Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008690.1 Hibiscus syriacus cultivar Beakdansim tig00111718_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 531595
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 3
Found at i:218012 original size:4 final size:4
Alignment explanation
Indices: 218003--218034 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
217993 TATGTAAAAC
218003 TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA
1 TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA
218035 AATGAAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
TGAA
Found at i:222366 original size:17 final size:16
Alignment explanation
Indices: 222318--222366 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
222308 CTGACACATA
* *
222318 TAAAAATAACTTTTAA
1 TAAAAATAAATTTTAT
*
222334 TAAAAACAAA-TTTAT
1 TAAAAATAAATTTTAT
222349 TAAAATATAAATTTTAT
1 TAAAA-ATAAATTTTAT
222366 T
1 T
222367 TTTAATATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 9 0.33
16 12 0.44
17 6 0.22
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAAATAAATTTTAT
Found at i:222495 original size:21 final size:21
Alignment explanation
Indices: 222469--222508 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
222459 CAACTTTTTG
* *
222469 ATAAGATTCATTTTATAATTT
1 ATAAGATTAATTGTATAATTT
222490 ATAAGATTAATTGTATAAT
1 ATAAGATTAATTGTATAAT
222509 ATTTTATAGT
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:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (21 bp):
ATAAGATTAATTGTATAATTT
Found at i:222946 original size:45 final size:45
Alignment explanation
Indices: 222895--222981 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 45
222885 AGAAGTATGC
* * *
222895 TTTGTAGAACTTGCTTTTACT-ATGTGGAATGTCTTGTGTGCATGT
1 TTTGTAGAACTTGCTCTTA-TAAAGTGAAATGTCTTGTGTGCATGT
222940 TTTGTAGAACTTGCTCTTATAAAGTGAAATGTCTTGTGTGCA
1 TTTGTAGAACTTGCTCTTATAAAGTGAAATGTCTTGTGTGCA
222982 AAGTGTGTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 1 0.03
45 37 0.97
ACGTcount: A:0.22, C:0.11, G:0.23, T:0.44
Consensus pattern (45 bp):
TTTGTAGAACTTGCTCTTATAAAGTGAAATGTCTTGTGTGCATGT
Found at i:224494 original size:39 final size:39
Alignment explanation
Indices: 224440--224517 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
224430 TTGCCTTGGT
224440 AAATTATCATGTTTCTGATACAGATTTGTTGATTTCTAA
1 AAATTATCATGTTTCTGATACAGATTTGTTGATTTCTAA
*
224479 AAATTATGATGTTTCTGATACAGATTTGTTGATTTCTAA
1 AAATTATCATGTTTCTGATACAGATTTGTTGATTTCTAA
224518 TGTTAATCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (39 bp):
AAATTATCATGTTTCTGATACAGATTTGTTGATTTCTAA
Found at i:224514 original size:21 final size:21
Alignment explanation
Indices: 224451--224515 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
224441 AATTATCATG
224451 TTTCTGATACAGATTTGTTGA
1 TTTCTGATACAGATTTGTTGA
* *
224472 TTTCT-A-A-AAATTATGATG-
1 TTTCTGATACAGATT-TGTTGA
224490 TTTCTGATACAGATTTGTTGA
1 TTTCTGATACAGATTTGTTGA
224511 TTTCT
1 TTTCT
224516 AATGTTAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
18 9 0.26
19 6 0.17
20 6 0.17
21 14 0.40
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.49
Consensus pattern (21 bp):
TTTCTGATACAGATTTGTTGA
Found at i:232398 original size:41 final size:41
Alignment explanation
Indices: 232353--232432 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
232343 TCATAACAAC
*
232353 AATAAAATACTATTATCATATGCAATGGGAGGTAGGTTAAT
1 AATAAAATACTATTATCATATGCAATGGGAGATAGGTTAAT
*
232394 AATAAAATACTATTCTCATATGCAATGGGAGATAGGTTA
1 AATAAAATACTATTATCATATGCAATGGGAGATAGGTTA
232433 GTAAACTATC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (41 bp):
AATAAAATACTATTATCATATGCAATGGGAGATAGGTTAAT
Found at i:236254 original size:25 final size:25
Alignment explanation
Indices: 236207--236274 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
236197 AGTTTATATT
*
236207 GCACTTTCGAGTGTAAATCTACGAG
1 GCACTTTCGAGTGCAAATCTACGAG
* *
236232 GCACTTTCGAGTGCAATTGTACGAG
1 GCACTTTCGAGTGCAAATCTACGAG
* * *
236257 GAATTTTCGAATGCAAAT
1 GCACTTTCGAGTGCAAAT
236275 ATATCTACGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (25 bp):
GCACTTTCGAGTGCAAATCTACGAG
Found at i:241552 original size:31 final size:29
Alignment explanation
Indices: 241484--241614 Score: 70
Period size: 31 Copynumber: 4.3 Consensus size: 29
241474 AAATATTTTT
*
241484 TTATAATTTTATTAATAAAAATATTAATAG
1 TTAT-ATTTTATTAATAAAAATATTAATAA
241514 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
* * * * * *
241547 TTATATTAATTATTTATTAAAGTAATAGT-G
1 TTATATT--TTATTAATAAAAATATTAATAA
* * *
241577 TTATATTATATT-TTAAAAATATTAATTA
1 TTATATTTTATTAATAAAAATATTAATAA
*
241605 GTATATTTTA
1 TTATATTTTA
241615 AATATCTTTA
Statistics
Matches: 76, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
27 9 0.12
28 12 0.16
30 8 0.11
31 22 0.29
32 6 0.08
33 19 0.25
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:241633 original size:23 final size:23
Alignment explanation
Indices: 241584--241634 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
241574 GTGTTATATT
**
241584 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
241607 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
241630 ATATT
1 ATATT
241635 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:241846 original size:22 final size:22
Alignment explanation
Indices: 241815--241877 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
241805 TTTATTATAA
241815 TATTAAAAATA-TAATATAATAT
1 TATTAAAAATATTAATA-AATAT
*
241837 TATTAGAAATATTAATAAATAT
1 TATTAAAAATATTAATAAATAT
* * *
241859 ATTTTAAATATTTTAATAA
1 -TATTAAAAATATTAATAA
241878 TTAATATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TATTAAAAATATTAATAAATAT
Found at i:241861 original size:21 final size:22
Alignment explanation
Indices: 241814--241870 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
241804 TTTTATTATA
241814 ATATTAAAAATA-TAATATAAT
1 ATATTAAAAATATTAATATAAT
*
241835 ATTATTAGAAATATTAATA-AAT
1 A-TATTAAAAATATTAATATAAT
**
241857 ATATTTTAAATATT
1 ATATTAAAAATATT
241871 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 12 0.39
22 14 0.45
23 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATATTAAAAATATTAATATAAT
Found at i:242136 original size:38 final size:38
Alignment explanation
Indices: 242093--242166 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
242083 CCAAACACTA
*
242093 GAAAACATTTTCCGGAAAACGAATTACGTGAAACAAGG
1 GAAAACATTTTCCGAAAAACGAATTACGTGAAACAAGG
*
242131 GAAAACATTTTCCGAAAAATGAATTACGTGAAACAA
1 GAAAACATTTTCCGAAAAACGAATTACGTGAAACAA
242167 ACACAGAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.20
Consensus pattern (38 bp):
GAAAACATTTTCCGAAAAACGAATTACGTGAAACAAGG
Found at i:244857 original size:3 final size:3
Alignment explanation
Indices: 244849--244891 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
244839 TCATAAGAGC
244849 GTA GTA GTA GTA GTA GTA -TA GTA GTA GTA -TA GTA GTA GTA GTA
1 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA
244892 AAAATATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (3 bp):
GTA
Found at i:244872 original size:11 final size:11
Alignment explanation
Indices: 244849--244888 Score: 71
Period size: 11 Copynumber: 3.5 Consensus size: 11
244839 TCATAAGAGC
244849 GTAGTAGTAGTA
1 GTAGTA-TAGTA
244861 GTAGTATAGTA
1 GTAGTATAGTA
244872 GTAGTATAGTA
1 GTAGTATAGTA
244883 GTAGTA
1 GTAGTA
244889 GTAAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 22 0.79
12 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (11 bp):
GTAGTATAGTA
Found at i:244872 original size:14 final size:15
Alignment explanation
Indices: 244849--244891 Score: 72
Period size: 14 Copynumber: 3.0 Consensus size: 15
244839 TCATAAGAGC
244849 GTAGTAGTAGTAGTA
1 GTAGTAGTAGTAGTA
244864 GTA-TAGTAGTAGTA
1 GTAGTAGTAGTAGTA
244878 -TAGTAGTAGTAGTA
1 GTAGTAGTAGTAGTA
244892 AAAATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.07
14 22 0.81
15 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (15 bp):
GTAGTAGTAGTAGTA
Found at i:245479 original size:157 final size:157
Alignment explanation
Indices: 245193--245511 Score: 638
Period size: 157 Copynumber: 2.0 Consensus size: 157
245183 AAATCAAATG
245193 ATATGAAATAAAAAAGAGATAAAAATATATTAATCTTTAAAATTGACACTGTAAAAAAGAAAAAT
1 ATATGAAATAAAAAAGAGATAAAAATATATTAATCTTTAAAATTGACACTGTAAAAAAGAAAAAT
245258 AATATGTGAGTGAAAATAAAATAGTAATAATAACAATAATTAAATAAGATAAATACATAAAAATA
66 AATATGTGAGTGAAAATAAAATAGTAATAATAACAATAATTAAATAAGATAAATACATAAAAATA
245323 AATAAAAACACATTAATGTAAGGACCC
131 AATAAAAACACATTAATGTAAGGACCC
245350 ATATGAAATAAAAAAGAGATAAAAATATATTAATCTTTAAAATTGACACTGTAAAAAAGAAAAAT
1 ATATGAAATAAAAAAGAGATAAAAATATATTAATCTTTAAAATTGACACTGTAAAAAAGAAAAAT
245415 AATATGTGAGTGAAAATAAAATAGTAATAATAACAATAATTAAATAAGATAAATACATAAAAATA
66 AATATGTGAGTGAAAATAAAATAGTAATAATAACAATAATTAAATAAGATAAATACATAAAAATA
245480 AATAAAAACACATTAATGTAAGGACCC
131 AATAAAAACACATTAATGTAAGGACCC
245507 ATATG
1 ATATG
245512 TAAAAGAAAA
Statistics
Matches: 162, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 162 1.00
ACGTcount: A:0.59, C:0.06, G:0.10, T:0.25
Consensus pattern (157 bp):
ATATGAAATAAAAAAGAGATAAAAATATATTAATCTTTAAAATTGACACTGTAAAAAAGAAAAAT
AATATGTGAGTGAAAATAAAATAGTAATAATAACAATAATTAAATAAGATAAATACATAAAAATA
AATAAAAACACATTAATGTAAGGACCC
Found at i:247497 original size:29 final size:28
Alignment explanation
Indices: 247465--247540 Score: 102
Period size: 27 Copynumber: 2.7 Consensus size: 28
247455 CTATTATAAC
*
247465 TTATAAAAGGTTTTATCCTTAATTTTAAT
1 TTATAAAA-GTTTTGTCCTTAATTTTAAT
247494 TTATAAAAAG--TTGTCCTTAATTTTAAT
1 TTAT-AAAAGTTTTGTCCTTAATTTTAAT
247521 TTATATAAAGTTTTGTCCTT
1 TTATA-AAAGTTTTGTCCTT
247541 TTACTAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
26 1 0.02
27 24 0.57
29 13 0.31
30 4 0.10
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (28 bp):
TTATAAAAGTTTTGTCCTTAATTTTAAT
Found at i:247584 original size:26 final size:27
Alignment explanation
Indices: 247554--247610 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
247544 CTAAAATGTT
* *
247554 TTGTCCTTTAGTGTAATTTATAAA-AG
1 TTGTCCTTAAATGTAATTTATAAAGAG
*
247580 TTGTCCTTAAATGTGATTTATAAAGAG
1 TTGTCCTTAAATGTAATTTATAAAGAG
247607 TTGT
1 TTGT
247611 GTTGTATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.46
Consensus pattern (27 bp):
TTGTCCTTAAATGTAATTTATAAAGAG
Found at i:260012 original size:2 final size:2
Alignment explanation
Indices: 260000--260057 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
259990 AATTTTATTA
*
260000 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
260042 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
260058 TATTCCAACA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:261683 original size:20 final size:20
Alignment explanation
Indices: 261658--261696 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
261648 GTGTAGATTC
261658 TGCCACCTGTCCATGGCTTT
1 TGCCACCTGTCCATGGCTTT
261678 TGCCACCTGTCCATGGCTT
1 TGCCACCTGTCCATGGCTT
261697 GATTAAGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.36, G:0.21, T:0.33
Consensus pattern (20 bp):
TGCCACCTGTCCATGGCTTT
Found at i:275655 original size:5 final size:5
Alignment explanation
Indices: 275645--275670 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
275635 TCCATGTATG
275645 TTTGA TTTGA TTTGA TTTGA TTTGA T
1 TTTGA TTTGA TTTGA TTTGA TTTGA T
275671 GGGATAGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (5 bp):
TTTGA
Found at i:276190 original size:30 final size:30
Alignment explanation
Indices: 276154--276227 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
276144 AATGAATAAT
* *
276154 AGCTTAGTAAGGCTATTAGAGAGAGGGTAA
1 AGCTTAGCAAAGCTATTAGAGAGAGGGTAA
*
276184 AGCTTAGCAAAGCTATTAGAGAGAGGGTGA
1 AGCTTAGCAAAGCTATTAGAGAGAGGGTAA
276214 AGCTTAGCAAAGCT
1 AGCTTAGCAAAGCT
276228 TAGAATACTG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.36, C:0.11, G:0.31, T:0.22
Consensus pattern (30 bp):
AGCTTAGCAAAGCTATTAGAGAGAGGGTAA
Found at i:278430 original size:12 final size:12
Alignment explanation
Indices: 278400--278468 Score: 56
Period size: 12 Copynumber: 5.8 Consensus size: 12
278390 AAGGGAAAAT
278400 AAAATAAAATCAA
1 AAAATAAAAT-AA
*
278413 AGAA-AAAAT--
1 AAAATAAAATAA
278422 AAAATAAAATAA
1 AAAATAAAATAA
*
278434 AATCAT-AAATAAA
1 AA-AATAAAAT-AA
278447 AAAATAAAAATAA
1 AAAAT-AAAATAA
278460 AAAATAAAA
1 AAAATAAAA
278469 ATATTAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 15
0.70 0.06 0.23
Matches are distributed among these distances:
9 3 0.07
10 5 0.11
12 17 0.38
13 16 0.36
14 4 0.09
ACGTcount: A:0.80, C:0.03, G:0.01, T:0.16
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:278443 original size:22 final size:22
Alignment explanation
Indices: 278395--278468 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
278385 AATTAAAGGG
*
278395 AAAATAAAATAAAATCAAAGAA
1 AAAATAAAATAAAATAAAAGAA
**
278417 AAAATAAAATAAAATAAAATCA
1 AAAATAAAATAAAATAAAAGAA
* *
278439 TAAAT-AAA-AAAATAAAAATAA
1 AAAATAAAATAAAAT-AAAAGAA
278460 AAAATAAAA
1 AAAATAAAA
278469 ATATTAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
20 5 0.11
21 13 0.30
22 26 0.59
ACGTcount: A:0.80, C:0.03, G:0.01, T:0.16
Consensus pattern (22 bp):
AAAATAAAATAAAATAAAAGAA
Found at i:278462 original size:27 final size:27
Alignment explanation
Indices: 278395--278461 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
278385 AATTAAAGGG
278395 AAAATAAAATAAAATCAAAGAAAAAAT
1 AAAATAAAATAAAATCAAAGAAAAAAT
* *
278422 AAAATAAAATAAAATCATA-AATAAA-
1 AAAATAAAATAAAATCAAAGAAAAAAT
278447 AAAATAAAAATAAAA
1 AAAAT-AAAATAAAA
278462 AATAAAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
25 5 0.14
26 14 0.38
27 18 0.49
ACGTcount: A:0.79, C:0.03, G:0.01, T:0.16
Consensus pattern (27 bp):
AAAATAAAATAAAATCAAAGAAAAAAT
Found at i:278468 original size:5 final size:5
Alignment explanation
Indices: 278395--278461 Score: 66
Period size: 5 Copynumber: 12.8 Consensus size: 5
278385 AATTAAAGGG
*
278395 AAAAT AAAAT AAAAT CAAAGAA AAAAT AAAAT AAAAT AAAAT CATAAAT
1 AAAAT AAAAT AAAAT -AAA-AT AAAAT AAAAT AAAAT AAAAT -A-AAAT
278444 -AAA- AAAAT AAAAAT AAAA
1 AAAAT AAAAT -AAAAT AAAA
278462 AATAAAAATA
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
4 6 0.11
5 30 0.57
6 12 0.23
7 5 0.09
ACGTcount: A:0.79, C:0.03, G:0.01, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:278480 original size:13 final size:13
Alignment explanation
Indices: 278415--278471 Score: 60
Period size: 13 Copynumber: 4.1 Consensus size: 13
278405 AAAATCAAAG
*
278415 AAAAAATAAAATAA
1 AAAAAATAAAA-AT
*
278429 AATAAAATCATAAAT
1 AA-AAAAT-AAAAAT
278444 AAAAAAATAAAAAT
1 -AAAAAATAAAAAT
278458 AAAAAATAAAAAT
1 AAAAAATAAAAAT
278471 A
1 A
278472 TTAAATAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 14 0.38
14 7 0.19
15 11 0.30
16 5 0.14
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:279630 original size:20 final size:20
Alignment explanation
Indices: 279605--279648 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
279595 TATATTATAT
*
279605 AACTTCAAAAACGTTTTCAA
1 AACTTCAAAAACATTTTCAA
279625 AACTTCAAAAACATTTTCAA
1 AACTTCAAAAACATTTTCAA
279645 AACT
1 AACT
279649 AAATATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.30
Consensus pattern (20 bp):
AACTTCAAAAACATTTTCAA
Found at i:281124 original size:21 final size:21
Alignment explanation
Indices: 281098--281138 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
281088 TAGAAATTAA
*
281098 TTTTTTTTAAAATTGTTAATT
1 TTTTTTTTAAAATTGATAATT
281119 TTTTTTTTAAAATTGATAAT
1 TTTTTTTTAAAATTGATAAT
281139 CAAAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (21 bp):
TTTTTTTTAAAATTGATAATT
Found at i:283665 original size:2 final size:2
Alignment explanation
Indices: 283658--283683 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
283648 CCATATTTAA
283658 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
283684 TCCCCCCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:287209 original size:6 final size:6
Alignment explanation
Indices: 287198--287232 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
287188 ACCCGTGACT
* *
287198 CTCTCC CTCTCC CTCTCC CTCTCT CTCTCT CTCTC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
287233 TACCCTGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (6 bp):
CTCTCC
Found at i:287233 original size:12 final size:12
Alignment explanation
Indices: 287196--287233 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
287186 AAACCCGTGA
287196 CTCTCTCCCTCT
1 CTCTCTCCCTCT
*
287208 CCCTCTCCCTCT
1 CTCTCTCCCTCT
*
287220 CTCTCTCTCTCT
1 CTCTCTCCCTCT
287232 CT
1 CT
287234 ACCCTGATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (12 bp):
CTCTCTCCCTCT
Found at i:288780 original size:22 final size:22
Alignment explanation
Indices: 288739--288780 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
288729 TTTTAATAAT
* * *
288739 TTTACTTTTATGACATGTTTTC
1 TTTACTTATATGAAACGTTTTC
288761 TTTACTTATATGAAACGTTT
1 TTTACTTATATGAAACGTTT
288781 CTCTATATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.55
Consensus pattern (22 bp):
TTTACTTATATGAAACGTTTTC
Found at i:292625 original size:11 final size:12
Alignment explanation
Indices: 292607--292638 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
292597 ATGAATGAAG
292607 GAAAATTAATTT
1 GAAAATTAATTT
292619 G-AAATTAATTT
1 GAAAATTAATTT
292630 GAAAATTAA
1 GAAAATTAA
292639 ACGATGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (12 bp):
GAAAATTAATTT
Found at i:296647 original size:13 final size:13
Alignment explanation
Indices: 296629--296698 Score: 63
Period size: 13 Copynumber: 5.4 Consensus size: 13
296619 ATAAATAATA
*
296629 AAAAAATTACAAT
1 AAAAAACTACAAT
*
296642 AAAAAAGT-CTAAT
1 AAAAAACTAC-AAT
*
296655 AAACAACTACAAT
1 AAAAAACTACAAT
*
296668 AAAAAAGT-CTAAT
1 AAAAAACTAC-AAT
*
296681 AAACAACTACAAT
1 AAAAAACTACAAT
296694 AAAAA
1 AAAAA
296699 GTACTAAATA
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
12 2 0.04
13 41 0.91
14 2 0.04
ACGTcount: A:0.66, C:0.13, G:0.03, T:0.19
Consensus pattern (13 bp):
AAAAAACTACAAT
Found at i:296711 original size:25 final size:26
Alignment explanation
Indices: 296636--296724 Score: 128
Period size: 26 Copynumber: 3.5 Consensus size: 26
296626 ATAAAAAAAT
296636 TACAATAAAAAAGTCTAATAAACAAC
1 TACAATAAAAAAGTCTAATAAACAAC
296662 TACAATAAAAAAGTCTAATAAACAAC
1 TACAATAAAAAAGTCTAATAAACAAC
* *
296688 TACAAT-AAAAAGTACTAA-ATACAAA
1 TACAATAAAAAAGT-CTAATAAACAAC
*
296713 TATAATAAAAAA
1 TACAATAAAAAA
296725 AAAAATCTCT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
25 17 0.29
26 41 0.71
ACGTcount: A:0.64, C:0.12, G:0.03, T:0.20
Consensus pattern (26 bp):
TACAATAAAAAAGTCTAATAAACAAC
Found at i:296835 original size:3 final size:3
Alignment explanation
Indices: 296827--296858 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
296817 CTCCTCGCTG
*
296827 TCA TCA TCA TCA CCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
296859 GTCGTGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (3 bp):
TCA
Found at i:298559 original size:9 final size:9
Alignment explanation
Indices: 298545--298578 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
298535 TAAGTAAAAT
298545 ATTAAATAA
1 ATTAAATAA
298554 ATTAAAT-A
1 ATTAAATAA
*
298562 CTTAAATAA
1 ATTAAATAA
298571 ATTAAATA
1 ATTAAATA
298579 TAAAATATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:298559 original size:17 final size:16
Alignment explanation
Indices: 298541--298585 Score: 72
Period size: 17 Copynumber: 2.8 Consensus size: 16
298531 TAATTAAGTA
298541 AAATATTAAATAAATT
1 AAATATTAAATAAATT
298557 AAATACTTAAATAAATT
1 AAATA-TTAAATAAATT
*
298574 AAATATAAAATA
1 AAATATTAAATA
298586 TTGAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATATTAAATAAATT
Found at i:305077 original size:13 final size:14
Alignment explanation
Indices: 305054--305082 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
305044 GTAGTGGAAT
305054 TTTACAAATTTAAA
1 TTTACAAATTTAAA
305068 TTTA-AAATTTAAA
1 TTTACAAATTTAAA
305081 TT
1 TT
305083 ACGTTGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTACAAATTTAAA
Found at i:305568 original size:2 final size:2
Alignment explanation
Indices: 305561--305595 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
305551 ATGAAAATAA
305561 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
305596 ATTACCATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:308119 original size:24 final size:24
Alignment explanation
Indices: 308088--308136 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
308078 TATTAGTGAG
308088 AAAGTTTTGA-AAATGTTTGATGA
1 AAAGTTTTGAGAAATGTTTGATGA
*
308111 AAAGATTTTGAGAATTGTTTGATGA
1 AAAG-TTTTGAGAAATGTTTGATGA
308136 A
1 A
308137 GCTTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.17
24 6 0.26
25 13 0.57
ACGTcount: A:0.39, C:0.00, G:0.22, T:0.39
Consensus pattern (24 bp):
AAAGTTTTGAGAAATGTTTGATGA
Found at i:311655 original size:3 final size:3
Alignment explanation
Indices: 311647--311679 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
311637 GAGAGAGGAA
311647 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
311680 GAATAATCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:319338 original size:7 final size:7
Alignment explanation
Indices: 319326--319354 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
319316 TAAACTATTT
319326 CTTGCAA
1 CTTGCAA
319333 CTTGCAA
1 CTTGCAA
319340 CTTGCAA
1 CTTGCAA
319347 CTTGCAA
1 CTTGCAA
319354 C
1 C
319355 ATAAAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.31, G:0.14, T:0.28
Consensus pattern (7 bp):
CTTGCAA
Found at i:321370 original size:2 final size:2
Alignment explanation
Indices: 321363--321390 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
321353 GAGAATAAAT
321363 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
321391 GCGATGATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:321510 original size:144 final size:144
Alignment explanation
Indices: 321245--321523 Score: 540
Period size: 144 Copynumber: 1.9 Consensus size: 144
321235 GTGACCTCGT
321245 TGGCGATGATGGGGCGAGACTGGTTACCTCCGAGTCAGTTTATATAGTAGGGGTTGTTTACTACA
1 TGGCGATGATGGGGCGAGACTGGTTACCTCCGAGTCAGTTTATATAGTAGGGGTTGTTTACTACA
321310 AATTGGAGGTATGTTTTATTGTTTGGGTTTTGATGATTTATTTGAGAATAAATTGTGTGTGTGTG
66 AATTGGAGGTATGTTTTATTGTTTGGGTTTTGATGATTTATTTGAGAATAAATTGTGTGTGTGTG
321375 TGTGTGTGTGTGTG
131 TGTGTGTGTGTGTG
*
321389 TGGCGATGATGGGGCGAGGCTGGTTACCTCCGAGTCAGTTTATATAGTAGGGGTTGTTTACTACA
1 TGGCGATGATGGGGCGAGACTGGTTACCTCCGAGTCAGTTTATATAGTAGGGGTTGTTTACTACA
*
321454 AATTGGAGGTATGTTTTATTGTTTGGGTTTTGATGATTTATTTGAGAATAACTTGTGTGTGTGTG
66 AATTGGAGGTATGTTTTATTGTTTGGGTTTTGATGATTTATTTGAGAATAAATTGTGTGTGTGTG
321519 TGTGT
131 TGTGT
321524 ACGTGCGTGC
Statistics
Matches: 133, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 133 1.00
ACGTcount: A:0.19, C:0.08, G:0.32, T:0.41
Consensus pattern (144 bp):
TGGCGATGATGGGGCGAGACTGGTTACCTCCGAGTCAGTTTATATAGTAGGGGTTGTTTACTACA
AATTGGAGGTATGTTTTATTGTTTGGGTTTTGATGATTTATTTGAGAATAAATTGTGTGTGTGTG
TGTGTGTGTGTGTG
Found at i:321514 original size:4 final size:4
Alignment explanation
Indices: 321507--321578 Score: 63
Period size: 4 Copynumber: 18.0 Consensus size: 4
321497 GAGAATAACT
** * * * * * * *
321507 TGTG TGTG TGTG TGTG TACG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG
321555 TGTG TGTG TGTG TGTG TGTG TGTG
1 TGTG TGTG TGTG TGTG TGTG TGTG
321579 AGAGAGAAAG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 64 1.00
ACGTcount: A:0.01, C:0.11, G:0.49, T:0.39
Consensus pattern (4 bp):
TGTG
Found at i:339921 original size:68 final size:68
Alignment explanation
Indices: 339840--339982 Score: 216
Period size: 68 Copynumber: 2.1 Consensus size: 68
339830 TTAAACATTA
* *
339840 TATTTTATATTTGTTTTAAGTATTTTAGTTTAAATAGGTTTT-AGTATTTCAATTAGGATTTAAG
1 TATTTTATATTTGTTTTAAGTATTTTAGTTTAAATA-ATTTTAAGTATTTCAATTAGGATCTAAG
339904 ATAT
65 ATAT
* * * *
339908 TATTTTATTTTTGTTTTAGGTATTTTAGTTTAAATAATTTTAAGTGTTTTAATTAGGATCTAAGA
1 TATTTTATATTTGTTTTAAGTATTTTAGTTTAAATAATTTTAAGTATTTCAATTAGGATCTAAGA
339973 TAT
66 TAT
339976 TATTTTA
1 TATTTTA
339983 GGAATTTAGC
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
67 4 0.06
68 64 0.94
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (68 bp):
TATTTTATATTTGTTTTAAGTATTTTAGTTTAAATAATTTTAAGTATTTCAATTAGGATCTAAGA
TAT
Found at i:342689 original size:13 final size:13
Alignment explanation
Indices: 342671--342703 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
342661 ATTTTGATAT
342671 TCGAATAATTATA
1 TCGAATAATTATA
342684 TCGAATAATTATA
1 TCGAATAATTATA
342697 TCGAATA
1 TCGAATA
342704 TACTTAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (13 bp):
TCGAATAATTATA
Found at i:344619 original size:21 final size:21
Alignment explanation
Indices: 344590--344671 Score: 85
Period size: 21 Copynumber: 3.8 Consensus size: 21
344580 AGAACCCGTA
*
344590 GGGGTATCGATTCCC-TCAAG
1 GGGGAATCGATTCCCTTCAAG
*
344610 GAGGGAATCGGTTCCCATTCAAAG
1 G-GGGAATCGATTCCC-TTC-AAG
*
344634 GGGGAATCGGTTCCCCTTCAAG
1 GGGGAATCGATT-CCCTTCAAG
*
344656 GGGGTATCGATTCCCT
1 GGGGAATCGATTCCCT
344672 CTGCACTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
20 1 0.02
21 16 0.30
22 13 0.25
23 16 0.30
24 7 0.13
ACGTcount: A:0.21, C:0.24, G:0.30, T:0.24
Consensus pattern (21 bp):
GGGGAATCGATTCCCTTCAAG
Found at i:344638 original size:23 final size:22
Alignment explanation
Indices: 344605--344670 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 22
344595 ATCGATTCCC
344605 TCAAGGAGGGAATCGGTTCCCAT
1 TCAAGG-GGGAATCGGTTCCCAT
*
344628 TCAAAGGGGGAATCGGTTCCCCT
1 TC-AAGGGGGAATCGGTTCCCAT
* *
344651 TCAAGGGGGTATCGATTCCC
1 TCAAGGGGGAATCGGTTCCC
344671 TCTGCACTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
22 16 0.41
23 19 0.49
24 4 0.10
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (22 bp):
TCAAGGGGGAATCGGTTCCCAT
Found at i:348519 original size:22 final size:21
Alignment explanation
Indices: 348477--348516 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
348467 GAGTTTATTT
*
348477 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
348498 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
348517 ACAATTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:352635 original size:19 final size:20
Alignment explanation
Indices: 352611--352656 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
352601 CAAAATTGTC
352611 CAATTTC-ACA-TCCTAACAT
1 CAATTTCAACACT-CTAACAT
352630 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
352650 TAATTTC
1 CAATTTC
352657 TAGCATAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 7 0.29
20 16 0.67
21 1 0.04
ACGTcount: A:0.37, C:0.28, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:360061 original size:21 final size:21
Alignment explanation
Indices: 360035--360074 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
360025 CCCCCTTTGA
*
360035 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
360056 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
360075 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:362343 original size:44 final size:45
Alignment explanation
Indices: 362280--362369 Score: 173
Period size: 44 Copynumber: 2.0 Consensus size: 45
362270 GGGGGAGAAG
362280 AATAAGTGTTAAAGTAATGTTAAAGTAA-GGGGAGTAATTTCAAA
1 AATAAGTGTTAAAGTAATGTTAAAGTAAGGGGGAGTAATTTCAAA
362324 AATAAGTGTTAAAGTAATGTTAAAGTAAGGGGGAGTAATTTCAAA
1 AATAAGTGTTAAAGTAATGTTAAAGTAAGGGGGAGTAATTTCAAA
362369 A
1 A
362370 CTTGATTTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 28 0.62
45 17 0.38
ACGTcount: A:0.46, C:0.02, G:0.23, T:0.29
Consensus pattern (45 bp):
AATAAGTGTTAAAGTAATGTTAAAGTAAGGGGGAGTAATTTCAAA
Found at i:369272 original size:3 final size:3
Alignment explanation
Indices: 369247--369311 Score: 54
Period size: 3 Copynumber: 23.7 Consensus size: 3
369237 CTCCATTTTC
369247 TAT TA- TAT TAT T-T T-T TAT ATAT TAT TA- TAT TA- TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
* *
369287 TAT TA- TAT TAA AAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
369312 CAAACATGCC
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
2 14 0.27
3 34 0.67
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:369274 original size:22 final size:21
Alignment explanation
Indices: 369247--369292 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
369237 CTCCATTTTC
*
369247 TATTATATTATTTTTTATATAT
1 TATTATATTATATTTTAT-TAT
369269 TATTATATTATATTTTATTAT
1 TATTATATTATATTTTATTAT
369290 TAT
1 TAT
369293 ATTAAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTATATTATATTTTATTAT
Found at i:369289 original size:18 final size:20
Alignment explanation
Indices: 369261--369311 Score: 70
Period size: 18 Copynumber: 2.6 Consensus size: 20
369251 ATATTATTTT
*
369261 TTATATATTATTATATT-ATA
1 TTAT-TATTATTATATTAAAA
369281 TT-TTATTATTATATTAAAA
1 TTATTATTATTATATTAAAA
369300 TTATTATTATTA
1 TTATTATTATTA
369312 CAAACATGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 12 0.43
19 5 0.18
20 11 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATTATTATTATATTAAAA
Found at i:370876 original size:19 final size:18
Alignment explanation
Indices: 370854--370893 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
370844 CTATTTTATA
370854 AATTATATATTAATTATTT
1 AATTATATATTAATT-TTT
* *
370873 AATTATTTATTTATTTTT
1 AATTATATATTAATTTTT
370891 AAT
1 AAT
370894 ATCGAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
AATTATATATTAATTTTT
Found at i:378554 original size:44 final size:42
Alignment explanation
Indices: 378462--378544 Score: 125
Period size: 44 Copynumber: 2.0 Consensus size: 42
378452 TAGATAAACT
378462 TGTTTTTATTTAATTATGGACTTTTTATTTATTTTGTTTCTTAA
1 TGTTTTTATTTAATTATGGA--TTTTATTTATTTTGTTTCTTAA
*
378506 TGTTTTTATTTAATTTTGGA-TTT-TTTATTTTGTTTCTTA
1 TGTTTTTATTTAATTATGGATTTTATTTATTTTGTTTCTTA
378545 GGGTCTGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
40 16 0.42
41 3 0.08
44 19 0.50
ACGTcount: A:0.18, C:0.04, G:0.10, T:0.69
Consensus pattern (42 bp):
TGTTTTTATTTAATTATGGATTTTATTTATTTTGTTTCTTAA
Found at i:380539 original size:47 final size:46
Alignment explanation
Indices: 380480--380630 Score: 194
Period size: 47 Copynumber: 3.2 Consensus size: 46
380470 CTTAATGTTT
* * *
380480 TTATTTAATTATAGACTTTTTATTTATTTTGTTTCATAATGATTTTA
1 TTATTTAATTATAGA-TTTTTATTTATTATGTTTCTTAATGTTTTTA
* *
380527 TTATTTTATTATAGATTTTGTATTTATTATGTTTCTTGATGTTTTTA
1 TTATTTAATTATAGATTTT-TATTTATTATGTTTCTTAATGTTTTTA
* * * *
380574 TTAGTTAATTATGGATTTATTATTTATTCTATTTCTTAATGTTTTTA
1 TTATTTAATTATAGATTT-TTATTTATTATGTTTCTTAATGTTTTTA
380621 TTATTTAATT
1 TTATTTAATT
380631 GTGTGAATTG
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
46 4 0.04
47 85 0.94
48 1 0.01
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.64
Consensus pattern (46 bp):
TTATTTAATTATAGATTTTTATTTATTATGTTTCTTAATGTTTTTA
Found at i:380732 original size:16 final size:16
Alignment explanation
Indices: 380711--380742 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
380701 TATTTAATTT
*
380711 TCACTTGAGTAGCACA
1 TCACTTGAGTAACACA
380727 TCACTTGAGTAACACA
1 TCACTTGAGTAACACA
380743 ATAATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (16 bp):
TCACTTGAGTAACACA
Found at i:390352 original size:12 final size:12
Alignment explanation
Indices: 390335--390359 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
390325 TTCTCTCGGC
390335 ATAAAAAAACAA
1 ATAAAAAAACAA
390347 ATAAAAAAACAA
1 ATAAAAAAACAA
390359 A
1 A
390360 CCTTTCCCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
ATAAAAAAACAA
Found at i:397086 original size:10 final size:11
Alignment explanation
Indices: 397068--397094 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
397058 TATATTAATT
397068 TTAAAAAAATA
1 TTAAAAAAATA
397079 TTAAAAAAATA
1 TTAAAAAAATA
397090 TTAAA
1 TTAAA
397095 TTCTAATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TTAAAAAAATA
Found at i:397199 original size:97 final size:99
Alignment explanation
Indices: 397023--397201 Score: 276
Period size: 97 Copynumber: 1.8 Consensus size: 99
397013 ATTAATTATT
* * *
397023 AAAATATTACCTCTTTATTTAAAATTATTCTTTCTTATATTAATTTTAAAAAAATATTAAAAAAA
1 AAAATATCAACTCTTTATTTAAAATTATTCTTTCTAATATTAATTTTAAAAAAATATTAAAAAAA
*
397088 TATTAAATTCTAATGAAAAAGAATGTAAAACTAA
66 TATTAAAATCTAATGAAAAAGAATGTAAAACTAA
397122 AAAATATCAACTCTTTATTTAAAA-TATTCTTTCTAATATTAATTTT-AAAAAATA-TAAAATAA
1 AAAATATCAACTCTTTATTTAAAATTATTCTTTCTAATATTAATTTTAAAAAAATATTAAAA-AA
397184 ATATTAATAAT-TAATGAA
65 ATATTAA-AATCTAATGAA
397202 TAATAATTTA
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
96 5 0.07
97 24 0.32
98 23 0.31
99 22 0.30
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (99 bp):
AAAATATCAACTCTTTATTTAAAATTATTCTTTCTAATATTAATTTTAAAAAAATATTAAAAAAA
TATTAAAATCTAATGAAAAAGAATGTAAAACTAA
Found at i:397902 original size:44 final size:41
Alignment explanation
Indices: 397830--397916 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 41
397820 AAATAATTAT
*
397830 TATATATATATATACTATTAATAAATTTAATTTAAATTAATATA
1 TATATATATATATAATATTAATAAATTTAA-TTAAA-T-ATATA
*
397874 TATATATATATATAATATTTAAT-TATTTAATTAAATATATA
1 TATATATATATATAATA-TTAATAAATTTAATTAAATATATA
397915 TA
1 TA
397917 CCTGGCCTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
41 7 0.17
42 1 0.03
43 5 0.12
44 22 0.55
45 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (41 bp):
TATATATATATATAATATTAATAAATTTAATTAAATATATA
Found at i:402553 original size:13 final size:14
Alignment explanation
Indices: 402535--402565 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
402525 GTATCATATT
402535 TCACATA-TTCATA
1 TCACATAGTTCATA
402548 TCACATAGTTCATA
1 TCACATAGTTCATA
402562 TCAC
1 TCAC
402566 TTGCATAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (14 bp):
TCACATAGTTCATA
Found at i:405912 original size:34 final size:33
Alignment explanation
Indices: 405870--405957 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 33
405860 AATGGTAATA
*
405870 AACAAAATTAACCAAAATACATTAACAA-AAAGTCC
1 AACAAAATTAA-CAAAATAAATTAA-AATAAA-TCC
*
405905 AACAAATTTAACAAAATAAATTAAAATAAATCC
1 AACAAAATTAACAAAATAAATTAAAATAAATCC
**
405938 AACAAAATTAATGAAATAAA
1 AACAAAATTAACAAAATAAA
405958 GTAAGTATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 22 0.47
34 15 0.32
35 10 0.21
ACGTcount: A:0.64, C:0.14, G:0.02, T:0.20
Consensus pattern (33 bp):
AACAAAATTAACAAAATAAATTAAAATAAATCC
Found at i:408125 original size:18 final size:17
Alignment explanation
Indices: 408081--408126 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
408071 TAATAATCAC
408081 ATATTAAATAAATAAATT
1 ATATTAAA-AAATAAATT
*
408099 ATTACTAAAAAATTAAATT
1 A-TATTAAAAAA-TAAATT
408118 ATATTAAAA
1 ATATTAAAA
408127 TGTTAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
ATATTAAAAAATAAATT
Found at i:408248 original size:17 final size:19
Alignment explanation
Indices: 408228--408269 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
408218 ATTAATTAAA
408228 TAAAATA-TTAAA-AAATT
1 TAAAATACTTAAATAAATT
408245 T-AAATACTTAAATAAATT
1 TAAAATACTTAAATAAATT
*
408263 AAAAATA
1 TAAAATA
408270 AAATATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 6 0.29
18 5 0.24
19 5 0.24
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATACTTAAATAAATT
Found at i:408257 original size:24 final size:23
Alignment explanation
Indices: 408213--408290 Score: 56
Period size: 24 Copynumber: 3.3 Consensus size: 23
408203 TATATCTGTA
*
408213 AAAAAATTAATTAA-ATAAAATATT
1 AAAAAATTAA--AATATTAAATATT
*
408237 AAAAAATTTAAATACTTAAATAAATT
1 AAAAAATTAAAATA-TTAAAT--ATT
408263 -AAAAA-TAAAATATTAAATA-T
1 AAAAAATTAAAATATTAAATATT
408283 AATAAAAT
1 AA-AAAAT
408291 ATACCTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
20 1 0.02
21 2 0.05
22 6 0.14
23 7 0.16
24 20 0.45
25 5 0.11
26 3 0.07
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (23 bp):
AAAAAATTAAAATATTAAATATT
Found at i:409614 original size:202 final size:202
Alignment explanation
Indices: 409268--409672 Score: 801
Period size: 202 Copynumber: 2.0 Consensus size: 202
409258 ATCGAAGACC
409268 AGAAAGAGAGAAGATAGAGTTCCACAAGAAGTCAGCCATAAGACAATGGAGAAATAAGTGATCCC
1 AGAAAGAGAGAAGATAGAGTTCCACAAGAAGTCAGCCATAAGACAATGGAGAAATAAGTGATCCC
409333 TAGTTTCTAATGGTTCATCACAAAACATACATTGGCAATCATTGATAAGCCCCATATGAAGAAGT
66 TAGTTTCTAATGGTTCATCACAAAACATACATTGGCAATCATTGATAAGCCCCATATGAAGAAGT
409398 ATATCTTTAGTAGGGAGTCAATCAAGTAAAGCCATCTAAGAAATTAAGATGTGTTTTGGTAAATG
131 ATATCTTTAGTAGGGAGTCAATCAAGTAAAGCCATCTAAGAAATTAAGATGTGTTTTGGTAAATG
409463 GAGAGGA
196 GAGAGGA
409470 AGAAAGAGAGAAGATAGAGTTCCACAAGAAGTCAGCCATAAGACAATGGAGAAATAAGTGATCCC
1 AGAAAGAGAGAAGATAGAGTTCCACAAGAAGTCAGCCATAAGACAATGGAGAAATAAGTGATCCC
409535 TAGTTTCTAATGGTTCATCACAAAACATACATTGGCAATCATTGATAAGCCCCATATGAAGAAGT
66 TAGTTTCTAATGGTTCATCACAAAACATACATTGGCAATCATTGATAAGCCCCATATGAAGAAGT
*
409600 CTATCTTTAGTAGGGAGTCAATCAAGTAAAGCCATCTAAGAAATTAAGATGTGTTTTGGTAAATG
131 ATATCTTTAGTAGGGAGTCAATCAAGTAAAGCCATCTAAGAAATTAAGATGTGTTTTGGTAAATG
409665 GAGAGGA
196 GAGAGGA
409672 A
1 A
409673 ACCAGATAAT
Statistics
Matches: 202, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
202 202 1.00
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (202 bp):
AGAAAGAGAGAAGATAGAGTTCCACAAGAAGTCAGCCATAAGACAATGGAGAAATAAGTGATCCC
TAGTTTCTAATGGTTCATCACAAAACATACATTGGCAATCATTGATAAGCCCCATATGAAGAAGT
ATATCTTTAGTAGGGAGTCAATCAAGTAAAGCCATCTAAGAAATTAAGATGTGTTTTGGTAAATG
GAGAGGA
Found at i:417022 original size:4 final size:4
Alignment explanation
Indices: 417015--417044 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
417005 TGAATGAATG
417015 AATA AATA AATA ATATA AATA AATA AATA A
1 AATA AATA AATA A-ATA AATA AATA AATA A
417045 TTTTTTAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:417034 original size:13 final size:12
Alignment explanation
Indices: 417015--417044 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
417005 TGAATGAATG
417015 AATAAATAAATA
1 AATAAATAAATA
417027 ATATAAATAAATA
1 A-ATAAATAAATA
417040 AATAA
1 AATAA
417045 TTTTTTAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AATAAATAAATA
Found at i:418448 original size:39 final size:39
Alignment explanation
Indices: 418394--418476 Score: 157
Period size: 39 Copynumber: 2.1 Consensus size: 39
418384 AAGAATAGAA
418394 GGGTGGGTCGGGGGAGTCCAAAATAACTTTACCAAGTAG
1 GGGTGGGTCGGGGGAGTCCAAAATAACTTTACCAAGTAG
*
418433 GGGTGGGTCGGGGGAGTCCAAAATAACTTTAGCAAGTAG
1 GGGTGGGTCGGGGGAGTCCAAAATAACTTTACCAAGTAG
418472 GGGTG
1 GGGTG
418477 TGTATTATCG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.27, C:0.13, G:0.40, T:0.20
Consensus pattern (39 bp):
GGGTGGGTCGGGGGAGTCCAAAATAACTTTACCAAGTAG
Found at i:424486 original size:17 final size:19
Alignment explanation
Indices: 424460--424507 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
424450 ACGCATATGA
*
424460 AATTTCAAAAAT-TATT-T
1 AATTTAAAAAATATATTAT
*
424477 TATTTAAAAAATACTATTAT
1 AATTTAAAAAATA-TATTAT
424497 AATTTAAAAAA
1 AATTTAAAAAA
424508 AGTATTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
19 4 0.16
20 11 0.44
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTTAAAAAATATATTAT
Found at i:424992 original size:65 final size:64
Alignment explanation
Indices: 424850--424999 Score: 180
Period size: 65 Copynumber: 2.3 Consensus size: 64
424840 CACCTTAAAA
* *
424850 ATATAAC-ATAAAAAATATTAAACACATATTATTAATAAAAATTTCTTTAAATATCAAATCATAT
1 ATATAACGATAAAAAATATTAAACACATATTATTAATAAAAAATTCTTTAAATACCAAAT-ATAT
* * *
424914 ATATAACGA-AAAAAATATTAAATATATATTTATTAATAAAAAATTCTTTAAATACCGAAT-TAT
1 ATATAACGATAAAAAATATTAAACACATA-TTATTAATAAAAAATTCTTTAAATACCAAATATAT
* *
424977 ATTTAAGGACTAAAAATATATTA
1 ATATAACGA-TAAAAA-ATATTA
425000 TTAAGCGTCT
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
63 10 0.14
64 24 0.32
65 34 0.46
66 6 0.08
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (64 bp):
ATATAACGATAAAAAATATTAAACACATATTATTAATAAAAAATTCTTTAAATACCAAATATAT
Found at i:429191 original size:21 final size:21
Alignment explanation
Indices: 429165--429205 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
429155 TGGTAAAATA
429165 CTACCGATTTTATTATTTTTT
1 CTACCGATTTTATTATTTTTT
*
429186 CTACCGATTTTTTTATTTTT
1 CTACCGATTTTATTATTTTT
429206 GGGTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.15, G:0.05, T:0.63
Consensus pattern (21 bp):
CTACCGATTTTATTATTTTTT
Found at i:429622 original size:27 final size:27
Alignment explanation
Indices: 429569--429624 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
429559 TTATTATTTG
*
429569 TACAAGTTTTATTATTATTGGGAGCTT
1 TACAAGTTTTATTATTATTGGAAGCTT
*
429596 TACAAGTTTTTTTATTATT-GAACGCTT
1 TACAAGTTTTATTATTATTGGAA-GCTT
429623 TA
1 TA
429625 TTGATTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (27 bp):
TACAAGTTTTATTATTATTGGAAGCTT
Found at i:429716 original size:12 final size:12
Alignment explanation
Indices: 429699--429762 Score: 57
Period size: 12 Copynumber: 5.7 Consensus size: 12
429689 AATATTAAAA
429699 AAATAATATTTT
1 AAATAATATTTT
*
429711 AAATAA-A--AT
1 AAATAATATTTT
429720 -AATAATATTTT
1 AAATAATATTTT
429731 AAATAATATTTT
1 AAATAATATTTT
* *
429743 -ATTAATTTTATT
1 AAATAATATT-TT
429755 AAATAATA
1 AAATAATA
429763 ATAATAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
8 5 0.12
9 2 0.05
11 9 0.22
12 19 0.47
13 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:429723 original size:20 final size:20
Alignment explanation
Indices: 429694--429736 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
429684 TCGAAAATAT
429694 TAAAAAAATAATATTTTAAA
1 TAAAAAAATAATATTTTAAA
*
429714 TAAAATAATAATATTTTAAA
1 TAAAAAAATAATATTTTAAA
429734 TAA
1 TAA
429737 TATTTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAAAATAATATTTTAAA
Found at i:429998 original size:2 final size:2
Alignment explanation
Indices: 429991--430037 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
429981 TAAATAAATA
429991 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
430033 AT AT A
1 AT AT A
430038 AACAAATCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:434451 original size:11 final size:11
Alignment explanation
Indices: 434418--434451 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
434408 ATAAATCAGC
434418 ATTTTTAATT-
1 ATTTTTAATTA
434428 ATTTTTAATTTA
1 ATTTTTAA-TTA
434440 ATTTTTAATTA
1 ATTTTTAATTA
434451 A
1 A
434452 AAGTAATGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.36
11 6 0.27
12 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTTTAATTA
Found at i:435607 original size:20 final size:20
Alignment explanation
Indices: 435584--435688 Score: 174
Period size: 20 Copynumber: 5.2 Consensus size: 20
435574 GAGGGTTATA
435584 GTATCGATATCGGATGCTCG
1 GTATCGATATCGGATGCTCG
435604 GTATCGATATCGGATGCTCG
1 GTATCGATATCGGATGCTCG
435624 GTATCGATATCGGATGCTCG
1 GTATCGATATCGGATGCTCG
*
435644 GTATCGATATCGTATGCTCG
1 GTATCGATATCGGATGCTCG
* * *
435664 ATATCGATATCGGAAGTTCG
1 GTATCGATATCGGATGCTCG
435684 GTATC
1 GTATC
435689 AATACAACGA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (20 bp):
GTATCGATATCGGATGCTCG
Found at i:435742 original size:21 final size:21
Alignment explanation
Indices: 435715--435769 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
435705 ATACTGGAGG
435715 ACTGGTATCCATACCAGATGA
1 ACTGGTATCCATACCAGATGA
** *
435736 GTTGGTATCCATACCGGATGA
1 ACTGGTATCCATACCAGATGA
435757 ACTGGTATCCATA
1 ACTGGTATCCATA
435770 TAGAAGATTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (21 bp):
ACTGGTATCCATACCAGATGA
Found at i:437878 original size:35 final size:35
Alignment explanation
Indices: 437833--437899 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
437823 AATTCATGCC
* *
437833 AAAAGAATCTATTGAGTTGAAATTTTAATTCACTT
1 AAAAAAATCTATGGAGTTGAAATTTTAATTCACTT
**
437868 AAAAAAATCTATGGAGTTGCGATTTTAATTCA
1 AAAAAAATCTATGGAGTTGAAATTTTAATTCA
437900 GTTAGATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (35 bp):
AAAAAAATCTATGGAGTTGAAATTTTAATTCACTT
Found at i:438182 original size:32 final size:32
Alignment explanation
Indices: 438122--438184 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
438112 TTAATTGAAA
* *
438122 AAAAATATAGAGTGATATTTTACAATTATCTC
1 AAAAATATAGAGAGATATTATACAATTATCTC
*
438154 AAAAATATA-AGAGATAATTATACTATTATCT
1 AAAAATATAGAGAGAT-ATTATACAATTATCT
438185 TGGATTGGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.37
Consensus pattern (32 bp):
AAAAATATAGAGAGATATTATACAATTATCTC
Found at i:449621 original size:15 final size:15
Alignment explanation
Indices: 449601--449635 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
449591 TTGTAGGACC
449601 ACTACGTCCCGA-AGG
1 ACTACGTCCC-ATAGG
449616 ACTACGTCCCATAGG
1 ACTACGTCCCATAGG
449631 ACTAC
1 ACTAC
449636 AATACCCTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.05
15 18 0.95
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (15 bp):
ACTACGTCCCATAGG
Found at i:450278 original size:34 final size:34
Alignment explanation
Indices: 450240--450307 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
450230 TTTCATTTAG
*
450240 GGGGAATTAATACCCCCCAGGGGGAATCTGTTCC
1 GGGGAATCAATACCCCCCAGGGGGAATCTGTTCC
*
450274 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCC
1 GGGGAATCAATACCCCCCAGGGGGAATCTGTTCC
450308 CCCTGCACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.22, C:0.28, G:0.31, T:0.19
Consensus pattern (34 bp):
GGGGAATCAATACCCCCCAGGGGGAATCTGTTCC
Found at i:450309 original size:20 final size:20
Alignment explanation
Indices: 450252--450310 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
450242 GGAATTAATA
450252 CCCCCCAGGGGGAATCTGTT
1 CCCCCCAGGGGGAATCTGTT
*
450272 ----CC--GGGGAATC-GATA
1 CCCCCCAGGGGGAATCTG-TT
450286 CCCCCCAGGGGGAATCTGTT
1 CCCCCCAGGGGGAATCTGTT
450306 CCCCC
1 CCCCC
450311 TGCACATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 16
0.62 0.04 0.34
Matches are distributed among these distances:
13 1 0.03
14 9 0.31
16 2 0.07
18 2 0.07
20 14 0.48
21 1 0.03
ACGTcount: A:0.17, C:0.37, G:0.29, T:0.17
Consensus pattern (20 bp):
CCCCCCAGGGGGAATCTGTT
Found at i:452805 original size:17 final size:17
Alignment explanation
Indices: 452783--452820 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
452773 ATCCTTTCCA
452783 CTTAGAATTGAAAAATT
1 CTTAGAATTGAAAAATT
452800 CTTAGAATTGAAAAATT
1 CTTAGAATTGAAAAATT
452817 CTTA
1 CTTA
452821 CTTTTATACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.37
Consensus pattern (17 bp):
CTTAGAATTGAAAAATT
Found at i:453506 original size:2 final size:2
Alignment explanation
Indices: 453499--453525 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
453489 ATCAAATTAT
453499 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
453526 TCTAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:455886 original size:14 final size:14
Alignment explanation
Indices: 455867--455894 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
455857 ATATCATATA
455867 TCTTATGTTTATGC
1 TCTTATGTTTATGC
455881 TCTTATGTTTATGC
1 TCTTATGTTTATGC
455895 ATATCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
TCTTATGTTTATGC
Found at i:476185 original size:45 final size:45
Alignment explanation
Indices: 476129--476233 Score: 113
Period size: 46 Copynumber: 2.3 Consensus size: 45
476119 GCACCAATCC
* *
476129 ATGCATTGATGCACTAATGAATAAATTG-AACATCGAATGCAGTTT
1 ATGCATCGATGCACTAAGGAATAAA-TGAAACATCGAATGCAGTTT
* ** * * *
476174 ATGCATCGATGCACTCAGGTTTTAATGAAAACATCGATTGCATTTT
1 ATGCATCGATGCACTAAGGAATAAATG-AAACATCGAATGCAGTTT
476220 ATGCATCGATGCAC
1 ATGCATCGATGCAC
476234 ACACCATGCA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
44 2 0.04
45 19 0.38
46 29 0.58
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (45 bp):
ATGCATCGATGCACTAAGGAATAAATGAAACATCGAATGCAGTTT
Found at i:476273 original size:64 final size:65
Alignment explanation
Indices: 476174--476299 Score: 200
Period size: 64 Copynumber: 2.0 Consensus size: 65
476164 AATGCAGTTT
* * *
476174 ATGCATCGATGCACTCAGGTTTTAATGAAAACATCGATTGCATTTTATGCATCGATGCACACACC
1 ATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTTATGCATCGATGCACACACC
* *
476239 ATGCATCGATGCACTTAGG-CTTATTCAAAACATCGAATGCATTTTATGCATCGATGCACAC
1 ATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTTATGCATCGATGCACAC
476300 TTAGTGCACC
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
64 38 0.68
65 18 0.32
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (65 bp):
ATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTTATGCATCGATGCACACACC
Found at i:481864 original size:24 final size:24
Alignment explanation
Indices: 481828--481909 Score: 64
Period size: 24 Copynumber: 3.5 Consensus size: 24
481818 ACTGAACAGC
*
481828 GCATCGATGCATCCCTTTGTATGT
1 GCATCGATACATCCCTTTGTATGT
* * *
481852 GCATTGATACAT--C-ATG-AAGAT
1 GCATCGATACATCCCTTTGTATG-T
* *
481873 GCACCGATGCATCCCTTTGTATGT
1 GCATCGATACATCCCTTTGTATGT
*
481897 GCATTGATACATC
1 GCATCGATACATC
481910 ATGAAGATGC
Statistics
Matches: 41, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
20 2 0.05
21 12 0.29
22 1 0.02
23 1 0.02
24 23 0.56
25 2 0.05
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (24 bp):
GCATCGATACATCCCTTTGTATGT
Found at i:481887 original size:45 final size:45
Alignment explanation
Indices: 481832--481944 Score: 185
Period size: 45 Copynumber: 2.5 Consensus size: 45
481822 AACAGCGCAT
481832 CGATGCATCCCTTTGTATGTGCATTGATACATCATGAAGATGCAC
1 CGATGCATCCCTTTGTATGTGCATTGATACATCATGAAGATGCAC
*
481877 CGATGCATCCCTTTGTATGTGCATTGATACATCATGAAGATGCAT
1 CGATGCATCCCTTTGTATGTGCATTGATACATCATGAAGATGCAC
*
481922 CGATGCA-CTCC-TTGAATGTGCAT
1 CGATGCATC-CCTTTGTATGTGCAT
481945 CGATGCACAA
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
44 12 0.18
45 53 0.82
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (45 bp):
CGATGCATCCCTTTGTATGTGCATTGATACATCATGAAGATGCAC
Found at i:483971 original size:565 final size:565
Alignment explanation
Indices: 482902--484035 Score: 2268
Period size: 565 Copynumber: 2.0 Consensus size: 565
482892 CGCATTTTCT
482902 ACTCTAATACAATATGTATTCAAAACCAGACTCAATGTGGGACTATAGCAATCAGATCCTACCTT
1 ACTCTAATACAATATGTATTCAAAACCAGACTCAATGTGGGACTATAGCAATCAGATCCTACCTT
482967 TTAGGACAATATGTTAATATTGACTCCGAGACTATAGCTTCACATTTTGGGCTAGATGACGATGG
66 TTAGGACAATATGTTAATATTGACTCCGAGACTATAGCTTCACATTTTGGGCTAGATGACGATGG
483032 TTTATATAATGAGAAAGAAACTGTGGAATATCCCTATGTTCCAAATGCTAGTGTTAGTACTCTAC
131 TTTATATAATGAGAAAGAAACTGTGGAATATCCCTATGTTCCAAATGCTAGTGTTAGTACTCTAC
483097 GATCTCATCACGATCGTTTTCTTCATTTGATGATCTCTTGGTGGTTTAGACCATCCGGAGGTAGG
196 GATCTCATCACGATCGTTTTCTTCATTTGATGATCTCTTGGTGGTTTAGACCATCCGGAGGTAGG
483162 TACTCCACTCTTCGTATTAGGGATTTATGGTGGATGCACTGTATCAAGAATAAGAACAAAATAAA
261 TACTCCACTCTTCGTATTAGGGATTTATGGTGGATGCACTGTATCAAGAATAAGAACAAAATAAA
483227 TTTTCCACATATTATATTTAGTGAGCTAGTGGATACCATAAACATTATTCATTCAAAACATGTTG
326 TTTTCCACATATTATATTTAGTGAGCTAGTGGATACCATAAACATTATTCATTCAAAACATGTTG
483292 AAACATTAGTTTATGGATGTCTTCTTATTAATCTTTTTGTATCAAACTCAGTCTTAACGTCTCTC
391 AAACATTAGTTTATGGATGTCTTCTTATTAATCTTTTTGTATCAAACTCAGTCTTAACGTCTCTC
483357 TTGACAATCCCATTCCTCTTCAAAACCAAATCAATCTCACCTCGTTGAAGAAAGCTGATTGGAAA
456 TTGACAATCCCATTCCTCTTCAAAACCAAATCAATCTCACCTCGTTGAAGAAAGCTGATTGGAAA
483422 CAGGACGAGGAAACTGGTAAATGGGTTTATCGACCTTCTAAGCAA
521 CAGGACGAGGAAACTGGTAAATGGGTTTATCGACCTTCTAAGCAA
483467 ACTCTAATACAATATGTATTCAAAACCAGACTCAATGTGGGACTATAGCAATCAGATCCTACCTT
1 ACTCTAATACAATATGTATTCAAAACCAGACTCAATGTGGGACTATAGCAATCAGATCCTACCTT
483532 TTAGGACAATATGTTAATATTGACTCCGAGACTATAGCTTCACATTTTGGGCTAGATGACGATGG
66 TTAGGACAATATGTTAATATTGACTCCGAGACTATAGCTTCACATTTTGGGCTAGATGACGATGG
483597 TTTATATAATGAGAAAGAAACTGTGGAATATCCCTATGTTCCAAATGCTAGTGTTAGTACTCTAC
131 TTTATATAATGAGAAAGAAACTGTGGAATATCCCTATGTTCCAAATGCTAGTGTTAGTACTCTAC
483662 GATCTCATCACGATCGTTTTCTTCATTTGATGATCTCTTGGTGGTTTAGACCATCCGGAGGTAGG
196 GATCTCATCACGATCGTTTTCTTCATTTGATGATCTCTTGGTGGTTTAGACCATCCGGAGGTAGG
483727 TACTCCACTCTTCGTATTAGGGATTTATGGTGGATGCACTGTATCAAGAATAAGAACAAAATAAA
261 TACTCCACTCTTCGTATTAGGGATTTATGGTGGATGCACTGTATCAAGAATAAGAACAAAATAAA
483792 TTTTCCACATATTATATTTAGTGAGCTAGTGGATACCATAAACATTATTCATTCAAAACATGTTG
326 TTTTCCACATATTATATTTAGTGAGCTAGTGGATACCATAAACATTATTCATTCAAAACATGTTG
483857 AAACATTAGTTTATGGATGTCTTCTTATTAATCTTTTTGTATCAAACTCAGTCTTAACGTCTCTC
391 AAACATTAGTTTATGGATGTCTTCTTATTAATCTTTTTGTATCAAACTCAGTCTTAACGTCTCTC
483922 TTGACAATCCCATTCCTCTTCAAAACCAAATCAATCTCACCTCGTTGAAGAAAGCTGATTGGAAA
456 TTGACAATCCCATTCCTCTTCAAAACCAAATCAATCTCACCTCGTTGAAGAAAGCTGATTGGAAA
483987 CAGGACGAGGAAACTGGTAAATGGGTTTATCGACCTTCTAAGCAA
521 CAGGACGAGGAAACTGGTAAATGGGTTTATCGACCTTCTAAGCAA
484032 ACTC
1 ACTC
484036 CGGGAGCGAG
Statistics
Matches: 569, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
565 569 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (565 bp):
ACTCTAATACAATATGTATTCAAAACCAGACTCAATGTGGGACTATAGCAATCAGATCCTACCTT
TTAGGACAATATGTTAATATTGACTCCGAGACTATAGCTTCACATTTTGGGCTAGATGACGATGG
TTTATATAATGAGAAAGAAACTGTGGAATATCCCTATGTTCCAAATGCTAGTGTTAGTACTCTAC
GATCTCATCACGATCGTTTTCTTCATTTGATGATCTCTTGGTGGTTTAGACCATCCGGAGGTAGG
TACTCCACTCTTCGTATTAGGGATTTATGGTGGATGCACTGTATCAAGAATAAGAACAAAATAAA
TTTTCCACATATTATATTTAGTGAGCTAGTGGATACCATAAACATTATTCATTCAAAACATGTTG
AAACATTAGTTTATGGATGTCTTCTTATTAATCTTTTTGTATCAAACTCAGTCTTAACGTCTCTC
TTGACAATCCCATTCCTCTTCAAAACCAAATCAATCTCACCTCGTTGAAGAAAGCTGATTGGAAA
CAGGACGAGGAAACTGGTAAATGGGTTTATCGACCTTCTAAGCAA
Found at i:486079 original size:26 final size:24
Alignment explanation
Indices: 486040--486087 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 24
486030 AAAAATCAAT
486040 ATTAAAAATAAATAGATTCCATATCC
1 ATTAAAAATAAATAG--TCCATATCC
486066 ATTAATAAAT-AATAGTCCATAT
1 ATTAA-AAATAAATAGTCCATAT
486088 TACAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 7 0.33
26 10 0.48
27 4 0.19
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.33
Consensus pattern (24 bp):
ATTAAAAATAAATAGTCCATATCC
Found at i:487908 original size:21 final size:21
Alignment explanation
Indices: 487869--487909 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
487859 TTTTAATATT
**
487869 TTAAATATAATTTAAAAAAAA
1 TTAAATATAAAATAAAAAAAA
*
487890 TTAAATATAAAATATAAAAA
1 TTAAATATAAAATAAAAAAA
487910 GCTGACATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
TTAAATATAAAATAAAAAAAA
Found at i:488234 original size:37 final size:37
Alignment explanation
Indices: 488161--488235 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
488151 GTTAGAAAAT
* *
488161 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
488198 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
488235 A
1 A
488236 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:489470 original size:20 final size:21
Alignment explanation
Indices: 489445--489496 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
489435 TTTTCCCAAT
*
489445 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
489465 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
489486 TCGCAATGCGA
1 TCGCAATGCGA
489497 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:489575 original size:20 final size:20
Alignment explanation
Indices: 489527--489579 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
489517 TAATACAAAA
* *
489527 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
489547 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
489567 TCGTAACGCGATT
1 TCGCAACGCGATT
489580 TACATAGCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:490145 original size:19 final size:19
Alignment explanation
Indices: 490099--490138 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
490089 ATGAAAATCA
*
490099 CAACGCGAAATAAAAAACG
1 CAACGCGAAACAAAAAACG
*
490118 CAACGCGAAACAAAAATCG
1 CAACGCGAAACAAAAAACG
490137 CA
1 CA
490139 TTGCGAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.55, C:0.25, G:0.15, T:0.05
Consensus pattern (19 bp):
CAACGCGAAACAAAAAACG
Found at i:490156 original size:19 final size:19
Alignment explanation
Indices: 490134--490202 Score: 95
Period size: 19 Copynumber: 3.6 Consensus size: 19
490124 GAAACAAAAA
*
490134 TCGCATTGCGAATTTTATT
1 TCGCGTTGCGAATTTTATT
*
490153 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGAATTTTATT
490172 TCGCGGTTGC-AATTTTCATT
1 TCGC-GTTGCGAATTTT-ATT
490192 TCGCGTTGCGA
1 TCGCGTTGCGA
490203 TTGTCTGGTC
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
19 31 0.70
20 13 0.30
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGAATTTTATT
Found at i:490186 original size:20 final size:19
Alignment explanation
Indices: 490146--490200 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
490136 GCATTGCGAA
*
490146 TTTTATTTCGCGTTGCGAT
1 TTTTATTTCGCGTTGCAAT
490165 TTTTATTTCGCGGTTGCAAT
1 TTTTATTTCGC-GTTGCAAT
*
490185 TTTCATTTCGCGTTGC
1 TTTTATTTCGCGTTGC
490201 GATTGTCTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.51
Consensus pattern (19 bp):
TTTTATTTCGCGTTGCAAT
Found at i:490215 original size:39 final size:39
Alignment explanation
Indices: 490139--490215 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
490129 AAAAATCGCA
* **
490139 TTGCGAATTTTATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGAATTTTATTTCGCGTTGCGATTTCTAGGTCGCGG
490178 TTGC-AATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGAATTTT-ATTTCGCGTTGCGATT-TCTAGGTCGCG
490216 ATAGTCATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 6 0.18
39 25 0.76
40 2 0.06
ACGTcount: A:0.12, C:0.18, G:0.25, T:0.45
Consensus pattern (39 bp):
TTGCGAATTTTATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:490269 original size:34 final size:33
Alignment explanation
Indices: 490187--490274 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
490177 GTTGCAATTT
* *
490187 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
490220 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
490253 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
490275 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:490276 original size:20 final size:20
Alignment explanation
Indices: 490242--490299 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
490232 GCGATTCTCT
**
490242 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
490262 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
490282 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
490300 AATCAAAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:492368 original size:42 final size:42
Alignment explanation
Indices: 492288--492380 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
492278 GCCCAACTCG
* * * *
492288 CCTATCATCCCTCAAGAGTCCACTTCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
492330 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
492372 ACTGTCATC
1 CCTATCATC
492381 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.25
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:493788 original size:14 final size:14
Alignment explanation
Indices: 493769--493804 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
493759 ATTGTTTAAT
493769 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
493783 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
493797 TGATTTGT
1 TGATTTGT
493805 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:494029 original size:33 final size:32
Alignment explanation
Indices: 493987--494113 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
493977 ATTAAATTTG
*
493987 CGTTGCGATTTTCATTTCGCATTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
494020 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
494053 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
494086 CGTTGCGATTTTCATTTCTCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
494114 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:494046 original size:19 final size:19
Alignment explanation
Indices: 493989--494113 Score: 73
Period size: 19 Copynumber: 7.4 Consensus size: 19
493979 TAAATTTGCG
493989 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* **
494008 TTGTGA--TTC-CCTCG--
1 TTGCGATTTTCATTTCGCA
494022 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* * *
494041 TTGCGA-----AATTAGCG
1 TTGCGATTTTCATTTCGCA
494055 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
494074 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
494088 TTGCGATTTTCATTTCTCA
1 TTGCGATTTTCATTTCGCA
494107 TTGCGAT
1 TTGCGAT
494114 AGTAATTTCC
Statistics
Matches: 76, Mismatches: 15, Indels: 30
0.63 0.12 0.25
Matches are distributed among these distances:
14 22 0.29
16 13 0.17
17 12 0.16
19 29 0.38
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:494076 original size:66 final size:66
Alignment explanation
Indices: 493980--494112 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
493970 ACGCGAAATT
* *
493980 AAATTTGCGTTGCGATTTTCATTTCGCATTGTGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
494045 G
66 G
* *
494046 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCTCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
494111 G
66 G
494112 A
1 A
494113 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.44
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:496423 original size:12 final size:12
Alignment explanation
Indices: 496406--496430 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
496396 TCTTCGGGGA
496406 CTTTTTCTTCTT
1 CTTTTTCTTCTT
496418 CTTTTTCTTCTT
1 CTTTTTCTTCTT
496430 C
1 C
496431 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:496639 original size:24 final size:24
Alignment explanation
Indices: 496605--496658 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
496595 CTGAAACATC
* *
496605 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
496629 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
496653 ATCAAA
1 ATCAAA
496659 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:497740 original size:20 final size:20
Alignment explanation
Indices: 497715--497772 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
497705 ATTCATTTGA
497715 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
497735 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
497755 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
497773 CGCAATGCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:497832 original size:19 final size:19
Alignment explanation
Indices: 497791--497858 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
497781 GAAATGAAAA
497791 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
497807 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
497824 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
497843 TCGCATTACGATTTTC
1 TCGCATTGCGATTTTC
497859 TCGTTGCGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
14 10 0.23
16 3 0.07
17 3 0.07
19 28 0.64
ACGTcount: A:0.15, C:0.21, G:0.16, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:497994 original size:14 final size:14
Alignment explanation
Indices: 497975--498011 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
497965 CATCAATTAA
497975 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
497989 ACAAATCATCTTTT
1 ACAAATCAACATTT
498003 ACAAATCAA
1 ACAAATCAA
498012 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Done.