C
64 CGGCGTCTTATC
20883526 AAATAAACGCCACTAAT
1 -AATAAACGCCACTAAT
20883543 GATGTTCTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
74 4 0.05
75 60 0.80
76 11 0.15
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (75 bp):
AATAAACGCCACTAATACTAATATACCTCAAAACCAAACGCTGCATTTTGGTTAAGATATTTGCG
GCGTCTTATC
Found at i:20883857 original size:74 final size:75
Alignment explanation
Indices: 20883777--20883916 Score: 192
Period size: 74 Copynumber: 1.9 Consensus size: 75
20883767 GTTTTTTTAA
* * *
20883777 AAACGCCACTAACACTAATCTACCTCAAGACCAAACGGTGCGTTTTCGTTAAGATA-TTTGCGGC
1 AAACGCCACTAACACTAATATACCTCAAAACCAAACGCTGCGTTTTCGTTAAGATATTTTGCGGC
20883841 GTTTTATCGT
66 GTTTTATCGT
** * * * *
20883851 AAACGCCACTAATTCTAATATACCTCAAAACCAAGCGCTGTGTTTTGGTTAAGGTATTTTGCGGC
1 AAACGCCACTAACACTAATATACCTCAAAACCAAACGCTGCGTTTTCGTTAAGATATTTTGCGGC
20883916 G
66 G
20883917 CTTACAAATA
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
74 47 0.84
75 9 0.16
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (75 bp):
AAACGCCACTAACACTAATATACCTCAAAACCAAACGCTGCGTTTTCGTTAAGATATTTTGCGGC
GTTTTATCGT
Found at i:20883968 original size:188 final size:189
Alignment explanation
Indices: 20883651--20884052 Score: 562
Period size: 188 Copynumber: 2.1 Consensus size: 189
20883641 TTCTTTAGCT
* * ** * *
20883651 GCGTTTTATAGAAAACGCCACTAATTCTAATATACAATTGATCCAAACGCTGCGTTTTGGTTAAT
1 GCGTTTTATCGTAAACGCCACTAATTCTAATATACAATAAAACCAAACGCTGCGTTTTGGTTAAG
* * *
20883716 GTATTTTGCGGCGCTTGAAAGTAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTTTAAAAAC
66 GTATTTTGCGGCGCTTGAAAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTGTTTAAAAAC
*
20883781 GCCACTAACACTAATCTACCTCAAGACCAAACGGTGCGTTTTCGTTAAGATA-TTTGCG
131 GCCACTAACACTAATCTACCTCAAGACCAAACGCTGCGTTTTCGTTAAGATATTTTGCG
* * *
20883839 GCGTTTTATCGTAAACGCCACTAATTCTAATATAC-CTCAAAACCAAGCGCTGTGTTTTGGTTAA
1 GCGTTTTATCGTAAACGCCACTAATTCTAATATACAAT-AAAACCAAACGCTGCGTTTTGGTTAA
20883903 GGTATTTTGCGGCGCTT-ACAAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTGTTTAAAA
65 GGTATTTTGCGGCGCTTGA-AAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTGTTTAAAA
* * * * *
20883967 ACGTCACTAATACTAATCTACCTCGAGACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCG
129 ACGCCACTAACACTAATCTACCTCAAGACCAAACGCTGCGTTTTCGTTAAGATATTTTGCG
* *
20884028 GCG-CTTA-CAATAAACGCCACTAATT
1 GCGTTTTATC-GTAAACGCCACTAATT
20884053 ATGTTCTTTT
Statistics
Matches: 190, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
187 3 0.02
188 178 0.94
189 9 0.05
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (189 bp):
GCGTTTTATCGTAAACGCCACTAATTCTAATATACAATAAAACCAAACGCTGCGTTTTGGTTAAG
GTATTTTGCGGCGCTTGAAAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTGTTTAAAAAC
GCCACTAACACTAATCTACCTCAAGACCAAACGCTGCGTTTTCGTTAAGATATTTTGCG
Found at i:20884037 original size:114 final size:113
Alignment explanation
Indices: 20883851--20884088 Score: 368
Period size: 114 Copynumber: 2.1 Consensus size: 113
20883841 GTTTTATCGT
* * *
20883851 AAACGCCACTAATTCTAATATACCTCAAAACCAAGCGCTGTGTTTTGGTTAAGGTATTTTGCGGC
1 AAACGCCACTAATACTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
20883916 GCTTACAAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTGTTTAA
66 GCTTAC-AATAAACGCCACTAATGATGTTCTTTTACGGCGTTTGTTTAA
* * * *
20883965 AAACGTCACTAATACTAATCTACCTCGAGACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
1 AAACGCCACTAATACTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
* * *
20884030 GCTTACAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTTTAG
66 GCTTACAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTGTTTAA
*
20884078 AAATGCCACTA
1 AAACGCCACTA
20884089 GTTGTTCAGG
Statistics
Matches: 112, Mismatches: 12, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
113 48 0.43
114 64 0.57
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (113 bp):
AAACGCCACTAATACTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
GCTTACAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTGTTTAA
Found at i:20885245 original size:20 final size:19
Alignment explanation
Indices: 20885220--20885269 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
20885210 TAATTTAACC
20885220 TTTTATATATTTTTTTTAGA
1 TTTTATATATTTTTTTTA-A
**
20885240 TTTTAT-T-TACTTTTTAA
1 TTTTATATATTTTTTTTAA
20885257 -TTTATATATTTTT
1 TTTTATATATTTTT
20885270 ATAAAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
16 5 0.21
17 2 0.08
18 10 0.42
19 1 0.04
20 6 0.25
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTTATATATTTTTTTTAA
Found at i:20885786 original size:7 final size:7
Alignment explanation
Indices: 20885774--20885798 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20885764 TTTATTATGA
20885774 TTATCTT
1 TTATCTT
20885781 TTATCTT
1 TTATCTT
20885788 TTATCTT
1 TTATCTT
20885795 TTAT
1 TTAT
20885799 TAGGATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (7 bp):
TTATCTT
Found at i:20888312 original size:23 final size:22
Alignment explanation
Indices: 20888281--20888337 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
20888271 CAATAGTGTA
*
20888281 TCCTCTGAGGAAGGGATAAAATG
1 TCCTTTGAGGAAGGGA-AAAATG
*
20888304 TCCTTTGA-GAAGGGAAAATTG
1 TCCTTTGAGGAAGGGAAAAATG
20888325 TACCTTATGAGGA
1 T-CCTT-TGAGGA
20888338 GATAATGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 6 0.21
22 11 0.38
23 10 0.34
24 2 0.07
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.26
Consensus pattern (22 bp):
TCCTTTGAGGAAGGGAAAAATG
Found at i:20892967 original size:17 final size:17
Alignment explanation
Indices: 20892923--20892969 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
20892913 AATTCAATTT
*
20892923 TAATATAAGT-ATTCAA
1 TAATATAAATAATTCAA
**
20892939 TAGGACTAAATAATTCAA
1 TAATA-TAAATAATTCAA
20892957 TAATATAAATAAT
1 TAATATAAATAAT
20892970 ATAAAATGTG
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
16 3 0.12
17 12 0.50
18 9 0.38
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (17 bp):
TAATATAAATAATTCAA
Found at i:20893265 original size:31 final size:30
Alignment explanation
Indices: 20893230--20893289 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
20893220 GGAGGTGGGA
*
20893230 TGGGAAGAGAATAAAAGTTTTAGGGAAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGAAAAAG
* * *
20893261 TGGGAGGGAGTAAAAATTTTAGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGAAAAA
20893290 TAAAATGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.45, C:0.00, G:0.35, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGAAAAAG
Found at i:20893521 original size:9 final size:9
Alignment explanation
Indices: 20893503--20893539 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
20893493 TATAGTTTGA
*
20893503 TATTCTAAT
1 TATTCGAAT
20893512 TATTCGAAT
1 TATTCGAAT
*
20893521 TATTCGAGT
1 TATTCGAAT
20893530 TATTCGAAT
1 TATTCGAAT
20893539 T
1 T
20893540 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:20898670 original size:22 final size:22
Alignment explanation
Indices: 20898645--20898695 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 22
20898635 TCTTAACTCT
20898645 TATTTACTGAA-ATATTTAGGCG
1 TATTTACT-AATATATTTAGGCG
*
20898667 TATTTTCTAACTTATATTTAGGCG
1 TATTTACTAA--TATATTTAGGCG
20898691 TATTT
1 TATTT
20898696 TCTTTGCTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 2 0.08
22 7 0.28
24 16 0.64
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (22 bp):
TATTTACTAATATATTTAGGCG
Found at i:20902125 original size:50 final size:50
Alignment explanation
Indices: 20902040--20902500 Score: 260
Period size: 50 Copynumber: 9.3 Consensus size: 50
20902030 AACTGTGATG
* * * * * *
20902040 TCGGGAAAGTAAGATTCGCTGTCGTAGCTTTAATCTATTCCATTACACCGC
1 TCGGG-AAGTAAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGC
* * ** ***
20902091 TAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT-TCTTAACTGCA-ATT
1 TCGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTAT-TCCACTGCACCGC
* * *
20902140 TCGAGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCATCGC
1 TCG-GGAAGTAAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGC
** **
20902191 -CTGGGAAGTAAGATTCACCGTTGTAGCTTCAA--TATTTAACTGCAATG-
1 TC-GGGAAGTAAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGC
** ** * * * *
20902238 TCGGGAAAACAAGATTCGTCGTTGTGGCTTTAATCTGTTCCATTGCACCGC
1 TCGGG-AAGTAAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGC
* * * * ** * **
20902289 TTGGGAAGTAAGATTCGCTGTTGTAGCTTCAATAT-TTTAACTGGAATG-
1 TCGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGC
** ** * *
20902337 TCGGGAAAACAAGATTTGCTGTTGTGGCTTCAATCTATTCCACTGCACCGC
1 TCGGG-AAGTAAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGC
* * ** **
20902388 -CTGAGAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAACTGCAATG-
1 TC-GGGAAGTAAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGC
* * * * * *
20902437 TCGGGGAAGCAAGGTTCGCCATTGTTGCTTCAATCTGTTCCACTGCACCGC
1 TC-GGGAAGTAAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGC
*
20902488 -CTAGGAAGTAAGA
1 TC-GGGAAGTAAGA
20902501 CCTGATGCGA
Statistics
Matches: 302, Mismatches: 92, Indels: 33
0.71 0.22 0.08
Matches are distributed among these distances:
47 3 0.01
48 36 0.12
49 35 0.12
50 216 0.72
51 12 0.04
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (50 bp):
TCGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGC
Found at i:20902197 original size:100 final size:99
Alignment explanation
Indices: 20902021--20902500 Score: 570
Period size: 100 Copynumber: 4.8 Consensus size: 99
20902011 TCGTAACTTT
** ** * * * * * * *
20902021 AATCTGTTTAACTGTGATGTCGGGAAAGTAAGATTCGCTGTCGTAGCTTTAATCTATTCCATTAC
1 AATCT-TTTAACTGCAATGTCGGGAAAACAAGATTCGCCGTTGTGGCTTCAATCTGTTCCACTGC
*
20902086 ACCG-CTAGGGAAGTAAGATTCACCGTTGTGGCTTC
65 ACCGCCT-GGGAAGTAAGATTCACCGTTGTAGCTTC
* * * *
20902121 AATCTTCTTAACTGCAATTTCGAGG-AAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTG
1 AATCTT-TTAACTGCAATGTCG-GGAAAACAAGATTCGCCGTTGTGGCTTCAATCTGTTCCACTG
*
20902185 CATCGCCTGGGAAGTAAGATTCACCGTTGTAGCTTC
64 CACCGCCTGGGAAGTAAGATTCACCGTTGTAGCTTC
* * * *
20902221 AAT-ATTTAACTGCAATGTCGGGAAAACAAGATTCGTCGTTGTGGCTTTAATCTGTTCCATTGCA
1 AATCTTTTAACTGCAATGTCGGGAAAACAAGATTCGCCGTTGTGGCTTCAATCTGTTCCACTGCA
* * *
20902285 CCGCTTGGGAAGTAAGATTCGCTGTTGTAGCTTC
66 CCGCCTGGGAAGTAAGATTCACCGTTGTAGCTTC
* * * * *
20902319 AATATTTTAACTGGAATGTCGGGAAAACAAGATTTGCTGTTGTGGCTTCAATCTATTCCACTGCA
1 AATCTTTTAACTGCAATGTCGGGAAAACAAGATTCGCCGTTGTGGCTTCAATCTGTTCCACTGCA
*
20902384 CCGCCTGAGAAGTAAGATTCACCGTTGTAGCTTC
66 CCGCCTGGGAAGTAAGATTCACCGTTGTAGCTTC
* * * * *
20902418 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGGTTCGCCATTGTTGCTTCAATCTGTTCCACTGC
1 AATC-TTTTAACTGCAATGTCGGGAAAACAAGATTCGCCGTTGTGGCTTCAATCTGTTCCACTGC
*
20902483 ACCGCCTAGGAAGTAAGA
65 ACCGCCTGGGAAGTAAGA
20902501 CCTGATGCGA
Statistics
Matches: 325, Mismatches: 49, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
97 2 0.01
98 82 0.25
99 88 0.27
100 149 0.46
101 4 0.01
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (99 bp):
AATCTTTTAACTGCAATGTCGGGAAAACAAGATTCGCCGTTGTGGCTTCAATCTGTTCCACTGCA
CCGCCTGGGAAGTAAGATTCACCGTTGTAGCTTC
Found at i:20902716 original size:44 final size:45
Alignment explanation
Indices: 20902519--20902718 Score: 133
Period size: 44 Copynumber: 4.5 Consensus size: 45
20902509 GATCTACTCT
* * * * * *
20902519 ACTGCAACCTCAGAGAGATAAGA-TCTATTGT-TTTAATCCGCTCC
1 ACTGCAACCTCAGGGAGATAAGATTC-ACTATCTTCAGTCTGCTCC
* * * * ** *
20902563 ATTGTAACTTCAGGGAGATAGGATT-ACTGGCTTCAATCTGCTCC
1 ACTGCAACCTCAGGGAGATAAGATTCACTATCTTCAGTCTGCTCC
* *
20902607 ACTGCAAACTCAGGGAGATAAGATTCACTATCTTCAGTCTGCCCC
1 ACTGCAACCTCAGGGAGATAAGATTCACTATCTTCAGTCTGCTCC
* * * * * *
20902652 ACTACAACTTTATGGG-GATAATACTT-GCTTTCTT-AGTCTGCTCC
1 ACTGCAACCTCA-GGGAGATAAGA-TTCACTATCTTCAGTCTGCTCC
*
20902696 GCTGCAACCTCAGGGAGATAAGA
1 ACTGCAACCTCAGGGAGATAAGA
20902719 CCTGATGCGA
Statistics
Matches: 119, Mismatches: 31, Indels: 12
0.73 0.19 0.07
Matches are distributed among these distances:
43 6 0.05
44 72 0.61
45 36 0.30
46 5 0.04
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (45 bp):
ACTGCAACCTCAGGGAGATAAGATTCACTATCTTCAGTCTGCTCC
Found at i:20902903 original size:88 final size:88
Alignment explanation
Indices: 20902811--20903083 Score: 312
Period size: 88 Copynumber: 3.1 Consensus size: 88
20902801 GGATTATTGG
* * * * * * ** *
20902811 CTTCGATCTGCTTCATTGCCAATACAAGAAGGCAAGATCTGGTGTTTTTGACCTGCTCCGTTGCA
1 CTTCGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTGCA
*
20902876 ACCCAGGGAGGCAAGGCTGGTGT
66 ACCCAGGGAGGCAAGGCTAGTGT
* * * * * * *
20902899 CTTCGATCTACTACGCTACCAGTATAGGAAGGCAAGATCTGCTATCTTCAACTTGCTCCACTGCA
1 CTTCGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTGCA
*
20902964 ACCCAGGGAGGTAAGGCTAGTGT
66 ACCCAGGGAGGCAAGGCTAGTGT
* ** * * *
20902987 CTTCGATCTGTTTCACTGTTAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTACTCTGCTGTA
1 CTTCGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTGCA
*
20903052 ACCCCGGGAGGCAAGGCTAGTGT
66 ACCCAGGGAGGCAAGGCTAGTGT
*
20903075 CTTTGATCT
1 CTTCGATCT
20903084 ACTCTACTAT
Statistics
Matches: 151, Mismatches: 34, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
88 151 1.00
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (88 bp):
CTTCGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTGCA
ACCCAGGGAGGCAAGGCTAGTGT
Found at i:20904430 original size:21 final size:21
Alignment explanation
Indices: 20904406--20904454 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
20904396 TAGCCTCTCT
20904406 ATTTTTACTTTTTCATTTTTC
1 ATTTTTACTTTTTCATTTTTC
* * *
20904427 ATTTTCATTTTTTTATTTTTC
1 ATTTTTACTTTTTCATTTTTC
20904448 ACTTTTT
1 A-TTTTT
20904455 TTCGACTCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.73
Consensus pattern (21 bp):
ATTTTTACTTTTTCATTTTTC
Found at i:20904439 original size:15 final size:17
Alignment explanation
Indices: 20904421--20904457 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
20904411 TACTTTTTCA
20904421 TTTTTCA-TTTTCA-TT
1 TTTTTCATTTTTCACTT
20904436 TTTTT-ATTTTTCACTT
1 TTTTTCATTTTTCACTT
20904452 TTTTTC
1 TTTTTC
20904458 GACTCAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.05
15 11 0.58
16 7 0.37
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCATTTTTCACTT
Found at i:20905299 original size:13 final size:13
Alignment explanation
Indices: 20905270--20905347 Score: 72
Period size: 12 Copynumber: 6.1 Consensus size: 13
20905260 TTTTTCTTTC
20905270 TTTTTATTTTGATT
1 TTTTTATTTTGA-T
20905284 TTTTTATTTTGAT
1 TTTTTATTTTGAT
**
20905297 TTTTTA-TTAAAT
1 TTTTTATTTTGAT
*
20905309 TTTTTATTTCGA-
1 TTTTTATTTTGAT
* *
20905321 TTTTTCTTTT-CT
1 TTTTTATTTTGAT
20905333 TTTTTGATTTTGAT
1 TTTTT-ATTTTGAT
20905347 T
1 T
20905348 GTGATTTTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
12 23 0.45
13 14 0.27
14 14 0.27
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.74
Consensus pattern (13 bp):
TTTTTATTTTGAT
Found at i:20905299 original size:25 final size:24
Alignment explanation
Indices: 20905271--20905347 Score: 73
Period size: 25 Copynumber: 3.1 Consensus size: 24
20905261 TTTTCTTTCT
*
20905271 TTTTATTTTGATTTTTTTATTTTGA
1 TTTT-TTTTAATTTTTTTATTTTGA
* *
20905296 TTTTTTATTAAATTTTTTATTTCGA
1 TTTTTT-TTAATTTTTTTATTTTGA
** *
20905321 TTTTTCTTTTCTTTTTTGATTTTGA
1 TTTTT-TTTAATTTTTTTATTTTGA
20905346 TT
1 TT
20905348 GTGATTTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
24 2 0.05
25 39 0.93
26 1 0.02
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.74
Consensus pattern (24 bp):
TTTTTTTTAATTTTTTTATTTTGA
Found at i:20914341 original size:30 final size:30
Alignment explanation
Indices: 20914296--20914417 Score: 145
Period size: 30 Copynumber: 4.1 Consensus size: 30
20914286 CATGGCCGTA
* *
20914296 TGTCTAGCCCGTGTGTCTCACACGACTGTG
1 TGTCCAGCTCGTGTGTCTCACACGACTGTG
* * *
20914326 TGTCCAGCTCGTGTGTCTCACATGGCTATG
1 TGTCCAGCTCGTGTGTCTCACACGACTGTG
* * ** *
20914356 TGTCCAGCTCATGTGTCTCACAAGGTTGTA
1 TGTCCAGCTCGTGTGTCTCACACGACTGTG
*
20914386 TGTCCAGCTCGTGTGTCTCACACGACCGTG
1 TGTCCAGCTCGTGTGTCTCACACGACTGTG
20914416 TG
1 TG
20914418 GGAAGGCCTA
Statistics
Matches: 76, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 76 1.00
ACGTcount: A:0.15, C:0.28, G:0.26, T:0.31
Consensus pattern (30 bp):
TGTCCAGCTCGTGTGTCTCACACGACTGTG
Found at i:20916036 original size:6 final size:6
Alignment explanation
Indices: 20916025--20916076 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
20916015 GAAATCTAAG
* * *
20916025 AAATAA AAATAAA ACAACTAA AAACAA AAACAA AAATAA AACTAA AAATAA
1 AAATAA AAAT-AA A-AA-TAA AAATAA AAATAA AAATAA AAATAA AAATAA
20916076 A
1 A
20916077 TTTGAAAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 28 0.72
7 5 0.13
8 5 0.13
9 1 0.03
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.12
Consensus pattern (6 bp):
AAATAA
Found at i:20916065 original size:12 final size:13
Alignment explanation
Indices: 20916028--20916076 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
20916018 ATCTAAGAAA
20916028 TAAAAATAAAACAAC
1 TAAAAAT-AAA-AAC
*
20916043 TAAAAACAAAAAC
1 TAAAAATAAAAAC
20916056 -AAAAAT-AAAAC
1 TAAAAATAAAAAC
20916067 TAAAAATAAA
1 TAAAAATAAA
20916077 TTTGAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 5 0.17
12 11 0.37
13 5 0.17
14 3 0.10
15 6 0.20
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (13 bp):
TAAAAATAAAAAC
Found at i:20918828 original size:12 final size:12
Alignment explanation
Indices: 20918811--20918840 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
20918801 CATGGCTTAA
20918811 CACACGACCTAG
1 CACACGACCTAG
20918823 CACACGACCTAG
1 CACACGACCTAG
20918835 CACACG
1 CACACG
20918841 GAGGTCTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.43, G:0.17, T:0.07
Consensus pattern (12 bp):
CACACGACCTAG
Found at i:20926064 original size:20 final size:20
Alignment explanation
Indices: 20926041--20926088 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
20926031 AACCACTCCG
*
20926041 TTTACTTTCTTACCATTCCA
1 TTTACTTACTTACCATTCCA
* * *
20926061 TTTACTCACTTTCCATTTCA
1 TTTACTTACTTACCATTCCA
20926081 TTTACTTA
1 TTTACTTA
20926089 GCATAAACTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.27, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTACTTACTTACCATTCCA
Found at i:20926996 original size:35 final size:35
Alignment explanation
Indices: 20926957--20927033 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
20926947 CCTGCAAAAT
20926957 ACACCAATGCTCATAAA-AGCTAGTCCAACCGAAAC
1 ACACCAATGCTCA-AAAGAGCTAGTCCAACCGAAAC
***
20926992 ACACCAATGCTCAAAAGAGCTAGTCCCTTCGAAAC
1 ACACCAATGCTCAAAAGAGCTAGTCCAACCGAAAC
20927027 ACACCAA
1 ACACCAA
20927034 ACAGAGAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 3 0.08
35 35 0.92
ACGTcount: A:0.42, C:0.32, G:0.12, T:0.14
Consensus pattern (35 bp):
ACACCAATGCTCAAAAGAGCTAGTCCAACCGAAAC
Found at i:20931318 original size:25 final size:24
Alignment explanation
Indices: 20931290--20931336 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
20931280 AATGTAAATG
*
20931290 TAAAAATTAAATTAAAACAAAATTA
1 TAAAAA-TAAAATAAAACAAAATTA
*
20931315 TAAAAATAAAATAAAATAAAAT
1 TAAAAATAAAATAAAACAAAAT
20931337 AATGGCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (24 bp):
TAAAAATAAAATAAAACAAAATTA
Found at i:20931366 original size:31 final size:31
Alignment explanation
Indices: 20931319--20931393 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
20931309 AAATTATAAA
* *
20931319 AATA-AAATAAAATAAAATAATGGCTAAATT
1 AATAGAAATAAAGTAAAATAATAGCTAAATT
20931349 AATAGAAATAAAGTAAAATAATAGCTAAATT
1 AATAGAAATAAAGTAAAATAATAGCTAAATT
20931380 AATAGAAATAAAGT
1 AATAGAAATAAAGT
20931394 GTTCCTAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
30 4 0.10
31 38 0.90
ACGTcount: A:0.63, C:0.03, G:0.09, T:0.25
Consensus pattern (31 bp):
AATAGAAATAAAGTAAAATAATAGCTAAATT
Found at i:20942876 original size:16 final size:15
Alignment explanation
Indices: 20942852--20942881 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
20942842 TGGGTTGAGA
20942852 AAATTATTTAATTAG
1 AAATTATTTAATTAG
20942867 AAATTAATTTAATTA
1 AAATT-ATTTAATTA
20942882 ATTAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AAATTATTTAATTAG
Found at i:20942896 original size:20 final size:20
Alignment explanation
Indices: 20942859--20942897 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20942849 AGAAAATTAT
*
20942859 TTAATTAGAAATTAATTTAA
1 TTAATTAGAAATAAATTTAA
20942879 TTAATTA-AAATAATATTTA
1 TTAATTAGAAATAA-ATTTA
20942898 TTTTGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TTAATTAGAAATAAATTTAA
Found at i:20945076 original size:22 final size:22
Alignment explanation
Indices: 20944998--20945069 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
20944988 CTTACGCAAA
* **
20944998 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
20945020 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
20945042 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
20945064 CATGAG
1 CATGAG
20945070 GGTTTAGAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:20959248 original size:171 final size:172
Alignment explanation
Indices: 20958915--20959248 Score: 442
Period size: 171 Copynumber: 1.9 Consensus size: 172
20958905 TTATATATCA
*
20958915 TAATTTAATATCAAGTACCATTAAGGTAATCTATACATGTATCATCACATTTCATAGCATATTGC
1 TAATTTAATATCAAGTACCATTAAGG-AATCTATACATGTATCATCACATTTCATAGCATATTAC
* ** *
20958980 TTTGATGTTATGAATTGAGAGTCTCAACTAAGGTCTTTAGACCATATAGGTCTATACCATATTTC
65 TTTGATATTATGAATTGAGAGTCTCAACTAAGGTCTTTAGACCATATAAATCCATACCATATTTC
* * *
20959045 ATTCATATCACTATGGCCACTCACATCAAAGTTACATTATTCT
130 ATTCATATCACTACGACCACTCACACCAAAGTTACATTATTCT
* * * * *
20959088 TAATTTCATATCAAGTGCCATTAAGG-CTCTATACATGTATCATCACTTTTCATAGCATATTATT
1 TAATTTAATATCAAGTACCATTAAGGAATCTATACATGTATCATCACATTTCATAGCATATTACT
* * *
20959152 TTGATATTATTAACTT-AG-GTTCTCAGCTAAGGTCTTTAGACCATATAAATCCATACCATGTTT
66 TTGATATTATGAA-TTGAGAG-TCTCAACTAAGGTCTTTAGACCATATAAATCCATACCATATTT
* *
20959215 CATTCATATTC-CTACGACCACTTATACCAAAGTT
129 CATTCATA-TCACTACGACCACTCACACCAAAGTT
20959249 GTAATGACCT
Statistics
Matches: 140, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
170 1 0.01
171 111 0.79
172 4 0.03
173 24 0.17
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (172 bp):
TAATTTAATATCAAGTACCATTAAGGAATCTATACATGTATCATCACATTTCATAGCATATTACT
TTGATATTATGAATTGAGAGTCTCAACTAAGGTCTTTAGACCATATAAATCCATACCATATTTCA
TTCATATCACTACGACCACTCACACCAAAGTTACATTATTCT
Found at i:20959655 original size:24 final size:24
Alignment explanation
Indices: 20959628--20959675 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
20959618 TTTAAAGAAA
20959628 AATAAATCTTGTCATCCTTTTTAT
1 AATAAATCTTGTCATCCTTTTTAT
* *
20959652 AATAAATCTTTTCATCTTTTTTAT
1 AATAAATCTTGTCATCCTTTTTAT
20959676 TCTTCTCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.15, G:0.02, T:0.54
Consensus pattern (24 bp):
AATAAATCTTGTCATCCTTTTTAT
Found at i:20976077 original size:2 final size:2
Alignment explanation
Indices: 20976028--20976062 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
20976018 ATGTGATTTG
20976028 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20976063 GCTTTCTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20978931 original size:127 final size:126
Alignment explanation
Indices: 20978680--20978907 Score: 291
Period size: 127 Copynumber: 1.8 Consensus size: 126
20978670 AAAGTCATAA
* * *
20978680 TTTAAAAGGATATTTTGCTATTTAGGTTTAACGAAAAGATCGAAACCCCGTAAGTTAGGGTACAA
1 TTTAAAACGATATTTTGCTATTCAGGTTTAACGAAAAAATCGAAACCCCGTAAGTTAGGGTACAA
* * ** *
20978745 TTCCTCGAATCACCAAAGCGCATAAATATTGCCTTATCGGGACTTCATTTATCTTTTGAAAT
66 TTCCTCGAATCACCAAAGCACAGAAATATTGCCTTATCGAAAATT-ATTTATCTTTTGAAAT
* * * *
20978807 TTTAAAACGATATTTTGCTATTCAGTTTTAGC-AAGAAAATCGAAACCCTGTAAGTTAGGGTACG
1 TTTAAAACGATATTTTGCTATTCAGGTTTAACGAA-AAAATCGAAACCCCGTAAGTTAGGGTACA
*
20978871 ATTTCTCGAATCACCGAAA-CAC-GAAATATTGCCTTAT
65 ATTCCTCGAATCACC-AAAGCACAGAAATATTGCCTTAT
20978908 TTTTAAAATT
Statistics
Matches: 89, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
126 16 0.18
127 70 0.79
128 3 0.03
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (126 bp):
TTTAAAACGATATTTTGCTATTCAGGTTTAACGAAAAAATCGAAACCCCGTAAGTTAGGGTACAA
TTCCTCGAATCACCAAAGCACAGAAATATTGCCTTATCGAAAATTATTTATCTTTTGAAAT
Found at i:20981195 original size:89 final size:89
Alignment explanation
Indices: 20981043--20981502 Score: 668
Period size: 89 Copynumber: 5.2 Consensus size: 89
20981033 TGACATGATG
* * * * * *
20981043 AGATCCGCTATCTACAGTCTGCTCCACTGCAAACTCAAGGAGACGAGGCTGGTGTCTTTGATCTG
1 AGATCTGCTATCTTCAGTCTGCTCCGCTGCAAACTCAGGGAGGCGAGGCTGGTGTCTTCGATCTG
* * *
20981108 CTTCGCTGCCAATATATGAAGACA
66 CTTCGCTGCTAATACAGGAAGACA
*
20981132 AGATCTGCTATCTTCAGTCTGCTCCGCTGTAAACTCAGGGAGGCGAGGCTGGTGTCTTCGATCTG
1 AGATCTGCTATCTTCAGTCTGCTCCGCTGCAAACTCAGGGAGGCGAGGCTGGTGTCTTCGATCTG
* * *
20981197 TTTCGCTGCTAATACAAGAAGATA
66 CTTCGCTGCTAATACAGGAAGACA
* * * * *
20981221 AGACCTGATATCTTCAGTCTGCTCCGCTGTAAACTCAAGGAGGCGAGGCTAGTGTCTTCGATCTG
1 AGATCTGCTATCTTCAGTCTGCTCCGCTGCAAACTCAGGGAGGCGAGGCTGGTGTCTTCGATCTG
20981286 CTTCGCTGCTAATACAGGAAGACA
66 CTTCGCTGCTAATACAGGAAGACA
* * * *
20981310 AGATCTACTATCTTCAGTCTACTCCACTGCAAACTCAGGGAGGTGAGGCTGGTGTCTTCGATCTG
1 AGATCTGCTATCTTCAGTCTGCTCCGCTGCAAACTCAGGGAGGCGAGGCTGGTGTCTTCGATCTG
20981375 CTTCGCTGCTAATACAGGAAGACA
66 CTTCGCTGCTAATACAGGAAGACA
* * * * * *
20981399 AGATCTGCTATATTTAGTCTGCTCTGCTGCAAACTCAGGGAGGCGATGCTGTTGTCTTCGATTTG
1 AGATCTGCTATCTTCAGTCTGCTCCGCTGCAAACTCAGGGAGGCGAGGCTGGTGTCTTCGATCTG
20981464 CTTCGCTGCTAATACAGGAAGACA
66 CTTCGCTGCTAATACAGGAAGACA
20981488 AGATCTGCTATCTTC
1 AGATCTGCTATCTTC
20981503 TTCAATCCAT
Statistics
Matches: 331, Mismatches: 40, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 331 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (89 bp):
AGATCTGCTATCTTCAGTCTGCTCCGCTGCAAACTCAGGGAGGCGAGGCTGGTGTCTTCGATCTG
CTTCGCTGCTAATACAGGAAGACA
Found at i:20981204 original size:44 final size:44
Alignment explanation
Indices: 20981073--20981293 Score: 130
Period size: 44 Copynumber: 5.0 Consensus size: 44
20981063 GCTCCACTGC
* * *
20981073 AAACTCAAGGAGACGAGGCTGGTGTCTTTGATCTGCTTCGCTGCC
1 AAACTCAAGGAGGCGAGGCTGGTGTCTTCGATCTGCTTCGCTG-T
* * * * * * * *
20981118 AATA-T-ATGAAGACAAGATCTGCTATCTTC-AGTCTGCTCCGCTGT
1 AA-ACTCAAGGAGGCGAG-GCTGGTGTCTTCGA-TCTGCTTCGCTGT
* *
20981162 AAACTCAGGGAGGCGAGGCTGGTGTCTTCGATCTGTTTCGCTGCT
1 AAACTCAAGGAGGCGAGGCTGGTGTCTTCGATCTGCTTCGCTG-T
* *** * * * *
20981207 -AA-TACAAGAAGATAAGACCTGATATCTTC-AGTCTGCTCCGCTGT
1 AAACT-CAAGGAGGCGAG-GCTGGTGTCTTCGA-TCTGCTTCGCTGT
*
20981251 AAACTCAAGGAGGCGAGGCTAGTGTCTTCGATCTGCTTCGCTG
1 AAACTCAAGGAGGCGAGGCTGGTGTCTTCGATCTGCTTCGCTG
20981294 CTAATACAGG
Statistics
Matches: 126, Mismatches: 37, Indels: 27
0.66 0.19 0.14
Matches are distributed among these distances:
43 2 0.02
44 61 0.48
45 61 0.48
46 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (44 bp):
AAACTCAAGGAGGCGAGGCTGGTGTCTTCGATCTGCTTCGCTGT
Found at i:20981502 original size:45 final size:45
Alignment explanation
Indices: 20981097--20981502 Score: 191
Period size: 45 Copynumber: 9.1 Consensus size: 45
20981087 GAGGCTGGTG
* * * *
20981097 TCTTTGATCTGCTTCGCTGCCAATATATGAAGACAAGATCTGCTA
1 TCTTCGATCTGCTTCGCTGCTAATACAGGAAGACAAGATCTGCTA
* * * * * * *
20981142 TCTTC-AGTCTGCTCCGCTG-TAA-ACTCAGGGAGGCGAG-GCTGGTG
1 TCTTCGA-TCTGCTTCGCTGCTAATA--CAGGAAGACAAGATCTGCTA
* * * * *
20981186 TCTTCGATCTGTTTCGCTGCTAATACAAGAAGATAAGACCTGATA
1 TCTTCGATCTGCTTCGCTGCTAATACAGGAAGACAAGATCTGCTA
* * * * *
20981231 TCTTC-AGTCTGCTCCGCTG-TAA-ACTCAAGG-AGGCGAG-GCTAG-TG
1 TCTTCGA-TCTGCTTCGCTGCTAATA--C-AGGAAGACAAGATCT-GCTA
*
20981275 TCTTCGATCTGCTTCGCTGCTAATACAGGAAGACAAGATCTACTA
1 TCTTCGATCTGCTTCGCTGCTAATACAGGAAGACAAGATCTGCTA
* * * * * *** * * *
20981320 TCTTC-AGTCTACTCCACTGCAAACT-CAGGGAGGTGAG-GCTGGTG
1 TCTTCGA-TCTGCTTCGCTGCTAA-TACAGGAAGACAAGATCTGCTA
20981364 TCTTCGATCTGCTTCGCTGCTAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTGCTTCGCTGCTAATACAGGAAGACAAGATCTGCTA
* * * * * * *
20981409 TATT-TAGTCTGC-TCTGCTGCAAACT-CAGGGAGGC--GATGCTGTTG
1 TCTTCGA-TCTGCTTC-GCTGCTAA-TACAGGAAGACAAGAT-CTGCTA
*
20981453 TCTTCGATTTGCTTCGCTGCTAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTGCTTCGCTGCTAATACAGGAAGACAAGATCTGCTA
20981498 TCTTC
1 TCTTC
20981503 TTCAATCCAT
Statistics
Matches: 256, Mismatches: 73, Indels: 64
0.65 0.19 0.16
Matches are distributed among these distances:
43 10 0.04
44 115 0.45
45 122 0.48
46 9 0.04
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (45 bp):
TCTTCGATCTGCTTCGCTGCTAATACAGGAAGACAAGATCTGCTA
Found at i:21002275 original size:41 final size:41
Alignment explanation
Indices: 21002215--21002295 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
21002205 TTTAAAATTT
* *
21002215 ATTTTCTTTGCATGGTTTTAAAGATCTATCGTAAGAGAATC
1 ATTTTCTTTGCATGATTTTAAACATCTATCGTAAGAGAATC
*
21002256 ATTTTTTTTGCATGATTTTAAACATCTATCGTAAGAGAAT
1 ATTTTCTTTGCATGATTTTAAACATCTATCGTAAGAGAAT
21002296 AGATCCAACC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (41 bp):
ATTTTCTTTGCATGATTTTAAACATCTATCGTAAGAGAATC
Found at i:21006816 original size:24 final size:24
Alignment explanation
Indices: 21006770--21006816 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
21006760 GAAGAATTGG
* * *
21006770 TGGCTTCGTCCACGACTTGCATGA
1 TGGCTTCGTCCACAACATACATGA
*
21006794 TGGCTTTGTCCACAACATACATG
1 TGGCTTCGTCCACAACATACATG
21006817 GTAGCTTGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (24 bp):
TGGCTTCGTCCACAACATACATGA
Found at i:21007776 original size:19 final size:18
Alignment explanation
Indices: 21007735--21007777 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
21007725 GTTTTTTGTC
*
21007735 ATAAAATAATTAATTTTT
1 ATAAAATAATTAATTTAT
21007753 ATAAAATAATTGAATTGTAT
1 ATAAAATAATT-AATT-TAT
21007773 -TAAAA
1 ATAAAA
21007778 ATTTGAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
19 9 0.41
20 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
ATAAAATAATTAATTTAT
Found at i:21015962 original size:6 final size:6
Alignment explanation
Indices: 21015947--21016077 Score: 135
Period size: 6 Copynumber: 22.5 Consensus size: 6
21015937 ATTTGAATAT
* * * * * *
21015947 AAAATG AAATTG -AAATG AAATTG AAATTG AAATTG AAATTG AAATTG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
* *
21015994 -AAATG AAAATG AAAATG AAAATG AGAATG -ATATG AAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
* * *
21016040 AAAATG AAAATG AGAATG -ATATG AAAATG GAAATG AAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAA
21016078 CGAATTACAG
Statistics
Matches: 107, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
5 14 0.13
6 93 0.87
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (6 bp):
AAAATG
Found at i:21016049 original size:35 final size:35
Alignment explanation
Indices: 21015959--21016077 Score: 161
Period size: 35 Copynumber: 3.4 Consensus size: 35
21015949 AATGAAATTG
* * * *
21015959 AAATGAAATTGAAATTGAAATTGA-AATTGAAATTG-
1 AAATGAAAATGAAAATGAAAATGAGAA-TGATA-TGA
21015994 AAATGAAAATGAAAATGAAAATGAGAATGATATGA
1 AAATGAAAATGAAAATGAAAATGAGAATGATATGA
21016029 AAATGAAAATGAAAATGAAAATGAGAATGATATGA
1 AAATGAAAATGAAAATGAAAATGAGAATGATATGA
*
21016064 AAATGGAAATGAAA
1 AAATGAAAATGAAA
21016078 CGAATTACAG
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
34 2 0.03
35 73 0.95
36 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (35 bp):
AAATGAAAATGAAAATGAAAATGAGAATGATATGA
Found at i:21016063 original size:29 final size:28
Alignment explanation
Indices: 21015947--21016077 Score: 147
Period size: 29 Copynumber: 4.5 Consensus size: 28
21015937 ATTTGAATAT
* *
21015947 AAAATGAAATTGAAATGAAATTGAAATTG
1 AAAATGAAAATGAAATGAAA-TGAAAATG
* *
21015976 AAATTGAAATTGAAATTGAAATGAAAATG
1 AAAATGAAAATGAAA-TGAAATGAAAATG
*
21016005 AAAATGAAAATGAGAATGATATGAAAATG
1 AAAATGAAAATGA-AATGAAATGAAAATG
*
21016034 AAAATGAAAATGAAAATGAGAATG-ATATG
1 AAAATGAAAATG-AAATGA-AATGAAAATG
*
21016063 AAAATGGAAATGAAA
1 AAAATGAAAATGAAA
21016078 CGAATTACAG
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
28 3 0.03
29 76 0.84
30 11 0.12
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (28 bp):
AAAATGAAAATGAAATGAAATGAAAATG
Found at i:21016749 original size:4 final size:4
Alignment explanation
Indices: 21016740--21016766 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
21016730 AATAAAATAA
21016740 TTAG TTAG TTAG TTAG TTAG TTAG TTA
1 TTAG TTAG TTAG TTAG TTAG TTAG TTA
21016767 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TTAG
Found at i:21016802 original size:18 final size:17
Alignment explanation
Indices: 21016760--21016802 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
21016750 AGTTAGTTAG
*
21016760 TTAGTTAATAATAATAA
1 TTAGTTAATAAAAATAA
*
21016777 TTGGGTTAATAAAAATAGA
1 TT-AGTTAATAAAAATA-A
21016796 TTAGTTA
1 TTAGTTA
21016803 GGATTAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.10
18 16 0.76
19 3 0.14
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.40
Consensus pattern (17 bp):
TTAGTTAATAAAAATAA
Found at i:21017979 original size:26 final size:28
Alignment explanation
Indices: 21017913--21017983 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 28
21017903 TGTCCAAACC
* *
21017913 TATATGATATGCGAGCCCTGATATGTTTA
1 TATATGATGTGCGAACCCTGATATG-TTA
21017942 TATATGATGTGCGAACCCTGATATG-TA
1 TATATGATGTGCGAACCCTGATATGTTA
*
21017969 -ATATTATGTGCGAAC
1 TATATGATGTGCGAAC
21017984 TCTTAAAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 14 0.36
27 2 0.05
29 23 0.59
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (28 bp):
TATATGATGTGCGAACCCTGATATGTTA
Found at i:21018048 original size:18 final size:19
Alignment explanation
Indices: 21018027--21018062 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21018017 CCTATATGCT
21018027 ATGC-AAACCCTATGTGAC
1 ATGCGAAACCCTATGTGAC
*
21018045 ATGCGAAGCCCTATGTGA
1 ATGCGAAACCCTATGTGA
21018063 ACCCTATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (19 bp):
ATGCGAAACCCTATGTGAC
Found at i:21018103 original size:34 final size:34
Alignment explanation
Indices: 21018057--21018134 Score: 113
Period size: 34 Copynumber: 2.3 Consensus size: 34
21018047 GCGAAGCCCT
* *
21018057 ATGTGAACCCTATGTTATGCGAATCC-TATGTGAC
1 ATGTGAACCCTATATTATGCG-AGCCATATGTGAC
*
21018091 ATGTGAAGCCTATATTATGCGAGCCATATGTGAC
1 ATGTGAACCCTATATTATGCGAGCCATATGTGAC
21018125 ATGTGAACCC
1 ATGTGAACCC
21018135 ACGGTTATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 3 0.08
34 36 0.92
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (34 bp):
ATGTGAACCCTATATTATGCGAGCCATATGTGAC
Found at i:21024745 original size:18 final size:18
Alignment explanation
Indices: 21024705--21024745 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
21024695 GCAATGCTTC
*
21024705 TAAAAAACACTTTTGGGA
1 TAAAAAACACTTTTGAGA
* *
21024723 CAAAAAACGCTTTTGAGA
1 TAAAAAACACTTTTGAGA
21024741 TAAAA
1 TAAAA
21024746 GCTTTCCTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (18 bp):
TAAAAAACACTTTTGAGA
Found at i:21026966 original size:42 final size:42
Alignment explanation
Indices: 21026912--21027005 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
21026902 TGTTAACTCA
* * *
21026912 TATGAGTTTCTGTTTAACCCTAATAGGTTTTCGTTTAGCTCT
1 TATGAGCTTCTGTTTAACCCTAATAGGTTTTCATTTAGCTAT
* * *
21026954 TTTGAGCTTCTGTTTAACCCTTATGGGTTTTCATTTAGCTAT
1 TATGAGCTTCTGTTTAACCCTAATAGGTTTTCATTTAGCTAT
21026996 TATGAGCTTC
1 TATGAGCTTC
21027006 CATTCAACCC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (42 bp):
TATGAGCTTCTGTTTAACCCTAATAGGTTTTCATTTAGCTAT
Found at i:21027015 original size:42 final size:42
Alignment explanation
Indices: 21026927--21027046 Score: 127
Period size: 42 Copynumber: 2.9 Consensus size: 42
21026917 GTTTCTGTTT
* * * * * ** *
21026927 AACCCTAATAGGTTTTCGTTTAGCTCTTTTGAGCTTCTGTTT
1 AACCCTTATGGGTTTTCATTTAGCTATTATGAGCTTCCATTC
21026969 AACCCTTATGGGTTTTCATTTAGCTATTATGAGCTTCCATTC
1 AACCCTTATGGGTTTTCATTTAGCTATTATGAGCTTCCATTC
*
21027011 AACCCTTACGGG-TTTCTATTTAGC-ATTTATGAGCTT
1 AACCCTTATGGGTTTTC-ATTTAGCTA-TTATGAGCTT
21027047 TTATTTAGCA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 5 0.07
42 62 0.93
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (42 bp):
AACCCTTATGGGTTTTCATTTAGCTATTATGAGCTTCCATTC
Found at i:21033920 original size:42 final size:43
Alignment explanation
Indices: 21033860--21033969 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 43
21033850 CATAGGATTC
* * * *
21033860 CGATATGTGATTACGTGTAAGACCATGTTTGGGACATTGGCGT
1 CGATATATGATTACGTGTAAGACCATATCTGGGACAGTGGCGT
* *
21033903 CG-TATATGATTTCGTGTAAGACCCTATCTGGGACAGTGGCGT
1 CGATATATGATTACGTGTAAGACCATATCTGGGACAGTGGCGT
* *
21033945 CGATATTTGATTACATGTAAGACCA
1 CGATATATGATTACGTGTAAGACCA
21033970 CGTCTAGGAC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 36 0.64
43 20 0.36
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.32
Consensus pattern (43 bp):
CGATATATGATTACGTGTAAGACCATATCTGGGACAGTGGCGT
Found at i:21037108 original size:21 final size:21
Alignment explanation
Indices: 21037082--21037136 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
21037072 AACAGCGGTG
* *
21037082 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTATA
*
21037103 GCGGTGAGATTGGGTACTATA
1 GCGGTGAGATTAGGTACTATA
21037124 GCGGTGAGATTAG
1 GCGGTGAGATTAG
21037137 AAATAATGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTATA
Found at i:21041023 original size:31 final size:30
Alignment explanation
Indices: 21040987--21041182 Score: 278
Period size: 31 Copynumber: 6.6 Consensus size: 30
21040977 CTACTTTATA
21040987 ATTTTTTTATTTTTAAAATACACTACATAT
1 ATTTTTTTATTTTTAAAATACACTACATAT
*
21041017 ATTTTTTTTACTTTTAAAATACACTACATAT
1 A-TTTTTTTATTTTTAAAATACACTACATAT
*
21041048 A------TATATTTAAAATACACTACATAT
1 ATTTTTTTATTTTTAAAATACACTACATAT
21041072 ATATTTTTTATTTTTAAAATACACTACATAT
1 AT-TTTTTTATTTTTAAAATACACTACATAT
21041103 ATTTTTTTATTTTTAAAATACACTACATAT
1 ATTTTTTTATTTTTAAAATACACTACATAT
**
21041133 ATATTTTTTATTTTTAAAATACACTACACGT
1 AT-TTTTTTATTTTTAAAATACACTACATAT
*
21041164 ATTTTTTAATTTTTAAAAT
1 ATTTTTTTATTTTTAAAAT
21041183 TTTAAATACA
Statistics
Matches: 150, Mismatches: 7, Indels: 18
0.86 0.04 0.10
Matches are distributed among these distances:
24 22 0.15
30 47 0.31
31 81 0.54
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.51
Consensus pattern (30 bp):
ATTTTTTTATTTTTAAAATACACTACATAT
Found at i:21041056 original size:24 final size:24
Alignment explanation
Indices: 21041029--21041075 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
21041019 TTTTTTTACT
21041029 TTTAAAATACACTACATATATATA
1 TTTAAAATACACTACATATATATA
21041053 TTTAAAATACACTACATATATAT
1 TTTAAAATACACTACATATATAT
21041076 TTTTTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (24 bp):
TTTAAAATACACTACATATATATA
Found at i:21041057 original size:55 final size:56
Alignment explanation
Indices: 21040993--21041160 Score: 248
Period size: 55 Copynumber: 2.9 Consensus size: 56
21040983 TATAATTTTT
* * *
21040993 TTATTTTTAAAATACACTACATATATTTTTTTTACTTTTAAAATACACTACATATA
1 TTATATTTAAAATACACTACATATATATTTTTTATTTTTAAAATACACTACATATA
21041049 -TATATTTAAAATACACTACATATATATTTTTTATTTTTAAAATACACTACATATA
1 TTATATTTAAAATACACTACATATATATTTTTTATTTTTAAAATACACTACATATA
*
21041104 TTTTTTTATTTTTAAAATACACTACATATATATTTTTTATTTTTAAAATACACTACA
1 -----TTATATTTAAAATACACTACATATATATTTTTTATTTTTAAAATACACTACA
21041161 CGTATTTTTT
Statistics
Matches: 102, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
55 52 0.51
61 50 0.49
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (56 bp):
TTATATTTAAAATACACTACATATATATTTTTTATTTTTAAAATACACTACATATA
Found at i:21041118 original size:61 final size:61
Alignment explanation
Indices: 21040987--21041182 Score: 296
Period size: 61 Copynumber: 3.3 Consensus size: 61
21040977 CTACTTTATA
* *
21040987 ATTTTTTTATTTTTAAAATACACTACATATATTTTTTTTACTTTTAAAATACACTACATAT
1 ATTTTTTTATTTTTAAAATACACTACATATATATTTTTTATTTTTAAAATACACTACATAT
*
21041048 A------TATATTTAAAATACACTACATATATATTTTTTATTTTTAAAATACACTACATAT
1 ATTTTTTTATTTTTAAAATACACTACATATATATTTTTTATTTTTAAAATACACTACATAT
**
21041103 ATTTTTTTATTTTTAAAATACACTACATATATATTTTTTATTTTTAAAATACACTACACGT
1 ATTTTTTTATTTTTAAAATACACTACATATATATTTTTTATTTTTAAAATACACTACATAT
*
21041164 ATTTTTTAATTTTTAAAAT
1 ATTTTTTTATTTTTAAAAT
21041183 TTTAAATACA
Statistics
Matches: 122, Mismatches: 7, Indels: 12
0.87 0.05 0.09
Matches are distributed among these distances:
55 52 0.43
61 70 0.57
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.51
Consensus pattern (61 bp):
ATTTTTTTATTTTTAAAATACACTACATATATATTTTTTATTTTTAAAATACACTACATAT
Found at i:21041249 original size:16 final size:16
Alignment explanation
Indices: 21041210--21041250 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
21041200 TTCTCCATTC
21041210 CCATCTCCCCTCTTCCA
1 CCAT-TCCCCTCTTCCA
*
21041227 TCATTCCCCTCTTCCA
1 CCATTCCCCTCTTCCA
*
21041243 CCGTTCCC
1 CCATTCCC
21041251 TCCTCCCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.10, C:0.56, G:0.02, T:0.32
Consensus pattern (16 bp):
CCATTCCCCTCTTCCA
Done.