Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397264.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_130.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8132550
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 35170 characters in sequence are not A, C, G, or T
File 9 of 14
Found at i:4424200 original size:31 final size:30
Alignment explanation
Indices: 4424148--4424239 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 30
4424138 AAAATATAAT
* *
4424148 ATTAATTTTAAAATTATTTTTATTTATTAAA
1 ATTAAATTTAATA-TATTTTTATTTATTAAA
* **
4424179 ATATAAATTTAATATATTTTTATTTTTTATT
1 AT-TAAATTTAATATATTTTTATTTATTAAA
* * * *
4424210 ATTAATTTTTATATAATATTATTTATTAAA
1 ATTAAATTTAATATATTTTTATTTATTAAA
4424240 TACATTTTTA
Statistics
Matches: 48, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
30 21 0.44
31 18 0.38
32 9 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
ATTAAATTTAATATATTTTTATTTATTAAA
Found at i:4424286 original size:13 final size:13
Alignment explanation
Indices: 4424200--4424318 Score: 59
Period size: 13 Copynumber: 8.7 Consensus size: 13
4424190 ATATATTTTT
4424200 ATTTTTTATTATTA
1 ATTTTTTATTA-TA
4424214 A-TTTTTA-TATA
1 ATTTTTTATTATA
4424225 ATATTATTTATTA-A
1 AT-TT-TTTATTATA
* *
4424239 ATACATTTTTAATGTA
1 AT---TTTTTATTATA
*
4424255 ATGTATTTTACTT-TC
1 AT-T-TTTTA-TTATA
4424270 ATTTTTTATTATA
1 ATTTTTTATTATA
*
4424283 ATTTTATATATT-TT
1 ATTTT-T-TATTATA
*
4424297 ATTTTTTAATATA
1 ATTTTTTATTATA
4424310 ATTTTTTAT
1 ATTTTTTAT
4424319 ATTATATATT
Statistics
Matches: 82, Mismatches: 10, Indels: 27
0.69 0.08 0.23
Matches are distributed among these distances:
11 3 0.04
12 7 0.09
13 29 0.35
14 17 0.21
15 19 0.23
16 7 0.09
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.64
Consensus pattern (13 bp):
ATTTTTTATTATA
Found at i:4424300 original size:27 final size:27
Alignment explanation
Indices: 4424270--4424340 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
4424260 TTTTACTTTC
*
4424270 ATTTTTTATTATAATTTTATATATTTT
1 ATTTTTTATTATAATTTTATATATTAT
* *
4424297 ATTTTTTAATATAATTTTTTATATTAT
1 ATTTTTTATTATAATTTTATATATTAT
* * *
4424324 ATATTATATTTTAATTT
1 ATTTTTTATTATAATTT
4424341 CTTTTACTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (27 bp):
ATTTTTTATTATAATTTTATATATTAT
Found at i:4424302 original size:15 final size:15
Alignment explanation
Indices: 4424284--4424415 Score: 65
Period size: 16 Copynumber: 8.2 Consensus size: 15
4424274 TTTATTATAA
4424284 TTTTATATATTTTATT
1 TTTTATATATTTTA-T
4424300 TTTTAATATAATTTT-T
1 TTTT-ATAT-ATTTTAT
*
4424316 TATATTATATATTATAT
1 T-T-TTATATATTTTAT
* * *
4424333 TTTAATTTCTTTTACT
1 TTTTATATATTTTA-T
4424349 TATATTATATAAATTTTAATT
1 T-T-TTATAT--ATTTT-A-T
*
4424370 TTTTATATTTTTTAAT
1 TTTTATATATTTT-AT
4424386 TTTTA-AT-TTTT-T
1 TTTTATATATTTTAT
*
4424398 TATTATATATTTTAT
1 TTTTATATATTTTAT
4424413 TTT
1 TTT
4424416 AATTACAACA
Statistics
Matches: 90, Mismatches: 12, Indels: 29
0.69 0.09 0.22
Matches are distributed among these distances:
12 5 0.06
13 2 0.02
14 8 0.09
15 13 0.14
16 19 0.21
17 18 0.20
18 11 0.12
19 6 0.07
20 5 0.06
21 3 0.03
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTATATATTTTAT
Found at i:4424372 original size:7 final size:8
Alignment explanation
Indices: 4424362--4424397 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
4424352 ATTATATAAA
4424362 TTTTAATT
1 TTTTAATT
4424370 TTTTATATT
1 TTTTA-ATT
4424379 TTTTAA-T
1 TTTTAATT
4424386 TTTTAATT
1 TTTTAATT
4424394 TTTT
1 TTTT
4424398 TATTATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 7 0.27
8 11 0.42
9 8 0.31
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTAATT
Found at i:4424375 original size:24 final size:24
Alignment explanation
Indices: 4424348--4424406 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
4424338 TTTCTTTTAC
4424348 TTATATTATATAAATTTTAATTTT
1 TTATATTATATAAATTTTAATTTT
* * *
4424372 TTATATTTTTTAATTTTTAATTTT
1 TTATATTATATAAATTTTAATTTT
4424396 TT-TATTATATA
1 TTATATTATATA
4424407 TTTTATTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 7 0.23
24 23 0.77
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
TTATATTATATAAATTTTAATTTT
Found at i:4436463 original size:45 final size:45
Alignment explanation
Indices: 4436399--4436489 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
4436389 TAATATTAGC
* *
4436399 GAAGACGAAAGCAAGCTACATCATGAAAAT-CCTGCAGACAAGCAG
1 GAAGAAGAAAACAAGCTACATCATGAAAATACC-GCAGACAAGCAG
4436444 GAAGAAGAAAACAAGCTACATCATGAAAATACCGCAGACAAGCAG
1 GAAGAAGAAAACAAGCTACATCATGAAAATACCGCAGACAAGCAG
4436489 G
1 G
4436490 TACACAACCA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 41 0.95
46 2 0.05
ACGTcount: A:0.47, C:0.21, G:0.22, T:0.10
Consensus pattern (45 bp):
GAAGAAGAAAACAAGCTACATCATGAAAATACCGCAGACAAGCAG
Found at i:4440390 original size:227 final size:217
Alignment explanation
Indices: 4439992--4440443 Score: 618
Period size: 227 Copynumber: 2.0 Consensus size: 217
4439982 CAGGAAACTT
4439992 AGTTGAGAGCATCAAGTTTCACAGCAACATAAGACAACAATTACTNNNNNNNNNNTAACTACACA
1 AGTTGAGAGCATCAAGTTTCACAGCAACATAAGACAACAATTACT----------TAACTACACA
* *
4440057 TGTTGAAAATGTGAGTAGCAAAGCCCTTGTAATGTGTAACAGAAACAAAAAGATTGAGCTCCAGA
56 TGTTGAAAATGTGAATAGCAAAGCCCTTGTAATGTGTAACAGAAACAAAAAGATTCAGCTCCAGA
* * *
4440122 GAAACACGTATCCATTCAATGCTGTGGCGCAAAGCCTCTTAAGATATCAGGCAGAAAATTTGATA
121 GAAACACATATCCATTCAATGCTGTGGAGCAAAGACTCTTAAGATATCAGGCAGAAAATTTGATA
4440187 TGCCAACAGACATGCCAAAAAGTTCAGAGATG
186 TGCCAACAGACATGCCAAAAAGTTCAGAGATG
* *
4440219 AGTTGAGAGTATCAAGTTTCGCAGCAACATAAGACAACAATTACTNNNNNNNNNNTAACTACACA
1 AGTTGAGAGCATCAAGTTTCACAGCAACATAAGACAACAATTACT----------TAACTACACA
4440284 TGTTGAAAATGTGAATAGCAAAGCCCTTGTAATGTGTAAC-GAAAACAAAAAGATTCAGCTCCAG
56 TGTTGAAAATGTGAATAGCAAAGCCCTTGTAATGTGTAACAG-AAACAAAAAGATTCAGCTCCAG
* *
4440348 AGAATCTCATATCCATTCAATGCTGTGGAGCAAAGACTCTTAAGATATCAGGCAGAAAATTTGAT
120 AGAAACACATATCCATTCAATGCTGTGGAGCAAAGACTCTTAAGATATCAGGCAGAAAATTTGAT
*
4440413 ATGCCAACAGACATGCCAAAAAGTTGAGAGA
185 ATGCCAACAGACATGCCAAAAAGTTCAGAGA
4440444 CGAGAAACAT
Statistics
Matches: 214, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
226 1 0.00
227 213 1.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.22
Consensus pattern (217 bp):
AGTTGAGAGCATCAAGTTTCACAGCAACATAAGACAACAATTACTTAACTACACATGTTGAAAAT
GTGAATAGCAAAGCCCTTGTAATGTGTAACAGAAACAAAAAGATTCAGCTCCAGAGAAACACATA
TCCATTCAATGCTGTGGAGCAAAGACTCTTAAGATATCAGGCAGAAAATTTGATATGCCAACAGA
CATGCCAAAAAGTTCAGAGATG
Found at i:4459265 original size:43 final size:43
Alignment explanation
Indices: 4459204--4459291 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
4459194 TTTCCGTTTC
4459204 CTGTGTAACAAGCTTGTTGAGTTCTTACCAGGAGTAACTAGTT
1 CTGTGTAACAAGCTTGTTGAGTTCTTACCAGGAGTAACTAGTT
4459247 CTGTGTAACAAGCTTGTTGAGTTCTTACCAGGAGTAACTAGTT
1 CTGTGTAACAAGCTTGTTGAGTTCTTACCAGGAGTAACTAGTT
4459290 CT
1 CT
4459292 TTTGCTTTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (43 bp):
CTGTGTAACAAGCTTGTTGAGTTCTTACCAGGAGTAACTAGTT
Found at i:4462519 original size:16 final size:16
Alignment explanation
Indices: 4462500--4462553 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
4462490 TCATATATTA
4462500 ATATTAACATATCAAT
1 ATATTAACATATCAAT
4462516 ATATT-ACATTATC-AT
1 ATATTAACA-TATCAAT
*
4462531 CAT-TATGACATATCAAT
1 -ATAT-TAACATATCAAT
4462548 ATATTA
1 ATATTA
4462554 TATTAAGATC
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
15 6 0.19
16 19 0.61
17 6 0.19
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.41
Consensus pattern (16 bp):
ATATTAACATATCAAT
Found at i:4466402 original size:21 final size:22
Alignment explanation
Indices: 4466378--4466423 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
4466368 TCAATTATAA
* *
4466378 TCAATACATAATTAGAT-AAAT
1 TCAATACAAAATTAAATCAAAT
*
4466399 TCAATATAAAATTAAATCAAAT
1 TCAATACAAAATTAAATCAAAT
4466421 TCA
1 TCA
4466424 CACATAGTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (22 bp):
TCAATACAAAATTAAATCAAAT
Found at i:4492923 original size:25 final size:24
Alignment explanation
Indices: 4492872--4492948 Score: 66
Period size: 26 Copynumber: 3.1 Consensus size: 24
4492862 AAAATTATTT
* *
4492872 TTTATTATAATATATAATTTTTTA
1 TTTATTATAATATATAATTTATAA
4492896 TTTATTA-AATATTTATAATTTATAA
1 TTTATTATAATA--TATAATTTATAA
* * *
4492921 TTTAAATATTAATATTTTATTTATAA
1 TTT-ATTA-TAATATATAATTTATAA
4492947 TT
1 TT
4492949 GACATATTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
23 4 0.09
24 7 0.16
25 13 0.30
26 15 0.35
28 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTATTATAATATATAATTTATAA
Found at i:4492955 original size:26 final size:28
Alignment explanation
Indices: 4492898--4492957 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 28
4492888 ATTTTTTATT
*
4492898 TATTAAATATTTATAATTTATAATTTAAA
1 TATT-AATATTTATAATTTATAATTGAAA
*
4492927 TATTAATATTT-T-ATTTATAATTGACA
1 TATTAATATTTATAATTTATAATTGAAA
4492953 TATTA
1 TATTA
4492958 TTATGAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 17 0.59
27 1 0.03
28 7 0.24
29 4 0.14
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (28 bp):
TATTAATATTTATAATTTATAATTGAAA
Found at i:4502274 original size:6 final size:6
Alignment explanation
Indices: 4502263--4502295 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
4502253 TTTTAGTATA
4502263 ATTAGG ATTAGG ATTAGG ATTAGG ATTAGG ATT
1 ATTAGG ATTAGG ATTAGG ATTAGG ATTAGG ATT
4502296 GCTATTCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.36
Consensus pattern (6 bp):
ATTAGG
Found at i:4511357 original size:6 final size:5
Alignment explanation
Indices: 4511327--4511383 Score: 78
Period size: 5 Copynumber: 10.6 Consensus size: 5
4511317 TTATATTTTG
4511327 TTTAT TTTAT TTTAT TTTAT TTTATT TTTATT TTTATT TTTAT TTTATT
1 TTTAT TTTAT TTTAT TTTAT TTTA-T TTTA-T TTTA-T TTTAT TTTA-T
4511376 TTTAT TTT
1 TTTAT TTT
4511384 GACAATGATC
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
5 28 0.56
6 22 0.44
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:4511357 original size:11 final size:11
Alignment explanation
Indices: 4511327--4511383 Score: 91
Period size: 11 Copynumber: 5.3 Consensus size: 11
4511317 TTATATTTTG
4511327 TTTA-TTTTAT
1 TTTATTTTTAT
4511337 TTTA-TTTTAT
1 TTTATTTTTAT
4511347 TTTATTTTTATT
1 TTTATTTTTA-T
4511359 TTTATTTTTAT
1 TTTATTTTTAT
4511370 TTTATTTTTAT
1 TTTATTTTTAT
4511381 TTT
1 TTT
4511384 GACAATGATC
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
10 14 0.31
11 20 0.44
12 11 0.24
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:4513595 original size:25 final size:25
Alignment explanation
Indices: 4513561--4513611 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
4513551 AGGGAGTATC
4513561 CAAGTTGATATTAATGTTCCTTCTA
1 CAAGTTGATATTAATGTTCCTTCTA
4513586 CAAGTTGATATTAATGTTCCTTCTA
1 CAAGTTGATATTAATGTTCCTTCTA
4513611 C
1 C
4513612 TTTCTAGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (25 bp):
CAAGTTGATATTAATGTTCCTTCTA
Found at i:4526826 original size:24 final size:23
Alignment explanation
Indices: 4526767--4526820 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
4526757 CATCCATAAT
**
4526767 TATAAAATATATAAATTATGTATA
1 TATAAAATAT-TATTTTATGTATA
*
4526791 TATAATATATTATTTTAT-TATA
1 TATAAAATATTATTTTATGTATA
4526813 TATAAAAT
1 TATAAAAT
4526821 TAATTACACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 11 0.42
23 6 0.23
24 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TATAAAATATTATTTTATGTATA
Found at i:4527338 original size:30 final size:28
Alignment explanation
Indices: 4527304--4527359 Score: 85
Period size: 30 Copynumber: 1.9 Consensus size: 28
4527294 ATTCTTGTTA
4527304 ATATAATATAAAAATATTATATATTAATAT
1 ATATAATATAAAAA-ATTA-ATATTAATAT
*
4527334 ATATAATATAAAAAATTAATTTTAAT
1 ATATAATATAAAAAATTAATATTAAT
4527360 TTTTTTATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 7 0.28
29 4 0.16
30 14 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
ATATAATATAAAAAATTAATATTAATAT
Found at i:4528412 original size:16 final size:16
Alignment explanation
Indices: 4528391--4528421 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4528381 TATGTTAACG
4528391 TTAATATTATTAATTA
1 TTAATATTATTAATTA
4528407 TTAATATTATTAATT
1 TTAATATTATTAATT
4528422 CGTATCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAATATTATTAATTA
Found at i:4530295 original size:23 final size:23
Alignment explanation
Indices: 4530243--4530295 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
4530233 TAAAATATTT
* * *
4530243 AAAAATATTATTATATTTGAGAC
1 AAAAATATTATTATATATAAGAA
4530266 AAAAATATTATTATA-ATAAGAA
1 AAAAATATTATTATATATAAGAA
4530288 AAAGAATA
1 AAA-AATA
4530296 AAGGAGAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (23 bp):
AAAAATATTATTATATATAAGAA
Found at i:4531465 original size:27 final size:27
Alignment explanation
Indices: 4531433--4531549 Score: 112
Period size: 27 Copynumber: 4.3 Consensus size: 27
4531423 ATATGAATGA
* *
4531433 TAAATTTTTAACATGATGTGTAATAAT
1 TAAATTTTTAACATGATATATAATAAT
4531460 TAAATTTTTAACAT-AGTATATAATAACT
1 TAAATTTTTAACATGA-TATATAATAA-T
* * *
4531488 T-AATTTTCAATATGATATATAATTAT
1 TAAATTTTTAACATGATATATAATAAT
* * * *
4531514 TAAAATTTTTAACGTAACATATAATAAA
1 T-AAATTTTTAACATGATATATAATAAT
4531542 TAAATTTT
1 TAAATTTT
4531550 CAATCTGACG
Statistics
Matches: 73, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
26 3 0.04
27 48 0.66
28 22 0.30
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.44
Consensus pattern (27 bp):
TAAATTTTTAACATGATATATAATAAT
Found at i:4531537 original size:55 final size:54
Alignment explanation
Indices: 4531432--4531584 Score: 153
Period size: 55 Copynumber: 2.8 Consensus size: 54
4531422 GATATGAATG
* * * * **
4531432 ATAAATTTTTAACATGATGTGTAATAATTAAATTTTTAACATAGTATATAATAA
1 ATAAATTTTCAATATGATATATAATAATTAAATTTTTAACATAACATATAATAA
* * * *
4531486 CTTAATTTTCAATATGATATATAATTATTAAAATTTTTAACGTAACATATAATAA
1 ATAAATTTTCAATATGATATATAATAATT-AAATTTTTAACATAACATATAATAA
* ** * *
4531541 ATAAATTTTCAATCTGACGTGTAATAATTACATTTTTAAACATA
1 ATAAATTTTCAATATGATATATAATAATTAAATTTTT-AACATA
4531585 TAACAACTAA
Statistics
Matches: 78, Mismatches: 19, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
54 29 0.37
55 49 0.63
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.42
Consensus pattern (54 bp):
ATAAATTTTCAATATGATATATAATAATTAAATTTTTAACATAACATATAATAA
Found at i:4534484 original size:2 final size:2
Alignment explanation
Indices: 4534463--4534511 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
4534453 AAAAGAGGCA
* *
4534463 AG AG AG AA AG AG -G AG A- AG AG AG AG AG AG AG AG AG AG AG AT
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4534503 A- AG AG AG AG
1 AG AG AG AG AG
4534512 CTAAGATCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.53, C:0.00, G:0.45, T:0.02
Consensus pattern (2 bp):
AG
Found at i:4534516 original size:11 final size:11
Alignment explanation
Indices: 4534463--4534517 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
4534453 AAAAGAGGCA
4534463 AGAGAGA-AAG
1 AGAGAGATAAG
4534473 AG-GAGA-AGAG
1 AGAGAGATA-AG
*
4534483 AGAGAGAGAGAG
1 AGAGAGATA-AG
4534495 AGAGAGATAAG
1 AGAGAGATAAG
*
4534506 AGAGAGCTAAG
1 AGAGAGATAAG
4534517 A
1 A
4534518 TCTTTCATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
9 5 0.12
10 6 0.15
11 17 0.43
12 12 0.30
ACGTcount: A:0.53, C:0.02, G:0.42, T:0.04
Consensus pattern (11 bp):
AGAGAGATAAG
Found at i:4534997 original size:12 final size:12
Alignment explanation
Indices: 4534982--4535021 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
4534972 GATCGAGAAA
4534982 GAGAAAGGGAAC
1 GAGAAAGGGAAC
* *
4534994 GAGAACGGGATC
1 GAGAAAGGGAAC
*
4535006 GAGATAGGGAAC
1 GAGAAAGGGAAC
4535018 GAGA
1 GAGA
4535022 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.10, G:0.42, T:0.05
Consensus pattern (12 bp):
GAGAAAGGGAAC
Found at i:4534997 original size:24 final size:24
Alignment explanation
Indices: 4534969--4535036 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
4534959 AAAGAAGGAT
*
4534969 CGAGATCGAGAAAGAGAAAGGGAA
1 CGAGAACGAGAAAGAGAAAGGGAA
* ** *
4534993 CGAGAACGGGATCGAGATAGGGAA
1 CGAGAACGAGAAAGAGAAAGGGAA
*
4535017 CGAGAGA-GAGAGAGAGAAAG
1 CGAGA-ACGAGAAAGAGAAAG
4535037 AGATCGCTTG
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
24 33 0.97
25 1 0.03
ACGTcount: A:0.46, C:0.09, G:0.41, T:0.04
Consensus pattern (24 bp):
CGAGAACGAGAAAGAGAAAGGGAA
Found at i:4542544 original size:12 final size:12
Alignment explanation
Indices: 4542527--4542563 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
4542517 TACTAAGTCT
4542527 AATATATATAT-
1 AATATATATATA
4542538 AA-ATATATATA
1 AATATATATATA
4542549 AATATATATATA
1 AATATATATATA
4542561 AAT
1 AAT
4542564 TTGAGTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 8 0.33
11 4 0.17
12 12 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AATATATATATA
Found at i:4542545 original size:10 final size:10
Alignment explanation
Indices: 4542530--4542558 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
4542520 TAAGTCTAAT
4542530 ATATATATAA
1 ATATATATAA
4542540 ATATATATAA
1 ATATATATAA
4542550 ATATATATA
1 ATATATATA
4542559 TAAATTTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATATAA
Found at i:4556176 original size:2 final size:2
Alignment explanation
Indices: 4556169--4556203 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4556159 CTTTTATCGC
*
4556169 CT CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4556204 ACATCAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:4559353 original size:2 final size:2
Alignment explanation
Indices: 4559346--4559379 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4559336 ATTAGAATTG
*
4559346 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4559380 GTGTTAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4566478 original size:32 final size:30
Alignment explanation
Indices: 4566411--4566479 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
4566401 TGAATATGAC
4566411 GTGTAATAACAATATTTTTTCAACATGGCT
1 GTGTAATAACAATATTTTTTCAACATGGCT
* *
4566441 -AGTAATAACAGTATTCTTTTTACAACATGG-T
1 GTGTAATAACAATA-T-TTTTT-CAACATGGCT
4566472 GTGTAATA
1 GTGTAATA
4566480 TCCTTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
29 11 0.34
30 1 0.03
31 6 0.19
32 14 0.44
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (30 bp):
GTGTAATAACAATATTTTTTCAACATGGCT
Found at i:4566574 original size:24 final size:23
Alignment explanation
Indices: 4566539--4566583 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
4566529 AACAGTATTT
*
4566539 TTTTTAATATGACGTGTAACATA
1 TTTTTAACATGACGTGTAACATA
4566562 TTTTTATACATGACGTGTAACA
1 TTTTTA-ACATGACGTGTAACA
4566584 ACATGACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.42
Consensus pattern (23 bp):
TTTTTAACATGACGTGTAACATA
Found at i:4566700 original size:45 final size:45
Alignment explanation
Indices: 4566559--4566707 Score: 167
Period size: 45 Copynumber: 3.3 Consensus size: 45
4566549 GACGTGTAAC
* * * * *
4566559 ATATTTTTATACATGACGTGTAACAACATGACTATGGCGTGTCAT
1 ATATTTTTGTACATGACGTGTAACAACCTAACCATGGCGTGTTAT
* * ** *
4566604 AT-TTTTTGTACATGACATATAACAACCTAACCATAACGTG-TAGC
1 ATATTTTTGTACATGACGTGTAACAACCTAACCATGGCGTGTTA-T
* *
4566648 ATGTTTTTGTACATGACGTGTAACAACCTAACCATGGTGTGTTAT
1 ATATTTTTGTACATGACGTGTAACAACCTAACCATGGCGTGTTAT
4566693 ATATTTTTGTACATG
1 ATATTTTTGTACATG
4566708 GCATATTAGG
Statistics
Matches: 84, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
43 1 0.01
44 32 0.38
45 49 0.58
46 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (45 bp):
ATATTTTTGTACATGACGTGTAACAACCTAACCATGGCGTGTTAT
Found at i:4566793 original size:21 final size:21
Alignment explanation
Indices: 4566747--4566786 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4566737 TTGTACATGG
*
4566747 CGTGTTACAACCTAACCATAA
1 CGTGTAACAACCTAACCATAA
4566768 CGTGTAACAACCTAACCAT
1 CGTGTAACAACCTAACCAT
4566787 GATGTGTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.30, G:0.10, T:0.23
Consensus pattern (21 bp):
CGTGTAACAACCTAACCATAA
Found at i:4566806 original size:104 final size:104
Alignment explanation
Indices: 4566663--4566873 Score: 314
Period size: 104 Copynumber: 2.0 Consensus size: 104
4566653 TTTGTACATG
* * * * *
4566663 ACGTGTAACAACCTAACCATGGTGTGTTATATATTTTTGTACATGGCATATTAGGTTAAGCGTGT
1 ACGTGTAACAACCTAACCATGATGTGTCACATATATTTGTACATGGCATATTAGGTTAAGCGGGT
* * *
4566728 AATATATTTTTGTACATGGCGTGTTACAACCTAACCATA
66 AACATATTTTTGTACATGACGTGTAACAACCTAACCATA
* *
4566767 ACGTGTAACAACCTAACCATGATGTGTCACATATATTTGTACATGGCATGTTAGGTTAGGCGGGT
1 ACGTGTAACAACCTAACCATGATGTGTCACATATATTTGTACATGGCATATTAGGTTAAGCGGGT
* *
4566832 AACATATTTTTGTACATGACGTGTAACAATCTAACTATA
66 AACATATTTTTGTACATGACGTGTAACAACCTAACCATA
4566871 ACG
1 ACG
4566874 CATCACATGT
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
104 95 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (104 bp):
ACGTGTAACAACCTAACCATGATGTGTCACATATATTTGTACATGGCATATTAGGTTAAGCGGGT
AACATATTTTTGTACATGACGTGTAACAACCTAACCATA
Found at i:4566902 original size:45 final size:44
Alignment explanation
Indices: 4566833--4566983 Score: 158
Period size: 45 Copynumber: 3.4 Consensus size: 44
4566823 TAGGCGGGTA
*
4566833 ACATATTTTTGTACATGACGTGTAACAATCTAACTATAACGCATC
1 ACATATTTTTATACATGACGTGTAACAATCTAACTATAACG-ATC
* * *
4566878 ACATGTTTTTATACATGACGTGTAACAATCTAACTATAACATATA
1 ACATATTTTTATACATGACGTGTAACAATCTAACTATAAC-GATC
* * * * * * * * *
4566923 ACATGTATCTGTACATGGCGTGTAACAACCTAACCATGACAGGTC
1 ACATATTTTTATACATGACGTGTAACAATCTAACTATAAC-GATC
4566968 ACATATTTTTATACAT
1 ACATATTTTTATACAT
4566984 AGCGAGTAAC
Statistics
Matches: 87, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
45 87 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (44 bp):
ACATATTTTTATACATGACGTGTAACAATCTAACTATAACGATC
Found at i:4566993 original size:90 final size:90
Alignment explanation
Indices: 4566842--4567037 Score: 236
Period size: 90 Copynumber: 2.2 Consensus size: 90
4566832 AACATATTTT
* * * * *
4566842 TGTACATGACGTGTAACAATCTAACTATAACGCATCACATGTTTTTATACATGACGTGTAACAA-
1 TGTACATGGCGTGTAACAACCTAACCATAACGCATCACATATTTTTATACATGACGAGTAACAAC
*
4566906 TCTAACTATAACATATAACATGTATC
66 T-TAACCATAACATATAACATGTATC
* *
4566932 TGTACATGGCGTGTAACAACCTAACCATGACAG-GTCACATATTTTTATACAT-AGCGAGTAACA
1 TGTACATGGCGTGTAACAACCTAACCATAAC-GCATCACATATTTTTATACATGA-CGAGTAACA
* * * *
4566995 ACTTAACCATGACATGTAATATGTTTC
64 ACTTAACCATAACATATAACATGTATC
4567022 TGTACATGGCGTGTAA
1 TGTACATGGCGTGTAA
4567038 ATGCCTCCAA
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
89 1 0.01
90 88 0.97
91 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (90 bp):
TGTACATGGCGTGTAACAACCTAACCATAACGCATCACATATTTTTATACATGACGAGTAACAAC
TTAACCATAACATATAACATGTATC
Found at i:4567028 original size:45 final size:45
Alignment explanation
Indices: 4566880--4567037 Score: 151
Period size: 45 Copynumber: 3.5 Consensus size: 45
4566870 AACGCATCAC
* * * * * * *
4566880 ATGTTTTTATACATGACGTGTAACAA-TCTAACTATAACATATAAC
1 ATGTTTCTGTACATGGCGTGTAACAACT-TAACCATGACATGTAAT
* * *
4566925 ATGTATCTGTACATGGCGTGTAACAACCTAACCATGACAGGTCACAT
1 ATGTTTCTGTACATGGCGTGTAACAACTTAACCATGACATGT-A-AT
* * *
4566972 AT-TTT-TATACATAGCGAGTAACAACTTAACCATGACATGTAAT
1 ATGTTTCTGTACATGGCGTGTAACAACTTAACCATGACATGTAAT
4567015 ATGTTTCTGTACATGGCGTGTAA
1 ATGTTTCTGTACATGGCGTGTAA
4567038 ATGCCTCCAA
Statistics
Matches: 89, Mismatches: 19, Indels: 10
0.75 0.16 0.08
Matches are distributed among these distances:
43 4 0.04
44 4 0.04
45 75 0.84
46 3 0.03
47 3 0.03
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (45 bp):
ATGTTTCTGTACATGGCGTGTAACAACTTAACCATGACATGTAAT
Found at i:4585649 original size:14 final size:14
Alignment explanation
Indices: 4585632--4585670 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
4585622 TGTTTTTATC
4585632 TCTTTTTTTTTCTA
1 TCTTTTTTTTTCTA
* *
4585646 TCTTTCTTTTTCTT
1 TCTTTTTTTTTCTA
4585660 TCTTTTTTTTT
1 TCTTTTTTTTT
4585671 TGTCCTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (14 bp):
TCTTTTTTTTTCTA
Found at i:4585655 original size:16 final size:15
Alignment explanation
Indices: 4585624--4585680 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 15
4585614 TTCCTATCTG
4585624 TTTTTATCTCTTTTT
1 TTTTTATCTCTTTTT
*
4585639 TTTTCTATCT-TTCTT
1 TTTT-TATCTCTTTTT
*
4585654 TTTCT-T-TCTTTTT
1 TTTTTATCTCTTTTT
*
4585667 TTTTTGTC-CTTTTT
1 TTTTTATCTCTTTTT
4585681 CTTATACTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
12 1 0.03
13 9 0.26
14 8 0.24
15 11 0.32
16 5 0.15
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.79
Consensus pattern (15 bp):
TTTTTATCTCTTTTT
Found at i:4585749 original size:2 final size:2
Alignment explanation
Indices: 4585733--4585769 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
4585723 TTCTTTTTAA
*
4585733 AT AT AT -T AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4585770 GATTTGGGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4593996 original size:55 final size:56
Alignment explanation
Indices: 4593881--4594010 Score: 160
Period size: 55 Copynumber: 2.3 Consensus size: 56
4593871 TTCACTCTGA
* *
4593881 TAAAGTCTTAATAAATAATTATTATTATTAGAGTAGGACTACGAGATTTTACTCTCT
1 TAAAGTCTTAATAAATAA-TATTATTATTAAAGTAGGACTACCAGATTTTACTCTCT
*
4593938 TAAAATCTTAATAAA-AA-ATTATTATTAAAGTTAGGACTACCCA-ATTTTACTCAT-T
1 TAAAGTCTTAATAAATAATATTATTATTAAAG-TAGGACTA-CCAGATTTTACTC-TCT
*
4593993 TAAAGCCTTAATAAATAA
1 TAAAGTCTTAATAAATAA
4594011 GTACAGGATA
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
54 12 0.19
55 31 0.48
56 7 0.11
57 14 0.22
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (56 bp):
TAAAGTCTTAATAAATAATATTATTATTAAAGTAGGACTACCAGATTTTACTCTCT
Found at i:4596636 original size:42 final size:42
Alignment explanation
Indices: 4596577--4596663 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
4596567 TGTGATTTCC
4596577 TTTGGGTGTTTTACCGGTTGCTAGAAGAGGTGAAATAAGGGT
1 TTTGGGTGTTTTACCGGTTGCTAGAAGAGGTGAAATAAGGGT
4596619 TTTGGGTGTTTTACCGGTTGCTAGAAGAGGTGAAATAAGGGT
1 TTTGGGTGTTTTACCGGTTGCTAGAAGAGGTGAAATAAGGGT
4596661 TTT
1 TTT
4596664 TAGAAAGGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.23, C:0.07, G:0.34, T:0.36
Consensus pattern (42 bp):
TTTGGGTGTTTTACCGGTTGCTAGAAGAGGTGAAATAAGGGT
Found at i:4597675 original size:63 final size:61
Alignment explanation
Indices: 4597485--4597675 Score: 220
Period size: 63 Copynumber: 3.1 Consensus size: 61
4597475 TATATATATA
* * * * *
4597485 TTTGCTTTAATTTTTGCCTAAGTTGTCTTTTGAAAGATTTTCAACTTAGTAGATTTTTTTTT
1 TTTGTTTTAACTTTTGCCTAAGTTGTCTTTTTAAAGATTTTCAACTTAGCAG-GTTTTTTTT
* * * * * * *
4597547 TTTGTCTTAACTTTTACCTTAAGTTGTCCTATTAAGGATTTTTAACTTAGCGGGTTTTTTTT
1 TTTGTTTTAACTTTTGCC-TAAGTTGTCTTTTTAAAGATTTTCAACTTAGCAGGTTTTTTTT
* *
4597609 TTTGCCTTTTAACTTTTGCCTAAGTCGTCTTTTTAAAGATTTTCAACTTAGCAGGTTCTTTTT
1 TTTG--TTTTAACTTTTGCCTAAGTTGTCTTTTTAAAGATTTTCAACTTAGCAGGTTTTTTTT
4597672 TTTG
1 TTTG
4597676 GATACAGTTT
Statistics
Matches: 105, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
62 26 0.25
63 67 0.64
64 12 0.11
ACGTcount: A:0.19, C:0.13, G:0.14, T:0.54
Consensus pattern (61 bp):
TTTGTTTTAACTTTTGCCTAAGTTGTCTTTTTAAAGATTTTCAACTTAGCAGGTTTTTTTT
Found at i:4601206 original size:15 final size:15
Alignment explanation
Indices: 4601186--4601224 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
4601176 ATTACTATTT
* *
4601186 TATATAAACTTTTAG
1 TATATAAACTTTAAA
*
4601201 TATATATACTTTAAA
1 TATATAAACTTTAAA
4601216 TATATAAAC
1 TATATAAAC
4601225 ATATGGTAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (15 bp):
TATATAAACTTTAAA
Found at i:4602127 original size:34 final size:34
Alignment explanation
Indices: 4602088--4602166 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 34
4602078 GAACTTGTAA
* * *
4602088 TGTTATTTAAGTTGTTGTTT-AAATATTTGTTTT
1 TGTTATTTAAGTTGATATTTGAAATATTTATTTT
*
4602121 TAGTTATTTAAGTTGATATTTGAGATATTTATTTT
1 T-GTTATTTAAGTTGATATTTGAAATATTTATTTT
4602156 TGATTATTTAA
1 TG-TTATTTAA
4602167 ATTTAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 1 0.03
34 18 0.46
35 20 0.51
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (34 bp):
TGTTATTTAAGTTGATATTTGAAATATTTATTTT
Found at i:4603375 original size:14 final size:14
Alignment explanation
Indices: 4603356--4603399 Score: 61
Period size: 15 Copynumber: 3.0 Consensus size: 14
4603346 NNNNNNGATG
4603356 TTATTATTATTTTA
1 TTATTATTATTTTA
4603370 TTATTATTATTTTTA
1 TTATTATTA-TTTTA
*
4603385 TAATTATTGATTTTA
1 TTATTATT-ATTTTA
4603400 AATTTAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.33
15 17 0.63
16 1 0.04
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (14 bp):
TTATTATTATTTTA
Found at i:4609870 original size:14 final size:13
Alignment explanation
Indices: 4609857--4609895 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
4609847 TTAATTTTTA
4609857 ATTTAAAATATTT
1 ATTTAAAATATTT
*
4609870 ATTTCAAATAATTT
1 ATTTAAAAT-ATTT
*
4609884 ATTAAAAATATT
1 ATTTAAAATATT
4609896 AATAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (13 bp):
ATTTAAAATATTT
Found at i:4614808 original size:28 final size:29
Alignment explanation
Indices: 4614757--4614814 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
4614747 TAAAGATAAA
* *
4614757 AAATAAGTTACAAGCTGTGTGTTTCAAAAT
1 AAATAAGTTACAAGC-GTATGTTTAAAAAT
4614787 AAATAAGTTACAAGC-TATGTTTAAAAAT
1 AAATAAGTTACAAGCGTATGTTTAAAAAT
4614815 CTTATTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 11 0.42
30 15 0.58
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.33
Consensus pattern (29 bp):
AAATAAGTTACAAGCGTATGTTTAAAAAT
Found at i:4629451 original size:13 final size:13
Alignment explanation
Indices: 4629435--4629460 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4629425 TCCTGAGTTC
4629435 CTTTCTTTTTTTT
1 CTTTCTTTTTTTT
4629448 CTTTCTTTTTTTT
1 CTTTCTTTTTTTT
4629461 TTTTTTGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
CTTTCTTTTTTTT
Found at i:4637807 original size:26 final size:26
Alignment explanation
Indices: 4637758--4637807 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
4637748 ACCCCAATAT
** *
4637758 TTTTTTCCTTCATTTTTTTTTTTTGG
1 TTTTTTCCTTCATTTTCCTCTTTTGG
*
4637784 TTTTTTCTTTCATTTTCCTCTTTT
1 TTTTTTCCTTCATTTTCCTCTTTT
4637808 CCCTTGTTGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (26 bp):
TTTTTTCCTTCATTTTCCTCTTTTGG
Found at i:4640984 original size:22 final size:22
Alignment explanation
Indices: 4640959--4641001 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4640949 ATATTATATG
* *
4640959 ACTGCTTGATATGCATTACGTA
1 ACTGATTGATAAGCATTACGTA
4640981 ACTGATTGATAAGCATTACGT
1 ACTGATTGATAAGCATTACGT
4641002 GATTGGTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (22 bp):
ACTGATTGATAAGCATTACGTA
Found at i:4641090 original size:22 final size:22
Alignment explanation
Indices: 4641058--4641137 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
4641048 ACTTAGGGAT
4641058 TATCTAAAAATTAGTCACGTAA
1 TATCTAAAAATTAGTCACGTAA
* *
4641080 TATTTAAAAATTAGTCTATGTAA
1 TATCTAAAAATTAGTC-ACGTAA
* **
4641103 TACCT-AAAACCAGTCACGTAA
1 TATCTAAAAATTAGTCACGTAA
4641124 TATCTAAAAATTAG
1 TATCTAAAAATTAG
4641138 AGACGCAATG
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
21 9 0.20
22 29 0.63
23 8 0.17
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.33
Consensus pattern (22 bp):
TATCTAAAAATTAGTCACGTAA
Found at i:4641212 original size:22 final size:23
Alignment explanation
Indices: 4641164--4641220 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 23
4641154 TCATGCAATG
*
4641164 CCTAAAAACCAATCTCACAATAT
1 CCTAAAAACCAATCACACAATAT
* *
4641187 -CTAAAAACCAATGACATAAT-T
1 CCTAAAAACCAATCACACAATAT
*
4641208 CCTAAAAATCAAT
1 CCTAAAAACCAAT
4641221 AATGCAATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.51, C:0.25, G:0.02, T:0.23
Consensus pattern (23 bp):
CCTAAAAACCAATCACACAATAT
Found at i:4662883 original size:15 final size:15
Alignment explanation
Indices: 4662853--4662919 Score: 89
Period size: 15 Copynumber: 4.4 Consensus size: 15
4662843 CGTTTGGTAC
*
4662853 ATTACAATGCAATGTG
1 ATTACAA-GTAATGTG
*
4662869 ATTACAGGTAATGTG
1 ATTACAAGTAATGTG
4662884 ATTACAAGTAATGTG
1 ATTACAAGTAATGTG
* *
4662899 ATTGCAAGCAATGTG
1 ATTACAAGTAATGTG
4662914 ATTACA
1 ATTACA
4662920 GGGAAAATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
15 39 0.87
16 6 0.13
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.31
Consensus pattern (15 bp):
ATTACAAGTAATGTG
Found at i:4663165 original size:20 final size:20
Alignment explanation
Indices: 4663142--4663209 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 20
4663132 TCATATATTT
4663142 TATTTTTATTTATTATTAA-A
1 TATTTTTATTTATT-TTAATA
4663162 TATTTTATATTTTATTTTAATA
1 TATTTT-TA-TTTATTTTAATA
*
4663184 TATTTATATTT-TTTT-ATA
1 TATTTTTATTTATTTTAATA
4663202 -ATTTTTAT
1 TATTTTTAT
4663210 ATAATATCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
17 7 0.16
18 3 0.07
19 4 0.09
20 9 0.21
21 8 0.19
22 12 0.28
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTTTTATTTATTTTAATA
Found at i:4663176 original size:19 final size:19
Alignment explanation
Indices: 4663145--4663211 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 19
4663135 TATATTTTAT
4663145 TTTTAT-TTATTATTAAATA
1 TTTTATATT-TTATTAAATA
*
4663164 TTTTATATTTTATTTTAATA
1 TTTTATATTTTA-TTAAATA
*
4663184 TATTTATATTTTTTTATAAT-
1 T-TTTATATTTTATTA-AATA
4663204 TTTTATAT
1 TTTTATAT
4663212 AATATCATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
19 16 0.39
20 12 0.29
21 13 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTATATTTTATTAAATA
Found at i:4663244 original size:109 final size:112
Alignment explanation
Indices: 4663066--4663607 Score: 799
Period size: 109 Copynumber: 5.0 Consensus size: 112
4663056 AAAATATAAG
4663066 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTT-TTAAATATATTTTTAA
1 TTTAATATATTTATA-TTTTT-TTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
4663130 TATCATATATTTTATTTTTATTTATTATTA-AATATTTTATATTTTA-T
64 TATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
4663177 TTTAATATATTTATATTTTTTTA-TAATTTTTATATAATATCATTTCTTAAATATATTTTTAATA
1 TTTAATATATTTATATTTTTTTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATA
4663241 TCATATATTTTATTTTT-TATTATTATTATAATA-TTTATA-TTTATT
66 TCATATATTTTATTTTTAT-TTATTATTATAATATTTTATATTTTATT
4663286 TTTAATATA-TTATA-TTTTTTATTAATTTTTATATAATATCATTTCTT-AATATATTTTTAATA
1 TTTAATATATTTATATTTTTTTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATA
4663348 TCATATATTTTATTTTTATTT-TTATTATAATATTTTATATTTTA-T
66 TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
*
4663393 TTTAATATA-TTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATA-TTTTAAT
1 TTTAATATATTTATATTT-TTTTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
*
4663456 GTCATATA-TTTA-TTTTATTTATTATTATAATATTTTATA-TTTATT
65 ATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
*
4663501 TTTAATATATTTATATTTATATTATTAATTTTT-TATATATATCATATT-TTAAAATATATTTTT
1 TTTAATATATTTATATTT-TTTTATTAATTTTTATATA-ATATCAT-TTCTT-AAATATATTTTT
*
4663564 AATGTCATATA-TTTATTTTTTATTTA-T-TTAT-A-ATTTTATATTTT
62 AATATCATATATTTTA-TTTTTATTTATTATTATAATATTTTATATTTT
4663608 TTTCATTTCT
Statistics
Matches: 408, Mismatches: 2, Indels: 43
0.90 0.00 0.09
Matches are distributed among these distances:
106 11 0.03
107 74 0.18
108 100 0.25
109 147 0.36
110 28 0.07
111 38 0.09
112 1 0.00
113 9 0.02
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (112 bp):
TTTAATATATTTATATTTTTTTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATA
TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
Found at i:4663388 original size:15 final size:14
Alignment explanation
Indices: 4663071--4663647 Score: 164
Period size: 14 Copynumber: 42.2 Consensus size: 14
4663061 ATAAGTTTAA
4663071 TATATT-TATATTT
1 TATATTATATATTT
*
4663084 TTTATTAT-TAATTTT
1 TATATTATAT-A-TTT
*
4663099 TATATAATATCATTT
1 TATATTATAT-ATTT
*
4663114 T-TA-AATATATTTT
1 TATATTATATA-TTT
*
4663127 TAATATCATATATTT
1 T-ATATTATATATTT
4663142 TAT-TT-T-TA-TT
1 TATATTATATATTT
*
4663152 TATTATTAAATATTT
1 TA-TATTATATATTT
4663167 TATATT-T-TATTT
1 TATATTATATATTT
*
4663179 TAATATATTTATATTT
1 T-ATAT-TATATATTT
4663195 T-T-TTATA-ATTTT
1 TATATTATATA-TTT
*
4663207 TATATAATATCATTT
1 TATATTATAT-ATTT
*
4663222 CT-TA-AATATATTTT
1 -TATATTATATA-TTT
*
4663236 TAATATCATATATTT
1 T-ATATTATATATTT
* *
4663251 TAT-TT-TTTATTA
1 TATATTATATATTT
4663263 T-TATTATA-ATATT
1 TATATTATATAT-TT
4663276 TATATT-TAT-TTT
1 TATATTATATATTT
4663288 TA-ATATATTATATTT
1 TATAT-TA-TATATTT
*
4663303 TTTATTA-AT-TTT
1 TATATTATATATTT
*
4663315 TATATAATATCATTT
1 TATATTATAT-ATTT
*
4663330 CT-TAATATAT-TTT
1 -TATATTATATATTT
*
4663343 TAATATCATATATTT
1 T-ATATTATATATTT
4663358 TAT-TT-T-TATTT
1 TATATTATATATTT
4663369 T-TATTATAATATTT
1 TATATTAT-ATATTT
4663383 TATATT-T-TATTT
1 TATATTATATATTT
4663395 TA-A-TATATTATATT
1 TATATTATA-TAT-TT
4663409 TATATTAT-TAATTTT
1 TATATTATAT-A-TTT
*
4663424 TATATAATATCATTT
1 TATATTATAT-ATTT
*
4663439 CT-TA-AATATATTT
1 -TATATTATATATTT
4663452 TA-ATGTCATATA-TT
1 TATAT-T-ATATATTT
*
4663466 TAT-TT-TAT-TTA
1 TATATTATATATTT
4663477 T-TATTATAATATTT
1 TATATTAT-ATATTT
4663491 TATATT-TAT-TTT
1 TATATTATATATTT
*
4663503 TA-ATATATTTATATT
1 TATAT-TATATAT-TT
*
4663518 TATATTATTAATTTTT
1 TATATTA-T-ATATTT
4663534 TATATATATCATATTT
1 TATAT-TAT-ATATTT
* *
4663550 TAAAATATAT-TTT
1 TATATTATATATTT
4663563 TA-ATGTCATATA-TT
1 TATAT-T-ATATATTT
*
4663577 TAT-TT-TTTA-TT
1 TATATTATATATTT
4663588 TAT-TTATA-ATTT
1 TATATTATATATTT
* *
4663600 TATATTTTTTTCATTT
1 TATA-TTATAT-ATTT
* * *
4663616 CTTTAATATATTTTT
1 -TATATTATATATTT
4663631 TATATTATATATTT
1 TATATTATATATTT
4663645 TAT
1 TAT
4663648 TTTAATTTGT
Statistics
Matches: 426, Mismatches: 49, Indels: 177
0.65 0.08 0.27
Matches are distributed among these distances:
10 7 0.02
11 37 0.09
12 66 0.15
13 60 0.14
14 98 0.23
15 95 0.22
16 56 0.13
17 7 0.02
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (14 bp):
TATATTATATATTT
Found at i:4663463 original size:216 final size:217
Alignment explanation
Indices: 4663066--4663607 Score: 838
Period size: 216 Copynumber: 2.5 Consensus size: 217
4663056 AAAATATAAG
4663066 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTTTAAATATATTTTTAAT
1 TTTAATATATTTATA--TTTTATTATTAATTTTTATATAATATCATTTTTAAATATATTTTTAAT
4663131 ATCATATATTTTATTTTTATTTATTATTA-AATATTTTATATTTTATTTTAATATATTTATATTT
64 ATCATATATTTTATTTTTATTT-TTATTATAATATTTTATATTTTATTTTAATATATTTATATTT
* *
4663195 TTTTATAATTTTTATATAATATCATTTCTTAAATATATTTTTAATATCATATATTTTATTTTTTA
128 TATTATAATTTTTATATAATATCATTTCTTAAATATATTTTTAATATCATATA-TTTATTTTAT-
4663260 TTATTATTATAATA-TTTATATTTATT
191 TTATTATTATAATATTTTATATTTATT
4663286 TTTAATATA-TTATATTTT-TTATTAATTTTTATATAATATCATTTCTT-AATATATTTTTAATA
1 TTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATTT-TTAAATATATTTTTAATA
4663348 TCATATATTTTATTTTTATTTTTATTATAATATTTTATATTTTATTTTAATATA-TTATATTTAT
65 TCATATATTTTATTTTTATTTTTATTATAATATTTTATATTTTATTTTAATATATTTATATTT-T
*
4663412 ATTATTAATTTTTATATAATATCATTTCTTAAATATA-TTTTAATGTCATATATTTATTTTATTT
129 ATTA-TAATTTTTATATAATATCATTTCTTAAATATATTTTTAATATCATATATTTATTTTATTT
4663476 ATTATTATAATATTTTATATTTATT
193 ATTATTATAATATTTTATATTTATT
4663501 TTTAATATATTTATATTTATATTATTAATTTTT-TATATATATCATATTTTAAAATATATTTTTA
1 TTTAATATATTTATATTT-TATTATTAATTTTTATATA-ATATCAT-TTTT-AAATATATTTTTA
* *
4663565 ATGTCATATA-TTTATTTTT-TATTTATT-T-ATAATTTTATATTTT
62 ATATCATATATTTTATTTTTATTTTTATTATAAT-ATTTTATATTTT
4663608 TTTCATTTCT
Statistics
Matches: 304, Mismatches: 5, Indels: 29
0.90 0.01 0.09
Matches are distributed among these distances:
214 14 0.05
215 44 0.14
216 116 0.38
217 56 0.18
218 28 0.09
219 16 0.05
220 30 0.10
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (217 bp):
TTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATTTTTAAATATATTTTTAATAT
CATATATTTTATTTTTATTTTTATTATAATATTTTATATTTTATTTTAATATATTTATATTTTAT
TATAATTTTTATATAATATCATTTCTTAAATATATTTTTAATATCATATATTTATTTTATTTATT
ATTATAATATTTTATATTTATT
Found at i:4663722 original size:22 final size:23
Alignment explanation
Indices: 4663678--4663723 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
4663668 TATATAAATA
*
4663678 TTAATTTTTTATATTTTATTTAT
1 TTAATTTTTTATATCTTATTTAT
4663701 TTAA-TTTTTAT-TCTTATATTAT
1 TTAATTTTTTATATCTTAT-TTAT
4663723 T
1 T
4663724 ATTTATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 12 0.57
23 4 0.19
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (23 bp):
TTAATTTTTTATATCTTATTTAT
Found at i:4663731 original size:24 final size:25
Alignment explanation
Indices: 4663697--4663746 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
4663687 TATATTTTAT
* * *
4663697 TTATTTAATTTTTATTCTTATATTA
1 TTATTTAATTTTAATTATAATATTA
4663722 TTATTT-ATTTTAATTATAATATTA
1 TTATTTAATTTTAATTATAATATTA
4663746 T
1 T
4663747 AAAATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (25 bp):
TTATTTAATTTTAATTATAATATTA
Found at i:4663744 original size:18 final size:20
Alignment explanation
Indices: 4663698--4663744 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 20
4663688 ATATTTTATT
*
4663698 TATT-TAATTTTTATTCTTA
1 TATTATAATATTTATTCTTA
4663717 TATTAT--TATTTATT-TTA
1 TATTATAATATTTATTCTTA
4663734 -ATTATAATATT
1 TATTATAATATT
4663745 ATAAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
16 5 0.21
17 3 0.12
18 11 0.46
19 4 0.17
20 1 0.04
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTATAATATTTATTCTTA
Found at i:4663746 original size:29 final size:28
Alignment explanation
Indices: 4663686--4663747 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
4663676 TATTAATTTT
* * *
4663686 TTATATTTTATTTATTTAATTTTTATTC
1 TTATATTTTATTTATTTAATTTATAATA
4663714 TTATATTATTATTTATTTTAA-TTATAATA
1 TTATATT-TTATTTA-TTTAATTTATAATA
4663743 TTATA
1 TTATA
4663748 AAATATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 7 0.24
29 17 0.59
30 5 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (28 bp):
TTATATTTTATTTATTTAATTTATAATA
Found at i:4690845 original size:17 final size:17
Alignment explanation
Indices: 4690823--4690884 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
4690813 ATTTCAAGAT
4690823 TTATTTACATATGAATA
1 TTATTTACATATGAATA
* *
4690840 TTATTTA-AGTAATTTCAAGA
1 TTATTTACA-T-A--TGAATA
4690860 TTTATTTACATATGAATA
1 -TTATTTACATATGAATA
4690878 TTATTTA
1 TTATTTA
4690885 AGTAATAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
16 1 0.03
17 15 0.43
18 5 0.14
20 5 0.14
21 8 0.23
22 1 0.03
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (17 bp):
TTATTTACATATGAATA
Found at i:4690845 original size:21 final size:21
Alignment explanation
Indices: 4690821--4690884 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
4690811 ATATTTCAAG
4690821 ATTTATTTACATATGAATATT
1 ATTTATTTACATATGAATATT
** ** *
4690842 ATTTAAGTA-AT-TTCA-A-G
1 ATTTATTTACATATGAATATT
4690859 ATTTATTTACATATGAATATT
1 ATTTATTTACATATGAATATT
4690880 ATTTA
1 ATTTA
4690885 AGTAATAATG
Statistics
Matches: 29, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
17 7 0.24
18 3 0.10
19 4 0.14
20 3 0.10
21 12 0.41
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (21 bp):
ATTTATTTACATATGAATATT
Found at i:4690864 original size:38 final size:38
Alignment explanation
Indices: 4690813--4690890 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
4690803 CAGTATAGAT
4690813 ATTTCAAGATTTATTTACATATGAATATTATTTAAGTA
1 ATTTCAAGATTTATTTACATATGAATATTATTTAAGTA
4690851 ATTTCAAGATTTATTTACATATGAATATTATTTAAGTA
1 ATTTCAAGATTTATTTACATATGAATATTATTTAAGTA
4690889 AT
1 AT
4690891 AATGTGAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (38 bp):
ATTTCAAGATTTATTTACATATGAATATTATTTAAGTA
Found at i:4693377 original size:16 final size:16
Alignment explanation
Indices: 4693337--4693378 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4693327 GTATTAATTT
* *
4693337 ACCCTAGAAGTGGTAA
1 ACCCTAGAAGCGATAA
4693353 ACTCC-AGAAGCGATAA
1 AC-CCTAGAAGCGATAA
4693369 ACCCTAGAAG
1 ACCCTAGAAG
4693379 TGACAATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 2 0.09
16 18 0.82
17 2 0.09
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.14
Consensus pattern (16 bp):
ACCCTAGAAGCGATAA
Found at i:4693840 original size:80 final size:78
Alignment explanation
Indices: 4693690--4693844 Score: 195
Period size: 80 Copynumber: 2.0 Consensus size: 78
4693680 AATACGAGAT
* *
4693690 TTATAAAAAAAAATAATATATTTTAGAGATGCATCTTAATACAAGATTGTGATAGTCATTAATTT
1 TTATAAAAAAAAATAATATAATTTAGAGATGCATCTTAATACAAGATTGTAATAGTCATTAATTT
4693755 ATAAAGTGCTTTAA
66 ATAAAG-GCTTTAA
* * * * * * *
4693769 TTATAAATAAAAGATAATGTAATTTAGAGATGTATTTTAATAGAAGATTGTAATAGTTATTGATC
1 TTATAAA-AAAAAATAATATAATTTAGAGATGCATCTTAATACAAGATTGTAATAGTCATTAAT-
4693834 TT-TAAAGGCTT
64 TTATAAAGGCTT
4693845 CACCTGTAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
79 11 0.17
80 52 0.80
81 2 0.03
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.39
Consensus pattern (78 bp):
TTATAAAAAAAAATAATATAATTTAGAGATGCATCTTAATACAAGATTGTAATAGTCATTAATTT
ATAAAGGCTTTAA
Found at i:4694350 original size:6 final size:6
Alignment explanation
Indices: 4694339--4694365 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4694329 CTCCCTCCAT
4694339 TTCCCC TTCCCC TTCCCC TTCCCC TTC
1 TTCCCC TTCCCC TTCCCC TTCCCC TTC
4694366 ATCCGAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
TTCCCC
Found at i:4702531 original size:84 final size:85
Alignment explanation
Indices: 4702346--4702531 Score: 272
Period size: 84 Copynumber: 2.2 Consensus size: 85
4702336 CAAGTTGTTT
* * * *
4702346 TTATCACA-ATT-TTGTATGTTGCAGCCAAATTGCATTTTAATGCATATTATTATCTTTTTTTTT
1 TTATCACAGATTATTGTAGGTTGCAGCCAAATTGCATTTTAATGCATATTATAATCTATATTTTT
* *
4702409 TTTATAGGAGCATGTTGTAA
66 TTTATAAGAGCATGTTATAA
4702429 TTATCACAGATTATTGTAGGTTGCAGCCAAATTGCATTATT-ATGCATATTATAAT-TATATTTT
1 TTATCACAGATTATTGTAGGTTGCAGCCAAATTGCATT-TTAATGCATATTATAATCTATATTTT
4702492 TTTTATAAGAGCATGTTATAA
65 TTTTATAAGAGCATGTTATAA
*
4702513 TTATCATAGATTATTGTAG
1 TTATCACAGATTATTGTAG
4702532 ACTTCTATCT
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
83 8 0.09
84 46 0.49
85 37 0.40
86 2 0.02
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (85 bp):
TTATCACAGATTATTGTAGGTTGCAGCCAAATTGCATTTTAATGCATATTATAATCTATATTTTT
TTTATAAGAGCATGTTATAA
Found at i:4712603 original size:35 final size:35
Alignment explanation
Indices: 4712557--4712628 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
4712547 TAGATGTAGC
4712557 TTGCATAATTCTAACAAGTAAAGATTCATTGTCTT
1 TTGCATAATTCTAACAAGTAAAGATTCATTGTCTT
4712592 TTGCATAATTCTAACAAGTAAAGATTCATTGTCTT
1 TTGCATAATTCTAACAAGTAAAGATTCATTGTCTT
4712627 TT
1 TT
4712629 TTAATGTCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (35 bp):
TTGCATAATTCTAACAAGTAAAGATTCATTGTCTT
Found at i:4719148 original size:30 final size:31
Alignment explanation
Indices: 4719108--4719166 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
4719098 TAGTCATAAT
4719108 ATTTTATTTGA-TTCAAAATAAAAATATAAAA
1 ATTTTATTTGACTT-AAAATAAAAATATAAAA
*
4719139 ATTTT-TTTGACTTAAAATAAAAGTATAA
1 ATTTTATTTGACTTAAAATAAAAATATAA
4719167 GAGTTTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (31 bp):
ATTTTATTTGACTTAAAATAAAAATATAAAA
Found at i:4732540 original size:35 final size:35
Alignment explanation
Indices: 4732500--4732601 Score: 195
Period size: 35 Copynumber: 2.9 Consensus size: 35
4732490 GGGCTGGCAC
*
4732500 CCTCTTGGGCCTCCTGGCGGGTCTGGACTGTGTCA
1 CCTCTTGGGCCTCCTGGTGGGTCTGGACTGTGTCA
4732535 CCTCTTGGGCCTCCTGGTGGGTCTGGACTGTGTCA
1 CCTCTTGGGCCTCCTGGTGGGTCTGGACTGTGTCA
4732570 CCTCTTGGGCCTCCTGGTGGGTCTGGACTGTG
1 CCTCTTGGGCCTCCTGGTGGGTCTGGACTGTG
4732602 GCCCGTGACA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.05, C:0.29, G:0.35, T:0.30
Consensus pattern (35 bp):
CCTCTTGGGCCTCCTGGTGGGTCTGGACTGTGTCA
Found at i:4737842 original size:35 final size:34
Alignment explanation
Indices: 4737778--4737878 Score: 159
Period size: 35 Copynumber: 2.9 Consensus size: 34
4737768 TGGCTGGCAC
*
4737778 CCTCTTGGGCCTCCTGG-CGGTCTGAACTGTGTCA
1 CCTCTTGGGCCTCCTGGTGGGTCTG-ACTGTGTCA
4737812 CCTCTTGGGCCTCCTGGTGGGTCTAGACTGTGTCA
1 CCTCTTGGGCCTCCTGGTGGGTCT-GACTGTGTCA
4737847 CCTCTTGGGCCTCCTGGTGGGTCTGGACTGTG
1 CCTCTTGGGCCTCCTGGTGGGTCT-GACTGTG
4737879 GCGCCGGTGA
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
34 17 0.27
35 45 0.71
36 1 0.02
ACGTcount: A:0.07, C:0.30, G:0.33, T:0.31
Consensus pattern (34 bp):
CCTCTTGGGCCTCCTGGTGGGTCTGACTGTGTCA
Found at i:4780008 original size:2 final size:2
Alignment explanation
Indices: 4780001--4780025 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4779991 GAATTCTCTA
4780001 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4780026 CATACACAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4784513 original size:2 final size:2
Alignment explanation
Indices: 4784506--4784547 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
4784496 TAGAAGTCTT
*
4784506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4784548 ATGATTTGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4795469 original size:5 final size:5
Alignment explanation
Indices: 4795459--4795485 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
4795449 TTTTGCAGCT
4795459 CTTGG CTTGG CTTGG CTTGG CTTGG CT
1 CTTGG CTTGG CTTGG CTTGG CTTGG CT
4795486 GATTTTCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.22, G:0.37, T:0.41
Consensus pattern (5 bp):
CTTGG
Found at i:4800950 original size:6 final size:6
Alignment explanation
Indices: 4800939--4800965 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4800929 TTTTTTTTAT
4800939 ACTAGC ACTAGC ACTAGC ACTAGC ACT
1 ACTAGC ACTAGC ACTAGC ACTAGC ACT
4800966 CTTGCTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.33, G:0.15, T:0.19
Consensus pattern (6 bp):
ACTAGC
Found at i:4807748 original size:7 final size:7
Alignment explanation
Indices: 4807732--4807768 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
4807722 CCAAAGCACT
*
4807732 CCTTTGC
1 CCTTTCC
4807739 CCTTTCC
1 CCTTTCC
4807746 CCTTTCC
1 CCTTTCC
4807753 CCTTTCC
1 CCTTTCC
4807760 CCTTTCC
1 CCTTTCC
4807767 CC
1 CC
4807769 CAACTCCAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.00, C:0.57, G:0.03, T:0.41
Consensus pattern (7 bp):
CCTTTCC
Found at i:4817577 original size:2 final size:2
Alignment explanation
Indices: 4817570--4817594 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4817560 TCCACGTCCC
4817570 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4817595 CTTTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4822056 original size:7 final size:7
Alignment explanation
Indices: 4822044--4822120 Score: 127
Period size: 7 Copynumber: 11.0 Consensus size: 7
4822034 CCCAAATAAT
4822044 TAACGGC
1 TAACGGC
4822051 TAACGGC
1 TAACGGC
4822058 TAACGGC
1 TAACGGC
4822065 TAACGGC
1 TAACGGC
4822072 TAACGGC
1 TAACGGC
4822079 TAACGGC
1 TAACGGC
4822086 TAACGGC
1 TAACGGC
*
4822093 TAACGGT
1 TAACGGC
*
4822100 TAACGGT
1 TAACGGC
*
4822107 TAACGGT
1 TAACGGC
4822114 TAACGGC
1 TAACGGC
4822121 CATTCCCGCC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 68 1.00
ACGTcount: A:0.29, C:0.25, G:0.29, T:0.18
Consensus pattern (7 bp):
TAACGGC
Found at i:4822614 original size:35 final size:35
Alignment explanation
Indices: 4822572--4822644 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
4822562 TTTTCATCTT
*
4822572 TTTCTTTTTACCCAATTATTTAATTAATTGATTTC
1 TTTCTTTTTACCCAATTATTTAATTAACTGATTTC
* * * *
4822607 TTTCTTTTTACCTAATTGTTTAGTTCACTGATTTC
1 TTTCTTTTTACCCAATTATTTAATTAACTGATTTC
4822642 TTT
1 TTT
4822645 ATCATCTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.21, C:0.15, G:0.05, T:0.59
Consensus pattern (35 bp):
TTTCTTTTTACCCAATTATTTAATTAACTGATTTC
Found at i:4827667 original size:29 final size:26
Alignment explanation
Indices: 4827625--4827687 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
4827615 GAGAAAAAAA
*
4827625 GAAAAAAAAAACCCACCCTCAGATTT
1 GAAAAAAAAAACCCACACTCAGATTT
*
4827651 GGAAAAAAAAACCACCCACACTGAGATTT
1 -GAAAAAAAAA--ACCCACACTCAGATTT
4827680 -AAAAAAAA
1 GAAAAAAAA
4827688 CAAAAAACCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 18 0.56
29 14 0.44
ACGTcount: A:0.56, C:0.22, G:0.10, T:0.13
Consensus pattern (26 bp):
GAAAAAAAAAACCCACACTCAGATTT
Found at i:4839454 original size:53 final size:54
Alignment explanation
Indices: 4839390--4839493 Score: 156
Period size: 53 Copynumber: 1.9 Consensus size: 54
4839380 GTAAAAAAAA
* *
4839390 TTTTTGAACATGACGTATAATAATAATA-TTTTTTTAATATGACATGTAACTTG
1 TTTTTGAACATGACGTATAACAATAATATTTTTTTTAATATGACATATAACTTG
* * *
4839443 TTTTTGTACATGAGGTGTAACAATAATATTTTTTTTAATATGACATATAAC
1 TTTTTGAACATGACGTATAACAATAATATTTTTTTTAATATGACATATAAC
4839494 AACTTTTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 24 0.53
54 21 0.47
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.45
Consensus pattern (54 bp):
TTTTTGAACATGACGTATAACAATAATATTTTTTTTAATATGACATATAACTTG
Found at i:4839501 original size:54 final size:53
Alignment explanation
Indices: 4839390--4839501 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 53
4839380 GTAAAAAAAA
* * ***
4839390 TTTTTGAACATGACGTATAATAATAATATTTTTTTAATATGACATGTAACTTG
1 TTTTTGAACATGACGTATAACAATAATATTTTTTTAATATGACATATAACAAC
* * *
4839443 TTTTTGTACATGAGGTGTAACAATAATATTTTTTTTAATATGACATATAACAAC
1 TTTTTGAACATGACGTATAACAATAATA-TTTTTTTAATATGACATATAACAAC
4839497 TTTTT
1 TTTTT
4839502 TTAATGACTT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
53 24 0.48
54 26 0.52
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (53 bp):
TTTTTGAACATGACGTATAACAATAATATTTTTTTAATATGACATATAACAAC
Found at i:4839517 original size:53 final size:53
Alignment explanation
Indices: 4839390--4839517 Score: 150
Period size: 53 Copynumber: 2.4 Consensus size: 53
4839380 GTAAAAAAAA
* * * ***
4839390 TTTTTGAACATGACGTATAATAATAATATTTTTTTAATATGACATGTAACTTG
1 TTTTTGTACATGACGTATAACAATAATATTTTTTTAATATGACATATAACAAC
* *
4839443 TTTTTGTACATGAGGTGTAACAATAATATTTTTTTTAATATGACATATAACAAC
1 TTTTTGTACATGACGTATAACAATAATA-TTTTTTTAATATGACATATAACAAC
* *
4839497 TTTTTTTA-ATGACTTATAACA
1 TTTTTGTACATGACGTATAACA
4839518 TGTTTTTATG
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
53 34 0.55
54 28 0.45
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (53 bp):
TTTTTGTACATGACGTATAACAATAATATTTTTTTAATATGACATATAACAAC
Found at i:4839523 original size:77 final size:78
Alignment explanation
Indices: 4839418--4839570 Score: 184
Period size: 77 Copynumber: 2.0 Consensus size: 78
4839408 AATAATAATA
* * * * * *
4839418 TTTTTTTAATATGACATGTAACTTGTTTTTGTACATGAGGTGTAACAATAATATTTTTTTTAATA
1 TTTTTTTAATATGACATATAACATGTTTTTATACATAAGATGTAACAATAATA-TTTTTTTAACA
4839483 TGACATATAACAAC
65 TGACATATAACAAC
* ** *
4839497 TTTTTTT-A-ATGACTTATAACATGTTTTTATGTATAATATGTAACAATAATATTTTTTTAACAT
1 TTTTTTTAATATGACATATAACATGTTTTTATACATAAGATGTAACAATAATATTTTTTTAACAT
*
4839560 GACGTATAACA
66 GACATATAACA
4839571 TCATGTGCAT
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
76 21 0.33
77 34 0.54
78 1 0.02
79 7 0.11
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.46
Consensus pattern (78 bp):
TTTTTTTAATATGACATATAACATGTTTTTATACATAAGATGTAACAATAATATTTTTTTAACAT
GACATATAACAAC
Found at i:4849365 original size:18 final size:18
Alignment explanation
Indices: 4849338--4849393 Score: 103
Period size: 18 Copynumber: 3.1 Consensus size: 18
4849328 AGAGCCCCAT
4849338 CTGGAGTAATCACTAGGC
1 CTGGAGTAATCACTAGGC
*
4849356 CTGGAATAATCACTAGGC
1 CTGGAGTAATCACTAGGC
4849374 CTGGAGTAATCACTAGGC
1 CTGGAGTAATCACTAGGC
4849392 CT
1 CT
4849394 ATTACCCCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (18 bp):
CTGGAGTAATCACTAGGC
Found at i:4850682 original size:31 final size:31
Alignment explanation
Indices: 4850627--4850685 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
4850617 GATAGAGGGA
*
4850627 AAATGTTCTCTTTCCTTTTCTTTTCACAACG
1 AAATGTTCTCTTTCCTTATCTTTTCACAACG
4850658 AAATGTTCTCTTTCCTTCAT-TTTTCACA
1 AAATGTTCTCTTTCCTT-ATCTTTTCACA
4850686 GCAAAGAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.20, C:0.25, G:0.05, T:0.49
Consensus pattern (31 bp):
AAATGTTCTCTTTCCTTATCTTTTCACAACG
Found at i:4851455 original size:18 final size:18
Alignment explanation
Indices: 4851419--4851455 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4851409 GACTAAAGAA
* *
4851419 AAAGAGAGAGAGATTGAG
1 AAAGAGAGAGAAATAGAG
4851437 AAAGAGAGAGAAATAGAG
1 AAAGAGAGAGAAATAGAG
4851455 A
1 A
4851456 CAGCACTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.35, T:0.08
Consensus pattern (18 bp):
AAAGAGAGAGAAATAGAG
Found at i:4856029 original size:14 final size:15
Alignment explanation
Indices: 4856004--4856032 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4855994 TTAAATTTTT
4856004 AATTATTTTTTAAAA
1 AATTATTTTTTAAAA
4856019 AATTA-TTTTTAAAA
1 AATTATTTTTTAAAA
4856033 TTTATGTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTATTTTTTAAAA
Found at i:4858886 original size:17 final size:17
Alignment explanation
Indices: 4858864--4858896 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4858854 TCTGTTAATG
4858864 ATTGTTTTTCATTTTCT
1 ATTGTTTTTCATTTTCT
4858881 ATTGTTTTTCATTTTC
1 ATTGTTTTTCATTTTC
4858897 AAAGCCAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.06, T:0.70
Consensus pattern (17 bp):
ATTGTTTTTCATTTTCT
Found at i:4868807 original size:101 final size:101
Alignment explanation
Indices: 4868632--4868834 Score: 343
Period size: 101 Copynumber: 2.0 Consensus size: 101
4868622 CTCTTTAGGG
*
4868632 ATACTTCTTGTTCTTATAAAAATCCTTACTGCATGAAATCAAGTTTATTGATCAGAAGGGCAGAA
1 ATACTTCTTGTTCTTATAAAAATCCTTACTGCATGAAATCAAGTTTATTGAACAGAAGGGCAGAA
4868697 ATGTATCAGGAATATACGAAGCAATTACCCATCCCA
66 ATGTATCAGGAATATACGAAGCAATTACCCATCCCA
** * *
4868733 ATACTTCTTGTTCTTATAAAAATCCTTGTTGCATGAAATCAGGTTTGTTGAACAGAAGGGCAGAA
1 ATACTTCTTGTTCTTATAAAAATCCTTACTGCATGAAATCAAGTTTATTGAACAGAAGGGCAGAA
* *
4868798 ATGTATCAGGACTATATGAAGCAATTACCCATCCCA
66 ATGTATCAGGAATATACGAAGCAATTACCCATCCCA
4868834 A
1 A
4868835 CACAGCGTGG
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 95 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (101 bp):
ATACTTCTTGTTCTTATAAAAATCCTTACTGCATGAAATCAAGTTTATTGAACAGAAGGGCAGAA
ATGTATCAGGAATATACGAAGCAATTACCCATCCCA
Found at i:4875251 original size:2 final size:2
Alignment explanation
Indices: 4875246--4875274 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4875236 ATATTGTGTG
4875246 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4875275 TCTAGAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4876227 original size:16 final size:16
Alignment explanation
Indices: 4876203--4876236 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4876193 AGCAAATAGC
4876203 TTGAATACTTGAATAA
1 TTGAATACTTGAATAA
* *
4876219 TTGAGTACTTGAGTAA
1 TTGAATACTTGAATAA
4876235 TT
1 TT
4876237 TGACTCTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (16 bp):
TTGAATACTTGAATAA
Found at i:4888814 original size:3 final size:3
Alignment explanation
Indices: 4888806--4888839 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4888796 TCATACAATG
4888806 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4888840 AAGGGTGCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4893484 original size:2 final size:2
Alignment explanation
Indices: 4893477--4893515 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4893467 ATATCAAAGT
4893477 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4893516 GCACACACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4894534 original size:2 final size:2
Alignment explanation
Indices: 4894527--4894558 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4894517 TTTCTTTTTG
4894527 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4894559 NNNNNNNNNN
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):
TA
Found at i:4894666 original size:2 final size:2
Alignment explanation
Indices: 4894659--4894697 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
4894649 NNNNNNNNNN
* * *
4894659 TA TA TA TA TA TA TA TA TA TG TA TG TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4894698 TGAGTGTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4897223 original size:30 final size:28
Alignment explanation
Indices: 4897156--4897210 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
4897146 TATTCGTTCA
* *
4897156 GTTATTTTTCATAACAATATTCAAATAAT
1 GTTATATTTCATAACAATATCCAAAT-AT
4897185 GTTATATTTCATAACAATATCCAAAT
1 GTTATATTTCATAACAATATCCAAAT
4897211 TGCTCATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.42
Consensus pattern (28 bp):
GTTATATTTCATAACAATATCCAAATAT
Found at i:4898077 original size:23 final size:23
Alignment explanation
Indices: 4898027--4898077 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
4898017 TAAAGTCTGT
4898027 TATAAATTACAATAATGCTTATG
1 TATAAATTACAATAATGCTTATG
*
4898050 AATAAATTA-AATATATG-TATATG
1 TATAAATTACAATA-ATGCT-TATG
4898073 TATAA
1 TATAA
4898078 TATATTACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (23 bp):
TATAAATTACAATAATGCTTATG
Found at i:4898430 original size:32 final size:31
Alignment explanation
Indices: 4898359--4898430 Score: 72
Period size: 32 Copynumber: 2.3 Consensus size: 31
4898349 TGACATGGTG
* * * *
4898359 TAATGTGATGATGTGGCATGCCACGTGGCAT
1 TAATATGATGATGTGACATGCCACATGGCAC
** *
4898390 TAGCATGATGATGTGACAATGTCACATGGCAC
1 TAATATGATGATGTGAC-ATGCCACATGGCAC
4898422 TAATATGAT
1 TAATATGAT
4898431 AATATAGCCA
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (31 bp):
TAATATGATGATGTGACATGCCACATGGCAC
Found at i:4901908 original size:23 final size:22
Alignment explanation
Indices: 4901864--4901908 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
4901854 GCTTAGATGA
* * *
4901864 TAGCAAAGAAGGAAATTTATGG
1 TAGCAAAGAAAGAAAATCATGG
4901886 TAGCAAAAGAAAGAAAATCATGG
1 TAGC-AAAGAAAGAAAATCATGG
4901909 CTTTTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (22 bp):
TAGCAAAGAAAGAAAATCATGG
Found at i:4905404 original size:26 final size:27
Alignment explanation
Indices: 4905354--4905407 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
4905344 ACACTTAGCC
4905354 CTTTTTCTCTTCCCTAATCTCCTTTCT
1 CTTTTTCTCTTCCCTAATCTCCTTTCT
4905381 CTTTTTCTCTTCCCTAATCT-CTTTCT
1 CTTTTTCTCTTCCCTAATCTCCTTTCT
4905407 C
1 C
4905408 CTCCTCTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.07, C:0.37, G:0.00, T:0.56
Consensus pattern (27 bp):
CTTTTTCTCTTCCCTAATCTCCTTTCT
Found at i:4906783 original size:14 final size:15
Alignment explanation
Indices: 4906764--4906792 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4906754 TAATAGTTTT
4906764 TAAATTAAA-TAAAA
1 TAAATTAAATTAAAA
4906778 TAAATTAAATTAAAA
1 TAAATTAAATTAAAA
4906793 AGAGAATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAATTAAATTAAAA
Found at i:4909750 original size:18 final size:18
Alignment explanation
Indices: 4909688--4909757 Score: 54
Period size: 18 Copynumber: 3.7 Consensus size: 18
4909678 ACCGCGTAGG
4909688 TTTTT-GAAACCCTCGAA
1 TTTTTCGAAACCCTCGAA
**
4909705 TTTTTC-AAACCCTTAAACCGGT
1 TTTTTCGAAACCC-T----CGAA
4909727 TTTTTCGAAACCCTCGAA
1 TTTTTCGAAACCCTCGAA
*
4909745 TTTTTCAAAACCC
1 TTTTTCGAAACCC
4909758 GGTTTTAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 13
0.69 0.08 0.22
Matches are distributed among these distances:
17 11 0.27
18 15 0.37
22 9 0.22
23 6 0.15
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.36
Consensus pattern (18 bp):
TTTTTCGAAACCCTCGAA
Found at i:4916814 original size:29 final size:29
Alignment explanation
Indices: 4916759--4916817 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
4916749 TAGTATAGAT
**
4916759 TTGATGAATATTAATTTTTTAAAAAAAAA
1 TTGATGAATATTAATTAATTAAAAAAAAA
**
4916788 TTGATGAATATTAA-TAATTAATTAAAAA
1 TTGATGAATATTAATTAATTAAAAAAAAA
4916816 TT
1 TT
4916818 TAAAAATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 12 0.46
29 14 0.54
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (29 bp):
TTGATGAATATTAATTAATTAAAAAAAAA
Found at i:4918211 original size:2 final size:2
Alignment explanation
Indices: 4918204--4918233 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4918194 GATACAGTAA
4918204 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
4918234 CAAAGTGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4919619 original size:30 final size:30
Alignment explanation
Indices: 4919563--4919621 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
4919553 TAATATATAA
**
4919563 TTTTTATTTAAAAAATAAATTTTAAAAATT
1 TTTTTATTTAAAAAATAAATAATAAAAATT
*
4919593 TTTTTA-TTAAAAAATATATAAATAAAAAT
1 TTTTTATTTAAAAAATAAAT-AATAAAAAT
4919622 GGTTGAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
TTTTTATTTAAAAAATAAATAATAAAAATT
Found at i:4924123 original size:48 final size:48
Alignment explanation
Indices: 4924052--4924147 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
4924042 AAAGAATAAT
*
4924052 AATCGGGCGACAATGATGTAGTTCAACCCTTTACTTCTCTCTGTACCC
1 AATCGGGCGACAATGATGTAGTTCAACCCTTTACTTCTCGCTGTACCC
4924100 AATCGGGCGACAATGATGTAGTTCAACCCTTTACTTCTCGCTGTACCC
1 AATCGGGCGACAATGATGTAGTTCAACCCTTTACTTCTCGCTGTACCC
4924148 GAGTACTTAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (48 bp):
AATCGGGCGACAATGATGTAGTTCAACCCTTTACTTCTCGCTGTACCC
Found at i:4926370 original size:21 final size:21
Alignment explanation
Indices: 4926329--4926379 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
4926319 AAATAATAAA
* * *
4926329 AATTTAAAATATTTTTTTATT
1 AATTTAAAAAATTATTATATT
4926350 AATTTAAAAAATTATTATATT
1 AATTTAAAAAATTATTATATT
4926371 --TTTAAAAAA
1 AATTTAAAAAA
4926380 AAACTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 9 0.33
21 18 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTAAAAAATTATTATATT
Found at i:4926737 original size:18 final size:19
Alignment explanation
Indices: 4926714--4926752 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
4926704 TTATATATCT
4926714 AATAAAAAATAT-TTTTAA
1 AATAAAAAATATATTTTAA
* *
4926732 AATAAAATATTTATTTTAA
1 AATAAAAAATATATTTTAA
4926751 AA
1 AA
4926753 ATTAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATAAAAAATATATTTTAA
Found at i:4933839 original size:3 final size:3
Alignment explanation
Indices: 4933831--4933855 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4933821 CATTCGCAGG
4933831 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
4933856 CAATCTCTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4943915 original size:125 final size:125
Alignment explanation
Indices: 4943618--4943990 Score: 696
Period size: 125 Copynumber: 3.0 Consensus size: 125
4943608 TTAAAACCTT
4943618 TAACTCAATGCATTTATTGTATATTGTAGTTATACGAATATTGCATAATTATCAAAGTACTAATT
1 TAACTCAATGCATTTATTGTATATTGTAGTTATACGAATATTGCATAATTATCAAAGTACTAATT
* *
4943683 ATCATTATTTTATATA-TTATTTAATTAAAACAAGTTCATGAATATAATTAATCTTATTA
66 ATCATTATTCTATATATTTGTTTAATTAAAACAAGTTCATGAATATAATTAATCTTATTA
4943742 T-ACTCAATGCATTTATTGTATATTGTAGTTATACGAATATTGCATAATTATCAAAGTACTAATT
1 TAACTCAATGCATTTATTGTATATTGTAGTTATACGAATATTGCATAATTATCAAAGTACTAATT
4943806 ATCATTATTCTATATATTTGTTTAATTAAAACAAGTTCATGAATATAATTAATCTTATTA
66 ATCATTATTCTATATATTTGTTTAATTAAAACAAGTTCATGAATATAATTAATCTTATTA
* *
4943866 TAACTCAATGCATTTATTGTATATTGTAGTTATACAAATATTGCATAATTATCAAAGTACTAACT
1 TAACTCAATGCATTTATTGTATATTGTAGTTATACGAATATTGCATAATTATCAAAGTACTAATT
4943931 ATCATTATTCTATATATTTGTTTAATTAAAACAAGTTCATGAATATAATTAATCTTATTA
66 ATCATTATTCTATATATTTGTTTAATTAAAACAAGTTCATGAATATAATTAATCTTATTA
4943991 AATAAAAGTT
Statistics
Matches: 243, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
123 78 0.32
124 44 0.18
125 121 0.50
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.44
Consensus pattern (125 bp):
TAACTCAATGCATTTATTGTATATTGTAGTTATACGAATATTGCATAATTATCAAAGTACTAATT
ATCATTATTCTATATATTTGTTTAATTAAAACAAGTTCATGAATATAATTAATCTTATTA
Found at i:4955750 original size:7 final size:7
Alignment explanation
Indices: 4955738--4955771 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
4955728 ATCCCCCCAG
4955738 AAAAAAT
1 AAAAAAT
4955745 AAAAAAT
1 AAAAAAT
4955752 AAAAAAT
1 AAAAAAT
4955759 AAAAAAT
1 AAAAAAT
4955766 AAAAAA
1 AAAAAA
4955772 GAAAGTCCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:4996034 original size:24 final size:26
Alignment explanation
Indices: 4995996--4996043 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
4995986 GGAATTTCGT
*
4995996 TAGGTCAGTGGACTCGGGTGGGGGAA
1 TAGGTCAGTGGACTCGGGAGGGGGAA
4996022 TAGGTC-G-GGACTCGGGAGGGGG
1 TAGGTCAGTGGACTCGGGAGGGGG
4996044 GGTGTGGTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.67
25 1 0.05
26 6 0.29
ACGTcount: A:0.17, C:0.12, G:0.54, T:0.17
Consensus pattern (26 bp):
TAGGTCAGTGGACTCGGGAGGGGGAA
Found at i:5002088 original size:21 final size:21
Alignment explanation
Indices: 5002062--5002101 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5002052 TTTTATTTTT
*
5002062 TAAAATTAAAATCATAGAACA
1 TAAAATTAAAATAATAGAACA
*
5002083 TAAAATTAAGATAATAGAA
1 TAAAATTAAAATAATAGAA
5002102 AAAAAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.25
Consensus pattern (21 bp):
TAAAATTAAAATAATAGAACA
Found at i:5002108 original size:21 final size:21
Alignment explanation
Indices: 5002063--5002108 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5002053 TTTATTTTTT
* * *
5002063 AAAATTAAAATCATAGAACAT
1 AAAATTAAAATAATAGAAAAA
*
5002084 AAAATTAAGATAATAGAAAAA
1 AAAATTAAAATAATAGAAAAA
5002105 AAAA
1 AAAA
5002109 CATGACAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.70, C:0.04, G:0.07, T:0.20
Consensus pattern (21 bp):
AAAATTAAAATAATAGAAAAA
Done.