Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 166 of 226
Found at i:52985161 original size:27 final size:26
Alignment explanation
Indices: 52985131--52985190 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 26
52985121 AGGGAGAGAG
*
52985131 AAGAAAGGGAAAGGAAAAGGAGGAA-GA
1 AAGAAA-GGAAAAGAAAAGGA-GAAGGA
52985158 AAGAGAAGGAAAAGAAAAGGAGAAGGA
1 AAGA-AAGGAAAAGAAAAGGAGAAGGA
52985185 AAGAAA
1 AAGAAA
52985191 AAGAGAGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
27 23 0.77
28 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (26 bp):
AAGAAAGGAAAAGAAAAGGAGAAGGA
Found at i:52985182 original size:17 final size:16
Alignment explanation
Indices: 52985157--52985196 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
52985147 AAGGAGGAAG
52985157 AAAGAGAAGGAAAAGAA
1 AAAGAGAAGG-AAAGAA
*
52985174 AAGGAGAAGGAAAGAA
1 AAAGAGAAGGAAAGAA
52985190 AAAGAGA
1 AAAGAGA
52985197 GAGACGAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
AAAGAGAAGGAAAGAA
Found at i:52985237 original size:20 final size:20
Alignment explanation
Indices: 52985211--52985257 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
52985201 CGAGGAGAGG
52985211 AAAAGAAA-GAAGAGAAAAGA
1 AAAAGAAAGGAA-AGAAAAGA
* *
52985231 GAAAGAAAGGAAAGCAAAGA
1 AAAAGAAAGGAAAGAAAAGA
52985251 AAAAGAA
1 AAAAGAA
52985258 GGATAAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (20 bp):
AAAAGAAAGGAAAGAAAAGA
Found at i:52985243 original size:16 final size:16
Alignment explanation
Indices: 52985157--52985243 Score: 50
Period size: 16 Copynumber: 5.1 Consensus size: 16
52985147 AAGGAGGAAG
* *
52985157 AAAGAGAAGGAAAAGA
1 AAAGAGAAAGAAAGGA
* *
52985173 AAAGGAGAAGGAAAGAA
1 AAA-GAGAAAGAAAGGA
* *
52985190 AAAGAGAGAGACGAGGA
1 AAAGAGAAAGA-AAGGA
*
52985207 GAGGAAAAGAAAG-AAGAGA
1 -A--AAGAGAAAGAAAG-GA
52985226 AAAGAGAAAGAAAGGA
1 AAAGAGAAAGAAAGGA
52985242 AA
1 AA
52985244 GCAAAGAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
16 21 0.39
17 20 0.37
18 4 0.07
19 2 0.04
20 7 0.13
ACGTcount: A:0.64, C:0.01, G:0.34, T:0.00
Consensus pattern (16 bp):
AAAGAGAAAGAAAGGA
Found at i:52989052 original size:13 final size:14
Alignment explanation
Indices: 52989022--52989050 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
52989012 ATGATAAATC
52989022 AATTTAATTAAAAA
1 AATTTAATTAAAAA
52989036 AATTTAATTAAAAA
1 AATTTAATTAAAAA
52989050 A
1 A
52989051 TTGAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTTAATTAAAAA
Found at i:52990914 original size:52 final size:52
Alignment explanation
Indices: 52990845--52990945 Score: 159
Period size: 52 Copynumber: 1.9 Consensus size: 52
52990835 TTTTTATTGT
* *
52990845 TAATTTTTACTTAATTTAAAATTATTATGTAAATATTTCTTTTATTTTTAAA
1 TAATTTTTAATTAATTTAAAATTATTATGTAAAGATTTCTTTTATTTTTAAA
*
52990897 TAATTATTTAATT-ATTTAAAATTATTCTGTAAAGATTTCTTTTATTTTT
1 TAATT-TTTAATTAATTTAAAATTATTATGTAAAGATTTCTTTTATTTTT
52990946 TCTGTTAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 39 0.87
53 6 0.13
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (52 bp):
TAATTTTTAATTAATTTAAAATTATTATGTAAAGATTTCTTTTATTTTTAAA
Found at i:52992215 original size:13 final size:13
Alignment explanation
Indices: 52992197--52992221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52992187 GGATAAATCA
52992197 ATTTAATTAAAAC
1 ATTTAATTAAAAC
52992210 ATTTAATTAAAA
1 ATTTAATTAAAA
52992222 AAATTGAAAA
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTTAATTAAAAC
Found at i:52994247 original size:23 final size:22
Alignment explanation
Indices: 52994221--52994399 Score: 84
Period size: 26 Copynumber: 7.8 Consensus size: 22
52994211 TGGGGGGGCA
52994221 GAAGGAGAGGGAAAGAAAGAAAG
1 GAAGGAGA-GGAAAGAAAGAAAG
52994244 GAAGGAGAGGAAAGAAAGAAA-
1 GAAGGAGAGGAAAGAAAGAAAG
52994265 -AA-GA-AGGAAAGAAAAGGAAAG
1 GAAGGAGAGGAAAG-AAA-GAAAG
* **
52994286 GAGAAGAGAAAAAAAGAAAGAAGAG
1 GA-AGGAG-AGGAAAGAAAGAA-AG
*
52994311 GAAAAGGAAAGGAGAAGAAA-AAA-
1 G--AAGGAGAGGA-AAGAAAGAAAG
* * *
52994334 GAAAGA-AAGAAGGAAAGAAAAG
1 GAAGGAGAGGAAAGAAAG-AAAG
* *
52994356 GAAAGGAGAAGAGAAAAAAAGAAGAA
1 G-AAGGAG-AG-GAAAGAAAGAA-AG
* *
52994382 GAAGAAGAGGGAAGAAAG
1 GAAGGAGAGGAAAGAAAG
52994400 GAGAAGAAAA
Statistics
Matches: 119, Mismatches: 17, Indels: 40
0.68 0.10 0.23
Matches are distributed among these distances:
18 7 0.06
19 10 0.08
20 9 0.08
21 7 0.06
22 15 0.13
23 21 0.18
24 8 0.07
25 18 0.15
26 23 0.19
27 1 0.01
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (22 bp):
GAAGGAGAGGAAAGAAAGAAAG
Found at i:52994256 original size:18 final size:18
Alignment explanation
Indices: 52994235--52994364 Score: 70
Period size: 18 Copynumber: 6.9 Consensus size: 18
52994225 GAGAGGGAAA
52994235 GAAAGAAAGGAAGGAGAG
1 GAAAGAAAGGAAGGAGAG
**
52994253 GAAAGAAA-GAAAAAGAAG
1 GAAAGAAAGGAAGGAG-AG
52994271 GAAAGAAAAGGAAAGGAGAAG
1 GAAAG-AAAGG-AAGGAG-AG
* * *
52994292 AGAAAAAAAGAAAGAAGAG
1 -GAAAGAAAGGAAGGAGAG
* *
52994311 GAAAAGGAAAGG-AGAAGAA
1 G-AAA-GAAAGGAAGGAGAG
* *
52994330 AAAAGAAA-GAAAGA-AG
1 GAAAGAAAGGAAGGAGAG
52994346 GAAAGAAAAGGAAAGGAGA
1 GAAAG-AAAGG-AAGGAGA
52994365 AGAGAAAAAA
Statistics
Matches: 84, Mismatches: 16, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
16 6 0.07
17 14 0.17
18 20 0.24
19 18 0.21
20 11 0.13
21 11 0.13
22 4 0.05
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (18 bp):
GAAAGAAAGGAAGGAGAG
Found at i:52994330 original size:34 final size:34
Alignment explanation
Indices: 52994240--52994415 Score: 142
Period size: 39 Copynumber: 4.8 Consensus size: 34
52994230 GGAAAGAAAG
* *
52994240 AAAGG-AAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGA
1 AAAGGAAAGGAGAAGAAA-AAA-AGAAAGAA-G-AAGA
*
52994277 AAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAGAGGA
1 AAAGGAAAGGAG-A-AGAAAAAAAGAAAGAAGAAGA
52994313 AAAGGAAAGGAGAAGAAAAAAGAAAGAAAGAAGGAAAGA
1 AAAGGAAAGGAGAAG--AAAA-AAAGAAAGAA-G-AAGA
52994352 AAAGGAAAGGAGAAGAGAAAAAA-AGAAGAAGAAGA
1 AAAGGAAAGGAGAAGA-AAAAAAGA-AAGAAGAAGA
*
52994387 AGAGGGAAGAAAGGAGAAG-AAAAAAGAAA
1 A-A---AGGAAAGGAGAAGAAAAAAAGAAA
52994416 AGAAAGGTAT
Statistics
Matches: 119, Mismatches: 5, Indels: 30
0.77 0.03 0.19
Matches are distributed among these distances:
34 2 0.02
35 6 0.05
36 22 0.18
37 33 0.28
38 18 0.15
39 34 0.29
40 4 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (34 bp):
AAAGGAAAGGAGAAGAAAAAAAGAAAGAAGAAGA
Found at i:52994354 original size:75 final size:74
Alignment explanation
Indices: 52994240--52994421 Score: 253
Period size: 75 Copynumber: 2.4 Consensus size: 74
52994230 GGAAAGAAAG
*
52994240 AAAGG-AAGGAGAGGAAAGAAAG-AA-AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAG
1 AAAGGAAAGGAGAAGAAA-AAAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAG
*
52994302 AAAGAAGAGGA
65 -AAGAAGAAGA
52994313 AAAGGAAAGGAGAAGAAAAAAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGA
1 AAAGGAAAGGAGAAGAAAAAAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGA
52994378 AGAAGAAGA
66 AGAAGAAGA
*
52994387 AGAGGGAAGAAAGGAGAAGAAAAAAGAAAAGAAAG
1 A-A---AGGAAAGGAGAAGAAAAAAG-AAAGAAAG
52994422 GTATTTTTTT
Statistics
Matches: 98, Mismatches: 3, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
73 9 0.09
74 23 0.23
75 39 0.40
78 19 0.19
79 8 0.08
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (74 bp):
AAAGGAAAGGAGAAGAAAAAAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGA
AGAAGAAGA
Found at i:52994738 original size:27 final size:27
Alignment explanation
Indices: 52994700--52994758 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
52994690 ATCTTGGTCA
*
52994700 TGCCAAAGCCATTGGCGGCAACAAAGG
1 TGCCAAAACCATTGGCGGCAACAAAGG
* * *
52994727 TGCCAAAACCATTTGCGGCACCAATGG
1 TGCCAAAACCATTGGCGGCAACAAAGG
52994754 TGCCA
1 TGCCA
52994759 TACTGATTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.29, G:0.25, T:0.15
Consensus pattern (27 bp):
TGCCAAAACCATTGGCGGCAACAAAGG
Found at i:52994839 original size:9 final size:9
Alignment explanation
Indices: 52994825--52994855 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
52994815 GAAAAATCAA
52994825 AAGAAAAAG
1 AAGAAAAAG
52994834 AAGAAAAAG
1 AAGAAAAAG
52994843 AAGAAAAAG
1 AAGAAAAAG
52994852 AAGA
1 AAGA
52994856 GGTGCTGCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:52994882 original size:11 final size:11
Alignment explanation
Indices: 52994866--52994905 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
52994856 GGTGCTGCGG
52994866 AAAAGAAGAGA
1 AAAAGAAGAGA
*
52994877 AAAAG-ATAGA
1 AAAAGAAGAGA
52994887 AAAAGAAGAGA
1 AAAAGAAGAGA
52994898 AAAAGAAG
1 AAAAGAAG
52994906 GTATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:52994967 original size:19 final size:21
Alignment explanation
Indices: 52994929--52994967 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
52994919 AATAATTGAT
*
52994929 TATATTTTTGTTATTATTTTG
1 TATATTTTTGTTAATATTTTG
52994950 TATA-TTTTG-TAATATTTT
1 TATATTTTTGTTAATATTTT
52994968 TTGTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 5 0.29
21 4 0.24
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (21 bp):
TATATTTTTGTTAATATTTTG
Found at i:52998575 original size:101 final size:104
Alignment explanation
Indices: 52998455--52998952 Score: 445
Period size: 101 Copynumber: 4.9 Consensus size: 104
52998445 AAAAATTATT
52998455 TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCA-AC-AGTAAAAAAAATTTCTTTTTTTT-TGT
1 TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGACAAGTAAAAAAAATTTCTTTTTTTTCTGT
*
52998517 CAGAATAAGATATAAATATACGAAAAAAATAAAAAAAAA
66 CAGAGTAAGATATAAATATACGAAAAAAATAAAAAAAAA
* ***
52998556 TTTTGGGTGCTGGCCTGTCAATGGCCGTCACCCAGTACAA-T--TTTAAA--T-TTTTTTTTCGT
1 TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAG-ACAAGTAAAAAAAATTTCTTTTTTTTC-T
*
52998615 GTCAGAGTCAGATATAAATATACGAAAAAAAT-------AA
64 GTCAGAGTAAGATATAAATATACGAAAAAAATAAAAAAAAA
* * * * *****
52998649 TTTT-GGTGCCGGCTTGTCAATGGTCGGCACCCAGTACAATTTTAAATTTTTTTTACTTTTTTTT
1 TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAG-ACAA--GTAAAAAAAATTT-CTTTTTTTT
*
52998713 CGTGTCAGAGTAAGATATAAATATAACG-AAAAATTAAAAAAAAA
62 C-TGTCAGAGTAAGATATAAATAT-ACGAAAAAAATAAAAAAAAA
* *
52998757 TTTTTGGGTGCTGGCCTGTCAATGGCCTGCACCCAGTACAAATTAAAAAAAATTTCTTTTTTTTC
1 -TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAG-AC-AAGTAAAAAAAATTTCTTTTTTTTC
* **
52998822 GTGTCAGAGTCAGATATAAATATATTAAAAAAATTAAAAAAAAA
63 -TGTCAGAGTAAGATATAAATATACGAAAAAAA-TAAAAAAAAA
* *
52998866 -TTTGGGTGCTGGCCTGTCAATGGTCC-GCACCCAGTACAA-T---TAAAA-TT-TTTTTTTCCA
1 TTTTGGGTGCTGGCCTGTCAATGG-CCGGCACCCAG-ACAAGTAAAAAAAATTTCTTTTTTTTC-
* *
52998923 TGTCAGAGTCAGATATAGATATACGAAAAA
63 TGTCAGAGTAAGATATAAATATACGAAAAA
52998953 TATGCGCTAT
Statistics
Matches: 334, Mismatches: 35, Indels: 57
0.78 0.08 0.13
Matches are distributed among these distances:
92 31 0.09
93 6 0.02
95 1 0.00
97 2 0.01
98 8 0.02
99 2 0.01
100 66 0.20
101 75 0.22
102 7 0.02
103 3 0.01
104 1 0.00
105 1 0.00
106 2 0.01
107 35 0.10
108 41 0.12
109 22 0.07
110 29 0.09
111 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (104 bp):
TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGACAAGTAAAAAAAATTTCTTTTTTTTCTGT
CAGAGTAAGATATAAATATACGAAAAAAATAAAAAAAAA
Found at i:52998789 original size:110 final size:106
Alignment explanation
Indices: 52998639--52998918 Score: 350
Period size: 107 Copynumber: 2.6 Consensus size: 106
52998629 TAAATATACG
* * *
52998639 AAAAAAATAATTTT-GGTGCCGGCTTGTCAATGGTCGGCACCCAGTACAATTTTAAATTTTTTTT
1 AAAAAAA-AATTTTGGGTGCTGGCCTGTCAATGG-CCGCACCCAGTACAA-TTTAAATTTTTTTT
*
52998703 ACTTTTTTTTCGTGTCAGAGTAAGATATAAATATA-ACGAAAAATT
63 -CTTTTTTTTCGTGTCAGAGTAAGATATAAATATATA-AAAAAATT
* *****
52998748 AAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCTGCACCCAGTACAAATTAAAAAAAATTTC
1 AAAAAAAAA-TTTTGGGTGCTGGCCTGTCAATGGCC-GCACCCAGTACAATTTAAATTTTTTTTC
*
52998813 TTTTTTTTCGTGTCAGAGTCAGATATAAATATATTAAAAAAATT
64 TTTTTTTTCGTGTCAGAGTAAGATATAAATATA-TAAAAAAATT
*
52998857 AAAAAAAAA-TTTGGGTGCTGGCCTGTCAATGGTCCGCACCCAGTACAATTAAAATTTTTTTT
1 AAAAAAAAATTTTGGGTGCTGGCCTGTCAATGG-CCGCACCCAGTACAATTTAAATTTTTTTT
52998919 TCCATGTCAG
Statistics
Matches: 147, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
107 43 0.29
108 37 0.25
109 36 0.24
110 31 0.21
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (106 bp):
AAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGCACCCAGTACAATTTAAATTTTTTTTCTT
TTTTTTCGTGTCAGAGTAAGATATAAATATATAAAAAAATT
Found at i:52998840 original size:108 final size:100
Alignment explanation
Indices: 52998704--52998953 Score: 328
Period size: 108 Copynumber: 2.4 Consensus size: 100
52998694 ATTTTTTTTA
*
52998704 CTTTTTTTTCGTGTCAGAGTAAGATATAAATATAACGAAAAATTAAAAAAAAATTTTTGGGTGCT
1 CTTTTTTTTCGTGTCAGAGTCAGATATAAATATAACGAAAAATTAAAAAAAAA--TTTGGGTGCT
52998769 GGCCTGTCAATGG-CCTGCACCCAGTACAAATTAAAAAAAATTT
64 GGCCTGTCAATGGTCC-GCACCCAGTAC-AATT----AAAA-TT
*
52998812 CTTTTTTTTCGTGTCAGAGTCAGATATAAATATATTA-AAAAAATTAAAAAAAAATTTGGGTGCT
1 CTTTTTTTTCGTGTCAGAGTCAGATATAAATATA--ACGAAAAATTAAAAAAAAATTTGGGTGCT
52998876 GGCCTGTCAATGGTCCGCACCCAGTACAATTAAAATT
64 GGCCTGTCAATGGTCCGCACCCAGTACAATTAAAATT
* * *
52998913 -TTTTTTTCCATGTCAGAGTCAGATATAGATAT-ACGAAAAAT
1 CTTTTTTTTCGTGTCAGAGTCAGATATAAATATAACGAAAAAT
52998954 ATGCGCTATT
Statistics
Matches: 132, Mismatches: 6, Indels: 18
0.85 0.04 0.12
Matches are distributed among these distances:
97 1 0.01
98 6 0.05
100 29 0.22
101 2 0.02
102 4 0.03
106 4 0.03
107 34 0.26
108 35 0.27
109 16 0.12
110 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (100 bp):
CTTTTTTTTCGTGTCAGAGTCAGATATAAATATAACGAAAAATTAAAAAAAAATTTGGGTGCTGG
CCTGTCAATGGTCCGCACCCAGTACAATTAAAATT
Found at i:52998965 original size:107 final size:105
Alignment explanation
Indices: 52998639--52998952 Score: 322
Period size: 108 Copynumber: 3.0 Consensus size: 105
52998629 TAAATATACG
* * * * * **
52998639 AAAAAAATAATTTT-GGTGCCGGCTTGTCAATGGTCGGCACCCAGTACAATTTTAAATTTTTTTT
1 AAAAAAA-AATTTTGGGTGCTGGCCTGTCAATGGCCTGCACCCAGTACAA-ATTAAA---AATTT
* * *
52998703 ACTTTTTTTTCGTGTCAGAGTAAGATATAAATATAACG--AAAAATT
61 -CTTTTTTTCCATGTCAGAGTCAGATATAAATAT-ACGAAAAAAATT
52998748 AAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCTGCACCCAGTACAAATTAAAAAAAATTTC
1 AAAAAAAAA-TTTTGGGTGCTGGCCTGTCAATGGCCTGCACCCAGTACAAATT---AAAAATTTC
* * **
52998813 TTTTTTTTCGTGTCAGAGTCAGATATAAATATATTAAAAAAATT
62 TTTTTTTCCATGTCAGAGTCAGATATAAATATACGAAAAAAATT
52998857 AAAAAAAAA-TTTGGGTGCTGGCCTGTCAATGGTCC-GCACCCAGTAC-AATT-AAAA-TT-TTT
1 AAAAAAAAATTTTGGGTGCTGGCCTGTCAATGG-CCTGCACCCAGTACAAATTAAAAATTTCTTT
*
52998916 TTTTCCATGTCAGAGTCAGATATAGATATACGAAAAA
65 TTTTCCATGTCAGAGTCAGATATAAATATACGAAAAA
52998953 TATGCGCTAT
Statistics
Matches: 182, Mismatches: 15, Indels: 25
0.82 0.07 0.11
Matches are distributed among these distances:
100 35 0.19
101 2 0.01
102 4 0.02
106 4 0.02
107 35 0.19
108 36 0.20
109 32 0.18
110 31 0.17
112 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (105 bp):
AAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCTGCACCCAGTACAAATTAAAAATTTCTTTT
TTTCCATGTCAGAGTCAGATATAAATATACGAAAAAAATT
Found at i:53002053 original size:105 final size:105
Alignment explanation
Indices: 53001811--53002123 Score: 442
Period size: 104 Copynumber: 3.0 Consensus size: 105
53001801 CTGGGTGCTG
53001811 ATTTTTTTTTATTTTTTCGTATATTTATATCTGACTCTGACACGAAAAAAAAAGTAAATTTTTTT
1 ATTTTTTTTTATTTTTTCGTATATTTATATCTGACTCTGACACG-AAAAAAAAG-AAATTTTTTT
** *
53001876 TAAATTGTACTGGGTGCCACCCATTGACAGGCCGGCACCCAA
64 TAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
*
53001918 AATTTTTTTTATTTTTTCGTATATTTATATCTGACTCTGACACGAAAAAAAAG-AATTTTTTTTA
1 ATTTTTTTTTATTTTTTCGTATATTTATATCTGACTCTGACACGAAAAAAAAGAAATTTTTTTTA
* * *
53001982 AATTGTACTGGGTGCCGGCAATTGACAGGCTAGTACCCAA
66 AATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
* *
53002022 ATTTTTTTTTATTTTTTTCGTATATTTATATCTTATTCTGACA--AAAAAAAAGGAAATTTTTTT
1 ATTTTTTTTTA-TTTTTTCGTATATTTATATCTGACTCTGACACGAAAAAAAA-GAAATTTTTTT
* *
53002085 T--ACTGT--TGGGTGCCGGCCATTGACAGGCCAGCAACCAA
64 TAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
53002123 A
1 A
53002124 AAATATTTTT
Statistics
Matches: 188, Mismatches: 15, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
101 29 0.15
103 12 0.06
104 56 0.30
105 39 0.21
106 9 0.05
107 43 0.23
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.40
Consensus pattern (105 bp):
ATTTTTTTTTATTTTTTCGTATATTTATATCTGACTCTGACACGAAAAAAAAGAAATTTTTTTTA
AATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
Found at i:53005938 original size:18 final size:18
Alignment explanation
Indices: 53005915--53005949 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
53005905 ATCCCAATGA
53005915 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
53005933 TCGCCACCACCTTCTTC
1 TCGCCACCACCTTCTTC
53005950 ACCACCAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.51, G:0.06, T:0.31
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:53006820 original size:3 final size:3
Alignment explanation
Indices: 53006812--53006870 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
53006802 TCTTAATACT
* *
53006812 AAC AAC AAC AAC AAC AAC AAC AAC AAC GAC AAC AAC AAC AAT AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
53006860 AAC AAC AAC AA
1 AAC AAC AAC AA
53006871 TAATAATAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.66, C:0.31, G:0.02, T:0.02
Consensus pattern (3 bp):
AAC
Found at i:53006960 original size:19 final size:21
Alignment explanation
Indices: 53006936--53006974 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
53006926 AACTAAAACA
*
53006936 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
53006955 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
53006975 ATCAATTAGT
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:53007144 original size:27 final size:27
Alignment explanation
Indices: 53007098--53007225 Score: 179
Period size: 27 Copynumber: 4.7 Consensus size: 27
53007088 AATACGAGTA
53007098 GTGCCGCCAAT--CAGTATGGCACCATTG
1 GTGCCGCCAATGGCA-T-TGGCACCATTG
*
53007125 GTGCCGCCAATGGCATTGGCAACATTG
1 GTGCCGCCAATGGCATTGGCACCATTG
53007152 GTGCCGCCAATGGCATTGGCACCATTG
1 GTGCCGCCAATGGCATTGGCACCATTG
** *
53007179 GTGCCGCCAATGGTTTTGGCACCTTTG
1 GTGCCGCCAATGGCATTGGCACCATTG
*
53007206 GTGCCGCCAATGGCTTTGGC
1 GTGCCGCCAATGGCATTGGC
53007226 GTGACCAAGG
Statistics
Matches: 93, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
27 90 0.97
28 1 0.01
29 2 0.02
ACGTcount: A:0.17, C:0.28, G:0.30, T:0.25
Consensus pattern (27 bp):
GTGCCGCCAATGGCATTGGCACCATTG
Found at i:53007824 original size:104 final size:104
Alignment explanation
Indices: 53007644--53007851 Score: 398
Period size: 104 Copynumber: 2.0 Consensus size: 104
53007634 TAATCTATTG
* *
53007644 AAGTTGTAATTTTAGTAAGTCAATATTTTGGAATTGATTTTGATTTTAAATTTTGGTGAGAAGAT
1 AAGTTGTAATTTTAGTAAGTAAATATTTTGCAATTGATTTTGATTTTAAATTTTGGTGAGAAGAT
53007709 CAATCGCGTTATGAAGGGTCACTGTAAACTCTCGAAAAT
66 CAATCGCGTTATGAAGGGTCACTGTAAACTCTCGAAAAT
53007748 AAGTTGTAATTTTAGTAAGTAAATATTTTGCAATTGATTTTGATTTTAAATTTTGGTGAGAAGAT
1 AAGTTGTAATTTTAGTAAGTAAATATTTTGCAATTGATTTTGATTTTAAATTTTGGTGAGAAGAT
53007813 CAATCGCGTTATGAAGGGTCACTGTAAACTCTCGAAAAT
66 CAATCGCGTTATGAAGGGTCACTGTAAACTCTCGAAAAT
53007852 TCAAATTATA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 102 1.00
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (104 bp):
AAGTTGTAATTTTAGTAAGTAAATATTTTGCAATTGATTTTGATTTTAAATTTTGGTGAGAAGAT
CAATCGCGTTATGAAGGGTCACTGTAAACTCTCGAAAAT
Found at i:53008964 original size:16 final size:17
Alignment explanation
Indices: 53008923--53008969 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
53008913 AGTAAAATAC
*
53008923 TAGTATTATTATTATGGT
1 TAGTATTATT-TTATAGT
53008941 TAGTTATTATTTT-TAGT
1 TAG-TATTATTTTATAGT
53008958 TAGTATTATTTT
1 TAGTATTATTTT
53008970 GAGTATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 9 0.33
17 6 0.22
18 5 0.19
19 7 0.26
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.62
Consensus pattern (17 bp):
TAGTATTATTTTATAGT
Found at i:53010058 original size:16 final size:17
Alignment explanation
Indices: 53010037--53010083 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 17
53010027 AATAATACTC
53010037 AAAATAATACTAAC-TA
1 AAAATAATACTAACATA
53010053 AAAATAATAACTAACAATA
1 AAAATAAT-ACTAAC-ATA
*
53010072 ATAATAATACTA
1 AAAATAATACTA
53010084 GTTTTTTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 8 0.30
17 6 0.22
18 4 0.15
19 9 0.33
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATAATACTAACATA
Found at i:53010063 original size:13 final size:13
Alignment explanation
Indices: 53010042--53010075 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
53010032 TACTCAAAAT
*
53010042 AATACTAACTAAA
1 AATAATAACTAAA
*
53010055 AATAATAACTAAC
1 AATAATAACTAAA
53010068 AATAATAA
1 AATAATAA
53010076 TAATACTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAATAACTAAA
Found at i:53011667 original size:49 final size:44
Alignment explanation
Indices: 53011578--53011706 Score: 123
Period size: 45 Copynumber: 2.8 Consensus size: 44
53011568 TACGAAATTT
* * * * *
53011578 TTTTTAGGTGCTAGCCTTTCAATGGCCGGTACTAATGTACGAAAAAAAA
1 TTTTT-GGTGCTGGCCTGTCAATGGCCGGCACCAACGTACG----AAAA
*
53011627 TTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGCGTACGAAAA
1 TTTTT-GGTGCTGGCCTGTCAATGGCCGGCACCAACGTACGAAAA
**
53011672 TTTTCTTTTGCTGGCCTGTCAATGGCCGGCACCAA
1 TTTT-TGGTGCTGGCCTGTCAATGGCCGGCACCAA
53011707 ATTTATCAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
45 34 0.49
46 1 0.01
49 34 0.49
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.29
Consensus pattern (44 bp):
TTTTTGGTGCTGGCCTGTCAATGGCCGGCACCAACGTACGAAAA
Found at i:53016822 original size:33 final size:33
Alignment explanation
Indices: 53016785--53016852 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
53016775 AGGCAACTCT
*
53016785 GACGACCAATGCGATTCACTCTCAACCACCGCC
1 GACGACCAATGCGATTCACCCTCAACCACCGCC
* * *
53016818 GACGACCACTGCTATTCACCCTTAACCACCGCC
1 GACGACCAATGCGATTCACCCTCAACCACCGCC
53016851 GA
1 GA
53016853 TCACTCCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.26, C:0.43, G:0.15, T:0.16
Consensus pattern (33 bp):
GACGACCAATGCGATTCACCCTCAACCACCGCC
Found at i:53018937 original size:31 final size:32
Alignment explanation
Indices: 53018880--53018951 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 32
53018870 CGACAATTTT
* *
53018880 AATTTTTCTGTTAATTTTTACTTTTATTTTAA
1 AATTTTTCTGTAAATATTTACTTTTATTTTAA
* *
53018912 AATTATTCTGTAAATATTT-CTTTTATTTTTA
1 AATTTTTCTGTAAATATTTACTTTTATTTTAA
53018943 AATTTTTCT
1 AATTTTTCT
53018952 TATTTTTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 19 0.54
32 16 0.46
ACGTcount: A:0.26, C:0.07, G:0.03, T:0.64
Consensus pattern (32 bp):
AATTTTTCTGTAAATATTTACTTTTATTTTAA
Found at i:53018950 original size:19 final size:17
Alignment explanation
Indices: 53018922--53018964 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
53018912 AATTATTCTG
53018922 TAAATATTTCTTTTATTTT
1 TAAATATTTC--TTATTTT
*
53018941 TAAATTTTTCTTATTTT
1 TAAATATTTCTTATTTT
53018958 T-AATATT
1 TAAATATT
53018965 AATTTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 8 0.36
19 9 0.41
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (17 bp):
TAAATATTTCTTATTTT
Found at i:53021539 original size:22 final size:21
Alignment explanation
Indices: 53021513--53021569 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
53021503 AACCCTTTTT
53021513 TTTCATTCAAAATTTATTTTAA
1 TTTCATT-AAAATTTATTTTAA
***
53021535 TTTCATTACTTTTTATTTTAA
1 TTTCATTAAAATTTATTTTAA
* *
53021556 TTTCCTTTAAATTT
1 TTTCATTAAAATTT
53021570 TCCTAATATC
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTCATTAAAATTTATTTTAA
Found at i:53021766 original size:13 final size:14
Alignment explanation
Indices: 53021740--53021776 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
53021730 TAATTTCATT
53021740 TTTTTCATTT-AATA
1 TTTTT-ATTTAAATA
53021754 -TTTTATTTAAATA
1 TTTTTATTTAAATA
53021767 TTTTTATTTA
1 TTTTTATTTA
53021777 TTTATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 4 0.19
13 8 0.38
14 9 0.43
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTTATTTAAATA
Found at i:53022009 original size:21 final size:22
Alignment explanation
Indices: 53021980--53022023 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
53021970 CATTTCAACA
53021980 TTTGTTTTTCATTTCATTTCAT
1 TTTGTTTTTCATTTCATTTCAT
*
53022002 TTTGTTTTT-ATTTGATTTCAT
1 TTTGTTTTTCATTTCATTTCAT
53022023 T
1 T
53022024 CTAATTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.14, C:0.09, G:0.07, T:0.70
Consensus pattern (22 bp):
TTTGTTTTTCATTTCATTTCAT
Found at i:53036361 original size:27 final size:27
Alignment explanation
Indices: 53036308--53036361 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
53036298 ATCGATTGCT
* *
53036308 TTAATAGTTGATGTCAAATAATTTATA
1 TTAATAGTTGATGTAAAATAATATATA
* *
53036335 TTAATAGTTTATGTAAAATTATATATA
1 TTAATAGTTGATGTAAAATAATATATA
53036362 ATTATTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (27 bp):
TTAATAGTTGATGTAAAATAATATATA
Found at i:53054041 original size:40 final size:41
Alignment explanation
Indices: 53053997--53054101 Score: 99
Period size: 40 Copynumber: 2.5 Consensus size: 41
53053987 AAAAAACTAG
* *
53053997 TATTATTATGGTTAGTTATTATTTTTAGTA-AAACCCTA-AT
1 TATTATTATGGTTAGTTATTATTTTGAGTATAAA-ACTATAT
* *
53054037 TATTATTGTTAGTTAG-TATTATTTTGAGTATAAAACTATTAT
1 TATTATT-ATGGTTAGTTATTATTTTGAGTATAAAACTA-TAT
*
53054079 TATTGTTATTGTGTTAGTTATTA
1 TATTATTA-TG-GTTAGTTATTA
53054102 GGGTTAGTGG
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
40 23 0.45
41 9 0.18
42 9 0.18
43 5 0.10
44 5 0.10
ACGTcount: A:0.30, C:0.04, G:0.12, T:0.53
Consensus pattern (41 bp):
TATTATTATGGTTAGTTATTATTTTGAGTATAAAACTATAT
Found at i:53059421 original size:11 final size:10
Alignment explanation
Indices: 53059393--53059423 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
53059383 ATTACTTTAA
53059393 AAAATATTAT
1 AAAATATTAT
53059403 AAAATATTAT
1 AAAATATTAT
53059413 AAAATTATTAT
1 AAAA-TATTAT
53059424 TAATTTAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.70
11 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AAAATATTAT
Found at i:53060065 original size:10 final size:10
Alignment explanation
Indices: 53060050--53060312 Score: 62
Period size: 10 Copynumber: 26.0 Consensus size: 10
53060040 AAAAATTACA
53060050 TTTTTCTTTC
1 TTTTTCTTTC
*
53060060 TTTTTCCTTC
1 TTTTTCTTTC
* ***
53060070 CTCCCCTCTTC
1 TTTTTCT-TTC
*
53060081 TTTTTTTTTTC
1 -TTTTTCTTTC
* *
53060092 TTCTCCTTTC
1 TTTTTCTTTC
*
53060102 CTTTTCTTTC
1 TTTTTCTTTC
53060112 ATTCTTTTTCTTTC
1 --T-T-TTTCTTTC
53060126 TTTTT-TCTTC
1 TTTTTCT-TTC
* * *
53060136 TTCTCCTTCC
1 TTTTTCTTTC
*
53060146 CTTTTCTTTC
1 TTTTTCTTTC
*
53060156 --CTTCTTT-
1 TTTTTCTTTC
53060163 TTCTTTCTTTC
1 TT-TTTCTTTC
* * *
53060174 CTCTCCTTTC
1 TTTTTCTTTC
*
53060184 CTTTTCTTTC
1 TTTTTCTTTC
*
53060194 ATTCTT-TTTC
1 -TTTTTCTTTC
*
53060204 TTTATTTTTTC
1 TTT-TTCTTTC
53060215 TTCTTCTCCTTTC
1 TT-TT-T-CTTTC
*
53060228 CTTTTCTTTC
1 TTTTTCTTTC
*
53060238 --CTTCTTT-
1 TTTTTCTTTC
53060245 TTCTTTCTTTC
1 TT-TTTCTTTC
* *
53060256 -TTTCCTCTC
1 TTTTTCTTTC
* * *
53060265 CTCTCCTTTC
1 TTTTTCTTTC
*
53060275 CTTTTCTTTC
1 TTTTTCTTTC
53060285 TTTTTCTTTC
1 TTTTTCTTTC
53060295 --TTTCTTTC
1 TTTTTCTTTC
*
53060303 TTCTTCTTTC
1 TTTTTCTTTC
53060313 CCTCTCATTC
Statistics
Matches: 181, Mismatches: 47, Indels: 50
0.65 0.17 0.18
Matches are distributed among these distances:
8 20 0.11
9 9 0.05
10 111 0.61
11 20 0.11
12 7 0.04
13 6 0.03
14 8 0.04
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:53060116 original size:24 final size:23
Alignment explanation
Indices: 53060080--53060309 Score: 135
Period size: 24 Copynumber: 10.7 Consensus size: 23
53060070 CTCCCCTCTT
*
53060080 CTTTT-TTTTTTCTTCTCCTTTC
1 CTTTTCTTTCTTCTTCTCCTTTC
* *
53060102 CTTTTCTTTCATTCTTTTTCTTT-
1 CTTTTCTTTC-TTCTTCTCCTTTC
*
53060125 C-TTT-TTTCTTCTTCTCCTTCC
1 CTTTTCTTTCTTCTTCTCCTTTC
* *
53060146 CTTTTCTTTCCTTCTTTTTCTTT-
1 CTTTTCTTT-CTTCTTCTCCTTTC
* * *
53060169 C-TTTC-CTCTCCTT-TCCTTTT
1 CTTTTCTTTCTTCTTCTCCTTTC
*
53060189 C-TTTCATTCTT-TT-T-CTTT-
1 CTTTTCTTTCTTCTTCTCCTTTC
*
53060207 -ATTT-TTTCTTCTTCTCCTTTC
1 CTTTTCTTTCTTCTTCTCCTTTC
* *
53060228 CTTTTCTTTCCTTCTTTTTCTTT-
1 CTTTTCTTT-CTTCTTCTCCTTTC
*
53060251 C-TTTCTTTCCTCTCCTCTCCTTTC
1 CTTTTCTTT-CT-TCTTCTCCTTTC
53060275 CTTTTCTTTCTT-TT-T-CTTT-
1 CTTTTCTTTCTTCTTCTCCTTTC
53060294 C-TTTCTTTCTTCTTCT
1 CTTTTCTTTCTTCTTCT
53060310 TTCCCTCTCA
Statistics
Matches: 165, Mismatches: 22, Indels: 44
0.71 0.10 0.19
Matches are distributed among these distances:
17 5 0.03
18 15 0.09
19 13 0.08
20 31 0.19
21 10 0.06
22 29 0.18
23 21 0.13
24 34 0.21
25 7 0.04
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (23 bp):
CTTTTCTTTCTTCTTCTCCTTTC
Found at i:53060143 original size:44 final size:44
Alignment explanation
Indices: 53060082--53060310 Score: 301
Period size: 44 Copynumber: 5.3 Consensus size: 44
53060072 CCCCTCTTCT
*
53060082 TTTTTTTTTCTTCTCCTTTCCTTTTCTTTCATTCTTTTTCTTTC
1 TTTTTTCTTCTTCTCCTTTCCTTTTCTTTCATTCTTTTTCTTTC
* *
53060126 TTTTTTCTTCTTCTCCTTCCCTTTTCTTTCCTTCTTTTTCTTTC
1 TTTTTTCTTCTTCTCCTTTCCTTTTCTTTCATTCTTTTTCTTTC
*
53060170 ---TTTC--C-TCTCCTTTCCTTTTCTTTCATTCTTTTTCTTTA
1 TTTTTTCTTCTTCTCCTTTCCTTTTCTTTCATTCTTTTTCTTTC
*
53060208 TTTTTTCTTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTC
1 TTTTTTCTTCTTCTCCTTTCCTTTTCTTTCATTCTTTTTCTTTC
* *
53060252 TTTCTTTCCTCTCCTCTCCTTTCCTTTTCTTTC-TTTTTCTTTCTTTC
1 TTT-TTT-CT-TCTTCTCCTTTCCTTTTCTTTCATTCTT-TTTCTTTC
*
53060299 TTTCTTCTTCTT
1 TTTTTTCTTCTT
53060311 TCCCTCTCAT
Statistics
Matches: 163, Mismatches: 12, Indels: 20
0.84 0.06 0.10
Matches are distributed among these distances:
38 30 0.18
39 1 0.01
41 8 0.05
43 1 0.01
44 78 0.48
45 5 0.03
46 8 0.05
47 32 0.20
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (44 bp):
TTTTTTCTTCTTCTCCTTTCCTTTTCTTTCATTCTTTTTCTTTC
Found at i:53060171 original size:34 final size:36
Alignment explanation
Indices: 53060119--53060296 Score: 122
Period size: 38 Copynumber: 4.4 Consensus size: 36
53060109 TTCATTCTTT
* *
53060119 TTCTTTCTTTTTTCTTCTTCTCCTTCCCTTTTCTTTCC
1 TTCTTT-TTCTTTCTTC-TCTCCTTCCCTTTTCTTTCA
*
53060157 TTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTTCA
1 TTCTTTTTCTTTC-TT-CTCTCCTTCCCTTTTCTTTCA
* *
53060195 TTCTTTTTCTTTATTTTTTCTTCTTCTCCTTTCCTTTTCTTTCC
1 TTCTTTTTC-------TTTCTTC-TCTCCTTCCCTTTTCTTTCA
* *
53060239 TTCTTTTTCTTTCTTTCTTTCCTCTCCTCTCCTTTCCTTTTCT
1 TTCTTTTTCTTTC-TTCTCTCCT-TCC-CT--TTT-C-TTTCA
53060282 TTCTTTTTCTTTCTT
1 TTCTTTTTCTTTCTT
53060297 TCTTTCTTCT
Statistics
Matches: 116, Mismatches: 7, Indels: 30
0.76 0.05 0.20
Matches are distributed among these distances:
37 15 0.13
38 40 0.34
39 3 0.03
41 3 0.03
42 3 0.03
43 18 0.16
44 30 0.26
45 4 0.03
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (36 bp):
TTCTTTTTCTTTCTTCTCTCCTTCCCTTTTCTTTCA
Found at i:53060193 original size:82 final size:82
Alignment explanation
Indices: 53060077--53060309 Score: 337
Period size: 82 Copynumber: 2.8 Consensus size: 82
53060067 TTCCTCCCCT
*
53060077 CTTC-TTTT-TTT-TTTCTTCTCCTTTCCTTTTCTTTCATTCTTTTTCTTTCTTTTTTCTTCTTC
1 CTTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTTCATTCTTTTTCTTTCTTTTTTCTTCTTC
53060139 TCCTTCCCTTTTCTTTC
66 TCCTTCCCTTTTCTTTC
*
53060156 CTTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTTCATTCTTTTTCTTTATTTTTTCTTCTTC
1 CTTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTTCATTCTTTTTCTTTCTTTTTTCTTCTTC
*
53060221 TCCTTTCCTTTTCTTTC
66 TCCTTCCCTTTTCTTTC
* * *
53060238 CTTCTTTTTCTTTCTTTCTTTCCTCTCCTCTCCTTTCCTTTTCTTTCTTTTTCTTTCTTTCTTTC
1 CTTC---TT-TTTCTTTCTTTCCTCTCCTTTCCTTTTC-TTTCATTCTTTTTCTTTCTTT-TTTC
53060303 TTCTTCT
60 TTCTTCT
53060310 TTCCCTCTCA
Statistics
Matches: 138, Mismatches: 7, Indels: 9
0.90 0.05 0.06
Matches are distributed among these distances:
79 4 0.03
80 4 0.03
81 3 0.02
82 69 0.50
85 2 0.01
86 26 0.19
87 19 0.14
88 11 0.08
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (82 bp):
CTTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTTCATTCTTTTTCTTTCTTTTTTCTTCTTC
TCCTTCCCTTTTCTTTC
Found at i:53071722 original size:24 final size:24
Alignment explanation
Indices: 53071672--53071723 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
53071662 TTCGTAGGTC
* **
53071672 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATAAT
*
53071696 AAATATATTATACTAATAAATAAT
1 AAATAAATTATACTAATAAATAAT
53071720 AAAT
1 AAAT
53071724 CTTCTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATAAT
Found at i:53077913 original size:42 final size:42
Alignment explanation
Indices: 53077824--53077996 Score: 211
Period size: 42 Copynumber: 4.0 Consensus size: 42
53077814 AGGTAATCTG
* *
53077824 ATATGCGAACCCTTAGTGCAGGTTATGTGAACCCCCTTAGTGAAT
1 ATATGCGAACCCTTAGTACATG-TATGTG-A-CCCCTTAGTGAAT
* *
53077869 ATATGCAAACCCTTAGTACATGTATGAGACCCCTTAGTGAAT
1 ATATGCGAACCCTTAGTACATGTATGTGACCCCTTAGTGAAT
* * * *
53077911 ATATGTGAACCCTTAGTACATGTATGTGATCTCTTATTGAAT
1 ATATGCGAACCCTTAGTACATGTATGTGACCCCTTAGTGAAT
* * * *
53077953 ATATGTGAACCTTTAGTACATGTATGTGATCCATTAGTGAAT
1 ATATGCGAACCCTTAGTACATGTATGTGACCCCTTAGTGAAT
53077995 AT
1 AT
53077997 GAGTGAAACC
Statistics
Matches: 114, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
42 89 0.78
43 1 0.01
44 5 0.04
45 19 0.17
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (42 bp):
ATATGCGAACCCTTAGTACATGTATGTGACCCCTTAGTGAAT
Found at i:53077936 original size:21 final size:21
Alignment explanation
Indices: 53077825--53077990 Score: 113
Period size: 21 Copynumber: 7.8 Consensus size: 21
53077815 GGTAATCTGA
* * *
53077825 TATGCGAACCCTTAGTGCAGG
1 TATGTGAACCCTTAGTACATG
*
53077846 TTATGTGAACCCCCTTAGTGA-ATA
1 -TATGTGAA--CCCTTAGT-ACATG
**
53077870 TATGCAAACCCTTAGTACATG
1 TATGTGAACCCTTAGTACATG
* * *
53077891 TATGAGACCCCTTAGTGA-ATA
1 TATGTGAACCCTTAGT-ACATG
53077912 TATGTGAACCCTTAGTACATG
1 TATGTGAACCCTTAGTACATG
* * * *
53077933 TATGTGATCTCTTATTGA-ATA
1 TATGTGAACCCTTAGT-ACATG
*
53077954 TATGTGAACCTTTAGTACATG
1 TATGTGAACCCTTAGTACATG
* *
53077975 TATGTGATCCATTAGT
1 TATGTGAACCCTTAGT
53077991 GAATATGAGT
Statistics
Matches: 111, Mismatches: 25, Indels: 17
0.73 0.16 0.11
Matches are distributed among these distances:
20 3 0.03
21 84 0.76
22 9 0.08
23 6 0.05
24 9 0.08
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (21 bp):
TATGTGAACCCTTAGTACATG
Found at i:53078363 original size:3 final size:3
Alignment explanation
Indices: 53078355--53078401 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
53078345 GTGAGGTAAG
53078355 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
53078402 GGAATTAAAT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:53080985 original size:5 final size:5
Alignment explanation
Indices: 53080975--53081007 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
53080965 TTTGTTTCTT
*
53080975 TTTTA TTTTA TTTTA TTTCA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
53081008 GTTTTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:53081083 original size:19 final size:20
Alignment explanation
Indices: 53081059--53081097 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
53081049 ATTACTAAGC
53081059 AATACATAT-TTTATTATTA
1 AATACATATGTTTATTATTA
53081078 AATACATATGTTTATTATTA
1 AATACATATGTTTATTATTA
53081098 TTACAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (20 bp):
AATACATATGTTTATTATTA
Found at i:53081172 original size:16 final size:14
Alignment explanation
Indices: 53081102--53081172 Score: 51
Period size: 13 Copynumber: 5.1 Consensus size: 14
53081092 TTATTATTAC
53081102 AATAATAATAA-TT
1 AATAATAATAATTT
* *
53081115 -ACAACAATAATTT
1 AATAATAATAATTT
53081128 AAT-ATAATAATTT
1 AATAATAATAATTT
*
53081141 AATAA-ATATCTATTT
1 AATAATA-AT-AATTT
53081156 AATAATCAATATATTT
1 AATAAT-AATA-ATTT
53081172 A
1 A
53081173 TTACAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
12 8 0.18
13 15 0.34
14 4 0.09
15 9 0.20
16 7 0.16
17 1 0.02
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (14 bp):
AATAATAATAATTT
Found at i:53086802 original size:12 final size:12
Alignment explanation
Indices: 53086785--53086818 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
53086775 GCCACACGGT
*
53086785 CGTGTGCTTGGC
1 CGTGTGCTAGGC
*
53086797 CGTGTGGTAGGC
1 CGTGTGCTAGGC
53086809 CGTGTGCTAG
1 CGTGTGCTAG
53086819 ACCATGTGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.21, G:0.44, T:0.29
Consensus pattern (12 bp):
CGTGTGCTAGGC
Found at i:53087186 original size:341 final size:341
Alignment explanation
Indices: 53086554--53087204 Score: 857
Period size: 341 Copynumber: 1.9 Consensus size: 341
53086544 CTGTTCGTCC
* * * * *
53086554 AGCGGTAAGTGCTCTAATGTGTTCTTGGAGGGTTTTATTAGTTCGTTTGTGATCAATTTTTCTGA
1 AGCGGTAAGTGCTCGAAAGTGTTCCTGGAGGGTTTAATTAGTTCATTTGTGATCAATTTTTCTGA
* *
53086619 TTAAGTTTCACGAATCGATACTAAAATTAATTATGTTAAGTGTCAATTTAGGTGTAGGAGTACTC
66 TTAAGTTTCACGAATCGATACTAAAATTAATTATGCTAAGTGTCAATTTAGGTGTAGGAGTACAC
* ** *
53086684 GATTCTCGGTTTTATGTGAAAAAACCTCCAGGTGTGTAATAGAACTTGCAAAAACAACGAATGAT
131 GATTCTCGATTTTAACTGAAAAAACCTCCAGGTGTGTAATAGAACTTGCAAAAACAACGAACGAT
* * * * * *
53086749 GAAAGTCAAAAATTGGGGCTATCAATGCCACACGGTCGTGTGCTTGGCCGTGTGGTAGGCCGTGT
196 GAAAGCCAAAAATTGGGGCTATCAATGCCACACGCTCGTGTGCTAGGACGTGTGCTAGGCCATGT
* * * *
53086814 GCTAGACCATGTGAGACACACGATTTGGGCCAATTT-GGCCGTGTGAGCCATACAGGCTAGCTAA
261 ACTAGACCATATGAGACACACGATCTGGGCC-ATTTGGGCCGTGTAAGCCATACAGGCTAGCTAA
53086878 GTAGTTGTTATTTGTTT
325 GTAGTTGTTATTTGTTT
53086895 AGCGGTAAGTGCTCGAAAGTGTTCCTGGAGGGTTTAATTAGTTCATTTGTGATCAATTTTTCTGA
1 AGCGGTAAGTGCTCGAAAGTGTTCCTGGAGGGTTTAATTAGTTCATTTGTGATCAATTTTTCTGA
* * ** *
53086960 TTAAGTTTTGA-GAATCGATACTAAAATTAGTTATGCTAACG-GTTGATTTAGGTGTGGGAGTAC
66 TTAAG-TTTCACGAATCGATACTAAAATTAATTATGCTAA-GTGTCAATTTAGGTGTAGGAGTAC
* * * * * * *
53087023 ACTATTCTTGATTTTACACT-AGAAAACTTCCTGGTGTGTAAT-GAAACTTG-AGAAAATAGCGA
129 ACGATTCTCGATTTTA-ACTGAAAAAACCTCCAGGTGTGTAATAG-AACTTGCA-AAAACAACGA
*
53087085 ACGATGAAAGCCAAAAATTGGGGCTATCGATGCCACACAGCT-GTGTGCTAGGACGTGTGCTAGG
191 ACGATGAAAGCCAAAAATTGGGGCTATCAATGCCACAC-GCTCGTGTGCTAGGACGTGTGCTAGG
* * *
53087149 CCATGTACTGGACCGTATGAGACACACGGTCTGGGCCATTTGGGCCGTGTAAGCCA
255 CCATGTACTAGACCATATGAGACACACGATCTGGGCCATTTGGGCCGTGTAAGCCA
53087205 CATGGGCGTG
Statistics
Matches: 266, Mismatches: 37, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
340 6 0.02
341 252 0.95
342 8 0.03
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (341 bp):
AGCGGTAAGTGCTCGAAAGTGTTCCTGGAGGGTTTAATTAGTTCATTTGTGATCAATTTTTCTGA
TTAAGTTTCACGAATCGATACTAAAATTAATTATGCTAAGTGTCAATTTAGGTGTAGGAGTACAC
GATTCTCGATTTTAACTGAAAAAACCTCCAGGTGTGTAATAGAACTTGCAAAAACAACGAACGAT
GAAAGCCAAAAATTGGGGCTATCAATGCCACACGCTCGTGTGCTAGGACGTGTGCTAGGCCATGT
ACTAGACCATATGAGACACACGATCTGGGCCATTTGGGCCGTGTAAGCCATACAGGCTAGCTAAG
TAGTTGTTATTTGTTT
Found at i:53090122 original size:16 final size:15
Alignment explanation
Indices: 53090101--53090149 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 15
53090091 TCGAGAAAAA
53090101 AATAATGATAATTGTG
1 AATAATGATAATT-TG
*
53090117 AATAATGATACTTTG
1 AATAATGATAATTTG
* *
53090132 AATAGTCAT-ATTTG
1 AATAATGATAATTTG
53090146 AATA
1 AATA
53090150 TTTTAGGTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 8 0.28
15 9 0.31
16 12 0.41
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.39
Consensus pattern (15 bp):
AATAATGATAATTTG
Found at i:53090269 original size:169 final size:169
Alignment explanation
Indices: 53089944--53090290 Score: 411
Period size: 169 Copynumber: 2.1 Consensus size: 169
53089934 AATTGATGAC
*
53089944 TGTGAATAATAATACTTTGAGTAGTCAAATTTGAATATTTTAGGTAGCGTTGGAAGTGGGAACCC
1 TGTGAATAATAATACTTTGAATAGTCAAATTTGAATATTTTAGGTAGCGTTGGAAGTGGGAACCC
* * * * * * **
53090009 TTTGATATTTGCTTTTACATTTGTCCAAGTAGGAAGCAAGCAAGGGGATTAGTCATTGTTACCGA
66 TTTGATATTTACTTCTACATTTGTCCAAGTAGGAAGCAAACAAGAGAATTAGTCACTGCGACCGA
53090074 CAATAGACATCCTAATTTCGAGAAAAAAATAATGATAAT
131 CAATAGACATCCTAATTTCGAGAAAAAAATAATGATAAT
* * *
53090113 TGTGAATAATGATACTTTGAATAGTCATATTTGAATATTTTAGGTAGTC-TTGGGAGTGGG-ACC
1 TGTGAATAATAATACTTTGAATAGTCAAATTTGAATATTTTAGGTAG-CGTTGGAAGTGGGAACC
* * * *
53090176 CTTTGATTTTTACTTCTACATTTGT-C-AGTTGGAGGTAAACAAGAGAATTTA-TCACTGCGACC
65 CTTTGATATTTACTTCTACATTTGTCCAAGTAGGAAGCAAACAAGAGAA-TTAGTCACTGCGACC
* * * * * * *
53090238 GATAGTGGACATCCTAGTTTCGA-CAAGAAA-AATGGTAAT
129 GACAATAGACATCCTAATTTCGAGAAAAAAATAATGATAAT
*
53090277 TGTGAGTAATAATA
1 TGTGAATAATAATA
53090291 ATAATAATAA
Statistics
Matches: 151, Mismatches: 25, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
164 20 0.13
165 5 0.03
166 42 0.28
167 4 0.03
168 25 0.17
169 54 0.36
170 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (169 bp):
TGTGAATAATAATACTTTGAATAGTCAAATTTGAATATTTTAGGTAGCGTTGGAAGTGGGAACCC
TTTGATATTTACTTCTACATTTGTCCAAGTAGGAAGCAAACAAGAGAATTAGTCACTGCGACCGA
CAATAGACATCCTAATTTCGAGAAAAAAATAATGATAAT
Found at i:53090291 original size:3 final size:3
Alignment explanation
Indices: 53090283--53090314 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
53090273 TAATTGTGAG
53090283 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
53090315 GAAATCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:53092400 original size:15 final size:16
Alignment explanation
Indices: 53092362--53092393 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53092352 CTAGCCCCTA
53092362 ACCCTAGCCTGTTGCC
1 ACCCTAGCCTGTTGCC
53092378 ACCCTAGCCT-TTGCC
1 ACCCTAGCCTGTTGCC
53092393 A
1 A
53092394 TGCTAGCACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.16, C:0.44, G:0.16, T:0.25
Consensus pattern (16 bp):
ACCCTAGCCTGTTGCC
Found at i:53093325 original size:3 final size:3
Alignment explanation
Indices: 53093313--53093600 Score: 192
Period size: 3 Copynumber: 95.7 Consensus size: 3
53093303 ATACTACTAC
* *
53093313 TAT TAC TAT TAT TAT TAT TAG TAT TAT TGA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
** *
53093358 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CCT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
53093406 TAC TAT TAT TAG CAT TAT TAT CAT TAGT T-T TAT TGT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
* * * ** * * * *
53093450 TAC TAT TAA CAT TAT TAT TGG AAT TAT TAT TAA TGT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * **
53093498 TTT TTT TCT TAC TAT TAA TAT TAT T-T ATAT TAT TAT TAT AAT TGC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
* * * *
53093543 TAT TAT TAT T-T TCAT TAC CAT TAT TAT TA- TATT TCT TGT ATACT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TA-T TAT TAT -TA-T TAT
53093590 TAT TAT TAT TA
1 TAT TAT TAT TA
53093601 CCCTGTTGTT
Statistics
Matches: 216, Mismatches: 56, Indels: 26
0.72 0.19 0.09
Matches are distributed among these distances:
2 10 0.05
3 195 0.90
4 10 0.05
5 1 0.00
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:53098459 original size:44 final size:44
Alignment explanation
Indices: 53098394--53098928 Score: 432
Period size: 44 Copynumber: 11.8 Consensus size: 44
53098384 GTCATCATGG
**
53098394 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * *
53098438 CTAATCTTATCCCCCTGAAGTTGCAGTAGG-GCAGATTGAAGAAA
1 CAAATCTTATCTCCCTGAAGTTGCAGT-GGAGCAGATTGAAGATA
* * * *
53098482 CAAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGATGG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-A
* * *
53098527 CAAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTGAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * ** *
53098571 CGAGTCTTATCTCTTTGAAGTTGCAGTGGAGCAGACTGAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * * * *
53098615 GCAAACCTTATCTACTTGAAGTTGCAGTGGAGCAGGTTAAAGATA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * *
53098660 CAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * * *
53098704 GCAAATCTTATTTCCCTGAAGTGGCAGTGGAACAGATTAAAGCTATA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--ATA
* * * * * *
53098751 -AGTTATAGGTCTTATCTCTCTGAAGTTGTAGTAGAACAGA-T-CATAT-
1 CA---A-A--TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * * * * *
53098797 CAAACCTTATCTCCCTGAAGTTGTAGTGGAGAAGGTTAAAAATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * *
53098841 AATCAATCTTATCTCCATGAAGTTGCAGTGGAGTAGATTGAAGACCGGCTA
1 CA--AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-----TA
* * * *
53098892 CAAATCCTATCTCCCTGAAGTTACAGTAGAGCGGATT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
53098929 AAAACAATGA
Statistics
Matches: 390, Mismatches: 77, Indels: 43
0.76 0.15 0.08
Matches are distributed among these distances:
41 25 0.06
42 1 0.00
43 5 0.01
44 148 0.38
45 110 0.28
46 33 0.08
47 6 0.02
48 1 0.00
49 31 0.08
50 1 0.00
51 29 0.07
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
Found at i:53098581 original size:89 final size:89
Alignment explanation
Indices: 53098398--53098884 Score: 493
Period size: 89 Copynumber: 5.4 Consensus size: 89
53098388 TCATGGCAAA
* ** * * *
53098398 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCA-CTAATCTTATCCCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACCTTATCTCCCTGAAGTTGC
* * *
53098462 AGTAGG-GCAGATTGAAGAAACAAG
66 AGT-GGAGCAGGTTAAAGATACAAG
* * *
53098486 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGATGGCAAACCTTATCTCTCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACCTTATCTCCCTGAAGTTGC
* *
53098551 AGTGGAGCAGGTTGAAGATACGAG
66 AGTGGAGCAGGTTAAAGATACAAG
** * *
53098575 TCTTATCTCTTTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACCTTATCTACTTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACCTTATCTCCCTGAAGTTGC
53098640 AGTGGAGCAGGTTAAAGATACAAG
66 AGTGGAGCAGGTTAAAGATACAAG
* * * *
53098664 TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTGGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACCTTATCTCCCTGAAGTTGC
* * *
53098729 AGTGGAACAGATTAAAGCTATAAGTTATAGG
66 AGTGGAGCAGGTTAAAG--AT-A--CA-A-G
* * * ** * *
53098760 TCTTATCTCTCTGAAGTTGTAGT--AG-A-ACAGATCATATCAAACCTTATCTCCCTGAAGTTGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACCTTATCTCCCTGAAGTTGC
* *
53098821 AGTGGAGAAGGTTAAAAATAAATCAA-
66 AGTGGAGCAGGTTAAAGAT--A-CAAG
* * *
53098847 TCTTATCTCCATGAAGTTGCAGTGGAGTAGATTGAAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA
53098885 CCGGCTACAA
Statistics
Matches: 330, Mismatches: 55, Indels: 25
0.80 0.13 0.06
Matches are distributed among these distances:
87 20 0.06
88 37 0.11
89 193 0.58
90 5 0.02
91 8 0.02
92 41 0.12
93 1 0.00
94 3 0.01
95 1 0.00
96 21 0.06
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.28
Consensus pattern (89 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACCTTATCTCCCTGAAGTTGC
AGTGGAGCAGGTTAAAGATACAAG
Found at i:53098669 original size:133 final size:133
Alignment explanation
Indices: 53098394--53098739 Score: 399
Period size: 133 Copynumber: 2.6 Consensus size: 133
53098384 GTCATCATGG
** * *
53098394 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAATCTTATCCCCCTGAAGT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACAAATCTTATCTCCCTGAAGT
* ** * *
53098459 TGCAGTAGG-GCAGATTGAAGAAACAAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAG
66 TGCAGT-GGAGCAGACTGAAGAAACAAACCTTATCTACCTGAAGTTGCAGTAGAGCAGACTAAAG
*
53098523 ATGG
130 ATGA
* * * * * **
53098527 CAAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTGAAGATACGAGTCTTATCTCTTTGAAGT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACAAATCTTATCTCCCTGAAGT
* * * **
53098592 TGCAGTGGAGCAGACTGAAGATAGCAAACCTTATCTACTTGAAGTTGCAGTGGAGCAGGTTAAAG
66 TGCAGTGGAGCAGACTGAAGA-AACAAACCTTATCTACCTGAAGTTGCAGTAGAGCAGACTAAAG
53098657 AT-A
130 ATGA
* * * *
53098660 CAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CAAATCTTATCTCCCTGAAG
* *
53098725 TGGCAGTGGAACAGA
65 TTGCAGTGGAGCAGA
53098740 TTAAAGCTAT
Statistics
Matches: 176, Mismatches: 34, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
132 2 0.01
133 110 0.62
134 64 0.36
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (133 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACAAATCTTATCTCCCTGAAGT
TGCAGTGGAGCAGACTGAAGAAACAAACCTTATCTACCTGAAGTTGCAGTAGAGCAGACTAAAGA
TGA
Found at i:53100621 original size:3 final size:3
Alignment explanation
Indices: 53100367--53100598 Score: 143
Period size: 3 Copynumber: 77.0 Consensus size: 3
53100357 ATACTACTAC
* * *
53100367 TAT TAC TAT TAT TAT TAG TAT TAT TGA- TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
** * * * *
53100412 TAT TAT TAT TAT CCT TAC TAT TAT TAT TAG CAT TAT TAT CAT TAGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
* * * *
53100458 T-T TAT TGT TAT T-T TAT TAC TAT TAA CAT TAT TAT TGGAGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T--A-T TAT TAT
* ** * * * * *
53100504 TAA TGC TAT TAC TAT TAT T-T TTT TCT TAC TAT TAA TAT TAT T-T ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * *
53100551 TAT TAT TAT TAT TAT TAC TAT TAT TAT T-T TCAT TAC CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
53100596 TAT
1 TAT
53100599 ATTCCTCGTA
Statistics
Matches: 171, Mismatches: 45, Indels: 26
0.71 0.19 0.11
Matches are distributed among these distances:
2 10 0.06
3 151 0.88
4 7 0.04
5 1 0.01
6 2 0.01
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:53104069 original size:24 final size:24
Alignment explanation
Indices: 53104035--53104092 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
53104025 TTTTTAGAAG
*
53104035 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGTATAATAT
53104059 ATTTAGCATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGTATAATAT
*
53104083 ATTTAACATT
1 ATTTAGCATT
53104093 GATTGGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAGTATAATAT
Found at i:53105950 original size:12 final size:12
Alignment explanation
Indices: 53105915--53105953 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
53105905 ATTTAAAGCT
53105915 TAGAAAACTATGA
1 TAGAAAACTA-GA
* *
53105928 TCGAGAACTAGA
1 TAGAAAACTAGA
53105940 TAGAAAACTAGA
1 TAGAAAACTAGA
53105952 TA
1 TA
53105954 AAACACCTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 14 0.64
13 8 0.36
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.21
Consensus pattern (12 bp):
TAGAAAACTAGA
Found at i:53107791 original size:24 final size:24
Alignment explanation
Indices: 53107728--53107779 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
53107718 TTTCTAGAAG
* **
53107728 ATTTAGTATTTATTAGTGTAATAT
1 ATTTAGCATTTATTAGCATAATAT
53107752 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
53107776 ATTT
1 ATTT
53107780 GACATTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:53110190 original size:15 final size:16
Alignment explanation
Indices: 53110170--53110199 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53110160 ATTCAAGATC
53110170 AATTTA-CTTGTTTGA
1 AATTTATCTTGTTTGA
53110185 AATTTATCTTGTTTG
1 AATTTATCTTGTTTG
53110200 CATGATTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.23, C:0.07, G:0.13, T:0.57
Consensus pattern (16 bp):
AATTTATCTTGTTTGA
Found at i:53116089 original size:8 final size:8
Alignment explanation
Indices: 53116076--53116100 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
53116066 ATATATACTA
53116076 AATAAAAT
1 AATAAAAT
53116084 AATAAAAT
1 AATAAAAT
53116092 AATAAAAT
1 AATAAAAT
53116100 A
1 A
53116101 TCTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:53118947 original size:19 final size:18
Alignment explanation
Indices: 53118919--53118962 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
53118909 ATTGATTAGT
**
53118919 TTAATTAATTTTTTAAAA
1 TTAATTAATTAATTAAAA
53118937 TTAATTTAATTAATTAAAA
1 TTAA-TTAATTAATTAAAA
*
53118956 TTTATTA
1 TTAATTA
53118963 TGAAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATTAATTAATTAAAA
Found at i:53120409 original size:43 final size:43
Alignment explanation
Indices: 53120357--53120455 Score: 180
Period size: 43 Copynumber: 2.3 Consensus size: 43
53120347 GCGCAGAAAA
53120357 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
53120400 AAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
53120443 AAACGCCACTAAA
1 AAACGCCGCTAAA
53120456 AACATGACTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.30, C:0.34, G:0.18, T:0.17
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:53120678 original size:18 final size:18
Alignment explanation
Indices: 53120655--53120714 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
53120645 TTAAAACAAG
53120655 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
*** * *
53120673 TTACATAAGAAAATT-G-T
1 TTACAT-TCTATATTAGAA
53120690 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
53120708 TTACATT
1 TTACATT
53120715 AGAATTACAT
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
16 4 0.14
17 7 0.24
18 14 0.48
19 4 0.14
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (18 bp):
TTACATTCTATATTAGAA
Found at i:53125084 original size:41 final size:41
Alignment explanation
Indices: 53125039--53125323 Score: 417
Period size: 41 Copynumber: 7.0 Consensus size: 41
53125029 ATATCTGATA
53125039 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGC
* * *
53125080 ATTAGCGGTGCTTCTTAAAAAACGCCGCTAAAGACCCGAGA
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGC
* * *
53125121 ATTAGCGGCGCTTCTTCAACAACGCCGCTAAATACCGGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGC
* *
53125162 ATTAGCAGCGCTTCTTCAAAAACGCCACTAAAGACCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGC
* * * *
53125203 ATTAGCGGCGCTTCTTTAAAAACGTCACTAAAGACCCGAAC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGC
* * *
53125244 ATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGACCTGATC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGC
* *
53125285 ATTAGCGGCGCTTCTTCAAAAACACCGCTAAAGCCCCGA
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGA
53125324 AAACTCAAAA
Statistics
Matches: 216, Mismatches: 28, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 216 1.00
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGC
Found at i:53125404 original size:39 final size:39
Alignment explanation
Indices: 53125355--53125489 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 39
53125345 TAGGCTTAGG
*
53125355 TTTTTTGCGGCGCTTTT-TGGAAAACGCCGCTAATGCTCA
1 TTTTTAGCGGCG-TTTTCTGGAAAACGCCGCTAATGCTCA
* * * * *
53125394 TTTTTAGCGGCGTTTTCTTGAAAGCGCAGCTAATACTCG
1 TTTTTAGCGGCGTTTTCTGGAAAACGCCGCTAATGCTCA
* * * *
53125433 TTCTTTAGCGACGTTTTCT-TAAAAGCGCCGGTAATGCTTGA
1 TT-TTTAGCGGCGTTTTCTGGAAAA-CGCCGCTAATGC-TCA
53125474 TTTTTAGCGGCGTTTT
1 TTTTTAGCGGCGTTTT
53125490 TTGTCCAAAC
Statistics
Matches: 77, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
38 4 0.05
39 33 0.43
40 37 0.48
41 3 0.04
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.39
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTCTGGAAAACGCCGCTAATGCTCA
Found at i:53126898 original size:44 final size:44
Alignment explanation
Indices: 53126812--53126898 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
53126802 TTTGGACTAG
* *
53126812 TAAACTTCCAATTTACTATCTCATGTGATTCAATTATACTAATA
1 TAAACTTCCAATTAACTATCTCATGTGATTCAACTATACTAATA
* * * *
53126856 TAAACTTCCAGTTAACTAT-TGCATGTGGTTTAACTATTCTAAT
1 TAAACTTCCAATTAACTATCT-CATGTGATTCAACTATACTAAT
53126899 GTATGCATAG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
43 1 0.03
44 35 0.97
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.41
Consensus pattern (44 bp):
TAAACTTCCAATTAACTATCTCATGTGATTCAACTATACTAATA
Found at i:53127329 original size:28 final size:28
Alignment explanation
Indices: 53127289--53127347 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
53127279 TTCTTGATAG
53127289 TATGCACTGTTGTATTGCCTACAGGTCA
1 TATGCACTGTTGTATTGCCTACAGGTCA
53127317 TATGCACTGTTGTATTGCCTACAGGTCA
1 TATGCACTGTTGTATTGCCTACAGGTCA
53127345 TAT
1 TAT
53127348 ATTTTCTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (28 bp):
TATGCACTGTTGTATTGCCTACAGGTCA
Found at i:53131095 original size:2 final size:2
Alignment explanation
Indices: 53131088--53131119 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
53131078 TCAACAAGAC
53131088 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
53131120 TTCTTTAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53132115 original size:16 final size:15
Alignment explanation
Indices: 53132094--53132134 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
53132084 GAGTCAAATA
53132094 AAATAAAGTTTGAATT-
1 AAATAAAGTTT--ATTC
53132110 AAATAAA-TTTATTC
1 AAATAAAGTTTATTC
53132124 AAATAAAGTTT
1 AAATAAAGTTT
53132135 TAAAAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 3 0.13
14 7 0.30
15 6 0.26
16 7 0.30
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (15 bp):
AAATAAAGTTTATTC
Found at i:53133279 original size:42 final size:42
Alignment explanation
Indices: 53133213--53133355 Score: 173
Period size: 42 Copynumber: 3.4 Consensus size: 42
53133203 GTATATGGCC
* * *
53133213 TTGGATATGGCATTGAAGATGGGAACCAGTTAGGTACAGCCA
1 TTGGATATGGCATTGGAGAAGGGAACCAGTTAGGTACAGGCA
*
53133255 TTGGATATGGCATTGGAGAAGGGAACCAGGTAGGTACAGGCA
1 TTGGATATGGCATTGGAGAAGGGAACCAGTTAGGTACAGGCA
* * **
53133297 TTGGAAATGGCA-TGG-GAAGTGGGAACCAGTTAGGAATGGGCA
1 TTGGATATGGCATTGGAGAA--GGGAACCAGTTAGGTACAGGCA
*
53133339 TTGGGTATGGCATTGGA
1 TTGGATATGGCATTGGA
53133356 AATGGGGGTC
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
40 3 0.03
41 3 0.03
42 77 0.90
43 3 0.03
ACGTcount: A:0.29, C:0.11, G:0.37, T:0.22
Consensus pattern (42 bp):
TTGGATATGGCATTGGAGAAGGGAACCAGTTAGGTACAGGCA
Found at i:53133374 original size:42 final size:42
Alignment explanation
Indices: 53133327--53133451 Score: 103
Period size: 42 Copynumber: 3.0 Consensus size: 42
53133317 GGGAACCAGT
53133327 TAGGAATGGGCATTGGGTATGGCATTGGAAATGGGGGTCA-A
1 TAGGAATGGGCATTGGGTATGGCATTGGAAATGGGGGTCAGA
* * * * * ***
53133368 TCAGGAAAT-AGCA-TGGGATTTGGTATCGGAAATGCGAACCAGA
1 T-AGG-AATGGGCATTGGG-TATGGCATTGGAAATGGGGGTCAGA
* * *
53133411 TGGGAATGGGTATCGGGTATGGCATTGGAAATGGGGGTCAG
1 TAGGAATGGGCATTGGGTATGGCATTGGAAATGGGGGTCAG
53133452 GCCGGAAATA
Statistics
Matches: 59, Mismatches: 19, Indels: 11
0.66 0.21 0.12
Matches are distributed among these distances:
41 8 0.14
42 43 0.73
43 8 0.14
ACGTcount: A:0.28, C:0.10, G:0.39, T:0.23
Consensus pattern (42 bp):
TAGGAATGGGCATTGGGTATGGCATTGGAAATGGGGGTCAGA
Found at i:53133538 original size:42 final size:42
Alignment explanation
Indices: 53133479--53133582 Score: 163
Period size: 42 Copynumber: 2.5 Consensus size: 42
53133469 ATATGGCATA
* *
53133479 GGATATGGCACTGGAAATGGGAACCAGTTAGGAACTGGTATT
1 GGATATGGTACTGGAAATGGGAACCAGTTAGGAACCGGTATT
*
53133521 GGATATGGTATTGGAAATGGGAACCAGTTAGGAACCGGTATT
1 GGATATGGTACTGGAAATGGGAACCAGTTAGGAACCGGTATT
* *
53133563 GGATTTGGTACCGGAAATGG
1 GGATATGGTACTGGAAATGG
53133583 AGGTCAGTCA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.30, C:0.11, G:0.35, T:0.25
Consensus pattern (42 bp):
GGATATGGTACTGGAAATGGGAACCAGTTAGGAACCGGTATT
Found at i:53134169 original size:29 final size:29
Alignment explanation
Indices: 53134121--53134195 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
53134111 TTAAATTAGT
* *
53134121 AAAATTA-AAATTATATTTTATTCC-TTA
1 AAAATTATAAATTATAATTTAATCCTTTA
*
53134148 AAAATTATTAAATTTTAATTTAATCCTTTA
1 AAAATTA-TAAATTATAATTTAATCCTTTA
53134178 AAAATTATAAATTCATAA
1 AAAATTATAAATT-ATAA
53134196 GCTATTAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 7 0.17
29 20 0.50
30 13 0.32
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (29 bp):
AAAATTATAAATTATAATTTAATCCTTTA
Found at i:53134805 original size:82 final size:84
Alignment explanation
Indices: 53134705--53134867 Score: 303
Period size: 85 Copynumber: 2.0 Consensus size: 84
53134695 TTGATGAAGC
53134705 AAATTATGATCTTGGGTTTCTAGGCATTT-TTTTTT-GTATACTTTTAATCAAATTTAGATGATA
1 AAATTATGATCTTGGGTTTCTAGGCATTTCTTTTTTGGTATACTTTTAATCAAATTTAGATGATA
53134768 AATTTATTTATTTTTAATT
66 AATTTATTTATTTTTAATT
53134787 AAATTATGATCTTGGGTTTCTAGGCATTTCCTTTTTTGGTATACTTTTAATCAAATTTAGATGAT
1 AAATTATGATCTTGGGTTTCTAGGCATTT-CTTTTTTGGTATACTTTTAATCAAATTTAGATGAT
53134852 AAATTTATTTATTTTT
65 AAATTTATTTATTTTT
53134868 TAGCTTTTTA
Statistics
Matches: 78, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
82 29 0.37
84 6 0.08
85 43 0.55
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.53
Consensus pattern (84 bp):
AAATTATGATCTTGGGTTTCTAGGCATTTCTTTTTTGGTATACTTTTAATCAAATTTAGATGATA
AATTTATTTATTTTTAATT
Found at i:53135339 original size:17 final size:18
Alignment explanation
Indices: 53135304--53135341 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
53135294 ATGACACAGA
53135304 TTTGTTATTTAATTATAT
1 TTTGTTATTTAATTATAT
* *
53135322 TTTGTT-TTTTATTTTAT
1 TTTGTTATTTAATTATAT
53135339 TTT
1 TTT
53135342 TATTTTTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTGTTATTTAATTATAT
Found at i:53136597 original size:19 final size:20
Alignment explanation
Indices: 53136559--53136596 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
53136549 TGGCCGGAAC
53136559 CCATGTATTTTTTTTAAAAT
1 CCATGTATTTTTTTTAAAAT
53136579 CCATGTATTTTTTTTAAA
1 CCATGTATTTTTTTTAAA
53136597 TATTGTATAA
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:0.29, C:0.11, G:0.05, T:0.55
Consensus pattern (20 bp):
CCATGTATTTTTTTTAAAAT
Found at i:53136754 original size:100 final size:99
Alignment explanation
Indices: 53136614--53136933 Score: 488
Period size: 100 Copynumber: 3.2 Consensus size: 99
53136604 TAATACTGAT
* * * * *
53136614 ATACGAAAAAGA-AAAAAAAA--TTTGGGTGTTGGCCTGTCAATGGCCGGCACCCAGTGA-ACAG
1 ATACGAAAAAAATAAAAAAAATTTTTGGGTGCTGGCCTATCAATGGCTGGCACCCAGT-ACACAA
53136675 TAAAATTTTTTTTCGTGTCAGAATAAGATATAAAA
65 TAAAATTTTTTTTCGTGTCAGAATAAGATATAAAA
53136710 ATACGAAAAAAATAAAAAAAATTTTTTGGGTGCTGGCCTATCAATGGCTGGCACCCAGTACACAA
1 ATACGAAAAAAATAAAAAAAA-TTTTTGGGTGCTGGCCTATCAATGGCTGGCACCCAGTACACAA
*
53136775 TAAATTTTTTTTTTCGTGTCAGAATAAGATATAAAA
65 TAAA-ATTTTTTTTCGTGTCAGAATAAGATATAAAA
53136811 ATACGAAAAAAATAAAAAAAATTTTTGGGTGCTGGCCTATCAATGGCTGGCACCCAGTACACAAT
1 ATACGAAAAAAATAAAAAAAATTTTTGGGTGCTGGCCTATCAATGGCTGGCACCCAGTACACAAT
* * *
53136876 -AAATTTTTTTTGTGTGTTAGAATCAGATATAAAA
66 AAAATTTTTTTT-CGTGTCAGAATAAGATATAAAA
53136910 ATACGAAAAAAATAAAAAAAATTT
1 ATACGAAAAAAATAAAAAAAATTT
53136934 CTATTTCCTC
Statistics
Matches: 207, Mismatches: 10, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
96 11 0.05
97 8 0.04
98 8 0.04
99 46 0.22
100 83 0.40
101 51 0.25
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (99 bp):
ATACGAAAAAAATAAAAAAAATTTTTGGGTGCTGGCCTATCAATGGCTGGCACCCAGTACACAAT
AAAATTTTTTTTCGTGTCAGAATAAGATATAAAA
Found at i:53141009 original size:114 final size:110
Alignment explanation
Indices: 53140713--53141104 Score: 521
Period size: 114 Copynumber: 3.5 Consensus size: 110
53140703 TATATATATG
* * * *
53140713 ATTGTACTAGGTGCCGGCCATTGACAGGTCAACACCCAAAAAATTTTTTTTTATTTTTTTCGTAT
1 ATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTTTTAATTTTTTTCGTAT
*
53140778 ATTTATATCTGACTCTGACACGAAAAAAA-AAA-TTTTTTTTAAAA
66 ATTTATATCTGACTCTGACA-AAAAAAAAGAAATTTTTTTTTAAAA
* * *
53140822 TTTGTACTGAGTGCCGGCCATTGA-AGGCCAGCACCC---AAATTTTTTTTTATTTTTTTCGTAT
1 ATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTTTTAATTTTTTTCGTAT
*
53140883 ATTTATATCTGACCCTGACAAAAAAAAAGAAATTTTTTTTTTAAAAAAA
66 ATTTATATCTGACTCTGACAAAAAAAAAGAAA-TTTTTTTTT---AAAA
53140932 ATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC-AAAAATTTTTTTTAAATTTTTTTCGTA
1 ATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTTTT-AATTTTTTTCGTA
53140996 TATTTATATCTGACTCTGACATGAAAAAAAAAAGTAAATTTTTTTTT-AAA
65 TATTTATATCTGACTCTGAC----AAAAAAAAAG-AAATTTTTTTTTAAAA
*
53141046 TTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAACTTTTTTTTTAATTTT
1 ATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAA--TTTTTTTTAATTTT
53141105 CCTTTNNNNN
Statistics
Matches: 253, Mismatches: 12, Indels: 29
0.86 0.04 0.10
Matches are distributed among these distances:
104 7 0.03
105 47 0.19
107 8 0.03
108 10 0.04
109 21 0.08
110 26 0.10
111 12 0.05
113 11 0.04
114 70 0.28
115 5 0.02
116 6 0.02
117 8 0.03
118 19 0.08
119 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (110 bp):
ATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTTTTAATTTTTTTCGTAT
ATTTATATCTGACTCTGACAAAAAAAAAGAAATTTTTTTTTAAAA
Found at i:53145710 original size:8 final size:8
Alignment explanation
Indices: 53145690--53145735 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
53145680 TCAGACTCAA
53145690 AAAAAAAT
1 AAAAAAAT
*
53145698 -CAAAAAT
1 AAAAAAAT
53145705 AAAAAAAT
1 AAAAAAAT
*
53145713 CAAAAAAT
1 AAAAAAAT
*
53145721 -CAAAAAT
1 AAAAAAAT
53145728 AAAAAAAT
1 AAAAAAAT
53145736 CAAAGAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
7 12 0.39
8 19 0.61
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAAAAT
Found at i:53145721 original size:23 final size:23
Alignment explanation
Indices: 53145691--53145739 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
53145681 CAGACTCAAA
53145691 AAAAAATCAAAAATAAAAAAATC
1 AAAAAATCAAAAATAAAAAAATC
53145714 AAAAAATCAAAAATAAAAAAATC
1 AAAAAATCAAAAATAAAAAAATC
53145737 AAA
1 AAA
53145740 GAAAAATAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (23 bp):
AAAAAATCAAAAATAAAAAAATC
Found at i:53145725 original size:15 final size:15
Alignment explanation
Indices: 53145692--53145739 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
53145682 AGACTCAAAA
*
53145692 AAAAATC-AAAAATAA
1 AAAAATCAAAAAAT-C
53145707 AAAAATCAAAAAATC
1 AAAAATCAAAAAATC
*
53145722 AAAAATAAAAAAATC
1 AAAAATCAAAAAATC
53145737 AAA
1 AAA
53145740 GAAAAATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 24 0.80
16 6 0.20
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAATCAAAAAATC
Found at i:53145775 original size:6 final size:6
Alignment explanation
Indices: 53145750--53145787 Score: 58
Period size: 6 Copynumber: 6.0 Consensus size: 6
53145740 GAAAAATAGG
53145750 AGAAAA AGAAAGA AGAAAAA AGAAAA AGAAAA AGAAAA
1 AGAAAA AGAAA-A AG-AAAA AGAAAA AGAAAA AGAAAA
53145788 GGAGAGGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 21 0.70
7 6 0.20
8 3 0.10
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:53146613 original size:9 final size:9
Alignment explanation
Indices: 53146599--53146629 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
53146589 TGAGTCAAAC
53146599 AAAAAATGA
1 AAAAAATGA
53146608 AAAAAATG-
1 AAAAAATGA
53146616 AAAAAATGA
1 AAAAAATGA
53146625 AAAAA
1 AAAAA
53146630 TAAAAATGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAAAATGA
Found at i:53146619 original size:7 final size:8
Alignment explanation
Indices: 53146599--53146635 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
53146589 TGAGTCAAAC
53146599 AAAAAATG
1 AAAAAATG
53146607 AAAAAAATG
1 -AAAAAATG
53146616 AAAAAATG
1 AAAAAATG
53146624 AAAAAAT-
1 AAAAAATG
53146631 AAAAA
1 AAAAA
53146636 TGGAGAGGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 5 0.18
8 15 0.54
9 8 0.29
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:53148086 original size:44 final size:44
Alignment explanation
Indices: 53147853--53148317 Score: 293
Period size: 44 Copynumber: 10.8 Consensus size: 44
53147843 AGAATTTCAG
* * * *
53147853 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT-
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGTA
* * *
53147896 ATCCTATCTCCCTGAGA-TACAGTGGAGCGGATT-AA---AG-G
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGTA
* * * * *
53147934 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCA-CCA--A
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCCAGTA
* * * * * ** * *
53147975 GTCTTATTTCTCTGAGATTACAGTGGAACAAACCGAAG-AATTGCA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCA--GTA
* *
53148020 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTA
1 -ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGTA
* * * * *
53148065 ATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAACCAAG-G
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCC-AGTA
* * * * *
53148109 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCA-CCAG--
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCCAGTA
* * * * * *
53148150 GTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAG-AATTTCA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCA-GT-A
* * *
53148195 GATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCCGGTA
1 -ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGTA
* * *
53148240 ATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCCGGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGTA
*
53148284 ATCCTATCTCCCTGAGATTACAGTGGAGCAGATT
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATT
53148318 AAAATAATGG
Statistics
Matches: 327, Mismatches: 71, Indels: 47
0.73 0.16 0.11
Matches are distributed among these distances:
37 1 0.00
38 14 0.04
39 12 0.04
40 1 0.00
41 57 0.17
42 18 0.06
43 19 0.06
44 135 0.41
45 6 0.02
46 63 0.19
47 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGTA
Found at i:53148218 original size:87 final size:87
Alignment explanation
Indices: 53147933--53148228 Score: 273
Period size: 87 Copynumber: 3.4 Consensus size: 87
53147923 CGGATTAAAG
* * * *
53147933 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAAGTCTTATTTCTCTGAGATTACAG
1 GATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCGCACCAGGTCTTATTTCCCTGAGATTACAG
* * *
53147998 TGGAACAAACCGAAGAATTGCA
66 TGGAACAGACTGAAGAATTCCA
* * * * * * * *
53148020 GATCTTATCTCCCTG-AGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGA-AGT
1 GATCTTATCTCCCTGAAG-TTACAGCAGAGTAGATCGCA-CCAG--GTCTTATTTCCCTGAGA-T
* * *
53148083 TACAGTGGAGCGGA-TTAA-AA--CCAA
61 TACAGTGGAACAGACTGAAGAATTCC-A
* *
53148107 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGGTCTTATTTCCCTGAGATTACA
1 -GATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCGCACCAGGTCTTATTTCCCTGAGATTACA
*
53148172 GTGGAACAGACTGAAGAATTTCA
65 GTGGAACAGACTGAAGAATTCCA
*
53148195 GATCTTATCTCCCTG-AGATTACAGCGGAGTAGAT
1 GATCTTATCTCCCTGAAG-TTACAGCAGAGTAGAT
53148229 TGAAGCCGGT
Statistics
Matches: 160, Mismatches: 35, Indels: 28
0.72 0.16 0.13
Matches are distributed among these distances:
85 25 0.16
86 9 0.06
87 63 0.39
88 34 0.21
89 6 0.04
90 23 0.14
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (87 bp):
GATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCGCACCAGGTCTTATTTCCCTGAGATTACAG
TGGAACAGACTGAAGAATTCCA
Found at i:53148307 original size:175 final size:172
Alignment explanation
Indices: 53147804--53148316 Score: 759
Period size: 175 Copynumber: 3.0 Consensus size: 172
53147794 GTTCATTATA
*
53147804 CAGGTCTTATTTCCCTGAGATTATAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
* * *
53147869 ATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTGAGA-TACAGTGGAGCGGATTAAA
66 ATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAA
53147932 --GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
131 CCGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
* * * *
53147972 CAAGTCTTATTTCTCTGAGATTACAGTGGAACAAACCGAAGAATTGCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
*
53148037 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAA
66 ATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATCTCCCTGAGA-TTACAGTGGAGCGGATT-A
53148101 AACCAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
129 AACC--GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
*
53148147 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
* * *
53148212 ATTACAGCGGAGTAGATTGAAGCCGGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
66 ATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAA
* * * *
53148277 GCCGGTAATCCTATCTCCCTG-AGATTACAGTGGAGCAGAT
131 -CCGG--ATCTTATCTCTCTGAAG-TTACAGTAGAGTAGAT
53148317 TAAAATAATG
Statistics
Matches: 310, Mismatches: 22, Indels: 19
0.88 0.06 0.05
Matches are distributed among these distances:
168 84 0.27
169 15 0.05
170 16 0.05
171 3 0.01
173 2 0.01
174 5 0.02
175 184 0.59
176 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (172 bp):
CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
ATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAA
CCGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
Found at i:53148336 original size:44 final size:43
Alignment explanation
Indices: 53147852--53148402 Score: 208
Period size: 44 Copynumber: 12.8 Consensus size: 43
53147842 AAGAATTTCA
* * * * *
53147852 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA-CAC
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGAT-TAAAATAAG
* * *
53147895 TATCCTATCTCCCTGAGA-TACAGTGGAGCGGATT---A-AAG
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAG
* * * *** **
53147933 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCACCAA-
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATAAG
* * * * ** *
53147975 G-TCTTATTTCTCTGAGATTACAGTGGAACAAACCGAAGAAT-TG
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-AATAAG
* **
53148018 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT-AG
1 --GATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATAAG
* * * *
53148063 TAATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAACCAAG
1 -GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAA-TAAG
* * * *** **
53148108 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGA-TCGCACCAG
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATAAG
* * * *
53148150 G-TCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCA-
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-AA--TAAG
* * * ***
53148195 GATCTTATCTCCCTGAGATTACAGCGGAGTAGATT-GAAGCCG
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAG
* ***
53148237 GTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAGCCG
1 G--ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAG
*
53148281 GTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAATG
1 G--ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAA-G
* ** * *** *
53148327 GATCTTATCTCTCTGA-AGTTACAGCAGAGTAGA-TCGCATCAG
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATAAG
*
53148369 G-TCTTATCTCCCTGAGATTACAGCGGAGCAGATT
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATT
53148403 GAAGACACAA
Statistics
Matches: 384, Mismatches: 92, Indels: 65
0.71 0.17 0.12
Matches are distributed among these distances:
37 1 0.00
38 15 0.04
39 12 0.03
41 75 0.20
42 25 0.07
43 31 0.08
44 156 0.41
45 10 0.03
46 59 0.15
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (43 bp):
GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAG
Found at i:53149197 original size:88 final size:88
Alignment explanation
Indices: 53148388--53149183 Score: 1234
Period size: 88 Copynumber: 9.0 Consensus size: 88
53148378 CCCTGAGATT
* * *
53148388 ACAGCGGAGCAGATTGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACA
1 ACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACA
53148453 AAAGATCTTGCCTTCCTGCATTG
66 AAAGATCTTGCCTTCCTGCATTG
* *
53148476 ACAGTGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGACGGAGCTGGTTGAAGACA
1 ACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACA
*
53148541 AAAGATCTTGCCTTCCTGTATTG
66 AAAGATCTTGCCTTCCTGCATTG
* * *
53148564 ACAGCGAAGTAGGTCGAAGACACAAACCTTGCCTCCCTCGGTTGTGATGGATCTGGTTGAAGACA
1 ACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACA
* *
53148629 ACAGATCTTGCCTTCTTGCATTG
66 AAAGATCTTGCCTTCCTGCATTG
* * *
53148652 ACAGTGAAACAGGTCGAAAACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACA
1 ACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACA
53148717 AAAGATCTTGCCTTCCTGCATTG
66 AAAGATCTTGCCTTCCTGCATTG
* * * *
53148740 ACAGCGAAGTAAGTCGAAGACACAAACCTTGCCACTCTCGGTTGTGATGGAGCTGGTCGAAGACA
1 ACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACA
53148805 AAAGATCTTGCCTTCCTGCATTG
66 AAAGATCTTGCCTTCCTGCATTG
* * * * *
53148828 ATAGCGAAGCAGGTCAAAGACACAAACCTTGTCTCTCTCAGTTGT-AGCGGAGCTGGTTGAAGAC
1 ACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGA-TGGAGCTGGTTGAAGAC
53148892 AAAAGATCTTGCCTTCCTGCATTG
65 AAAAGATCTTGCCTTCCTGCATTG
53148916 ACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACA
1 ACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACA
53148981 AAAGATCTTGCCTTCCTGCATTG
66 AAAGATCTTGCCTTCCTGCATTG
*
53149004 ACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCCCTCGGTTGTGATGGAGCTGGTTGAAGACA
1 ACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACA
* *
53149069 ACAGATCTTGCCTTCTTGCATTG
66 AAAGATCTTGCCTTCCTGCATTG
* * * * * *
53149092 ACAGCGAAACAGGTCAAAAACACAAACCTTACCTCTCTCGGTTGTGGTGAAGCTGGTTGAAGACA
1 ACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACA
** * * * *
53149157 GTAGATATTGCCCTCCTGTATCG
66 AAAGATCTTGCCTTCCTGCATTG
53149180 ACAG
1 ACAG
53149184 TGGGGCAGAT
Statistics
Matches: 646, Mismatches: 60, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
87 1 0.00
88 644 1.00
89 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.24
Consensus pattern (88 bp):
ACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACA
AAAGATCTTGCCTTCCTGCATTG
Found at i:53149439 original size:96 final size:96
Alignment explanation
Indices: 53149199--53149480 Score: 476
Period size: 96 Copynumber: 2.9 Consensus size: 96
53149189 CAGATCAAAT
* * *
53149199 ATGGAAAATTTTACCTCCCTGTGACTACAGTAGAGTACATTGAAGCCAATAATTCTATCTCCTTG
1 ATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTACATTGAAGCCGATAATTCTATCTCCCTG
*
53149264 GTTGGCAGTGGAATGGATTGAA-AATCGAAG
66 GTTGGCAGTGGAATAGATTGAAGAATCGAAG
53149294 ATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTACATTGAAGCCGATAATTCTATCTCCCTG
1 ATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTACATTGAAGCCGATAATTCTATCTCCCTG
* *
53149359 GTTGTCAGCGGAATAGATTGAAGAATCGAAG
66 GTTGGCAGTGGAATAGATTGAAGAATCGAAG
* * *
53149390 ATGGCAGATTTTACCTTCCTGTGACTACAGTAGAGTACATTGAATCCGATAATTCTATCTCCCTG
1 ATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTACATTGAAGCCGATAATTCTATCTCCCTG
53149455 GTTGGCAGTGGAATAGATTGAAGAAT
66 GTTGGCAGTGGAATAGATTGAAGAAT
53149481 TTCAGATCTT
Statistics
Matches: 175, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
95 81 0.46
96 94 0.54
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (96 bp):
ATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTACATTGAAGCCGATAATTCTATCTCCCTG
GTTGGCAGTGGAATAGATTGAAGAATCGAAG
Found at i:53149551 original size:44 final size:44
Alignment explanation
Indices: 53149490--53149645 Score: 147
Period size: 44 Copynumber: 3.5 Consensus size: 44
53149480 TTTCAGATCT
53149490 TATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCC
1 TATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCC
* * * ** ** * *
53149534 TATCTCTCTGA-AGTTACAGTGAAGCGGATT-AAAATAAAG-GATCT
1 TATCTCCCTGAGA-TTACAGCGGAGTAGATTGAAGCT--AGTAATCC
*
53149578 TATCTCCCTGAGATTACAGCAGAGTAGATTGAAGCTAGTAATCC
1 TATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCC
* * *
53149622 TATCTCTCTGAAATTACAGTGGAG
1 TATCTCCCTGAGATTACAGCGGAG
53149646 CGGATTAAAA
Statistics
Matches: 83, Mismatches: 23, Indels: 12
0.70 0.19 0.10
Matches are distributed among these distances:
43 6 0.07
44 71 0.86
45 6 0.07
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCC
Found at i:53149595 original size:88 final size:88
Alignment explanation
Indices: 53149485--53149694 Score: 350
Period size: 88 Copynumber: 2.4 Consensus size: 88
53149475 AAGAATTTCA
* *
53149485 GATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCTCTGAAGTTA
1 GATCTTATCTCCCTGAGATTACAGCAGAGTAGATTGAAGCTAGTAATCCTATCTCTCTGAAATTA
53149550 CAGTGAAGCGGATTAAAATAAAG
66 CAGTGAAGCGGATTAAAATAAAG
53149573 GATCTTATCTCCCTGAGATTACAGCAGAGTAGATTGAAGCTAGTAATCCTATCTCTCTGAAATTA
1 GATCTTATCTCCCTGAGATTACAGCAGAGTAGATTGAAGCTAGTAATCCTATCTCTCTGAAATTA
*
53149638 CAGTGGAGCGGATTAAAATAAAG
66 CAGTGAAGCGGATTAAAATAAAG
* * *
53149661 GATCTTATCTCTCT-AAAGTTACAGTAGAGTAGAT
1 GATCTTATCTCCCTGAGA-TTACAGCAGAGTAGAT
53149695 CACATCAGAT
Statistics
Matches: 115, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
87 2 0.02
88 113 0.98
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (88 bp):
GATCTTATCTCCCTGAGATTACAGCAGAGTAGATTGAAGCTAGTAATCCTATCTCTCTGAAATTA
CAGTGAAGCGGATTAAAATAAAG
Found at i:53149670 original size:44 final size:44
Alignment explanation
Indices: 53149534--53149685 Score: 148
Period size: 44 Copynumber: 3.5 Consensus size: 44
53149524 CTAGTAATCC
* *
53149534 TATCTCTCTGAAGTTACAGTGAAGCGGATTAAAATAAAGGATCT
1 TATCTCTCTGAAATTACAGTGGAGCGGATTAAAATAAAGGATCT
* * ** ** ** * *
53149578 TATCTCCCTGAGATTACAGCAGAGTAGATTGAAGCT--AGTAATCC
1 TATCTCTCTGAAATTACAGTGGAGCGGATT-AAAATAAAG-GATCT
53149622 TATCTCTCTGAAATTACAGTGGAGCGGATTAAAATAAAGGATCT
1 TATCTCTCTGAAATTACAGTGGAGCGGATTAAAATAAAGGATCT
53149666 TATCTCTCT-AAAGTTACAGT
1 TATCTCTCTGAAA-TTACAGT
53149686 AGAGTAGATC
Statistics
Matches: 81, Mismatches: 22, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
43 8 0.10
44 68 0.84
45 5 0.06
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (44 bp):
TATCTCTCTGAAATTACAGTGGAGCGGATTAAAATAAAGGATCT
Found at i:53149812 original size:44 final size:44
Alignment explanation
Indices: 53149700--53149826 Score: 123
Period size: 44 Copynumber: 2.9 Consensus size: 44
53149690 TAGATCACAT
* * **
53149700 CAGATTGAAGCCAGAGATCTTATCTCCCT-GAGATTACAATGGAG
1 CAGATTAAAGCCACAGATCTTATCTCCCTGGAG-TTACAGCGGAG
* * * *
53149744 TAGATTAAAGCTAGTA-ATCCTATCTCCCTGGAGTTACAGCGGAG
1 CAGATTAAAGCCA-CAGATCTTATCTCCCTGGAGTTACAGCGGAG
* * *
53149788 CAGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAG
1 CAGATTAAAGCCACAGATCTTATCTCCCTGGAGTTACAG
53149827 TAGAGTGGAT
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
43 1 0.02
44 61 0.92
45 4 0.06
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (44 bp):
CAGATTAAAGCCACAGATCTTATCTCCCTGGAGTTACAGCGGAG
Found at i:53149844 original size:142 final size:142
Alignment explanation
Indices: 53149573--53149837 Score: 397
Period size: 142 Copynumber: 1.9 Consensus size: 142
53149563 TAAAATAAAG
* * *
53149573 GATCTTATCTCCCTGAGATTACAGCAGAGTAGATTGAAGCTAGTAATCCTATCTCTCTGAAATTA
1 GATCTTATCTCCCTGAGATTACAACAGAGTAGATTAAAGCTAGTAATCCTATCTCCCTGAAATTA
* * *
53149638 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCACATCAG
66 CAGCGGAGCAGATTAAAACAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCACATCAG
53149703 ATTGAAGCCAGA
131 ATTGAAGCCAGA
** * *
53149715 GATCTTATCTCCCTGAGATTACAATGGAGTAGATTAAAGCTAGTAATCCTATCTCCCTGGAGTTA
1 GATCTTATCTCCCTGAGATTACAACAGAGTAGATTAAAGCTAGTAATCCTATCTCCCTGAAATTA
* * *
53149780 CAGCGGAGCAGATTAAAACCACA-GATCTTATCTCTCTGAAGTTACAGTAGAGTGGATC
66 CAGCGGAGCAGATTAAAA-CAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATC
53149838 GTATCAGGTC
Statistics
Matches: 109, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
142 107 0.98
143 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (142 bp):
GATCTTATCTCCCTGAGATTACAACAGAGTAGATTAAAGCTAGTAATCCTATCTCCCTGAAATTA
CAGCGGAGCAGATTAAAACAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCACATCAG
ATTGAAGCCAGA
Found at i:53151241 original size:3 final size:3
Alignment explanation
Indices: 53151233--53151263 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
53151223 GATTTAGTCC
53151233 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
53151264 TTCATTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:53151906 original size:108 final size:108
Alignment explanation
Indices: 53151710--53152231 Score: 650
Period size: 108 Copynumber: 4.8 Consensus size: 108
53151700 TCAAAAAAGG
53151710 AAAATATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
1 AAAAT-TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
* *
53151775 GGTTTCGATTTCTCGTTCGACCAAAT-GACTTAATATCCTTTTCA
65 GGTTTCGATTTCTCGTTCAACCAAATAG-CTAAATATCCTTTTCA
* *
53151819 AAAATTTTCAAAATAAAGCAATATTTTGTGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
1 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
53151884 GTTTCGATTTCTCGTTCAACCAAATAGCTAAATATCCTTTT-A
66 GTTTCGATTTCTCGTTCAACCAAATAGCTAAATATCCTTTTCA
* * ** ** * ** *
53151926 AAAACGTTTCAAAA-ATGGCTTTCA-GATGATGTATCT-CCACTT--AGGAACGTGCCCTAAGGT
1 AAAA-TTTTCAAAATAAGGCAAT-ATTTTG-CGT-T-TGGAAATTCGAGGAACGTGCCCTAAGGT
* *
53151986 ACTGGGTTTCGATTTCTCGTTCGACCAAAT-GACTTAATATCCTTTTCA
61 ACTGGGTTTCGATTTCTCGTTCAACCAAATAG-CTAAATATCCTTTTCA
* * *
53152034 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTG
1 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTACTG
*
53152099 GGTGTCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTCA
65 GGTTTCGA--TTTCTCGTTCAACCAAATAGCTAAATATCCTTTTCA
* * * *
53152145 AAAA-TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAGGAACGTGCTCTAAGGTGCTGG
1 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
53152209 GTTTCGATTTCTCG-TCTAACCAA
66 GTTTCGATTTCTCGTTC-AACCAA
53152232 CTTGACAAAT
Statistics
Matches: 357, Mismatches: 38, Indels: 38
0.82 0.09 0.09
Matches are distributed among these distances:
105 1 0.00
106 7 0.02
107 94 0.26
108 121 0.34
109 58 0.16
110 39 0.11
111 36 0.10
112 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (108 bp):
AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
GTTTCGATTTCTCGTTCAACCAAATAGCTAAATATCCTTTTCA
Found at i:53153683 original size:10 final size:10
Alignment explanation
Indices: 53153658--53153691 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
53153648 ACTTTGTTTC
53153658 TTCTTTTTCCTT
1 TTCTTTTT--TT
53153670 TTCTTTTTTT
1 TTCTTTTTTT
53153680 TTCTTTTTTT
1 TTCTTTTTTT
53153690 TT
1 TT
53153692 TTGGCAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.64
12 8 0.36
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:53153691 original size:15 final size:15
Alignment explanation
Indices: 53153654--53153693 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
53153644 TACTACTTTG
*
53153654 TTTCTTCTTTTTCCT
1 TTTCTTTTTTTTCCT
*
53153669 TTTCTTTTTTTTTCT
1 TTTCTTTTTTTTCCT
53153684 TTT-TTTTTTT
1 TTTCTTTTTTT
53153694 GGCAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTCTTTTTTTTCCT
Found at i:53157710 original size:13 final size:13
Alignment explanation
Indices: 53157692--53157716 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53157682 AATCTTCCCC
53157692 ATTTTTTTTTAAA
1 ATTTTTTTTTAAA
53157705 ATTTTTTTTTAA
1 ATTTTTTTTTAA
53157717 GCTTAAGATA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTTTTTAAA
Found at i:53160318 original size:27 final size:27
Alignment explanation
Indices: 53160254--53160329 Score: 116
Period size: 27 Copynumber: 2.8 Consensus size: 27
53160244 AAAAGATTTT
* *
53160254 CTTTCATATTACACCACAAAGGTGTTC
1 CTTTCATATTGCGCCACAAAGGTGTTC
53160281 CTTTCATATTGCGCCACAAAGGTGTTC
1 CTTTCATATTGCGCCACAAAGGTGTTC
* *
53160308 CTTTCATATTGTGCCATAAAGG
1 CTTTCATATTGCGCCACAAAGG
53160330 CATTCATTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (27 bp):
CTTTCATATTGCGCCACAAAGGTGTTC
Found at i:53162776 original size:13 final size:13
Alignment explanation
Indices: 53162737--53162789 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
53162727 AGTTTAGCAA
53162737 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
53162750 TG-TTATGGAAAAG
1 TGCTT-TTGAAAAG
*
53162763 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
53162776 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
53162789 T
1 T
53162790 TTGGTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 2 0.06
13 30 0.88
14 2 0.06
ACGTcount: A:0.30, C:0.06, G:0.26, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:53179137 original size:6 final size:7
Alignment explanation
Indices: 53179120--53179146 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
53179110 CAAGGTTGGT
53179120 TTTTTTA
1 TTTTTTA
53179127 TTTTTTA
1 TTTTTTA
53179134 TTTTTTA
1 TTTTTTA
53179141 TTTTTT
1 TTTTTT
53179147 TATAGGTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:53187874 original size:6 final size:7
Alignment explanation
Indices: 53187857--53187883 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
53187847 CAAGGTTGGT
53187857 TTTTTTA
1 TTTTTTA
53187864 TTTTTTA
1 TTTTTTA
53187871 TTTTTTA
1 TTTTTTA
53187878 TTTTTT
1 TTTTTT
53187884 TATAGGTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:53201706 original size:36 final size:36
Alignment explanation
Indices: 53201633--53201710 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
53201623 ACATTTCTCA
* **
53201633 CTTTTTCTCACTCACTTTCTTCTTTTTATTTTGCTT
1 CTTTTTCTAACTCACTTTCTTCTTTCAATTTTGCTT
* *
53201669 CTTTTTCTAACTCATTTTCTT-TTTCAATTTTCTCTT
1 CTTTTTCTAACTCACTTTCTTCTTTCAATTTT-GCTT
53201705 CTTTTT
1 CTTTTT
53201711 AACATTTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
35 8 0.22
36 28 0.78
ACGTcount: A:0.10, C:0.23, G:0.01, T:0.65
Consensus pattern (36 bp):
CTTTTTCTAACTCACTTTCTTCTTTCAATTTTGCTT
Found at i:53201840 original size:27 final size:26
Alignment explanation
Indices: 53201799--53201865 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
53201789 GTATCCGCTT
53201799 ATTTTCTCTTATTATCATCTCTTGTCTCTC
1 ATTTTCT-TT-TTAT-ATCT-TTGTCTCTC
* *
53201829 -TTTTCTTTTTATTTCTTTTTCTCTC
1 ATTTTCTTTTTATATCTTTGTCTCTC
*
53201854 ATTTTCTCTTTA
1 ATTTTCTTTTTA
53201866 GAAGATGAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 8 0.24
26 13 0.39
27 4 0.12
28 2 0.06
29 6 0.18
ACGTcount: A:0.10, C:0.22, G:0.01, T:0.66
Consensus pattern (26 bp):
ATTTTCTTTTTATATCTTTGTCTCTC
Found at i:53204326 original size:9 final size:9
Alignment explanation
Indices: 53204312--53204337 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
53204302 TAAAAACACA
53204312 AACTAAAAT
1 AACTAAAAT
53204321 AACTAAAAT
1 AACTAAAAT
53204330 AACTAAAA
1 AACTAAAA
53204338 ATTAATGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (9 bp):
AACTAAAAT
Found at i:53212872 original size:24 final size:25
Alignment explanation
Indices: 53212819--53212877 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
53212809 TCAACTTGAG
**
53212819 AGAGCTTACCGATATTCAGCTTGTA
1 AGAGCTTACCGATATTCAGCTCATA
*
53212844 TGAGCTTACCG-T-TTACAGCTCATA
1 AGAGCTTACCGATATT-CAGCTCATA
*
53212868 AGAGCATACC
1 AGAGCTTACC
53212878 AATTTAGAGC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 2 0.07
24 16 0.57
25 10 0.36
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (25 bp):
AGAGCTTACCGATATTCAGCTCATA
Found at i:53213101 original size:16 final size:17
Alignment explanation
Indices: 53213064--53213108 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
53213054 TAAATGATTT
*
53213064 TACATG-ATAT-ATTGA
1 TACATGAATATGAATGA
*
53213079 TATATGAA-ATGAATGA
1 TACATGAATATGAATGA
53213095 TACATGAATATGAA
1 TACATGAATATGAA
53213109 ATGAATGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 7 0.29
16 12 0.50
17 5 0.21
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (17 bp):
TACATGAATATGAATGA
Found at i:53218389 original size:13 final size:13
Alignment explanation
Indices: 53218358--53218391 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
53218348 TTCTCGATAG
*
53218358 GGGAAATCGACAA
1 GGGAAATGGACAA
53218371 -GGAAATGGACAA
1 GGGAAATGGACAA
53218383 GGGAAATGG
1 GGGAAATGG
53218392 GAAAACAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.38, T:0.09
Consensus pattern (13 bp):
GGGAAATGGACAA
Found at i:53225611 original size:19 final size:19
Alignment explanation
Indices: 53225587--53225628 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
53225577 ATGGCTCAGC
*
53225587 AAACACTGCTAGAAGCGCA
1 AAACACTGCTAAAAGCGCA
53225606 AAACACTGCTAAAAGCGCA
1 AAACACTGCTAAAAGCGCA
53225625 AAAC
1 AAAC
53225629 CGAGAATTAT
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:0.48, C:0.26, G:0.17, T:0.10
Consensus pattern (19 bp):
AAACACTGCTAAAAGCGCA
Found at i:53225753 original size:14 final size:14
Alignment explanation
Indices: 53225734--53225760 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53225724 GTGGTCCAGT
53225734 TGAACTGAACCGAG
1 TGAACTGAACCGAG
53225748 TGAACTGAACCGA
1 TGAACTGAACCGA
53225761 CCAAGAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:53233726 original size:69 final size:69
Alignment explanation
Indices: 53233541--53233717 Score: 196
Period size: 69 Copynumber: 2.6 Consensus size: 69
53233531 GCGTCACAGT
* * * *
53233541 GGACTCTACTCGTTGCCATAGTTGAGCTATGGTCTTACACCTTATATTCCCAGTGTTTATTGTCC
1 GGACTCTAATGGTTGTCATAGCTGAGCTATGGTCTTACACCTTATATTCCCAGTGTTTATTGTCC
53233606 CAAC
66 CAAC
** * * * *
53233610 AAACTC-AATTGGTTTTCTTAGCTGAGCTAAT-TTCTTACACCTTATATTCCCTGTGTTTATTGT
1 GGACTCTAA-TGGTTGTCATAGCTGAGCT-ATGGTCTTACACCTTATATTCCCAGTGTTTATTGT
***
53233673 CCCGGG
64 CCCAAC
*
53233679 GGACTCTAATGGTTGTCATAGCCGAGCTATGGTCTTACA
1 GGACTCTAATGGTTGTCATAGCTGAGCTATGGTCTTACA
53233718 ATCTATATTT
Statistics
Matches: 85, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
68 3 0.04
69 78 0.92
70 4 0.05
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (69 bp):
GGACTCTAATGGTTGTCATAGCTGAGCTATGGTCTTACACCTTATATTCCCAGTGTTTATTGTCC
CAAC
Found at i:53236474 original size:35 final size:35
Alignment explanation
Indices: 53236424--53236513 Score: 126
Period size: 35 Copynumber: 2.6 Consensus size: 35
53236414 TTTAACATAG
* *
53236424 TGGCATGCTTTACATGTGAATCAGAATCAGTATAC
1 TGGCATGCTTAACATGTGAATCAAAATCAGTATAC
* * *
53236459 TGGCATGCTTAACATGCGAATCAAAATTAGTATAG
1 TGGCATGCTTAACATGTGAATCAAAATCAGTATAC
*
53236494 TAGCATGCTTAACATGTGAA
1 TGGCATGCTTAACATGTGAA
53236514 ATTGATTATC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (35 bp):
TGGCATGCTTAACATGTGAATCAAAATCAGTATAC
Done.