Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007819.1 Hibiscus syriacus cultivar Beakdansim tig00110156_pilon, 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: 3855360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2745 characters in sequence are not A, C, G, or T
File 13 of 17
Found at i:2614073 original size:20 final size:20
Alignment explanation
Indices: 2614048--2614087 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2614038 CGACGTGCAT
*
2614048 GTCCCATGCACAGTTCCCAC
1 GTCCCATGCACAGCTCCCAC
2614068 GTCCCATGCACAGCTCCCAC
1 GTCCCATGCACAGCTCCCAC
2614088 ATGCATCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.47, G:0.15, T:0.17
Consensus pattern (20 bp):
GTCCCATGCACAGCTCCCAC
Found at i:2614099 original size:20 final size:20
Alignment explanation
Indices: 2614076--2614113 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2614066 ACGTCCCATG
*
2614076 CACAGCTCCCACATGCATCC
1 CACAACTCCCACATGCATCC
*
2614096 CACAACTCCCCCATGCAT
1 CACAACTCCCACATGCAT
2614114 GCTCCAATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.50, G:0.08, T:0.16
Consensus pattern (20 bp):
CACAACTCCCACATGCATCC
Found at i:2614207 original size:29 final size:29
Alignment explanation
Indices: 2614165--2614229 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
2614155 AACACCACAC
*
2614165 AGGTCGCTCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
2614194 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
2614223 AGGTCGC
1 AGGTCGC
2614230 TGTAGAATTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.17, C:0.35, G:0.32, T:0.15
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:2622631 original size:13 final size:13
Alignment explanation
Indices: 2622613--2622637 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2622603 AATGTATTTT
2622613 ATTCGAATAAATA
1 ATTCGAATAAATA
2622626 ATTCGAATAAAT
1 ATTCGAATAAAT
2622638 CATTATTCAA
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:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (13 bp):
ATTCGAATAAATA
Found at i:2622898 original size:13 final size:13
Alignment explanation
Indices: 2622880--2622921 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2622870 AGTACAGTAT
2622880 AAAATAATT-TTTA
1 AAAAT-ATTATTTA
2622893 AAAATATTATTTA
1 AAAATATTATTTA
* *
2622906 AAAGTATAATTTA
1 AAAATATTATTTA
2622919 AAA
1 AAA
2622922 TTTAACTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 3 0.12
13 23 0.88
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
AAAATATTATTTA
Found at i:2628130 original size:45 final size:47
Alignment explanation
Indices: 2628059--2628165 Score: 173
Period size: 45 Copynumber: 2.3 Consensus size: 47
2628049 TTATTTTCGT
2628059 TTTTTTCGAATAAATGCATGCGAATTAGATATCATGCGGTTAGG-TTTA
1 TTTTTT-GAAT-AATGCATGCGAATTAGATATCATGCGGTTAGGATTTA
2628107 TTTTTTGAATAAT-CATGCGAATTAGATATCATGCGGTTAGGATTTA
1 TTTTTTGAATAATGCATGCGAATTAGATATCATGCGGTTAGGATTTA
2628153 TTTTTGTGAATAA
1 TTTTT-TGAATAA
2628166 CAAAGCATAA
Statistics
Matches: 57, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
45 28 0.49
46 12 0.21
47 11 0.19
48 6 0.11
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (47 bp):
TTTTTTGAATAATGCATGCGAATTAGATATCATGCGGTTAGGATTTA
Found at i:2637525 original size:6 final size:6
Alignment explanation
Indices: 2637499--2637690 Score: 69
Period size: 6 Copynumber: 30.3 Consensus size: 6
2637489 ATTTCGCTTG
* * * *
2637499 AAGAAGA AATAAA AGAGAAA AAGAAAA AAGAAAA AATGAAA AA-AAT AATAAT
1 AAGAA-A AAGAAA A-AGAAA AAG-AAA AAG-AAA AA-GAAA AAGAAA AAGAAA
*
2637551 AATAAA AATGAGAA GAAGAAA AAGAAA AAGAAGAA AAGAAA AATGACAA
1 AAGAAA AA-GA-AA -AAGAAA AAGAAA AAG-A-AA AAGAAA AA-GA-AA
** *
2637600 AA-AAA TAA-AAA TGGTAA AAGAAGA AAGAAA AATG--- AAGAAA AATGAAA
1 AAGAAA -AAGAAA AAGAAA AAGAA-A AAGAAA AA-GAAA AAGAAA AA-GAAA
*
2637647 AGAGAAA ATA-AAA AATGAAA AAG-AA GA-AAA AAGAAA AAGAAA AA
1 A-AGAAA A-AGAAA AA-GAAA AAGAAA AAGAAA AAGAAA AAGAAA AA
2637691 AAAGGAGGGT
Statistics
Matches: 147, Mismatches: 14, Indels: 49
0.70 0.07 0.23
Matches are distributed among these distances:
3 1 0.01
4 2 0.01
5 13 0.09
6 58 0.39
7 56 0.38
8 15 0.10
9 2 0.01
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.08
Consensus pattern (6 bp):
AAGAAA
Found at i:2637526 original size:7 final size:7
Alignment explanation
Indices: 2637509--2637691 Score: 86
Period size: 7 Copynumber: 24.6 Consensus size: 7
2637499 AAGAAGAAAT
2637509 AAAAGAGA
1 AAAAGA-A
2637517 AAAAGAA
1 AAAAGAA
2637524 AAAAGAA
1 AAAAGAA
2637531 AAAATGAAA
1 AAAA-G-AA
*
2637540 AAAATAA
1 AAAAGAA
*
2637547 TAATAATAA
1 -AA-AAGAA
*
2637556 AAATGAGA
1 AAAAGA-A
*
2637564 AGAAG-A
1 AAAAGAA
2637570 AAAAG-A
1 AAAAGAA
2637576 AAAAGAA
1 AAAAGAA
2637583 GAAAAGAA
1 -AAAAGAA
*
2637591 AAATGACA
1 AAAAGA-A
*
2637599 AAAAAATA
1 AAAAGA-A
**
2637607 AAAATGGT
1 AAAA-GAA
2637615 AAAAGAA
1 AAAAGAA
*
2637622 GAAAGAAA
1 AAAAG-AA
2637630 AATGAAGAA
1 AA--AAGAA
*
2637639 AAATGAA
1 AAAAGAA
*
2637646 AAGAGAA
1 AAAAGAA
*
2637653 AATA-AA
1 AAAAGAA
*
2637659 AAATGAAA
1 AAAAG-AA
2637667 AAGAAGAA
1 AA-AAGAA
2637675 AAAAG-A
1 AAAAGAA
2637681 AAAAGAA
1 AAAAGAA
2637688 AAAA
1 AAAA
2637692 AAGGAGGGTT
Statistics
Matches: 135, Mismatches: 24, Indels: 33
0.70 0.12 0.17
Matches are distributed among these distances:
6 21 0.16
7 47 0.35
8 47 0.35
9 17 0.13
10 3 0.02
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.08
Consensus pattern (7 bp):
AAAAGAA
Found at i:2637529 original size:15 final size:15
Alignment explanation
Indices: 2637509--2637691 Score: 75
Period size: 15 Copynumber: 12.3 Consensus size: 15
2637499 AAGAAGAAAT
2637509 AAAAGAGAAAAAGAA
1 AAAAGAGAAAAAGAA
2637524 AAAAGA-AAAAATGAA
1 AAAAGAGAAAAA-GAA
*
2637539 AAAA-ATAATAATA-ATA
1 AAAAGAGAA-AA-AGA-A
*
2637555 AAAATGAGAAGAAG--
1 AAAA-GAGAAAAAGAA
2637569 AAAA-AGAAAAAGAA
1 AAAAGAGAAAAAGAA
*
2637583 GAAAAGA-AAAATGACA
1 -AAAAGAGAAAAAGA-A
* * **
2637599 AAAAAATAAAAATGGT
1 AAAAGAGAAAAA-GAA
*
2637615 AAAAGA-AGAAAGAA
1 AAAAGAGAAAAAGAA
*
2637629 AAATGAAGAAAAATG--
1 AAAAG-AGAAAAA-GAA
*
2637644 AAAAGAG-AAAATAA
1 AAAAGAGAAAAAGAA
*
2637658 AAAA-TGAAAAAGAA
1 AAAAGAGAAAAAGAA
*
2637672 GAAAAAAGAAAAAGAA
1 -AAAAGAGAAAAAGAA
2637688 AAAA
1 AAAA
2637692 AAGGAGGGTT
Statistics
Matches: 126, Mismatches: 19, Indels: 46
0.66 0.10 0.24
Matches are distributed among these distances:
12 7 0.06
13 5 0.04
14 27 0.21
15 48 0.38
16 32 0.25
17 4 0.03
18 3 0.02
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.08
Consensus pattern (15 bp):
AAAAGAGAAAAAGAA
Found at i:2637610 original size:31 final size:29
Alignment explanation
Indices: 2637516--2637690 Score: 81
Period size: 31 Copynumber: 5.6 Consensus size: 29
2637506 AATAAAAGAG
*
2637516 AAAAAGAAAAAAGAAAAAATGAAAAAAATAAT
1 AAAAAGAGAAAAG-AAAAATG-AAAAAA-AAT
* * * * *
2637548 AATAATA-AAAATG-AGAA-GAAGAAAAAG
1 AAAAAGAGAAAA-GAAAAATGAAAAAAAAT
2637575 AAAAAGAAGAAAAGAAAAATGACAAAAAAAT
1 AAAAAG-AGAAAAGAAAAATGA-AAAAAAAT
*
2637606 AAAAATGGTAAAAGAAGAAAGAAAAATGAAGAAAAAT
1 AAAAA--G----AG-A-AAAGAAAAATGAAAAAAAAT
* *
2637643 GAAAAGAGAAAATAAAAAATGAAAAAGAAGA-
1 AAAAAGAGAAAA-GAAAAATGAAAAA-AA-AT
2637674 AAAAAGA-AAAAGAAAAA
1 AAAAAGAGAAAAGAAAAA
2637691 AAAGGAGGGT
Statistics
Matches: 111, Mismatches: 16, Indels: 35
0.69 0.10 0.22
Matches are distributed among these distances:
27 6 0.05
28 7 0.06
29 16 0.14
30 21 0.19
31 25 0.23
32 7 0.06
33 1 0.01
35 1 0.01
36 3 0.03
37 12 0.11
38 12 0.11
ACGTcount: A:0.76, C:0.01, G:0.15, T:0.08
Consensus pattern (29 bp):
AAAAAGAGAAAAGAAAAATGAAAAAAAAT
Found at i:2637663 original size:30 final size:29
Alignment explanation
Indices: 2637627--2637683 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
2637617 AAGAAGAAAG
*
2637627 AAAAATGAAGAAA-AATGAAAAGAGAAAATA
1 AAAAATGAA-AAAGAA-GAAAAAAGAAAATA
2637657 AAAAATGAAAAAGAAGAAAAAAGAAAA
1 AAAAATGAAAAAGAAGAAAAAAGAAAA
2637684 AGAAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (29 bp):
AAAAATGAAAAAGAAGAAAAAAGAAAATA
Found at i:2637683 original size:36 final size:35
Alignment explanation
Indices: 2637526--2637693 Score: 125
Period size: 36 Copynumber: 4.7 Consensus size: 35
2637516 AAAAAGAAAA
* *
2637526 AAGAAAAAATGAAAAA-AATAATAATAAT-AAAAATG
1 AAGAAAAAA-GAAAAAGAA-AAAAAAAATGAAAAATG
* *
2637561 -AG-AAGAAGAAAAAGAAAAAGAAGAAAAGAAAAATG
1 AAGAAAAAAGAAAAAGAAAAA-AA-AAATGAAAAATG
* *
2637596 ACA-AAAAAATAAAAATGGTAAAAGAAGAAA-GAAAAATG
1 A-AGAAAAAAGAAAAA--G-AAAA-AAAAAATGAAAAATG
*
2637634 AAGAAAAATGAAAAGAGAAAATAAAAAATGAAAAA-G
1 AAGAAAAAAGAAAA-AGAAAA-AAAAAATGAAAAATG
2637670 AAGAAAAAAGAAAAAGAAAAAAAA
1 AAGAAAAAAGAAAAAGAAAAAAAA
2637694 GGAGGGTTCA
Statistics
Matches: 107, Mismatches: 12, Indels: 29
0.72 0.08 0.20
Matches are distributed among these distances:
32 8 0.07
33 8 0.07
34 8 0.07
35 13 0.12
36 23 0.21
37 18 0.17
38 18 0.17
39 5 0.05
40 5 0.05
41 1 0.01
ACGTcount: A:0.76, C:0.01, G:0.15, T:0.08
Consensus pattern (35 bp):
AAGAAAAAAGAAAAAGAAAAAAAAAATGAAAAATG
Found at i:2637692 original size:15 final size:15
Alignment explanation
Indices: 2637502--2637694 Score: 88
Period size: 17 Copynumber: 11.8 Consensus size: 15
2637492 TCGCTTGAAG
2637502 AAGAAATAAAAGAGAAA
1 AAGAAA-AAAA-AGAAA
2637519 AAGAAAAAAGAA-AAA
1 AAGAAAAAA-AAGAAA
* * *
2637534 ATG-AAAAAAATAAT
1 AAGAAAAAAAAGAAA
* * *
2637548 AATAATAAAAATG-AG
1 AAGAA-AAAAAAGAAA
*
2637563 AAGAAGAAAAAGAAA
1 AAGAAAAAAAAGAAA
*
2637578 AAG-AAGAAAAGAAA
1 AAGAAAAAAAAGAAA
*
2637592 AATGACAAAAAAATAAA
1 AA-GA-AAAAAAAGAAA
2637609 AATGGTAAAAGAAGAAAGAAA
1 AA--G--AAA-AA-AAAGAAA
*
2637630 AATGAAGAAAAATGAAA
1 AA-GAA-AAAAAAGAAA
2637647 AGAGAAAATAAAAAATGAAA
1 A-AG--AA-AAAAAA-GAAA
2637667 AAGAAGAAAAAAGAAA
1 AAGAA-AAAAAAGAAA
2637683 AAGAAAAAAAAG
1 AAGAAAAAAAAG
2637695 GAGGGTTCAA
Statistics
Matches: 136, Mismatches: 22, Indels: 38
0.69 0.11 0.19
Matches are distributed among these distances:
13 2 0.01
14 24 0.18
15 23 0.17
16 18 0.13
17 34 0.25
18 6 0.04
19 12 0.09
20 9 0.07
21 8 0.06
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.08
Consensus pattern (15 bp):
AAGAAAAAAAAGAAA
Found at i:2637740 original size:45 final size:45
Alignment explanation
Indices: 2637691--2637776 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 45
2637681 AAAAGAAAAA
*
2637691 AAAGGAGGGT-TCAA-TATGAAAATCC-GCAAAGGGCGTCTTGAAACC
1 AAAGGA-GGTCTCAAGT-TGAAAA-CCTGCAAAGGGCGACTTGAAACC
*
2637736 AAAGGAGGTCTCAAGTTGAAAACCTGTAAAGGGCGACTTGA
1 AAAGGAGGTCTCAAGTTGAAAACCTGCAAAGGGCGACTTGA
2637777 GTTTTAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
44 5 0.14
45 30 0.83
46 1 0.03
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.19
Consensus pattern (45 bp):
AAAGGAGGTCTCAAGTTGAAAACCTGCAAAGGGCGACTTGAAACC
Found at i:2638923 original size:36 final size:36
Alignment explanation
Indices: 2638872--2638942 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 36
2638862 AAACAGGTCA
2638872 ATCTTAAGCCTTCAC-GAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACC
*
2638907 ATCTGTAAGCCTTCACGGAAGATTAGTGAAGCAAAC
1 ATCT-TAAGCCTTCACGGAAGAGTAGTGAAGCAAAC
2638943 TCATTTTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 4 0.12
36 11 0.33
37 18 0.55
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (36 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACC
Found at i:2639004 original size:51 final size:51
Alignment explanation
Indices: 2638944--2639362 Score: 343
Period size: 55 Copynumber: 7.9 Consensus size: 51
2638934 GAAGCAAACT
* *
2638944 CATTTTATGAAGATCAAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CATTTTATGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
2638995 CATTTTATGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGC-GACA
1 CATTTTATGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * *
2639045 CGTTTGT-TAAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGAC-
1 CATTT-TATGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
2639095 C-TGTTTATAGAAGATTTTCCGAGT-TCTATACTCTCTGAAGAAATAGAGAGCGGACC
1 CAT-TTTAT-GAAGA---T-CGAGTCT-TATACTCTCTGAAGGAATAGGGAGCGGACA
* * * **
2639151 CATTTTATGGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGTAGACA
1 CATTTTAT-GAAGA----TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
2639207 C-GTTTATTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACC
1 CATTTTA-TGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * *
2639258 CGTTTGT-TGAAGATTATTTGAGTCTTATACTCTCTGAATGAATAGAGAGCATG-CA
1 CATTT-TATGAAG---A-TCGAGTCTTATACTCTCTGAAGGAATAGGGAGC-GGACA
*
2639313 CATTTTATGAAGATTGTTTGAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 CATTTTATGAAGA----TCGAGTCTTATACTCT-CTGAAGGAATAGGGAGC
2639363 ATGCTCGTCA
Statistics
Matches: 304, Mismatches: 37, Indels: 50
0.78 0.09 0.13
Matches are distributed among these distances:
49 2 0.01
50 47 0.15
51 90 0.30
52 3 0.01
53 1 0.00
54 4 0.01
55 109 0.36
56 43 0.14
57 5 0.02
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (51 bp):
CATTTTATGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
Found at i:2639256 original size:162 final size:158
Alignment explanation
Indices: 2638964--2639357 Score: 496
Period size: 162 Copynumber: 2.5 Consensus size: 158
2638954 AGATCAAGTC
*
2638964 CTATACTCTCTGAAGGAATAGGGAGCGGACACATTTTATGAAGA----TCGAGTCTTATACTCTC
1 CTATACTCTCTGAA-GAATAGAGAGCGGACACATTTTATGAAGATTGTTCGAGTCTTATACTCTC
* * * *
2639025 TGAAGGAATAGGGAGCGACACGTTTGTTAAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAG
65 TGAAGGAATAGAGAGAGACACGTTTATTAAAGATCGAGTCCTATACTCTCTGAAAGAATAGGGAG
*
2639090 CGGACCTGTTTATAGAAGATT-TTCCGAGTT
130 CGGACCCGTTTATAGAAGATTATT-CGAG-T
* *
2639120 CTATACTCTCTGAAGAAATAGAGAGCGGACCCATTTTATGGAAGATTGTTCAAGTCTTATACTCT
1 CTATACTCTCTGAAG-AATAGAGAGCGGACACATTTTAT-GAAGATTGTTCGAGTCTTATACTCT
* * * *
2639185 CTGAATGAATAGAGAGTAGACACGTTTATTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGG
64 CTGAAGGAATAGAGAG-AGACACGTTTATTAAAGATCGAGTCCTATACTCTCTGAAAGAATAGGG
* * *
2639250 AGCGGACCCGTTTGTTGAAGATTATTTGAGT
128 AGCGGACCCGTTTATAGAAGATTATTCGAGT
* *
2639281 CTTATACTCTCTGAATGAATAGAGAGCATG-CACATTTTATGAAGATTGTTTGAGTCTTATACT-
1 C-TATACTCTCTGAA-GAATAGAGAGC-GGACACATTTTATGAAGATTGTTCGAGTCTTATACTC
2639344 TCCTGAAGGAATAG
63 T-CTGAAGGAATAG
2639358 GGAGCATGCT
Statistics
Matches: 206, Mismatches: 20, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
155 1 0.00
156 35 0.17
157 5 0.02
160 1 0.00
161 63 0.31
162 97 0.47
163 4 0.02
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.31
Consensus pattern (158 bp):
CTATACTCTCTGAAGAATAGAGAGCGGACACATTTTATGAAGATTGTTCGAGTCTTATACTCTCT
GAAGGAATAGAGAGAGACACGTTTATTAAAGATCGAGTCCTATACTCTCTGAAAGAATAGGGAGC
GGACCCGTTTATAGAAGATTATTCGAGT
Found at i:2640123 original size:105 final size:104
Alignment explanation
Indices: 2639994--2640202 Score: 393
Period size: 105 Copynumber: 2.0 Consensus size: 104
2639984 TTCCCAGTTC
2639994 ATTTTTTCATTTTTGTATGCGATTGTTATTTAAAACTACAATTAGAGAGGGATTGGGAC-TACTT
1 ATTTTTTCATTTTTGTATGCGATTGTTATTTAAAACTACAATTAGAGAGGGATTGGGACTTACTT
2640058 AGACTGCTTGAACATAAATGGGGTCTTGTTGATTCCATT
66 AGACTGCTTGAACATAAATGGGGTCTTGTTGATTCCATT
2640097 ATTTTTTCATTTTTTTGTATGCGATTGTTATTTAAAACTACAATTAGAGAGGGATTGGGACTTAC
1 ATTTTTTCA--TTTTTGTATGCGATTGTTATTTAAAACTACAATTAGAGAGGGATTGGGACTTAC
2640162 TTAGACTGCTTGAACATAAATGGGGTCTTGTTGATTCCATT
64 TTAGACTGCTTGAACATAAATGGGGTCTTGTTGATTCCATT
2640203 TGTTCTTTGT
Statistics
Matches: 103, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
103 9 0.09
105 50 0.49
106 44 0.43
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (104 bp):
ATTTTTTCATTTTTGTATGCGATTGTTATTTAAAACTACAATTAGAGAGGGATTGGGACTTACTT
AGACTGCTTGAACATAAATGGGGTCTTGTTGATTCCATT
Found at i:2650823 original size:24 final size:22
Alignment explanation
Indices: 2650791--2650835 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2650781 TGTAAAAAGT
*
2650791 AAATGATTAAATAATAAAATATAA
1 AAATAATT-AATAA-AAAATATAA
2650815 AAATAATTAATAAAAAATATA
1 AAATAATTAATAAAAAATATA
2650836 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 5 0.25
24 7 0.35
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
AAATAATTAATAAAAAATATAA
Found at i:2650836 original size:24 final size:24
Alignment explanation
Indices: 2650791--2650836 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2650781 TGTAAAAAGT
* *
2650791 AAATGATTAAATAATAAAATATAA
1 AAATAATTAAATAAAAAAATATAA
2650815 AAATAATT-AATAAAAAATATAT
1 AAATAATTAAATAAAAAA-ATAT
2650837 TTTTTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
AAATAATTAAATAAAAAAATATAA
Found at i:2661955 original size:33 final size:33
Alignment explanation
Indices: 2661918--2661983 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
2661908 TATGGATGAT
2661918 GTTAGTATGAATTATTGATTTAATTCTGATGGA
1 GTTAGTATGAATTATTGATTTAATTCTGATGGA
2661951 GTTAGTATGAATTATTGATTTAATTCTGATGGA
1 GTTAGTATGAATTATTGATTTAATTCTGATGGA
2661984 AAATGGTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.03, G:0.21, T:0.45
Consensus pattern (33 bp):
GTTAGTATGAATTATTGATTTAATTCTGATGGA
Found at i:2666087 original size:151 final size:150
Alignment explanation
Indices: 2665800--2666100 Score: 561
Period size: 151 Copynumber: 2.0 Consensus size: 150
2665790 TTCGGTTTCA
2665800 TCCTGTTATCCATCTACAAATGGTTCATGTATTCCCATATTATTCCTTCTGTTGTGACTGTAGCT
1 TCCTGTTATCCATCTACAAATGGTTCATGTATTCCCATATTATTCCTTCTGTTGTGACTGTAGCT
2665865 GAGATTTGTTGTCTTGTCAATTGTTTTGCAGCTCTTTTCTATATATGCAGCCGGTATACAGTACC
66 GAGATTTGTTGTCTTGTCAATTGTTTTGCAGCTCTTTTCTATATATGCAGCCGGTATACAGTACC
2665930 TATTCCATTC-TGAGGGCAT
131 TATTCCATTCTTGAGGGCAT
2665949 TCCTGTTATCCATCACTACAAATGGTTCATGTATTCCCATATTATTCCTTCTGTTGTGACTGTAG
1 TCCTGTTATCCAT--CTACAAATGGTTCATGTATTCCCATATTATTCCTTCTGTTGTGACTGTAG
2666014 CTGAGATTTGTTGTCTTGTCAATTGTTTTGCAGCTC-TTTCTATATATGCAGCCGGTAATACAGT
64 CTGAGATTTGTTGTCTTGTCAATTGTTTTGCAGCTCTTTTCTATATATGCAGCCGGT-ATACAGT
2666078 ACCTATTCCATTCTTGAGGGCAT
128 ACCTATTCCATTCTTGAGGGCAT
2666101 CGGATATATC
Statistics
Matches: 148, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
149 13 0.09
150 20 0.14
151 106 0.72
152 9 0.06
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (150 bp):
TCCTGTTATCCATCTACAAATGGTTCATGTATTCCCATATTATTCCTTCTGTTGTGACTGTAGCT
GAGATTTGTTGTCTTGTCAATTGTTTTGCAGCTCTTTTCTATATATGCAGCCGGTATACAGTACC
TATTCCATTCTTGAGGGCAT
Found at i:2667383 original size:17 final size:17
Alignment explanation
Indices: 2667361--2667395 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2667351 TATAACCCTA
2667361 TTCCCATCATCCAAATG
1 TTCCCATCATCCAAATG
2667378 TTCCCATCATCCAAATG
1 TTCCCATCATCCAAATG
2667395 T
1 T
2667396 GTCGGACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.34, G:0.06, T:0.31
Consensus pattern (17 bp):
TTCCCATCATCCAAATG
Found at i:2670700 original size:24 final size:26
Alignment explanation
Indices: 2670654--2670705 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
2670644 TCACTTCTAT
*
2670654 TTTAATTATTAATTATTTAAAAAATAA
1 TTTAATTATT-ATAATTTAAAAAATAA
2670681 TTTAATTATT-TAATTT-AAAAATAA
1 TTTAATTATTATAATTTAAAAAATAA
2670705 T
1 T
2670706 AAAATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 9 0.38
25 5 0.21
27 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTAATTATTATAATTTAAAAAATAA
Found at i:2679418 original size:14 final size:15
Alignment explanation
Indices: 2679386--2679419 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
2679376 TATCTTTGCA
2679386 ATAAACCCTAAATTC
1 ATAAACCCTAAATTC
2679401 -TAAACCCTAAA-TC
1 ATAAACCCTAAATTC
2679414 ATAAAC
1 ATAAAC
2679420 TATAAACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (15 bp):
ATAAACCCTAAATTC
Found at i:2679439 original size:21 final size:21
Alignment explanation
Indices: 2679387--2679439 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2679377 ATCTTTGCAA
* * *
2679387 TAAACCCTAAATTCTAAACCC
1 TAAAACCTAAACTATAAACCC
* *
2679408 TAAATCATAAACTATAAACCC
1 TAAAACCTAAACTATAAACCC
2679429 TAAAACCTAAA
1 TAAAACCTAAA
2679440 TCTGATTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAAACCTAAACTATAAACCC
Found at i:2679801 original size:156 final size:156
Alignment explanation
Indices: 2679517--2679828 Score: 576
Period size: 156 Copynumber: 2.0 Consensus size: 156
2679507 ATGTACTCCT
2679517 AATAAATCAATCGCATACTTACACATAACATATCAACATGCAAATAAATATACACAACTAATTAA
1 AATAAATCAATCGCATACTTACACATAACATATCAACATGCAAATAAATATACACAACTAATTAA
2679582 AGAAAACAATCCTAAACATGGACTAAATTAGAGAAAACTAATGTTATGACCAATATAGCTAATAT
66 AGAAAACAATCCTAAACATGGACTAAATTAGAGAAAACTAATGTTATGACCAATATAGCTAATAT
2679647 ACTAACTTTAGAATGATGTTATGGGC
131 ACTAACTTTAGAATGATGTTATGGGC
2679673 AATAAATCAATCGCATACTTACACATAAACATATCAACATGCAAATAAATATACACAACTAATTA
1 AATAAATCAATCGCATACTTACACAT-AACATATCAACATGCAAATAAATATACACAACTAATTA
2679738 AAGAAAAC-ATCCT-AACATGGACTAAATTAAGAGAAAACTAATG-TATGACCAATATAAGCTAA
65 AAGAAAACAATCCTAAACATGGACTAAATT-AGAGAAAACTAATGTTATGACCAATAT-AGCTAA
2679800 TATACTAACTTTAGAATGATGTTATGGGC
128 TATACTAACTTTAGAATGATGTTATGGGC
2679829 TGTTAAAGGT
Statistics
Matches: 153, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
155 27 0.18
156 80 0.52
157 46 0.30
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.26
Consensus pattern (156 bp):
AATAAATCAATCGCATACTTACACATAACATATCAACATGCAAATAAATATACACAACTAATTAA
AGAAAACAATCCTAAACATGGACTAAATTAGAGAAAACTAATGTTATGACCAATATAGCTAATAT
ACTAACTTTAGAATGATGTTATGGGC
Found at i:2683061 original size:20 final size:20
Alignment explanation
Indices: 2683036--2683073 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2683026 ATCCTATTTC
2683036 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
2683056 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
2683074 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:2683538 original size:18 final size:19
Alignment explanation
Indices: 2683505--2683542 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2683495 ATCCCTATTG
2683505 TTATCATCCCCAAATTTAA
1 TTATCATCCCCAAATTTAA
*
2683524 TTATCA-CCTCAAATTTAA
1 TTATCATCCCCAAATTTAA
2683542 T
1 T
2683543 CATAATAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.37, C:0.24, G:0.00, T:0.39
Consensus pattern (19 bp):
TTATCATCCCCAAATTTAA
Found at i:2690229 original size:12 final size:12
Alignment explanation
Indices: 2690206--2690239 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
2690196 ACTGGTATTT
2690206 AAAAATGT-AAA
1 AAAAATGTAAAA
2690217 AAAAATGTAAAA
1 AAAAATGTAAAA
2690229 AAAAATG-AAAA
1 AAAAATGTAAAA
2690240 TACATGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (12 bp):
AAAAATGTAAAA
Found at i:2693335 original size:16 final size:17
Alignment explanation
Indices: 2693311--2693348 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
2693301 ATATTTTTAA
2693311 TATTT-TGTATTTAATT
1 TATTTATGTATTTAATT
2693327 T-TTTATGTATTTAATT
1 TATTTATGTATTTAATT
2693343 TATTTA
1 TATTTA
2693349 ATATTTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.15
16 13 0.65
17 4 0.20
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (17 bp):
TATTTATGTATTTAATT
Found at i:2695110 original size:30 final size:31
Alignment explanation
Indices: 2695075--2695142 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 31
2695065 CATATGTTAT
2695075 GCCGCCACCATTTC-CTTACCCGATG-CAGAC
1 GCCGCCACCATTTCTCTTACCCGATGCCA-AC
2695105 GCCG---CCA-TTCTCTTACCCGATGCCAAC
1 GCCGCCACCATTTCTCTTACCCGATGCCAAC
2695132 GCCGCCACCAT
1 GCCGCCACCAT
2695143 CACCTGGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
26 3 0.09
27 20 0.62
28 2 0.06
30 7 0.22
ACGTcount: A:0.19, C:0.46, G:0.16, T:0.19
Consensus pattern (31 bp):
GCCGCCACCATTTCTCTTACCCGATGCCAAC
Found at i:2695468 original size:9 final size:9
Alignment explanation
Indices: 2695454--2695481 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2695444 TTAGCTGCTC
2695454 AGGACGACG
1 AGGACGACG
2695463 AGGACGACG
1 AGGACGACG
2695472 AGGACGACG
1 AGGACGACG
2695481 A
1 A
2695482 TGATGATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.21, G:0.43, T:0.00
Consensus pattern (9 bp):
AGGACGACG
Found at i:2705892 original size:23 final size:23
Alignment explanation
Indices: 2705837--2705892 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
2705827 TATATATTTG
* *
2705837 TGACATGTTTATCTCTATCTTTA
1 TGACATGTTTATCTATACCTTTA
*
2705860 TGACACGTTTATCTATACCTTTA
1 TGACATGTTTATCTATACCTTTA
*
2705883 TGATATGTTT
1 TGACATGTTT
2705893 GTCTCTGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.23, C:0.16, G:0.11, T:0.50
Consensus pattern (23 bp):
TGACATGTTTATCTATACCTTTA
Found at i:2707902 original size:29 final size:29
Alignment explanation
Indices: 2707869--2707926 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
2707859 TGAAAATGTG
*
2707869 GTAGATATAAAAATATTAAGTACATATGA
1 GTAGATATAAAAATATTAAATACATATGA
2707898 GTAGATATAAAAATATTAAATACATATGA
1 GTAGATATAAAAATATTAAATACATATGA
2707927 AGATAAGGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.31
Consensus pattern (29 bp):
GTAGATATAAAAATATTAAATACATATGA
Found at i:2715495 original size:23 final size:24
Alignment explanation
Indices: 2715451--2715497 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
2715441 ATACATTGAC
*
2715451 AAATTATATAAATACAATAACATT
1 AAATTATATAAATACAAAAACATT
2715475 AAATTAT-TAGAA-ACAAAAACATT
1 AAATTATATA-AATACAAAAACATT
2715498 CATTTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.30
Consensus pattern (24 bp):
AAATTATATAAATACAAAAACATT
Found at i:2718734 original size:128 final size:128
Alignment explanation
Indices: 2718507--2719388 Score: 1522
Period size: 128 Copynumber: 6.9 Consensus size: 128
2718497 TAATCGGAGT
* *
2718507 ACTATTCACATGAAGGCGCGTTCTCGGGGGTGCGCCTTCCATTATTTTGTCA-AGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
2718571 AATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
2718634 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCATTCTATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
2718699 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
2718762 ACTATTCACATGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
2718827 CATTGTCCTATTATGTCACTCATGTCCCTCGGGGACACTAG--ATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
2718888 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAA
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
2718953 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** * * *
2719016 TC-AGGGGACTTGAAGGCACGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTA
2719080 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
2719144 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
2719209 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** * *
2719272 TC-AGGGGACTTGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTA
2719336 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
2719389 AATCAGGTTA
Statistics
Matches: 716, Mismatches: 33, Indels: 11
0.94 0.04 0.01
Matches are distributed among these distances:
126 123 0.17
127 50 0.07
128 542 0.76
129 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:2719741 original size:11 final size:11
Alignment explanation
Indices: 2719725--2719772 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 11
2719715 GTTATTTAAA
2719725 CGGGTATTGGG
1 CGGGTATTGGG
2719736 CGGGTA-TGGG
1 CGGGTATTGGG
2719746 TCGGGTATTATTGGG
1 -CGGG---TATTGGG
2719761 CGGGTATTGGG
1 CGGGTATTGGG
2719772 C
1 C
2719773 CGAGGGGTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
10 4 0.12
11 18 0.56
14 6 0.19
15 4 0.12
ACGTcount: A:0.10, C:0.10, G:0.50, T:0.29
Consensus pattern (11 bp):
CGGGTATTGGG
Found at i:2719942 original size:13 final size:13
Alignment explanation
Indices: 2719886--2719929 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
2719876 TTTAATATTT
*
2719886 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
2719898 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
2719911 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
2719924 ATCGGG
1 ATCGGG
2719930 TAATCGGGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.14, C:0.16, G:0.52, T:0.18
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:2721406 original size:34 final size:34
Alignment explanation
Indices: 2721368--2721468 Score: 139
Period size: 34 Copynumber: 3.0 Consensus size: 34
2721358 AAATTTAATG
*
2721368 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
2721402 TTAAATTTCGAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* *
2721436 TTAAATTTTGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
2721469 AATTTATCAA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:2722009 original size:21 final size:21
Alignment explanation
Indices: 2721979--2722042 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
2721969 TATGGTATAA
* *
2721979 AACCTTGCGGGCTAGGCATGT
1 AACCTGGCGGGCTAGGAATGT
2722000 AACCTGGCGGGCTAGGAATGT
1 AACCTGGCGGGCTAGGAATGT
* *
2722021 AACCCT-GTGGGCTCGGAATGT
1 AA-CCTGGCGGGCTAGGAATGT
2722042 A
1 A
2722043 GCCCTGCGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 35 0.92
22 3 0.08
ACGTcount: A:0.22, C:0.22, G:0.34, T:0.22
Consensus pattern (21 bp):
AACCTGGCGGGCTAGGAATGT
Found at i:2722081 original size:21 final size:21
Alignment explanation
Indices: 2722055--2722102 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2722045 CCTGCGGAGA
*
2722055 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
2722076 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
2722097 GGGCAT
1 TGGCAT
2722103 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:2723875 original size:14 final size:14
Alignment explanation
Indices: 2723822--2723888 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
2723812 ATAATTCTAA
*
2723822 ATAAATAATAATTAT
1 ATAAAT-ATATTTAT
*
2723837 ATAAAT-TATTTTAA
1 ATAAATATA-TTTAT
* *
2723851 AAAAATAATATTTAC
1 ATAAAT-ATATTTAT
*
2723866 ATAAATATATTAAT
1 ATAAATATATTTAT
2723880 ATAAATATA
1 ATAAATATA
2723889 ATAACTATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
13 2 0.05
14 23 0.55
15 15 0.36
16 2 0.05
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAAATATATTTAT
Found at i:2723885 original size:29 final size:29
Alignment explanation
Indices: 2723819--2723890 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
2723809 TTAATAATTC
* *
2723819 TAAATAAATAATAATTATATAAATTATTT
1 TAAATAAATAATAATTACATAAATTATAT
* *
2723848 TAAAAAAATAATATTTACATAAA-TATAT
1 TAAATAAATAATAATTACATAAATTATAT
2723876 TAATATAAAT-ATAAT
1 TAA-ATAAATAATAAT
2723891 AACTATTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 11 0.31
29 25 0.69
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (29 bp):
TAAATAAATAATAATTACATAAATTATAT
Found at i:2735839 original size:25 final size:25
Alignment explanation
Indices: 2735805--2735855 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
2735795 TGGTCGAGTC
2735805 GAGTCGAGTCTGATCAGGAATCAAG
1 GAGTCGAGTCTGATCAGGAATCAAG
*
2735830 GAGTCGAGTCTGGTCAGGAATCAAG
1 GAGTCGAGTCTGATCAGGAATCAAG
2735855 G
1 G
2735856 TTCTAAAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.35, T:0.20
Consensus pattern (25 bp):
GAGTCGAGTCTGATCAGGAATCAAG
Found at i:2737529 original size:21 final size:21
Alignment explanation
Indices: 2737512--2737571 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
2737502 CTAAAATTTA
*
2737512 AAACTCTAACCCCTAAATCAC
1 AAACTCTAAACCCTAAATCAC
* *
2737533 AAACTCTAAACCCT-AACCAT
1 AAACTCTAAACCCTAAATCAC
*
2737553 AAACTCAGAAACCCTAAAT
1 AAACTC-TAAACCCTAAAT
2737572 AGGACCATGG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 10 0.31
21 20 0.62
22 2 0.06
ACGTcount: A:0.47, C:0.33, G:0.02, T:0.18
Consensus pattern (21 bp):
AAACTCTAAACCCTAAATCAC
Found at i:2744172 original size:19 final size:18
Alignment explanation
Indices: 2744148--2744196 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 18
2744138 TTAGTTGAAC
2744148 AAAATTAGATATATTAATA
1 AAAATTA-ATATATTAATA
2744167 AAAATT-ATATA-TAATA
1 AAAATTAATATATTAATA
*
2744183 TAAATTAA-ATATTA
1 AAAATTAATATATTA
2744197 TTATAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 13 0.48
17 8 0.30
19 6 0.22
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
AAAATTAATATATTAATA
Found at i:2744201 original size:22 final size:23
Alignment explanation
Indices: 2744165--2744208 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
2744155 GATATATTAA
2744165 TAAAAATTATATATAATATAAAT
1 TAAAAATTATATATAATATAAAT
* *
2744188 TAAATATTAT-TATAATTTAAA
1 TAAAAATTATATATAATATAAA
2744209 AAGATTATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAAAATTATATATAATATAAAT
Found at i:2744614 original size:94 final size:92
Alignment explanation
Indices: 2744501--2744689 Score: 281
Period size: 94 Copynumber: 2.0 Consensus size: 92
2744491 ATCACTCATG
* *
2744501 TTATAATCACTGGTATTGTAATTCGAGATTTTTAAAAATAACAATTACTTCTTTAATCACTGAGA
1 TTATAATAACTGGTATTGTAATTCGAGATCTTTAAAAATAA-AATTACTTCTTTAATCA-TGAGA
**
2744566 TAATTTAATTCGTTTACAAC-TAAATATAT
64 TAATTTAATTCACTTAC-ACTTAAATATAT
* *
2744595 TTATAATAACTGGTGTTGTAATTCGAGATCTTTAAAAATAAAATTACTTCTTTAATTATGAGATA
1 TTATAATAACTGGTATTGTAATTCGAGATCTTTAAAAATAAAATTACTTCTTTAATCATGAGATA
*
2744660 ATTTGATTCACTTACACTTAAATATAT
66 ATTTAATTCACTTACACTTAAATATAT
2744687 TTA
1 TTA
2744690 AATCTAAATC
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
91 2 0.02
92 31 0.36
93 16 0.18
94 38 0.44
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (92 bp):
TTATAATAACTGGTATTGTAATTCGAGATCTTTAAAAATAAAATTACTTCTTTAATCATGAGATA
ATTTAATTCACTTACACTTAAATATAT
Found at i:2753108 original size:22 final size:22
Alignment explanation
Indices: 2753082--2753123 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2753072 CTACATCCTT
* *
2753082 CTTTTTCTTGTTCTTTTTTTTC
1 CTTTTTCTTCTTCTTCTTTTTC
2753104 CTTTTTCTTCTTCTTCTTTT
1 CTTTTTCTTCTTCTTCTTTT
2753124 GGAGTTTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (22 bp):
CTTTTTCTTCTTCTTCTTTTTC
Found at i:2755812 original size:18 final size:18
Alignment explanation
Indices: 2755786--2755821 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2755776 GTTGTCCATT
* *
2755786 TTATTATTTTAGTACCTA
1 TTATCATTTTAATACCTA
2755804 TTATCATTTTAATACCTA
1 TTATCATTTTAATACCTA
2755822 AAATGTAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.53
Consensus pattern (18 bp):
TTATCATTTTAATACCTA
Found at i:2755869 original size:20 final size:20
Alignment explanation
Indices: 2755844--2755898 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
2755834 TCACGCAATA
2755844 ATAATATATGAAAAATATGT
1 ATAATATATGAAAAATATGT
2755864 ATAATATATGAAAAATATGT
1 ATAATATATGAAAAATATGT
2755884 ATAATATATGAAAAA
1 ATAATATATGAAAAA
2755899 CATATATTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (20 bp):
ATAATATATGAAAAATATGT
Found at i:2755872 original size:11 final size:10
Alignment explanation
Indices: 2755844--2755894 Score: 52
Period size: 9 Copynumber: 5.1 Consensus size: 10
2755834 TCACGCAATA
2755844 ATAATATATG
1 ATAATATATG
*
2755854 A-AAAATATG
1 ATAATATATG
2755863 TATAATATATG
1 -ATAATATATG
*
2755874 A-AAAATATG
1 ATAATATATG
2755883 TATAATATATG
1 -ATAATATATG
2755894 A
1 A
2755895 AAAACATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
9 14 0.42
10 5 0.15
11 14 0.42
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (10 bp):
ATAATATATG
Found at i:2758479 original size:13 final size:14
Alignment explanation
Indices: 2758461--2758493 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2758451 TATTTTAAAC
2758461 CCTAAACC-TATAT
1 CCTAAACCATATAT
2758474 CCTAAACCATATAT
1 CCTAAACCATATAT
2758488 CCTAAA
1 CCTAAA
2758494 TCTTAAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.27
Consensus pattern (14 bp):
CCTAAACCATATAT
Found at i:2758500 original size:21 final size:20
Alignment explanation
Indices: 2758467--2758514 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
2758457 AAACCCTAAA
*
2758467 CCTATATCCTAAAC-CATATAT
1 CCTAAATCCTAAACTCA-A-AT
*
2758488 CCTAAATCTTAAACTCAAAT
1 CCTAAATCCTAAACTCAAAT
2758508 CCTAAAT
1 CCTAAAT
2758515 TATATCCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 13 0.54
22 2 0.08
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (20 bp):
CCTAAATCCTAAACTCAAAT
Found at i:2758873 original size:24 final size:24
Alignment explanation
Indices: 2758808--2758873 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
2758798 TAATATAGCA
* *
2758808 TATATTT-TGAAAATTAAAATTAT
1 TATATTTATTAAAATTTAAATTAT
*
2758831 TATTATTATATT-AAA-TTAAGTTAT
1 TA-TATT-TATTAAAATTTAAATTAT
2758855 TATATTTATTAAAATTTAA
1 TATATTTATTAAAATTTAA
2758874 CACATGATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
22 4 0.11
23 9 0.26
24 17 0.49
25 4 0.11
26 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (24 bp):
TATATTTATTAAAATTTAAATTAT
Found at i:2759611 original size:22 final size:22
Alignment explanation
Indices: 2759584--2759629 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
2759574 TTATGGGCAG
2759584 GGGTATGGTCGAGGGTGTGTAA
1 GGGTATGGTCGAGGGTGTGTAA
2759606 GGGTATGGTCGAGGGTGTGTAA
1 GGGTATGGTCGAGGGTGTGTAA
2759628 GG
1 GG
2759630 TGTGCCACCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.04, G:0.52, T:0.26
Consensus pattern (22 bp):
GGGTATGGTCGAGGGTGTGTAA
Found at i:2759738 original size:10 final size:10
Alignment explanation
Indices: 2759723--2759748 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2759713 TCGAGTATAT
2759723 TTATCAATTG
1 TTATCAATTG
2759733 TTATCAATTG
1 TTATCAATTG
2759743 TTATCA
1 TTATCA
2759749 TTAAGAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.50
Consensus pattern (10 bp):
TTATCAATTG
Found at i:2765660 original size:26 final size:27
Alignment explanation
Indices: 2765608--2765661 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
2765598 GTTTATATTG
* ** *
2765608 ATGATAAAACCATTTTTTTTTATAGAA
1 ATGATAAAACCATTTTTATACAAAGAA
2765635 ATGATAAAACCA-TTTTATACAAAGAA
1 ATGATAAAACCATTTTTATACAAAGAA
2765661 A
1 A
2765662 ATCTCAATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.35
Consensus pattern (27 bp):
ATGATAAAACCATTTTTATACAAAGAA
Found at i:2769881 original size:20 final size:20
Alignment explanation
Indices: 2769856--2769899 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2769846 AAATTCAACC
2769856 AAAATAA-AAAGAAATAAAAT
1 AAAATAATAAAGAAAT-AAAT
*
2769876 AAAATAATAAATAAATAAAT
1 AAAATAATAAAGAAATAAAT
2769896 AAAA
1 AAAA
2769900 CATAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (20 bp):
AAAATAATAAAGAAATAAAT
Found at i:2770664 original size:37 final size:37
Alignment explanation
Indices: 2770571--2770672 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
2770561 GTGCTTGTGG
* * ** * *
2770571 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
2770608 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
2770645 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
2770673 TAGGAAGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:2771247 original size:83 final size:83
Alignment explanation
Indices: 2771125--2771320 Score: 259
Period size: 83 Copynumber: 2.4 Consensus size: 83
2771115 AACTGAATGG
** * *
2771125 AATCGAACTCGACAAT-TTTGATGACAGATAACTCTTCTAGCCTTGAGTTATGCTGTAAACGATG
1 AATCGAACTCGACGGTCTTTGATGACAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAACGATG
*
2771189 TACCTTGGAGCTGAGCGT
66 CACCTTGGAGCTGAGCGT
* * * *
2771207 AGTCGAACTCGACGGTCTTTGCTGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATG
1 AATCGAACTCGACGGTCTTTGATGACAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAACGATG
* *
2771272 CGCCTTGGAGCTGAGTGT
66 CACCTTGGAGCTGAGCGT
* * *
2771290 AATCGAACTCGAAGGTCTTTGTTGATAGATA
1 AATCGAACTCGACGGTCTTTGATGACAGATA
2771321 CTTCTTCTTT
Statistics
Matches: 98, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
82 13 0.13
83 85 0.87
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (83 bp):
AATCGAACTCGACGGTCTTTGATGACAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAACGATG
CACCTTGGAGCTGAGCGT
Found at i:2771699 original size:106 final size:106
Alignment explanation
Indices: 2771508--2772460 Score: 1458
Period size: 106 Copynumber: 9.0 Consensus size: 106
2771498 GTACTGTTCC
* * * * * * * *
2771508 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGAGAAATTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * * * * * *
2771573 TCAGCCGCCCCTTTG-CTGTGAAGTTGAGCTTGTGCTATCTT
66 CCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCTG
* * *
2771614 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
2771679 CCAGCCGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2771720 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
2771785 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2771826 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
2771891 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2771932 GAGTCCAATATCTTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
2771997 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2772038 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
2772103 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2772144 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
2772209 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2772250 GAGTCCAATATCCTTCGTTGTGAAGCTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
2772315 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
2772356 GAGTCCAATATACTTCGTTGTGAAGTTGAAGTTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * * *
2772421 CCATCCGTCCCTTCATTGTGAAGTTGAGCTTGTGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
2772461 CTAGTGGCAC
Statistics
Matches: 792, Mismatches: 54, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
106 792 1.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2773395 original size:22 final size:22
Alignment explanation
Indices: 2773369--2773445 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
2773359 TTGTGTTTGG
2773369 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
2773391 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
2773413 TCAAAGGTTTGGCATTTGGTGC
1 TCAAAGGTTTGGCATTTGATGC
2773435 TCAAAGGTTTG
1 TCAAAGGTTTG
2773446 ATGGGGTAGC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.22, C:0.13, G:0.29, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:2774104 original size:20 final size:18
Alignment explanation
Indices: 2774077--2774151 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 18
2774067 TTTTTGTCCT
2774077 TTTTTCTTTTTTATTTTTG
1 TTTTTCTTTTTT-TTTTTG
*
2774096 TTATTTCTTTTTTCTTTTG
1 TT-TTTCTTTTTTTTTTTG
2774115 -TTTTC-TTTTTTTTTTG
1 TTTTTCTTTTTTTTTTTG
2774131 CTTCTTTTCTTTTTTCTTTTT
1 --T-TTTTCTTTTTT-TTTTT
2774152 TTCCTTTTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
16 10 0.21
17 4 0.09
18 1 0.02
19 7 0.15
20 15 0.32
21 5 0.11
22 5 0.11
ACGTcount: A:0.03, C:0.11, G:0.04, T:0.83
Consensus pattern (18 bp):
TTTTTCTTTTTTTTTTTG
Found at i:2774120 original size:10 final size:9
Alignment explanation
Indices: 2774076--2774165 Score: 57
Period size: 9 Copynumber: 9.9 Consensus size: 9
2774066 TTTTTTGTCC
2774076 TTTTTTCTT
1 TTTTTTCTT
2774085 TTTTATT-TT
1 TTTT-TTCTT
2774094 TGTTATTTC--
1 T-TT-TTTCTT
2774103 TTTTTTCTT
1 TTTTTTCTT
2774112 TTGTTTTCTT
1 TT-TTTTCTT
2774122 TTTTTT-TT
1 TTTTTTCTT
2774130 GCTTCTTTTC--
1 --TT-TTTTCTT
2774140 TTTTTTCTT
1 TTTTTTCTT
*
2774149 TTTTTCCTT
1 TTTTTTCTT
*
2774158 TTTGTTCT
1 TTTTTTCT
2774166 GATTGAATCT
Statistics
Matches: 65, Mismatches: 3, Indels: 26
0.69 0.03 0.28
Matches are distributed among these distances:
7 9 0.14
8 6 0.09
9 28 0.43
10 17 0.26
11 5 0.08
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.81
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:2774135 original size:25 final size:24
Alignment explanation
Indices: 2774107--2774153 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
2774097 TATTTCTTTT
* *
2774107 TTCTTTTGTTTTCTTTTTTTTTTGC
1 TTCTTTTCTTTT-TTCTTTTTTTGC
2774132 TTCTTTTCTTTTTTCTTTTTTT
1 TTCTTTTCTTTTTTCTTTTTTT
2774154 CCTTTTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (24 bp):
TTCTTTTCTTTTTTCTTTTTTTGC
Found at i:2774140 original size:37 final size:35
Alignment explanation
Indices: 2774076--2774160 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 35
2774066 TTTTTTGTCC
2774076 TTTTTTCTTTTTTATTTTTGTTATTTCTTTTTTCTT
1 TTTTTTC-TTTTTATTTTTGTTATTTCTTTTTTCTT
*
2774112 TTGTTTTCTTTTT-TTTTTGCTTCTTTTCTTTTTTCTT
1 TT-TTTTCTTTTTATTTTTG-TT-ATTTCTTTTTTCTT
*
2774149 TTTTTCCTTTTT
1 TTTTTTCTTTTT
2774161 GTTCTGATTG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
35 6 0.14
36 18 0.41
37 20 0.45
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.82
Consensus pattern (35 bp):
TTTTTTCTTTTTATTTTTGTTATTTCTTTTTTCTT
Found at i:2774160 original size:7 final size:7
Alignment explanation
Indices: 2774075--2774152 Score: 72
Period size: 7 Copynumber: 11.0 Consensus size: 7
2774065 CTTTTTTGTC
2774075 CTTTTTT
1 CTTTTTT
2774082 CTTTTTT
1 CTTTTTT
*
2774089 -ATTTTT
1 CTTTTTT
* *
2774095 GTTATTT
1 CTTTTTT
2774102 CTTTTTT
1 CTTTTTT
2774109 CTTTTGTT
1 CTTTT-TT
2774117 -TTCTTTT
1 CTT-TTTT
2774124 -TTTTTT
1 CTTTTTT
2774130 GCTTCTTTT
1 -CTT-TTTT
2774139 CTTTTTT
1 CTTTTTT
2774146 CTTTTTT
1 CTTTTTT
2774153 TCCTTTTTGT
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
6 9 0.15
7 38 0.63
8 9 0.15
9 4 0.07
ACGTcount: A:0.03, C:0.12, G:0.04, T:0.82
Consensus pattern (7 bp):
CTTTTTT
Found at i:2775352 original size:16 final size:16
Alignment explanation
Indices: 2775328--2775364 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
2775318 ATGCAAGAAT
*
2775328 GCATGAAATGTTCGAG
1 GCATTAAATGTTCGAG
2775344 GCATTAAATGTTCGAG
1 GCATTAAATGTTCGAG
2775360 GCATT
1 GCATT
2775365 GATCCAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (16 bp):
GCATTAAATGTTCGAG
Found at i:2777851 original size:4 final size:4
Alignment explanation
Indices: 2777829--2777990 Score: 53
Period size: 4 Copynumber: 40.2 Consensus size: 4
2777819 CATGTTAGAT
2777829 ATAA A-AA A-AA AT-A AT-A ATAA ATAAA ATAA ATAA ATAA ATTCAA CCA-AA
1 ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATAA A-T-AA --ATAA
* *
2777877 AT-A A-AA AGAA ATAAA ATAA A-ATA ATAA ATAA ATAA ATAA A-AC ATAGA
1 ATAA ATAA ATAA AT-AA ATAA ATA-A ATAA ATAA ATAA ATAA ATAA ATA-A
* * *
2777924 A-AA ATGATA GTAA AT-A ATAGT ATAA ATAT A-AA ATAA A-AA AGGTAA
1 ATAA AT-A-A ATAA ATAA ATA-A ATAA ATAA ATAA ATAA ATAA A--TAA
*
2777969 TATAT ATAA ATAA ATAA ATAA A
1 -ATAA ATAA ATAA ATAA ATAA A
2777991 ATACACATAA
Statistics
Matches: 122, Mismatches: 11, Indels: 50
0.67 0.06 0.27
Matches are distributed among these distances:
3 30 0.25
4 64 0.52
5 20 0.16
6 6 0.05
7 1 0.01
8 1 0.01
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:2777928 original size:50 final size:48
Alignment explanation
Indices: 2777829--2777919 Score: 123
Period size: 46 Copynumber: 1.9 Consensus size: 48
2777819 CATGTTAGAT
* *
2777829 ATAAAAAAAAATAATAATAAATAAAATAAATAAATAAATTCAACCAAA
1 ATAAAAAAAAATAATAATAAATAAAATAAATAAATAAATACAACAAAA
* * *
2777877 ATAAAAAGAAATAA-AATAAA-ATAATAAATAAATAAATAAAACA
1 ATAAAAAAAAATAATAATAAATAAAATAAATAAATAAATACAACA
2777920 TAGAAAAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
46 19 0.50
47 6 0.16
48 13 0.34
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.20
Consensus pattern (48 bp):
ATAAAAAAAAATAATAATAAATAAAATAAATAAATAAATACAACAAAA
Found at i:2778031 original size:78 final size:80
Alignment explanation
Indices: 2777899--2778052 Score: 185
Period size: 78 Copynumber: 1.9 Consensus size: 80
2777889 AAAATAAAAT
* *
2777899 AATAAATAAATAAATAAAACATAGAAAAATGATAGTAAATAATAGTATAAATATAA-AAT-AAAA
1 AATAAATAAATAAATAAAACATAAAAAAATGATAGCAAATAATAGTATAAATATAATAATGAAAA
2777962 AAGGTAATATATATA
66 AAGGTAATATATATA
* *
2777977 AATAAATAAATAAA-ATACACATAAAGAAAATGA-AGC-AATAAATA-TAATATATATAATAATG
1 AATAAATAAATAAATA-AAACATAAA-AAAATGATAGCAAAT-AATAGT-ATAAATATAATAATG
*
2778038 ATAAAAGGTAATATA
62 AAAAAAGGTAATATA
2778053 CGTAAATAGA
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
77 5 0.08
78 36 0.55
79 10 0.15
80 14 0.22
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.25
Consensus pattern (80 bp):
AATAAATAAATAAATAAAACATAAAAAAATGATAGCAAATAATAGTATAAATATAATAATGAAAA
AAGGTAATATATATA
Found at i:2778692 original size:37 final size:37
Alignment explanation
Indices: 2778598--2778695 Score: 115
Period size: 37 Copynumber: 2.6 Consensus size: 37
2778588 GTGCTTGTGG
* * * * *
2778598 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
* * * *
2778635 ATCCTATTTTTAAGAATTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
2778672 ATCCTATTTTTAGGAGTTTGAATC
1 ATCCTATTTTTAGGAGTTTGAATC
2778696 GTAGTAGGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
Found at i:2808199 original size:44 final size:44
Alignment explanation
Indices: 2808136--2808225 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
2808126 GCCTGCTGAA
2808136 ATCTCTACCTTGATGCACGCATAAGTAGCATTCTCTTTCATGTT
1 ATCTCTACCTTGATGCACGCATAAGTAGCATTCTCTTTCATGTT
* *
2808180 ATCTCTACTTTGATGCACGCATAGGTAGCATTCTCTTTCATGTT
1 ATCTCTACCTTGATGCACGCATAAGTAGCATTCTCTTTCATGTT
2808224 AT
1 AT
2808226 GCAGAATTAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.40
Consensus pattern (44 bp):
ATCTCTACCTTGATGCACGCATAAGTAGCATTCTCTTTCATGTT
Found at i:2809621 original size:11 final size:11
Alignment explanation
Indices: 2809605--2809637 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2809595 GATTTTTTAT
2809605 TTAATTTATAA
1 TTAATTTATAA
2809616 TTAATTT-TAA
1 TTAATTTATAA
*
2809626 TTATTTTATAA
1 TTAATTTATAA
2809637 T
1 T
2809638 ATTAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTAATTTATAA
Found at i:2810264 original size:12 final size:12
Alignment explanation
Indices: 2810239--2810277 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
2810229 GACGAGTCTA
2810239 TTTAAAAAATATT
1 TTTAAAAAA-ATT
2810252 TTTAAAAAAATT
1 TTTAAAAAAATT
*
2810264 TGTAAAAATAATT
1 TTTAAAAA-AATT
2810277 T
1 T
2810278 AAATTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (12 bp):
TTTAAAAAAATT
Found at i:2810301 original size:20 final size:19
Alignment explanation
Indices: 2810259--2810301 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
2810249 ATTTTTAAAA
*
2810259 AAATTTGTAAAAATAATTT
1 AAATTTGTAAAAATAAATT
2810278 AAATTT-TAAAACATAAAATT
1 AAATTTGTAAAA-AT-AAATT
2810298 AAAT
1 AAAT
2810302 CGATGTGACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 8 0.38
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
AAATTTGTAAAAATAAATT
Found at i:2814147 original size:19 final size:21
Alignment explanation
Indices: 2814125--2814181 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
2814115 AGAACCCCAG
2814125 GGGGGTATCGATTCCC-C-TA
1 GGGGGTATCGATTCCCTCATA
* *
2814144 GGGGGAATCGGTTCCCTCATA
1 GGGGGTATCGATTCCCTCATA
*
2814165 -TGGGTATCGATTCCCTC
1 GGGGGTATCGATTCCCTC
2814182 TGCACCAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 14 0.45
20 15 0.48
21 2 0.06
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
GGGGGTATCGATTCCCTCATA
Found at i:2814178 original size:20 final size:20
Alignment explanation
Indices: 2814125--2814182 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
2814115 AGAACCCCAG
2814125 GGGGGTATCGATTCCC-CTA
1 GGGGGTATCGATTCCCTCTA
* *
2814144 GGGGGAATCGGTTCCCTCATA
1 GGGGGTATCGATTCCCTC-TA
*
2814165 -TGGGTATCGATTCCCTCT
1 GGGGGTATCGATTCCCTCT
2814183 GCACCAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 15 0.47
20 15 0.47
21 2 0.06
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (20 bp):
GGGGGTATCGATTCCCTCTA
Found at i:2820099 original size:20 final size:20
Alignment explanation
Indices: 2820070--2820107 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2820060 CCCCTTCAAA
*
2820070 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
2820090 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
2820108 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:2824167 original size:117 final size:117
Alignment explanation
Indices: 2823945--2824168 Score: 283
Period size: 117 Copynumber: 1.9 Consensus size: 117
2823935 AACTTTCAAA
* *
2823945 TTGAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTAAAAGCTCTAAATCCTTCTTCAAGAT
1 TTGAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTAAAAGCTCTAAATCCTTCTTCAACAT
* *
2824010 TTCATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAAT
66 TTCATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAAT
* * * * *
2824062 TTGAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCCTT-TCTCAAC
1 TTGAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTAAAAGCTCTAAATCCTTCT-TCAAC
* * **
2824125 ATTTCATTTTGATTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
64 ATTTCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
2824169 ATCATTTTTA
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
116 2 0.02
117 85 0.93
118 4 0.04
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (117 bp):
TTGAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTAAAAGCTCTAAATCCTTCTTCAACAT
TTCATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAAT
Found at i:2826619 original size:22 final size:21
Alignment explanation
Indices: 2826577--2826616 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2826567 GAGTTTATTT
*
2826577 TCATTTTTACATTTTGAAACA
1 TCATTTTTACATTTTAAAACA
*
2826598 TCATTTTTATATTTTAAAA
1 TCATTTTTACATTTTAAAA
2826617 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTACATTTTAAAACA
Found at i:2830463 original size:235 final size:235
Alignment explanation
Indices: 2830052--2830521 Score: 940
Period size: 235 Copynumber: 2.0 Consensus size: 235
2830042 GGTTATTTTC
2830052 GTTTCTATATTGTATATCATACTTCAACTAAGACTCAACCAACTTGGGATGGAGCTTCATGGGAT
1 GTTTCTATATTGTATATCATACTTCAACTAAGACTCAACCAACTTGGGATGGAGCTTCATGGGAT
2830117 GCAATACAACACACTCAAGCATCTTCGACAAAACATACGAGTGAGGGTGAATGAGATCATATCAT
66 GCAATACAACACACTCAAGCATCTTCGACAAAACATACGAGTGAGGGTGAATGAGATCATATCAT
2830182 ATATAATCAACAAAGTAGCCAAGTCAATTCAGTAACGACAATGATGGCGTCAAATATCATAAGCA
131 ATATAATCAACAAAGTAGCCAAGTCAATTCAGTAACGACAATGATGGCGTCAAATATCATAAGCA
2830247 CATCACCATATTTCGAAGGTGGATCTTAAAGTGTGTTAAG
196 CATCACCATATTTCGAAGGTGGATCTTAAAGTGTGTTAAG
2830287 GTTTCTATATTGTATATCATACTTCAACTAAGACTCAACCAACTTGGGATGGAGCTTCATGGGAT
1 GTTTCTATATTGTATATCATACTTCAACTAAGACTCAACCAACTTGGGATGGAGCTTCATGGGAT
2830352 GCAATACAACACACTCAAGCATCTTCGACAAAACATACGAGTGAGGGTGAATGAGATCATATCAT
66 GCAATACAACACACTCAAGCATCTTCGACAAAACATACGAGTGAGGGTGAATGAGATCATATCAT
2830417 ATATAATCAACAAAGTAGCCAAGTCAATTCAGTAACGACAATGATGGCGTCAAATATCATAAGCA
131 ATATAATCAACAAAGTAGCCAAGTCAATTCAGTAACGACAATGATGGCGTCAAATATCATAAGCA
2830482 CATCACCATATTTCGAAGGTGGATCTTAAAGTGTGTTAAG
196 CATCACCATATTTCGAAGGTGGATCTTAAAGTGTGTTAAG
2830522 TACACCTCCT
Statistics
Matches: 235, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
235 235 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (235 bp):
GTTTCTATATTGTATATCATACTTCAACTAAGACTCAACCAACTTGGGATGGAGCTTCATGGGAT
GCAATACAACACACTCAAGCATCTTCGACAAAACATACGAGTGAGGGTGAATGAGATCATATCAT
ATATAATCAACAAAGTAGCCAAGTCAATTCAGTAACGACAATGATGGCGTCAAATATCATAAGCA
CATCACCATATTTCGAAGGTGGATCTTAAAGTGTGTTAAG
Found at i:2830735 original size:16 final size:16
Alignment explanation
Indices: 2830714--2830746 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2830704 TAATAAAATT
2830714 ATTAATTTACTTTTTA
1 ATTAATTTACTTTTTA
*
2830730 ATTAATTTATTTTTTA
1 ATTAATTTACTTTTTA
2830746 A
1 A
2830747 AATTTAATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTAATTTACTTTTTA
Found at i:2846387 original size:40 final size:40
Alignment explanation
Indices: 2846312--2846387 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
2846302 TCAAATACGT
**
2846312 AAAATATTTTTCAAAAAATATAATTCATTTTACAAAAAAA
1 AAAATATTTTTCAAAAAATATAATTCATTAAACAAAAAAA
* *
2846352 AAAATATTTTTCAAAAAATGT-TTTCAGTTAAACAAA
1 AAAATATTTTTCAAAAAATATAATTCA-TTAAACAAA
2846388 TGACCCGAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 4 0.13
40 27 0.87
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (40 bp):
AAAATATTTTTCAAAAAATATAATTCATTAAACAAAAAAA
Found at i:2847034 original size:2 final size:2
Alignment explanation
Indices: 2847027--2847051 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2847017 TTTAAATTAA
2847027 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
2847052 GAGAGAGAGA
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:2847056 original size:2 final size:2
Alignment explanation
Indices: 2847051--2847093 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2847041 ATATATATAT
2847051 AG AG AG AG AG AG 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 AG AG AG AG AG AG
2847093 A
1 A
2847094 AAACTTTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2847869 original size:20 final size:21
Alignment explanation
Indices: 2847844--2847900 Score: 91
Period size: 20 Copynumber: 2.8 Consensus size: 21
2847834 ATCCTATTCC
2847844 CTGGTAATCTTACATTCT-CA
1 CTGGTAATCTTACATTCTCCA
2847864 CTGGTAATCTTACATT-TCCA
1 CTGGTAATCTTACATTCTCCA
*
2847884 CTGGTAATCTTCCATTC
1 CTGGTAATCTTACATTC
2847901 CGTGAACCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 1 0.03
20 33 0.97
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.40
Consensus pattern (21 bp):
CTGGTAATCTTACATTCTCCA
Found at i:2858834 original size:24 final size:24
Alignment explanation
Indices: 2858790--2858835 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2858780 TGTTCTTTTG
* *
2858790 TCTTTGTGTGTGCATCTTAATTAA
1 TCTTTGCGTGTGCAACTTAATTAA
2858814 TCTTTGCGTGTGCCAAC-TAATT
1 TCTTTGCGTGTG-CAACTTAATT
2858836 TTTAATGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (24 bp):
TCTTTGCGTGTGCAACTTAATTAA
Found at i:2879472 original size:2 final size:2
Alignment explanation
Indices: 2879465--2879506 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2879455 AACAACTTTC
2879465 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2879507 TAAAATTCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2881435 original size:33 final size:33
Alignment explanation
Indices: 2881366--2881437 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
2881356 TAATGTGGTA
* *
2881366 TTTATTATTATTATTTTAATTTTTATATCATTT
1 TTTATTATTATAATTTTAATTTTTATATCATAT
*
2881399 TTTATTATTAGTAATTTTATATTTTTA-ATTA-AT
1 TTTATTATTA-TAATTTTA-ATTTTTATATCATAT
2881432 TTTATT
1 TTTATT
2881438 CGATTAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 17 0.50
34 10 0.29
35 7 0.21
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (33 bp):
TTTATTATTATAATTTTAATTTTTATATCATAT
Found at i:2894272 original size:28 final size:28
Alignment explanation
Indices: 2894241--2894308 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
2894231 TAATATAAAA
*
2894241 TAAAAATTAAGCGATAAGTAATATATTT
1 TAAAAATTAAACGATAAGTAATATATTT
*
2894269 TAAAAATTAAACGTTAAGTAATATATTT
1 TAAAAATTAAACGATAAGTAATATATTT
*
2894297 TAAAAATAAAAC
1 TAAAAATTAAAC
2894309 TTTAAATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.34
Consensus pattern (28 bp):
TAAAAATTAAACGATAAGTAATATATTT
Found at i:2900354 original size:17 final size:17
Alignment explanation
Indices: 2900332--2900366 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2900322 GTAGACTCAG
* *
2900332 AGTTATTACCATTAAAA
1 AGTTATTAACACTAAAA
2900349 AGTTATTAACACTAAAA
1 AGTTATTAACACTAAAA
2900366 A
1 A
2900367 CCTCTATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.31
Consensus pattern (17 bp):
AGTTATTAACACTAAAA
Found at i:2903061 original size:19 final size:19
Alignment explanation
Indices: 2903010--2903066 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
2903000 TTTGGATTAA
2903010 GGAATGTGTGATT-TCTATG
1 GGAATGTGTGATTCTC-ATG
*
2903029 GGAATGTGAGATTCTCATG
1 GGAATGTGTGATTCTCATG
*
2903048 GGAATGTGTGATTCCCATG
1 GGAATGTGTGATTCTCATG
2903067 TTTGGTTGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 32 0.94
20 2 0.06
ACGTcount: A:0.23, C:0.11, G:0.32, T:0.35
Consensus pattern (19 bp):
GGAATGTGTGATTCTCATG
Found at i:2903265 original size:19 final size:19
Alignment explanation
Indices: 2903241--2903282 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
2903231 ATTCTTCTGT
2903241 CATGGGAATGTGTGATTCC
1 CATGGGAATGTGTGATTCC
*
2903260 CATGGGAATGTGTGATTCT
1 CATGGGAATGTGTGATTCC
2903279 CATG
1 CATG
2903283 TTTGGTTGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.33
Consensus pattern (19 bp):
CATGGGAATGTGTGATTCC
Found at i:2903406 original size:216 final size:215
Alignment explanation
Indices: 2903026--2903458 Score: 812
Period size: 216 Copynumber: 2.0 Consensus size: 215
2903016 TGTGATTTCT
*
2903026 ATGGGAATGTGAGATTCTCATGGGAATGTGTGATTCCCATGTTTGGTTGGCCGGGAATCTCATTC
1 ATGGGAATGTGAGATTCCCATGGGAATGTGTGATTCCCATGTTTGGTTGGCCGGGAATCTCATTC
2903091 TCGATAATGTTTTATTATCAATAGTAAATTTTTTGAGGTATATTACCAAGAATATCATTACCTCC
66 TCGATAATGTTTTATTATCAATAGTAAATTTTTTGAGGTATATTACCAAGAATATCATTACCTCC
*
2903156 ATTTCCTTAGGTATTGTTGGATTACCGGCCTTTTATACTAAAATGCCCTTAATTTTTTTTTCTTT
131 ATTTCCTTAGGTATTGTTGGATTACCGACCTTTTATACTAAAATGCCCTTAATTTTTTTTTCTTT
2903221 CAAAAATATCATTCTTCTGTC
196 CAAAAATATCATT-TTCTGTC
* *
2903242 ATGGGAATGTGTGATTCCCATGGGAATGTGTGATTCTCATGTTTGGTTGGCCGGGAATCTCATTC
1 ATGGGAATGTGAGATTCCCATGGGAATGTGTGATTCCCATGTTTGGTTGGCCGGGAATCTCATTC
*
2903307 TCGGTAATGTTTTATTATCAATAGTAAATTTTTTGAGGTATATTACCAAGAATATCATTACCTCC
66 TCGATAATGTTTTATTATCAATAGTAAATTTTTTGAGGTATATTACCAAGAATATCATTACCTCC
2903372 ATTTCCTTAGGTATTGTTGGATTACCGACCTTTTATACTAAAATGCCCTTAATTTTTTTTTCTTT
131 ATTTCCTTAGGTATTGTTGGATTACCGACCTTTTATACTAAAATGCCCTTAATTTTTTTTTCTTT
2903437 CAAAAATATCATTTTCTGTC
196 CAAAAATATCATTTTCTGTC
2903457 AT
1 AT
2903459 TGGATAATAA
Statistics
Matches: 212, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
215 9 0.04
216 203 0.96
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (215 bp):
ATGGGAATGTGAGATTCCCATGGGAATGTGTGATTCCCATGTTTGGTTGGCCGGGAATCTCATTC
TCGATAATGTTTTATTATCAATAGTAAATTTTTTGAGGTATATTACCAAGAATATCATTACCTCC
ATTTCCTTAGGTATTGTTGGATTACCGACCTTTTATACTAAAATGCCCTTAATTTTTTTTTCTTT
CAAAAATATCATTTTCTGTC
Found at i:2903852 original size:62 final size:62
Alignment explanation
Indices: 2903740--2903863 Score: 167
Period size: 62 Copynumber: 2.0 Consensus size: 62
2903730 CCAATAATCT
* * *
2903740 TTTATTCATTTAATCAAACACGGCAATCTTATATTCATGCTAAACCAACCAAACACAAAATA
1 TTTATTCATTTAACCAAACACGGCAATCGTAGATTCATGCTAAACCAACCAAACACAAAATA
* * * * * *
2903802 TTTATTCCTTTAACCAAATACGGTAATCGTAGATTCCTGTTAAACTAACCAAACACAAAATA
1 TTTATTCATTTAACCAAACACGGCAATCGTAGATTCATGCTAAACCAACCAAACACAAAATA
2903864 CAACATTCCC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.30
Consensus pattern (62 bp):
TTTATTCATTTAACCAAACACGGCAATCGTAGATTCATGCTAAACCAACCAAACACAAAATA
Found at i:2903913 original size:20 final size:20
Alignment explanation
Indices: 2903888--2903925 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2903878 ATCCTATTCT
2903888 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
2903908 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
2903926 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:2906944 original size:24 final size:24
Alignment explanation
Indices: 2906927--2907052 Score: 107
Period size: 24 Copynumber: 5.2 Consensus size: 24
2906917 ATCAAAATAT
*
2906927 AAATCAGGTCAAGTATCATATCAG
1 AAATCAGGTCAAGTATCAAATCAG
* *
2906951 AAATCAGGTCAAGTAACAGATCAG
1 AAATCAGGTCAAGTATCAAATCAG
* *
2906975 -AATCCAAGTCAAGTATCAGATCAG
1 AAAT-CAGGTCAAGTATCAAATCAG
* *
2906999 -AATCCATGTC-AGATATCAGATCAG
1 AAAT-CAGGTCAAG-TATCAAATCAG
* *
2907023 -AATCCATGTCAAGTATCAGATCAG
1 AAAT-CAGGTCAAGTATCAAATCAG
2907047 AAATCA
1 AAATCA
2907053 AATCGAAAAT
Statistics
Matches: 93, Mismatches: 5, Indels: 8
0.88 0.05 0.08
Matches are distributed among these distances:
23 5 0.05
24 83 0.89
25 5 0.05
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (24 bp):
AAATCAGGTCAAGTATCAAATCAG
Found at i:2907019 original size:48 final size:47
Alignment explanation
Indices: 2906934--2907048 Score: 160
Period size: 48 Copynumber: 2.4 Consensus size: 47
2906924 TATAAATCAG
*
2906934 GTCAAGTATCATATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAG-AATCAGGTCAAGTAACAGATCAGAATCCAA
* * *
2906982 GTCAAGTATCAGATCAGAATCCATGTC-AGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAT-CAGGTCAAG-TAACAGATCAGAATCCAA
2907030 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
2907049 ATCAAATCGA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
47 5 0.08
48 56 0.92
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (47 bp):
GTCAAGTATCAGATCAGAATCAGGTCAAGTAACAGATCAGAATCCAA
Found at i:2907065 original size:48 final size:47
Alignment explanation
Indices: 2906934--2907065 Score: 151
Period size: 48 Copynumber: 2.7 Consensus size: 47
2906924 TATAAATCAG
* *
2906934 GTCAAGTATCATATCAGAAATCAGGTCAAGTAA-CAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAAATCAAGTCAA--AATCAGATCAGAATCCAA
* * *
2906982 GTCAAGTATCAGATCAG-AATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAAT-CAAGTCA-AAATCAGATCAGAATCCAA
*
2907030 GTCAAGTATCAGATCAGAAATCAAATCGAAAATCAG
1 GTCAAGTATCAGATCAGAAATCAAGTC-AAAATCAG
2907066 GTAAAATATT
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
47 4 0.06
48 63 0.88
49 5 0.07
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (47 bp):
GTCAAGTATCAGATCAGAAATCAAGTCAAAATCAGATCAGAATCCAA
Found at i:2909530 original size:13 final size:13
Alignment explanation
Indices: 2909512--2909588 Score: 58
Period size: 13 Copynumber: 6.2 Consensus size: 13
2909502 AACGGTCAAC
2909512 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
2909525 GGTCAATGGGTCG
1 GGTCAACGGGTCG
2909538 GGT---CGGGTCAACG
1 GGTCAACGGGT---CG
2909551 GGTC-A--GGTCG
1 GGTCAACGGGTCG
*
2909561 GGTAAACGGGTCG
1 GGTCAACGGGTCG
*
2909574 GGTAAACGGGTCG
1 GGTCAACGGGTCG
2909587 GG
1 GG
2909589 CCGGGTCAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
10 9 0.17
11 1 0.02
13 43 0.81
ACGTcount: A:0.17, C:0.18, G:0.48, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2909541 original size:18 final size:18
Alignment explanation
Indices: 2909518--2909612 Score: 110
Period size: 18 Copynumber: 5.6 Consensus size: 18
2909508 CAACGGTCAA
*
2909518 CGGGTCGGGTCAATGGGT
1 CGGGTCGGGTCAACGGGT
2909536 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
* *
2909554 CAGGTCGGGT-AA----A
1 CGGGTCGGGTCAACGGGT
*
2909567 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
*
2909585 CGGGCCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
2909603 CGGGTCGGGT
1 CGGGTCGGGT
2909613 TGTGACCGGT
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
13 9 0.14
14 2 0.03
17 2 0.03
18 51 0.80
ACGTcount: A:0.14, C:0.20, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:2909549 original size:31 final size:29
Alignment explanation
Indices: 2909512--2909608 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 29
2909502 AACGGTCAAC
2909512 GGTCAACGGGTCGGGTCAATGGGT-CGGGTCG
1 GGTCAACGGGTCGGGTC---GGGTACGGGTCG
*
2909543 GGTCAACGGGTCAGGTCGGGTAAACGGGTCG
1 GGTCAACGGGTCGGGTCGGGT--ACGGGTCG
* *
2909574 GGTAAACGGGTCGGGCCGGGTCAACGGGTCG
1 GGTCAACGGGTCGGGTCGGGT--ACGGGTCG
2909605 GGTC
1 GGTC
2909609 GGGTTGTGAC
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
28 4 0.07
31 53 0.93
ACGTcount: A:0.15, C:0.21, G:0.47, T:0.16
Consensus pattern (29 bp):
GGTCAACGGGTCGGGTCGGGTACGGGTCG
Found at i:2911136 original size:19 final size:19
Alignment explanation
Indices: 2911112--2911213 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
2911102 AGGAGCCGTT
*
2911112 TGAGCCGAGCCGCTTGAGC
1 TGAGCCGAGCCGTTTGAGC
2911131 TGAGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCGTTTGAGC
2911150 TGAGCCGAGCCGTTT---C
1 TGAGCCGAGCCGTTTGAGC
2911166 --AGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCGTTTGAGC
2911183 TGAGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCGTTTGAGC
*
2911202 TGAGCCAAGCCG
1 TGAGCCGAGCCG
2911214 AGCCGCCTAG
Statistics
Matches: 76, Mismatches: 2, Indels: 10
0.86 0.02 0.11
Matches are distributed among these distances:
14 13 0.17
16 1 0.01
17 1 0.01
19 61 0.80
ACGTcount: A:0.17, C:0.29, G:0.35, T:0.19
Consensus pattern (19 bp):
TGAGCCGAGCCGTTTGAGC
Found at i:2911170 original size:33 final size:33
Alignment explanation
Indices: 2911133--2911207 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
2911123 GCTTGAGCTG
2911133 AGCCGAGCCGTTTGAGCTGAGCCGAGCCGTTTC
1 AGCCGAGCCGTTTGAGCTGAGCCGAGCCGTTTC
*
2911166 AGCCGAGCCGTTTGAGCTGAGCCGAGCCGTTTG
1 AGCCGAGCCGTTTGAGCTGAGCCGAGCCGTTTC
*
2911199 AGCTGAGCC
1 AGCCGAGCC
2911208 AAGCCGAGCC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.16, C:0.29, G:0.35, T:0.20
Consensus pattern (33 bp):
AGCCGAGCCGTTTGAGCTGAGCCGAGCCGTTTC
Found at i:2911170 original size:52 final size:52
Alignment explanation
Indices: 2911104--2911213 Score: 193
Period size: 52 Copynumber: 2.1 Consensus size: 52
2911094 GAAGCCTGAG
*
2911104 GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCCGAGCCGTTTGAGCTGAGCC
1 GAGCCGTTTCAGCCGAGCCGCTTGAGCTGAGCCGAGCCGTTTGAGCTGAGCC
*
2911156 GAGCCGTTTCAGCCGAGCCGTTTGAGCTGAGCCGAGCCGTTTGAGCTGAGCC
1 GAGCCGTTTCAGCCGAGCCGCTTGAGCTGAGCCGAGCCGTTTGAGCTGAGCC
*
2911208 AAGCCG
1 GAGCCG
2911214 AGCCGCCTAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.16, C:0.29, G:0.35, T:0.19
Consensus pattern (52 bp):
GAGCCGTTTCAGCCGAGCCGCTTGAGCTGAGCCGAGCCGTTTGAGCTGAGCC
Found at i:2912394 original size:18 final size:18
Alignment explanation
Indices: 2912368--2912402 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2912358 TCGAAAGGAC
*
2912368 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
2912386 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
2912403 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:2916158 original size:14 final size:14
Alignment explanation
Indices: 2916139--2916204 Score: 69
Period size: 14 Copynumber: 4.4 Consensus size: 14
2916129 GAAGCCTGAG
2916139 GAGCCGTTTGAGCC
1 GAGCCGTTTGAGCC
2916153 GAGCCGCTTGAGCTGAGCC
1 GAGCCG-TT----TGAGCC
*
2916172 GAGCCGTTTCAGCC
1 GAGCCGTTTGAGCC
*
2916186 GAGCCGTTTGAGCT
1 GAGCCGTTTGAGCC
2916200 GAGCC
1 GAGCC
2916205 AAGCCGAGCC
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
14 28 0.64
15 2 0.05
18 2 0.05
19 12 0.27
ACGTcount: A:0.15, C:0.30, G:0.35, T:0.20
Consensus pattern (14 bp):
GAGCCGTTTGAGCC
Found at i:2916171 original size:19 final size:18
Alignment explanation
Indices: 2916147--2916210 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
2916137 AGGAGCCGTT
2916147 TGAGCCGAGCCGCTTGAGC
1 TGAGCCGAGCCG-TTGAGC
2916166 TGAGCCGAGCCGTT----
1 TGAGCCGAGCCGTTGAGC
*
2916180 TCAGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCG-TTGAGC
*
2916199 TGAGCCAAGCCG
1 TGAGCCGAGCCG
2916211 AGCCGCCTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 11 0.30
15 2 0.05
18 2 0.05
19 22 0.59
ACGTcount: A:0.17, C:0.31, G:0.34, T:0.17
Consensus pattern (18 bp):
TGAGCCGAGCCGTTGAGC
Found at i:2916176 original size:33 final size:33
Alignment explanation
Indices: 2916139--2916210 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
2916129 GAAGCCTGAG
*
2916139 GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
1 GAGCCGTTTCAGCCGAGCCGCTTGAGCTGAGCC
*
2916172 GAGCCGTTTCAGCCGAGCCGTTTGAGCTGAGCC
1 GAGCCGTTTCAGCCGAGCCGCTTGAGCTGAGCC
*
2916205 AAGCCG
1 GAGCCG
2916211 AGCCGCCTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.17, C:0.31, G:0.35, T:0.18
Consensus pattern (33 bp):
GAGCCGTTTCAGCCGAGCCGCTTGAGCTGAGCC
Found at i:2917385 original size:18 final size:18
Alignment explanation
Indices: 2917359--2917393 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2917349 TCGAAAGGAC
*
2917359 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
2917377 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
2917394 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:2919747 original size:21 final size:21
Alignment explanation
Indices: 2919721--2919773 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2919711 GTTTCCAGAT
2919721 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
* *
2919742 TCGCAACGTGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
*
2919763 TCGCAATGCGA
1 TCGCAACGCGA
2919774 TTTACATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:2919838 original size:40 final size:40
Alignment explanation
Indices: 2919791--2920042 Score: 398
Period size: 40 Copynumber: 6.2 Consensus size: 40
2919781 ATTCGCATTA
2919791 CGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTG
1 CGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTG
2919831 CGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTG
1 CGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTG
*
2919871 CGATAGTCAAAGTTCGCGTTGCGATTTTCCAAATTCGTTG
1 CGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTG
* * *
2919911 C-AGTAGTCAAAGTTCGCGTTGCGATTTTCTAAATTCGTTA
1 CGA-TAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTG
*
2919951 CGATAGTCGAAGTTCGCGTTGCGATTTATTTCAAATTCGTTG
1 CGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTG
*
2919993 CGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
1 CGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTG
2920035 CGATAGTC
1 CGATAGTC
2920043 CAAAATCGCA
Statistics
Matches: 199, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
39 1 0.01
40 136 0.68
41 3 0.02
42 59 0.30
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (40 bp):
CGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTG
Found at i:2920033 original size:21 final size:20
Alignment explanation
Indices: 2919807--2920038 Score: 135
Period size: 21 Copynumber: 11.4 Consensus size: 20
2919797 TCGAAGTTCG
2919807 CGTTGCGATT-TTCCAAATT
1 CGTTGCGATTATTCCAAATT
* * *
2919826 CGTTGCGA-TAGTCGAAGTT
1 CGTTGCGATTATTCCAAATT
2919845 CGCGTTGCGATT-TTCCAAATT
1 --CGTTGCGATTATTCCAAATT
*
2919866 CGTTGCGA-TAGT-CAAAGTT
1 CGTTGCGATTATTCCAAA-TT
2919885 CGCGTTGCGATT-TTCCAAATT
1 --CGTTGCGATTATTCCAAATT
* *
2919906 CGTTGC-AGTAGT-CAAAGTT
1 CGTTGCGATTATTCCAAA-TT
*
2919925 CGCGTTGCGATT-TTCTAAATT
1 --CGTTGCGATTATTCCAAATT
* * * *
2919946 CGTTACGA-TAGTCGAAGTT
1 CGTTGCGATTATTCCAAATT
*
2919965 CGCGTTGCGATTTATTTCAAATT
1 --CGTTGCGA-TTATTCCAAATT
* *
2919988 CGTTGCGA-TAGTCCAAGTT
1 CGTTGCGATTATTCCAAATT
2920007 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TTATTCCAAATT
2920030 CGTTGCGAT
1 CGTTGCGAT
2920039 AGTCCAAAAT
Statistics
Matches: 161, Mismatches: 27, Indels: 49
0.68 0.11 0.21
Matches are distributed among these distances:
18 13 0.08
19 55 0.34
20 1 0.01
21 65 0.40
22 11 0.07
23 16 0.10
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTATTCCAAATT
Found at i:2920723 original size:23 final size:23
Alignment explanation
Indices: 2920697--2920766 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
2920687 ACCAGTCGTT
2920697 GCGAATTTGGAATAAATCGCAAC
1 GCGAATTTGGAATAAATCGCAAC
* *
2920720 GCGAACTTGGACT--ATCGCAA-
1 GCGAATTTGGAATAAATCGCAAC
2920740 -CGAATTTGGAATAAATCGCAAC
1 GCGAATTTGGAATAAATCGCAAC
2920762 GCGAA
1 GCGAA
2920767 CTTCGACTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 10 0.26
21 14 0.36
23 15 0.38
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (23 bp):
GCGAATTTGGAATAAATCGCAAC
Found at i:2920738 original size:21 final size:20
Alignment explanation
Indices: 2920712--2920806 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 20
2920702 TTTGGAATAA
2920712 ATCGCAACGCGAACTTGGACT
1 ATCGCAA-GCGAACTTGGACT
* *
2920733 ATCGCAA-CGAATTTGGAAT
1 ATCGCAAGCGAACTTGGACT
*
2920752 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTGGACT
*
2920775 ATCGCAA-CAAACTTGGACT
1 ATCGCAAGCGAACTTGGACT
2920794 ATCGCAATGCGAA
1 ATCGCAA-GCGAA
2920807 TATGTAAATC
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
19 27 0.45
21 24 0.40
23 9 0.15
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAAGCGAACTTGGACT
Found at i:2920757 original size:42 final size:42
Alignment explanation
Indices: 2920698--2920791 Score: 161
Period size: 42 Copynumber: 2.2 Consensus size: 42
2920688 CCAGTCGTTG
*
2920698 CGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
2920740 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
* *
2920782 CAAACTTGGA
1 CGAATTTGGA
2920792 CTATCGCAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.21
Consensus pattern (42 bp):
CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
Found at i:2926680 original size:31 final size:34
Alignment explanation
Indices: 2926645--2926717 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 34
2926635 TCACAAAAGT
* *
2926645 TTATTTTTTAATTTAATTACT-TAAC-TTCCAA-
1 TTATTTTTTAATTTAATCACTCTAACTTTCAAAC
**
2926676 TTA-TTCCTAATTTAATCACTCTAACTTTCAAAC
1 TTATTTTTTAATTTAATCACTCTAACTTTCAAAC
2926709 TTATTTTTT
1 TTATTTTTT
2926718 TTATCTCGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
30 14 0.44
31 7 0.22
32 5 0.16
33 3 0.09
34 3 0.09
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.53
Consensus pattern (34 bp):
TTATTTTTTAATTTAATCACTCTAACTTTCAAAC
Done.