Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008001.1 Hibiscus syriacus cultivar Beakdansim tig00110458_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: 3902382
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 18
Found at i:222110 original size:39 final size:39
Alignment explanation
Indices: 222056--222178 Score: 210
Period size: 39 Copynumber: 3.2 Consensus size: 39
222046 ATGAAACCTA
* *
222056 GTGCATATGATGGGCACGACTTTATGTGTAAGCACTTCG
1 GTGCATATGGTGGGCACGACCTTATGTGTAAGCACTTCG
*
222095 GTGCATATGGTGGGCACGACCTTATGTGTAAGCACTTTG
1 GTGCATATGGTGGGCACGACCTTATGTGTAAGCACTTCG
*
222134 GTGCATATGGTGGGCACGACCTTATGTGTAAGCACTTCA
1 GTGCATATGGTGGGCACGACCTTATGTGTAAGCACTTCG
222173 GTGCAT
1 GTGCAT
222179 GTTTGACTTG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 79 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (39 bp):
GTGCATATGGTGGGCACGACCTTATGTGTAAGCACTTCG
Found at i:225577 original size:52 final size:52
Alignment explanation
Indices: 225502--225610 Score: 137
Period size: 52 Copynumber: 2.1 Consensus size: 52
225492 CTGGACATGG
* * * ** *
225502 GAAATCACGGGTTGAGCATGGAGATGTTACTCCATGTCCCAGGGTGAGCACA
1 GAAAGCACAGGTTGAGCAGGGAGATACTACTCCATGTCCCAAGGTGAGCACA
** *
225554 GAAAGCACAGGTTGAGCAGGGAGATACTGTTGCATGTCCCAAGGTGAGCACA
1 GAAAGCACAGGTTGAGCAGGGAGATACTACTCCATGTCCCAAGGTGAGCACA
225606 GAAAG
1 GAAAG
225611 ATGCATGTGG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.30, C:0.19, G:0.32, T:0.18
Consensus pattern (52 bp):
GAAAGCACAGGTTGAGCAGGGAGATACTACTCCATGTCCCAAGGTGAGCACA
Found at i:226341 original size:5 final size:6
Alignment explanation
Indices: 226306--226339 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
226296 TTAGGGATCA
226306 TTTTAT ATTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT -TTTTAT TTTTAT TTTTAT TTTTAT TTT
226340 ATGAAAGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:226398 original size:13 final size:13
Alignment explanation
Indices: 226382--226406 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
226372 AATAAAACAA
226382 TGTAATATTTAAG
1 TGTAATATTTAAG
226395 TGTAATATTTAA
1 TGTAATATTTAA
226407 ATTTTTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TGTAATATTTAAG
Found at i:229503 original size:32 final size:32
Alignment explanation
Indices: 229458--229518 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
229448 TCTCGCACCC
* *
229458 TTTCTTTTACTTTTGCTTTGTTTTCAATCCCA
1 TTTCTTTTACTTTTGATTTGTTTTAAATCCCA
*
229490 TTTCTTTTGCTTTTGATTTGTTTTAAATC
1 TTTCTTTTACTTTTGATTTGTTTTAAATC
229519 AAATAAGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.13, C:0.16, G:0.08, T:0.62
Consensus pattern (32 bp):
TTTCTTTTACTTTTGATTTGTTTTAAATCCCA
Found at i:229797 original size:29 final size:30
Alignment explanation
Indices: 229755--229825 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
229745 AATACACCTA
*
229755 AAGACGCCTAGATATCAAACATA-ACAATG
1 AAGACGCCTAGATATCAAACATAGAAAATG
* * *
229784 AAGACGTCTAGATATCCAAGATAGAAAATG
1 AAGACGCCTAGATATCAAACATAGAAAATG
229814 AAGACGCCTAGA
1 AAGACGCCTAGA
229826 GATCCAAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 20 0.56
30 16 0.44
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.17
Consensus pattern (30 bp):
AAGACGCCTAGATATCAAACATAGAAAATG
Found at i:229816 original size:30 final size:29
Alignment explanation
Indices: 229755--229833 Score: 104
Period size: 30 Copynumber: 2.7 Consensus size: 29
229745 AATACACCTA
* * *
229755 AAGACGCCTAGATATCAAACATAACAATG
1 AAGACGCCTAGATATCCAAGATAAAAATG
*
229784 AAGACGTCTAGATATCCAAGATAGAAAATG
1 AAGACGCCTAGATATCCAAGATA-AAAATG
*
229814 AAGACGCCTAGAGATCCAAG
1 AAGACGCCTAGATATCCAAG
229834 TTGAAGACGC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 20 0.47
30 23 0.53
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.16
Consensus pattern (29 bp):
AAGACGCCTAGATATCCAAGATAAAAATG
Found at i:233826 original size:31 final size:31
Alignment explanation
Indices: 233791--233888 Score: 144
Period size: 31 Copynumber: 3.2 Consensus size: 31
233781 CTTAGGCCTC
*
233791 AGTGATCACATCTTAATTAAATAAAAATGAA
1 AGTGATCAAATCTTAATTAAATAAAAATGAA
*
233822 AGTGA-CAAAATCTTAATTAAATAAAAACGAA
1 AGTGATC-AAATCTTAATTAAATAAAAATGAA
*
233853 AGTGATCAAATCTTAATTAAACAAAAATGAA
1 AGTGATCAAATCTTAATTAAATAAAAATGAA
*
233884 CGTGA
1 AGTGA
233889 CTAAATATTA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
30 1 0.02
31 58 0.97
32 1 0.02
ACGTcount: A:0.53, C:0.10, G:0.11, T:0.26
Consensus pattern (31 bp):
AGTGATCAAATCTTAATTAAATAAAAATGAA
Found at i:235206 original size:34 final size:34
Alignment explanation
Indices: 235155--235242 Score: 158
Period size: 34 Copynumber: 2.6 Consensus size: 34
235145 CTCGACTCGA
*
235155 CTCGACTCGTTGCTCGTTAATTCGTTAAAATTTTG
1 CTCGACTC-ATGCTCGTTAATTCGTTAAAATTTTG
235190 CTCGACTCATGCTCGTTAATTCGTTAAAATTTTG
1 CTCGACTCATGCTCGTTAATTCGTTAAAATTTTG
235224 CTCGACTCATGCTCGTTAA
1 CTCGACTCATGCTCGTTAA
235243 GAAAACTCGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 44 0.85
35 8 0.15
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.40
Consensus pattern (34 bp):
CTCGACTCATGCTCGTTAATTCGTTAAAATTTTG
Found at i:241768 original size:31 final size:31
Alignment explanation
Indices: 241733--241792 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
241723 GTCAAACGGT
*
241733 CGGTTATATCGGGAACCATACTGCAAACGAA
1 CGGTTATATCGGGAACCATACTACAAACGAA
* * *
241764 CGGTTATGTCGGGGACCATATTACAAACG
1 CGGTTATATCGGGAACCATACTACAAACG
241793 GATTAAATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (31 bp):
CGGTTATATCGGGAACCATACTACAAACGAA
Found at i:243288 original size:2 final size:2
Alignment explanation
Indices: 243281--243327 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
243271 GCATAACAAG
243281 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
243323 GA GA G
1 GA GA G
243328 CTCCAATTCC
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:249493 original size:18 final size:18
Alignment explanation
Indices: 249470--249505 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
249460 GTCCGAACCA
249470 ATTGCCAAGAAACTTGGC
1 ATTGCCAAGAAACTTGGC
249488 ATTGCCAAGAAACTTGGC
1 ATTGCCAAGAAACTTGGC
249506 CTTCATGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (18 bp):
ATTGCCAAGAAACTTGGC
Found at i:254009 original size:21 final size:21
Alignment explanation
Indices: 253983--254025 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
253973 ACGTAATATT
253983 AGAAGGGTG-CGTCGGAGAATC
1 AGAAGGGTGTC-TCGGAGAATC
*
254004 AGAAGGGTGTCTCGGAGGATC
1 AGAAGGGTGTCTCGGAGAATC
254025 A
1 A
254026 AATTGAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.28, C:0.14, G:0.42, T:0.16
Consensus pattern (21 bp):
AGAAGGGTGTCTCGGAGAATC
Found at i:254544 original size:2 final size:2
Alignment explanation
Indices: 254532--254589 Score: 75
Period size: 2 Copynumber: 29.0 Consensus size: 2
254522 AAATGTTCAA
*
254532 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
254575 AT ACT -T AT AT -T AT AT
1 AT A-T AT AT AT AT AT AT
254590 TAAAATAACA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
1 2 0.04
2 45 0.90
3 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:254625 original size:16 final size:17
Alignment explanation
Indices: 254600--254632 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
254590 TAAAATAACA
*
254600 TATTATAAAAT-TAAAT
1 TATTAGAAAATATAAAT
254616 TATTAGAAAATATAAAT
1 TATTAGAAAATATAAAT
254633 GCAAAAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
TATTAGAAAATATAAAT
Found at i:269648 original size:4 final size:4
Alignment explanation
Indices: 269634--269689 Score: 89
Period size: 4 Copynumber: 14.5 Consensus size: 4
269624 TTTAACCTTA
*
269634 ACAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC--
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
269680 ACAT ACAT AC
1 ACAT ACAT AC
269690 GCAATGTGGA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
4 46 0.96
ACGTcount: A:0.48, C:0.27, G:0.02, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:273279 original size:15 final size:15
Alignment explanation
Indices: 273259--273340 Score: 103
Period size: 15 Copynumber: 5.5 Consensus size: 15
273249 TTCCGGAAAA
*
273259 TGAATTACTGGAGTT
1 TGAATTACTGGAATT
273274 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
273289 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
*
273304 TGAATTACTAGAATT
1 TGAATTACTGGAATT
**
273319 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
273333 TGAATTAC
1 TGAATTAC
273341 ATTTCTGGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
14 11 0.19
15 46 0.81
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:273302 original size:45 final size:44
Alignment explanation
Indices: 273253--273340 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 44
273243 TTGGTTTTCC
* * **
273253 GGAAAATGAATTACTGGAGTTTGAATTACTGGAATTTGAATTACT
1 GGAAAATGAATTACTAGAATTTGAATT-CTGGAAAATGAATTACT
273298 GGAAAATGAATTACTAGAATTTGAATTCTGGAAAATGAATTAC
1 GGAAAATGAATTACTAGAATTTGAATTCTGGAAAATGAATTAC
273341 ATTTCTGGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (44 bp):
GGAAAATGAATTACTAGAATTTGAATTCTGGAAAATGAATTACT
Found at i:273338 original size:29 final size:30
Alignment explanation
Indices: 273259--273340 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
273249 TTCCGGAAAA
*** *
273259 TGAATTACTGGAGTTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTAGAATT
273289 TGAATTACTGGAAAATGAATTACTAGAATT
1 TGAATTACTGGAAAATGAATTACTAGAATT
273319 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
273341 ATTTCTGGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 16 0.33
30 32 0.67
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTAGAATT
Found at i:273346 original size:20 final size:20
Alignment explanation
Indices: 273323--273372 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
273313 AGAATTTGAA
273323 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
273343 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
273363 TTCTGGAAAA
1 TTCTGGAAAA
273373 CATCTGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:273612 original size:22 final size:25
Alignment explanation
Indices: 273560--273613 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
273550 CTTACTAAAA
*
273560 TATTATTGAAATATATAAATATTATT
1 TATTATT-AAATATATAAATATAATT
*
273586 CATTATT-AATATATAAA-A-AATT
1 TATTATTAAATATATAAATATAATT
273608 TATTAT
1 TATTAT
273614 ATTATAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 8 0.32
23 1 0.04
24 10 0.40
26 6 0.24
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
TATTATTAAATATATAAATATAATT
Found at i:273938 original size:41 final size:42
Alignment explanation
Indices: 273859--273976 Score: 204
Period size: 41 Copynumber: 2.9 Consensus size: 42
273849 ATGAATTACA
*
273859 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
273901 TTCCGGAAAACGAATTACGTG-AACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
273942 TT-CGGAAAACGAATTACGTGAAACAAACACTGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
273977 TTCGGGGAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
40 18 0.25
41 34 0.47
42 21 0.29
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:276568 original size:2 final size:2
Alignment explanation
Indices: 276561--276619 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
276551 AATGTATAAC
276561 AT AT AT AT AT AT AT AT AT AT AT -T 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
*
276602 AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT
276620 TCTTAAACGT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:294707 original size:16 final size:16
Alignment explanation
Indices: 294674--294707 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
294664 ATGAAATAAC
* *
294674 ATGTATATGTGAATAT
1 ATGTATATGAGAAGAT
294690 ATGTATATGAGAAGAT
1 ATGTATATGAGAAGAT
294706 AT
1 AT
294708 AAGAATAAGA
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:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (16 bp):
ATGTATATGAGAAGAT
Found at i:295452 original size:42 final size:42
Alignment explanation
Indices: 295406--295489 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
295396 GAATATAATC
295406 ATATATGTACATGTTTGTATTTGATATATGAATAGAAATATG
1 ATATATGTACATGTTTGTATTTGATATATGAATAGAAATATG
295448 ATATATGTACATGTTTGTATTTGATATATGAATAGAAATATG
1 ATATATGTACATGTTTGTATTTGATATATGAATAGAAATATG
295490 TTTTTTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (42 bp):
ATATATGTACATGTTTGTATTTGATATATGAATAGAAATATG
Found at i:295472 original size:23 final size:23
Alignment explanation
Indices: 295406--295477 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
295396 GAATATAATC
295406 ATATATGTACATGTTTGTATTTG
1 ATATATGTACATGTTTGTATTTG
** *
295429 ATATATG-A-ATAG---AAATATG
1 ATATATGTACAT-GTTTGTATTTG
295448 ATATATGTACATGTTTGTATTTG
1 ATATATGTACATGTTTGTATTTG
295471 ATATATG
1 ATATATG
295478 AATAGAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
19 11 0.30
20 2 0.05
21 4 0.11
22 2 0.05
23 18 0.49
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.46
Consensus pattern (23 bp):
ATATATGTACATGTTTGTATTTG
Found at i:298382 original size:24 final size:24
Alignment explanation
Indices: 298355--298403 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
298345 ACAAGGAATG
* *
298355 GAAATTTGAAGTTTGAAATCGCCT
1 GAAATTTGAAATTTGAAAACGCCT
298379 GAAATTTGAAATTTGAAAACGCCT
1 GAAATTTGAAATTTGAAAACGCCT
298403 G
1 G
298404 GTTAGAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (24 bp):
GAAATTTGAAATTTGAAAACGCCT
Found at i:306557 original size:19 final size:20
Alignment explanation
Indices: 306533--306579 Score: 87
Period size: 19 Copynumber: 2.4 Consensus size: 20
306523 TTGTATGCTT
306533 TTGATTATCAAGAGAAGC-C
1 TTGATTATCAAGAGAAGCTC
306552 TTGATTATCAAGAGAAGCTC
1 TTGATTATCAAGAGAAGCTC
306572 TTGATTAT
1 TTGATTAT
306580 TTCCCTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (20 bp):
TTGATTATCAAGAGAAGCTC
Found at i:309334 original size:23 final size:23
Alignment explanation
Indices: 309308--309364 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
309298 TGTGACATGT
309308 TCTCTTCCTTTATGGCACGTTTA
1 TCTCTTCCTTTATGGCACGTTTA
* * * *
309331 TCTCTGCCTTTGTGGCATGTTTT
1 TCTCTTCCTTTATGGCACGTTTA
*
309354 TCTCTTTCTTT
1 TCTCTTCCTTT
309365 TGGTAGCTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.07, C:0.25, G:0.14, T:0.54
Consensus pattern (23 bp):
TCTCTTCCTTTATGGCACGTTTA
Found at i:317179 original size:47 final size:47
Alignment explanation
Indices: 317091--317220 Score: 143
Period size: 47 Copynumber: 2.7 Consensus size: 47
317081 ATTTATTATG
* * ** * *
317091 TTAGTGCGAATATGCACTCTTGTATAGTACAACCGTGCACTCCTATA
1 TTAGTGCGAATACGCACTCCTGTATAGTACAATTGTACACTCATATA
*
317138 TTAGTGTGAATACGCACTCCTGTATAGTACAATTGTACACTCATATA
1 TTAGTGCGAATACGCACTCCTGTATAGTACAATTGTACACTCATATA
* ** * *
317185 TTTGTGCGAACGCACACTCCTATATTAGTACAATTG
1 TTAGTGCGAATACGCACTCCTGTA-TAGTACAATTG
317221 CGATCTAATA
Statistics
Matches: 69, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
47 58 0.84
48 11 0.16
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (47 bp):
TTAGTGCGAATACGCACTCCTGTATAGTACAATTGTACACTCATATA
Found at i:318547 original size:41 final size:42
Alignment explanation
Indices: 318334--318680 Score: 260
Period size: 41 Copynumber: 8.4 Consensus size: 42
318324 TCTTTAATTT
** * **
318334 ACTTTTTTTCTTTGTAATTGAGGTTCTTAATTTTGT-AATC-C
1 ACTTTTTACCTTTATAATTGAGGCCCTTAATTTT-TCAATCTC
* *
318375 TACTTTTTATCTTTATAATTGAGGCCCTTAATTTTTCAATCCC
1 -ACTTTTTACCTTTATAATTGAGGCCCTTAATTTTTCAATCTC
* * **
318418 A-TTTTTCCACATTTATAATTGATGATCTTAAGTTTTTCAATC-C
1 ACTTTTT--ACCTTTATAATTGAGGCCCTTAA-TTTTTCAATCTC
* * * *
318461 -CTTTGTACTTTTATAATTGA-GCTCCTGATTTTTTCAA--TC
1 ACTTTTTACCTTTATAATTGAGGC-CCTTAATTTTTCAATCTC
*
318500 ACTTTTTACCTTTATAATTGAGGCCCTTAATTTTTAAATCTC
1 ACTTTTTACCTTTATAATTGAGGCCCTTAATTTTTCAATCTC
* * *
318542 ATTTTTTTA-CTTATATAATCT-AGGCCCCTAATTTTTTCAACCTC
1 A-CTTTTTACCTT-TATAAT-TGAGGCCCTTAA-TTTTTCAATCTC
* * *
318586 AC--TTTACCTTTA-AATTGAAGCCCCTAATTTTTTAATCTC
1 ACTTTTTACCTTTATAATTGAGGCCCTTAATTTTTCAATCTC
*
318625 ACTTTTTACCTTTAT-ATTGAGG-TCTCTAATTTTTCAATCAT-
1 ACTTTTTACCTTTATAATTGAGGCCCT-TAATTTTTCAATC-TC
318666 ACTTTTTA-CTTTATA
1 ACTTTTTACCTTTATA
318681 GTTTAAGCCC
Statistics
Matches: 249, Mismatches: 32, Indels: 49
0.75 0.10 0.15
Matches are distributed among these distances:
39 14 0.06
40 57 0.23
41 66 0.27
42 45 0.18
43 45 0.18
44 22 0.09
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.50
Consensus pattern (42 bp):
ACTTTTTACCTTTATAATTGAGGCCCTTAATTTTTCAATCTC
Found at i:318560 original size:83 final size:80
Alignment explanation
Indices: 318376--318695 Score: 228
Period size: 84 Copynumber: 3.9 Consensus size: 80
318366 TTGTAATCCT
* * *
318376 ACTTTTTATCTTTATAATTGAGGC-CCTTAATTTTTCAATCCCATTTTTCCACATTTATAATTGA
1 ACTTTTTA-CTTTATAATTGA-GCTCC-TATTTTTTCAATCAC-TTTTT--ACCTTTATAATTGA
* ** * *
318440 TGATCTTAAGTTTTTCAATC-C
60 AGCCCCTAA-TTTTTAAATCTC
* *
318461 -CTTTGTACTTTTATAATTGAGCTCCTGATTTTTTCAATCACTTTTTACCTTTATAATTGAGGCC
1 ACTTTTTAC-TTTATAATTGAGCTCCT-ATTTTTTCAATCACTTTTTACCTTTATAATTGAAGCC
*
318525 CTTAATTTTTAAATCTC
64 CCTAATTTTTAAATCTC
* *
318542 ATTTTTTTACTTATATAATCT-AGGCCCCTAATTTTTTCAACCTCAC--TTTACCTTTA-AATTG
1 A-CTTTTTACTT-TATAAT-TGA-GCTCCT-ATTTTTTCAA--TCACTTTTTACCTTTATAATTG
*
318603 AAGCCCCTAATTTTTTAATCTC
59 AAGCCCCTAATTTTTAAATCTC
* * * *
318625 ACTTTTTACCTTTAT-ATTGAGGTCTCTAATTTTTCAATCATACTTTTTA-CTTTATAGTTTAAG
1 ACTTTTTA-CTTTATAATTGAGCTC-CTATTTTTTCAATC--ACTTTTTACCTTTATAATTGAAG
318688 -CCCTAATT
62 CCCCTAATT
318696 AATCATTTTT
Statistics
Matches: 195, Mismatches: 21, Indels: 42
0.76 0.08 0.16
Matches are distributed among these distances:
78 2 0.01
80 23 0.12
81 38 0.19
82 21 0.11
83 50 0.26
84 57 0.29
86 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.48
Consensus pattern (80 bp):
ACTTTTTACTTTATAATTGAGCTCCTATTTTTTCAATCACTTTTTACCTTTATAATTGAAGCCCC
TAATTTTTAAATCTC
Found at i:318616 original size:124 final size:124
Alignment explanation
Indices: 318376--318663 Score: 313
Period size: 124 Copynumber: 2.3 Consensus size: 124
318366 TTGTAATCCT
* *
318376 ACTTTTTATCTTTATAATTGAGGCCCTTAATTTTTCAATCCCATTTTTCCACATTTATAATTGAT
1 ACTTTTTACCTTTATAATTGAGGCCCTTAATTTTTCAATCCCATTTTTCCACATTTATAATTGAG
* * * * * *
318441 GATCTTAAGTTTTTCAATCCCTTTGTACTTTTATAATTGAGCTCCTGATTTTTTCAA-TC
66 GACCCTAAGTTTTTCAATCCCCTTGTACCTTTATAATTGAGCCCCTAATTTTTT-AACTC
* * **
318500 ACTTTTTACCTTTATAATTGAGGCCCTTAATTTTTAAATCTCATTTTTTTAC-TTATATAATCT-
1 ACTTTTTACCTTTATAATTGAGGCCCTTAATTTTTCAATCCCATTTTTCCACATT-TATAAT-TG
* *
318563 AGGCCCCTAATTTTTTCAA-CCTCACTT-TACCTTTA-AATTGAAGCCCCTAATTTTTTAATCTC
64 AGGACCCTAAGTTTTTCAATCC-C-CTTGTACCTTTATAATTG-AGCCCCTAATTTTTTAA-CTC
*
318625 ACTTTTTACCTTTAT-ATTGAGG-TCTCTAATTTTTCAATC
1 ACTTTTTACCTTTATAATTGAGGCCCT-TAATTTTTCAATC
318664 ATACTTTTTA
Statistics
Matches: 140, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
123 13 0.09
124 107 0.76
125 20 0.14
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.48
Consensus pattern (124 bp):
ACTTTTTACCTTTATAATTGAGGCCCTTAATTTTTCAATCCCATTTTTCCACATTTATAATTGAG
GACCCTAAGTTTTTCAATCCCCTTGTACCTTTATAATTGAGCCCCTAATTTTTTAACTC
Found at i:318640 original size:84 final size:83
Alignment explanation
Indices: 318488--318695 Score: 209
Period size: 83 Copynumber: 2.5 Consensus size: 83
318478 TGAGCTCCTG
* * *
318488 ATTTTTTCAATCACTTTTTACCTTTATAATTGAGGCCCTTAATTTTTAAATCTCATTTTTTTACT
1 ATTTTTTCAATCAC-TTTTACCTTTATAATTGAAGCCCCTAATTTTTAAATCTCATCTTTTTACT
318553 TATATAATCTAGGCCCCTA
65 TATATAATCTAGGCCCCTA
*
318572 ATTTTTTCAACCTCAC-TTTACCTTTA-AATTGAAGCCCCTAATTTTTTAATCTCA-CTTTTTAC
1 ATTTTTTCAA--TCACTTTTACCTTTATAATTGAAGCCCCTAATTTTTAAATCTCATCTTTTTA-
* *
318634 CTT-TAT-AT-TGAGGTCTCTA
63 CTTATATAATCT-AGGCCCCTA
* *
318653 A-TTTTTCAATCATACTTTTTA-CTTTATAGTTTAAG-CCCTAATT
1 ATTTTTTCAATC--AC-TTTTACCTTTATAATTGAAGCCCCTAATT
318696 AATCATTTTT
Statistics
Matches: 107, Mismatches: 8, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
78 2 0.02
80 11 0.10
81 23 0.21
82 19 0.18
83 28 0.26
84 20 0.19
86 4 0.04
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.49
Consensus pattern (83 bp):
ATTTTTTCAATCACTTTTACCTTTATAATTGAAGCCCCTAATTTTTAAATCTCATCTTTTTACTT
ATATAATCTAGGCCCCTA
Found at i:322751 original size:20 final size:20
Alignment explanation
Indices: 322715--322752 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
322705 AATCTATTCC
**
322715 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
322735 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
322753 GTGAAAACGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:324253 original size:17 final size:16
Alignment explanation
Indices: 324222--324263 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
324212 AAAATTGAAT
324222 TTTAATAATACATATATA
1 TTTAA-AATACATATA-A
*
324240 TTTAAAATATATATAA
1 TTTAAAATACATATAA
324256 TTTAAAAT
1 TTTAAAAT
324264 TTTTCAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 9 0.39
18 5 0.22
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTAAAATACATATAA
Found at i:328978 original size:2 final size:2
Alignment explanation
Indices: 328906--328961 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
328896 ATTCAAACAA
328906 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
328948 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
328962 CTTCATGATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:329351 original size:21 final size:21
Alignment explanation
Indices: 329318--329357 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
329308 AATTAGTAAA
329318 AAAATCAAAGGTAAATTATTT
1 AAAATCAAAGGTAAATTATTT
329339 AAAAT-AAAGGGTAAATTAT
1 AAAATCAAA-GGTAAATTAT
329358 ATCAGTGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.30
Consensus pattern (21 bp):
AAAATCAAAGGTAAATTATTT
Found at i:329796 original size:15 final size:14
Alignment explanation
Indices: 329758--329788 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
329748 TAATGGGGAG
329758 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
329772 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
329786 TAA
1 TAA
329789 ATCTCTGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:330374 original size:19 final size:20
Alignment explanation
Indices: 330328--330374 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
330318 TTAATTTATT
330328 AAAAATTAAATATTATATAA
1 AAAAATTAAATATTATATAA
** * *
330348 AATTATTAGATA-TATTTAA
1 AAAAATTAAATATTATATAA
330367 AAAAATTA
1 AAAAATTA
330375 TAAAAATATT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAAATTAAATATTATATAA
Found at i:346459 original size:2 final size:2
Alignment explanation
Indices: 346454--346508 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
346444 TTAATCATTA
346454 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
346496 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
346509 ACGTTATAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:347171 original size:26 final size:26
Alignment explanation
Indices: 347114--347171 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
347104 TAGGTAATTT
* *
347114 ATTTTCTTTTTCTATAAAATTTTTTA
1 ATTTTATTTTTCTATAAAATTTTTAA
* *
347140 AGTTTATTTTT-TCTAAAATTTTATAA
1 ATTTTATTTTTCTATAAAATTTT-TAA
347166 ATTTTA
1 ATTTTA
347172 AATTAAGCGG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (26 bp):
ATTTTATTTTTCTATAAAATTTTTAA
Found at i:348610 original size:12 final size:12
Alignment explanation
Indices: 348593--348626 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
348583 TACATATATG
348593 TATTATATAATA
1 TATTATATAATA
348605 TATTATAT-A-A
1 TATTATATAATA
348615 TATTATATAATA
1 TATTATATAATA
348627 CAATAATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.45
11 2 0.10
12 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATTATATAATA
Found at i:349269 original size:99 final size:99
Alignment explanation
Indices: 349134--349328 Score: 336
Period size: 99 Copynumber: 2.0 Consensus size: 99
349124 TTGTTTGTTA
* * * *
349134 ACAGTTAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCTAATATCCTTCGTTG
1 ACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCTTCATTG
*
349199 TGAAGTTGAAATTGACTCTGAGATTGGGAAGTTG
66 TGAAGTTGAAATTGACTCTGAAATTGGGAAGTTG
349233 ACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCTTCATTG
1 ACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCTTCATTG
*
349298 TGAAGTTGAAATTGGCTCTGAAATTGGGAAG
66 TGAAGTTGAAATTGACTCTGAAATTGGGAAG
349329 CCCCTTCGTT
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 90 1.00
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (99 bp):
ACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCTTCATTG
TGAAGTTGAAATTGACTCTGAAATTGGGAAGTTG
Found at i:350432 original size:12 final size:12
Alignment explanation
Indices: 350415--350473 Score: 57
Period size: 12 Copynumber: 4.6 Consensus size: 12
350405 ACCCACCTTA
350415 TTTTTTCTTTTC
1 TTTTTTCTTTTC
350427 TTTTTTCTTTTGTTC
1 TTTTTTC--TT-TTC
350442 TTTCTTT-TTTTC
1 TTT-TTTCTTTTC
*
350454 TCTTTTCCTTTTC
1 T-TTTTTCTTTTC
350467 TTTTTTC
1 TTTTTTC
350474 AATTAGGGCG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
12 18 0.46
13 10 0.26
14 2 0.05
15 6 0.15
16 3 0.08
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (12 bp):
TTTTTTCTTTTC
Found at i:350444 original size:20 final size:19
Alignment explanation
Indices: 350415--350473 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 19
350405 ACCCACCTTA
350415 TTTTTTCTTTTCTTTTTTC
1 TTTTTTCTTTTCTTTTTTC
350434 TTTTGTTC-TTTCTTTTTTTC
1 TTTT-TTCTTTTC-TTTTTTC
*
350454 TCTTTTCCTTTTCTTTTTTC
1 T-TTTTTCTTTTCTTTTTTC
350474 AATTAGGGCG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
19 8 0.23
20 20 0.57
21 7 0.20
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTTCTTTTCTTTTTTC
Found at i:362515 original size:16 final size:17
Alignment explanation
Indices: 362496--362528 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
362486 ATAATAATTT
362496 CTTAA-TATAAAAAAGG
1 CTTAAGTATAAAAAAGG
*
362512 CTTAAGTATACAAAAGG
1 CTTAAGTATAAAAAAGG
362529 TGCCCAGCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (17 bp):
CTTAAGTATAAAAAAGG
Found at i:363809 original size:41 final size:41
Alignment explanation
Indices: 363755--363868 Score: 103
Period size: 40 Copynumber: 2.8 Consensus size: 41
363745 CAATTTCTAG
*
363755 ATTCGCAACGCGATTATGACAATCGCAATGCGATTTT-CCA
1 ATTCGCAATGCGATTATGACAATCGCAATGCGATTTTCCCA
** *
363795 ATTTCGCGTTGCGATT-T-ACTTATTCGC-ATGCGATTTTCCCA
1 A-TTCGCAATGCGATTATGAC--AATCGCAATGCGATTTTCCCA
* *
363836 ATTCGCAATGCGAATAAGTA-AATCGCAATGCGA
1 ATTCGCAATGCGATTATG-ACAATCGCAATGCGA
363869 ATTTGGAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
39 2 0.04
40 28 0.49
41 26 0.46
43 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (41 bp):
ATTCGCAATGCGATTATGACAATCGCAATGCGATTTTCCCA
Found at i:363839 original size:20 final size:20
Alignment explanation
Indices: 363755--363848 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 20
363745 CAATTTCTAG
* **
363755 ATTCGCAACGCGATTATGACA
1 ATTCGCAATGCGATT-TTCCA
363776 A-TCGCAATGCGATTTTCCA
1 ATTCGCAATGCGATTTTCCA
** * **
363795 ATTTCGCGTTGCGATTTACTT
1 A-TTCGCAATGCGATTTTCCA
363816 ATTCGC-ATGCGATTTTCCCA
1 ATTCGCAATGCGATTTT-CCA
363836 ATTCGCAATGCGA
1 ATTCGCAATGCGA
363849 ATAAGTAAAT
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
19 12 0.21
20 24 0.42
21 21 0.37
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (20 bp):
ATTCGCAATGCGATTTTCCA
Found at i:363861 original size:20 final size:21
Alignment explanation
Indices: 363838--363889 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
363828 TTTTCCCAAT
*
363838 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
363858 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
363879 TCGCAATGCGA
1 TCGCAATGCGA
363890 TACTGACTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:363953 original size:57 final size:57
Alignment explanation
Indices: 363881--363988 Score: 162
Period size: 57 Copynumber: 1.9 Consensus size: 57
363871 TTGGAAAATC
* * *
363881 GCAATGCGATACTGACTGTCGCAACGCGATAATACAAAATCGCAACGCGATACTTTT
1 GCAACGCGATACTGACTATCGCAACGAGATAATACAAAATCGCAACGCGATACTTTT
* * *
363938 GCAACGCGATTCTGACTATCGCAACGAGATAATACAGAATCGCAATGCGAT
1 GCAACGCGATACTGACTATCGCAACGAGATAATACAAAATCGCAACGCGAT
363989 TTTCAAAGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.21
Consensus pattern (57 bp):
GCAACGCGATACTGACTATCGCAACGAGATAATACAAAATCGCAACGCGATACTTTT
Found at i:365979 original size:20 final size:20
Alignment explanation
Indices: 365954--366040 Score: 131
Period size: 20 Copynumber: 4.3 Consensus size: 20
365944 CAACGGGGAA
365954 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
365974 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
365994 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
366014 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGGAAATGACT
366034 ATCGCAA
1 ATCGCAA
366041 TGAGAGAATC
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 59 0.95
21 3 0.05
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:366101 original size:20 final size:20
Alignment explanation
Indices: 366076--366113 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
366066 AATCGCAACG
*
366076 TGAAAATCGCAATGCGAAGA
1 TGAAAATCGCAACGCGAAGA
366096 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
366114 TTTAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACGCGAAGA
Found at i:366136 original size:19 final size:19
Alignment explanation
Indices: 366109--366154 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
366099 AAATCGCAAC
* **
366109 GCGAATTTAGTTTTGCATT
1 GCGATTTTAGTTTCACATT
*
366128 GCGATTTTAGTTTCACGTT
1 GCGATTTTAGTTTCACATT
366147 GCGATTTT
1 GCGATTTT
366155 CTCGTTGCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.22, T:0.48
Consensus pattern (19 bp):
GCGATTTTAGTTTCACATT
Found at i:366160 original size:14 final size:14
Alignment explanation
Indices: 366138--366198 Score: 59
Period size: 14 Copynumber: 4.0 Consensus size: 14
366128 GCGATTTTAG
*
366138 TTTCACGTTGCGAT
1 TTTCTCGTTGCGAT
366152 TTTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
366166 TTTCATTTCGCATTGCGAT
1 TTTC---TCG--TTGCGAT
*
366185 TCTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
366199 AGTCAGTTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 24 0.60
16 3 0.08
17 3 0.08
19 10 0.25
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (14 bp):
TTTCTCGTTGCGAT
Found at i:366168 original size:33 final size:33
Alignment explanation
Indices: 366126--366198 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
366116 TAGTTTTGCA
* *
366126 TTGCGATTTT-AGTTTCACGTTGCGATTTTCTCG
1 TTGCGATTTTCA-TTTCACATTGCGATTCTCTCG
*
366159 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCACATTGCGATTCTCTCG
366192 TTGCGAT
1 TTGCGAT
366199 AGTCAGTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 35 0.97
34 1 0.03
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCACATTGCGATTCTCTCG
Found at i:366181 original size:19 final size:19
Alignment explanation
Indices: 366123--366185 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
366113 ATTTAGTTTT
366123 GCATTGCGATTTT-AGTTTC
1 GCATTGCGATTTTCA-TTTC
* *
366142 ACGTTGCGATTTTC---TC
1 GCATTGCGATTTTCATTTC
366158 G--TTGCGATTTTCATTTC
1 GCATTGCGATTTTCATTTC
366175 GCATTGCGATT
1 GCATTGCGATT
366186 CTCTCGTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
14 11 0.31
16 2 0.06
17 3 0.09
19 19 0.54
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.46
Consensus pattern (19 bp):
GCATTGCGATTTTCATTTC
Found at i:366344 original size:14 final size:14
Alignment explanation
Indices: 366325--366361 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
366315 CACCAATTAA
366325 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
366339 ACAAATCATCTTTT
1 ACAAATCAACATTT
366353 ACAAATCAA
1 ACAAATCAA
366362 TTAAACAATA
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
Found at i:367806 original size:21 final size:22
Alignment explanation
Indices: 367782--367842 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
367772 GAACGGTGGG
367782 AGGGGACTCTTGAGGGATGA-T
1 AGGGGACTCTTGAGGGATGATT
*
367803 AGGGGCCTCTTGA---ATGATT
1 AGGGGACTCTTGAGGGATGATT
*
367822 GGAGGGACTCTTGAGGGATGA
1 AG-GGGACTCTTGAGGGATGA
367843 CAGGTGAGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 4 0.12
19 2 0.06
20 10 0.31
21 12 0.38
23 4 0.12
ACGTcount: A:0.23, C:0.11, G:0.41, T:0.25
Consensus pattern (22 bp):
AGGGGACTCTTGAGGGATGATT
Found at i:367841 original size:41 final size:42
Alignment explanation
Indices: 367755--367846 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
367745 ACCTCTCAAC
* *
367755 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
* * *
367797 GATGATAGGGGCCTCTTGAATGATTGGA-GGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
367838 GATGACAGG
1 GATGACAGG
367847 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 21 0.48
42 23 0.52
ACGTcount: A:0.22, C:0.14, G:0.41, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
Found at i:368166 original size:20 final size:20
Alignment explanation
Indices: 368141--368184 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
368131 AATAGAATCT
*
368141 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGAAACAC
*
368161 GAAACTTAAAATCGAAACGC
1 GAAACTTAAAATCGAAACAC
368181 GAAA
1 GAAA
368185 ATGACTATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.20, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGAAACAC
Found at i:368194 original size:20 final size:20
Alignment explanation
Indices: 368171--368239 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
368161 GAAACTTAAA
*
368171 ATCGAAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
368191 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
**
368211 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
368231 ATCGCAACG
1 ATCGCAACG
368240 AGAGAATCGC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:368391 original size:33 final size:34
Alignment explanation
Indices: 368318--368393 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 34
368308 AACTAATTCG
* * * * *
368318 CATTGCGATTTTCATTTTCGCGTTGCGCTTTTGT
1 CATTGTGATTTTCATTTTCGCATTGCGATTCTCT
*
368352 CGTTGTGATTTTCA-TTTCGCATTGCGATTCTCT
1 CATTGTGATTTTCATTTTCGCATTGCGATTCTCT
368385 CATTGTGAT
1 CATTGTGAT
368394 AGTCAAATTC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
33 23 0.66
34 12 0.34
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.49
Consensus pattern (34 bp):
CATTGTGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:368424 original size:20 final size:20
Alignment explanation
Indices: 368401--368453 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
368391 GATAGTCAAA
368401 TTCGCGTTGCGATAGCCATT
1 TTCGCGTTGCGATAGCCATT
*
368421 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGCCATT
368441 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
368454 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.13, C:0.23, G:0.26, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGCCATT
Found at i:368463 original size:20 final size:20
Alignment explanation
Indices: 368401--368478 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
368391 GATAGTCAAA
** *
368401 TTCGCGTTGCGATAGCCATT
1 TTCGCGTTGCGATAGTAAGT
* *
368421 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTAAGT
**
368441 TTCGCGTTGCGATTTTAAGT
1 TTCGCGTTGCGATAGTAAGT
* *
368461 TTCGTGTTGCGAAAGTAA
1 TTCGCGTTGCGATAGTAA
368479 ACTATTCTTC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTAAGT
Found at i:370354 original size:20 final size:20
Alignment explanation
Indices: 370331--370402 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
370321 GAAACTTAAA
370331 ATCGCAACGAGAAAATGACT
1 ATCGCAACGAGAAAATGACT
370351 ATCGCAAC-ACGAAAATGACT
1 ATCGCAACGA-GAAAATGACT
*
370371 ATCGCAACGCTG-AAATGACT
1 ATCGCAACG-AGAAAATGACT
370391 ATCGCAACGAGA
1 ATCGCAACGAGA
370403 TAATTGCAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
19 2 0.04
20 43 0.93
21 1 0.02
ACGTcount: A:0.42, C:0.24, G:0.19, T:0.15
Consensus pattern (20 bp):
ATCGCAACGAGAAAATGACT
Found at i:370430 original size:17 final size:18
Alignment explanation
Indices: 370408--370455 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
370398 CGAGATAATT
370408 GCAATGCGAATTG-AATC
1 GCAATGCGAATTGAAATC
*
370425 GCAATGCGGAAATGAAATC
1 GCAATGC-GAATTGAAATC
*
370444 GCAACGCGAATT
1 GCAATGCGAATT
370456 TGGTTTCGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 7 0.27
18 9 0.35
19 10 0.38
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.19
Consensus pattern (18 bp):
GCAATGCGAATTGAAATC
Found at i:370497 original size:14 final size:12
Alignment explanation
Indices: 370464--370512 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 12
370454 TTTGGTTTCG
*
370464 CGTTGCGATTCT
1 CGTTGCGATTTT
370476 CGTTGCGATTATT
1 CGTTGCGATT-TT
370489 CGATTGCGATTCTCT
1 CG-TTGCGATT-T-T
370504 CGTTGCGAT
1 CGTTGCGAT
370513 AGTCATTTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 10 0.31
13 3 0.09
14 16 0.50
15 3 0.09
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.41
Consensus pattern (12 bp):
CGTTGCGATTTT
Found at i:370527 original size:20 final size:20
Alignment explanation
Indices: 370504--370550 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
370494 GCGATTCTCT
370504 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
370524 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
*
370544 TGTTGCG
1 CGTTGCG
370551 CGATTGAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.21, G:0.28, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:370575 original size:27 final size:26
Alignment explanation
Indices: 370522--370577 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
370512 TAGTCATTTC
*
370522 CGCGTTGCGATAGTCATTTTCGTGTTG
1 CGCGTTGAGATAGTCATTTTCG-GTTG
370549 CGCGATTGAGATAGTCATTTGTC-GTTG
1 CGCG-TTGAGATAGTCATTT-TCGGTTG
370576 CG
1 CG
370578 ATTCTCGCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 10 0.38
28 14 0.54
29 2 0.08
ACGTcount: A:0.14, C:0.18, G:0.30, T:0.38
Consensus pattern (26 bp):
CGCGTTGAGATAGTCATTTTCGGTTG
Found at i:370991 original size:22 final size:22
Alignment explanation
Indices: 370964--371021 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
370954 GATGGAGATA
370964 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
370986 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
371008 GACGGATGTCGCCG
1 GACGGATTTCGCCG
371022 TAGAGAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.17, C:0.19, G:0.45, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:371239 original size:20 final size:20
Alignment explanation
Indices: 371214--371301 Score: 106
Period size: 20 Copynumber: 4.3 Consensus size: 20
371204 TATTATCTCA
*
371214 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGTATCGCG
*
371234 TTGCGAAAGTCAGTATCGCG
1 TTGCGATAGTCAGTATCGCG
* *
371254 TTGCGATTTTGT-ATTATCGCG
1 TTGCGA--TAGTCAGTATCGCG
*
371275 TTGCGATAGTCAGTATCGCA
1 TTGCGATAGTCAGTATCGCG
371295 TTGCGAT
1 TTGCGAT
371302 TTTCCAAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
19 3 0.05
20 38 0.67
21 14 0.25
22 2 0.04
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAGTATCGCG
Found at i:371320 original size:41 final size:41
Alignment explanation
Indices: 371228--371322 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
371218 GATAGTCAGA
* * ** *
371228 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAAT
371269 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CAAAT
*
371311 -TCGCATTGCGAT
1 ATCGCGTTGCGAT
371323 TTACTTATTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAAT
Found at i:371334 original size:20 final size:21
Alignment explanation
Indices: 371290--371341 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
371280 ATAGTCAGTA
*
371290 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
371311 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
371331 TCGCATTGCGA
1 TCGCATTGCGA
371342 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:371383 original size:21 final size:22
Alignment explanation
Indices: 371331--371383 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
371321 ATTTACTTAT
371331 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
371352 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
371373 TCGCATTGCGA
1 TCGCATTGCGA
371384 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:372079 original size:37 final size:36
Alignment explanation
Indices: 372038--372108 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
372028 GAATGAGTAC
*
372038 TAAAATGAAACAAAAACTAAACTTAATGACATGATAT
1 TAAAATAAAACAAAAACTAAACTTAA-GACATGATAT
* *
372075 TAAAATAAAACAAAAACTGAACTTTAGACATGAT
1 TAAAATAAAACAAAAACTAAACTTAAGACATGAT
372109 TTTGAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 8 0.26
37 23 0.74
ACGTcount: A:0.56, C:0.11, G:0.08, T:0.24
Consensus pattern (36 bp):
TAAAATAAAACAAAAACTAAACTTAAGACATGATAT
Found at i:378161 original size:13 final size:14
Alignment explanation
Indices: 378137--378171 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
378127 ATTTAAAATT
*
378137 AATATTTGTATATAA
1 AATATTTATATA-AA
378152 AATATTTATATAAA
1 AATATTTATATAAA
378166 AATATT
1 AATATT
378172 ATTAATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (14 bp):
AATATTTATATAAA
Found at i:378498 original size:31 final size:32
Alignment explanation
Indices: 378434--378503 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 32
378424 AAATGTGTTC
378434 AACTAATGATGTGACATATACACATTACTTAA
1 AACTAATGATGTGACATATACACATTACTTAA
378466 AA-TAATGACT-TGACATATA-ACATATAAC-TAA
1 AACTAATGA-TGTGACATATACACAT-T-ACTTAA
378497 AACTAAT
1 AACTAAT
378504 AACGTAGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
30 4 0.12
31 21 0.62
32 9 0.26
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (32 bp):
AACTAATGATGTGACATATACACATTACTTAA
Found at i:379769 original size:35 final size:35
Alignment explanation
Indices: 379682--379806 Score: 119
Period size: 35 Copynumber: 3.6 Consensus size: 35
379672 TTACTTGAAA
* * * *
379682 AGACATCTTTTGATGAAGAGACACAACTGTTGGAG
1 AGACAACTCTTGATGAAGAGACACAACTTTTGGGG
* ****
379717 A-AGCAAC-CTTCGGTGAAGAGATGTGACTTTTGGGG
1 AGA-CAACTCTT-GATGAAGAGACACAACTTTTGGGG
379752 AGACAACTCTTGATGAAGAGACACAACTTTTGGGG
1 AGACAACTCTTGATGAAGAGACACAACTTTTGGGG
* *
379787 AGGCACCTCTTGATGAAGAG
1 AGACAACTCTTGATGAAGAG
379807 TAATGATCCT
Statistics
Matches: 70, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
34 3 0.04
35 63 0.90
36 4 0.06
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (35 bp):
AGACAACTCTTGATGAAGAGACACAACTTTTGGGG
Found at i:380264 original size:6 final size:6
Alignment explanation
Indices: 380253--380281 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
380243 CAATCATGAC
380253 ATGAAT ATGAAT ATGAAT ATGAAT A-GAAT
1 ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT
380282 GCACGAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.31
Consensus pattern (6 bp):
ATGAAT
Found at i:384954 original size:17 final size:17
Alignment explanation
Indices: 384932--384978 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
384922 GGTTGTGATT
*
384932 GTGTTGAGTTCATTTAG
1 GTGTTGAGCTCATTTAG
384949 GTGTTGAGCTCATTTAG
1 GTGTTGAGCTCATTTAG
*
384966 GTATTGAGC-CATT
1 GTGTTGAGCTCATT
384979 GATGCCCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 4 0.14
17 24 0.86
ACGTcount: A:0.19, C:0.11, G:0.28, T:0.43
Consensus pattern (17 bp):
GTGTTGAGCTCATTTAG
Found at i:386146 original size:21 final size:20
Alignment explanation
Indices: 386110--386151 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
386100 CTCTAACTTA
**
386110 AAACCTTAAATTATAATCCCT
1 AAACCTTAAACCATAA-CCCT
386131 AAACCTTAAACCATAACCCT
1 AAACCTTAAACCATAACCCT
386151 A
1 A
386152 TTACCTCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (20 bp):
AAACCTTAAACCATAACCCT
Found at i:389641 original size:22 final size:22
Alignment explanation
Indices: 389613--389694 Score: 105
Period size: 22 Copynumber: 3.7 Consensus size: 22
389603 ATATCCCCAA
389613 CAGTGCTAAGGCACTTTAGTAT
1 CAGTGCTAAGGCACTTTAGTAT
*
389635 CAGTGCTAATGCACTTCT-GTAT
1 CAGTGCTAAGGCACTT-TAGTAT
* *
389657 CAGTGCTGAGACACTTTAGTA-
1 CAGTGCTAAGGCACTTTAGTAT
389678 CTAGTGCTAAGGCACTT
1 C-AGTGCTAAGGCACTT
389695 CCGTGAATTG
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
21 2 0.04
22 48 0.94
23 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (22 bp):
CAGTGCTAAGGCACTTTAGTAT
Found at i:390672 original size:15 final size:15
Alignment explanation
Indices: 390652--390682 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
390642 AAGTTTTGAT
390652 AGTCTAGGTAATTAA
1 AGTCTAGGTAATTAA
390667 AGTCTAGGTAATTAA
1 AGTCTAGGTAATTAA
390682 A
1 A
390683 TTATATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (15 bp):
AGTCTAGGTAATTAA
Found at i:392042 original size:21 final size:21
Alignment explanation
Indices: 392016--392060 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
392006 CGAATGCCAT
392016 ATATTTGTCCCGAAGGACCAC
1 ATATTTGTCCCGAAGGACCAC
*
392037 ATATTTGTCCCGAAGGACTAC
1 ATATTTGTCCCGAAGGACCAC
392058 ATA
1 ATA
392061 AAACTCTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (21 bp):
ATATTTGTCCCGAAGGACCAC
Found at i:392652 original size:19 final size:21
Alignment explanation
Indices: 392604--392655 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
392594 ATCCCCCCCA
*
392604 GTACCGATACTTCTCTTCAAGG
1 GTACCGATAC-TCTCATCAAGG
*
392626 GTATCGATAC-CTCATCAA-G
1 GTACCGATACTCTCATCAAGG
392645 GTACCGATACT
1 GTACCGATACT
392656 AATTGGCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 7 0.27
22 9 0.35
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (21 bp):
GTACCGATACTCTCATCAAGG
Found at i:392715 original size:20 final size:21
Alignment explanation
Indices: 392678--392728 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
392668 ATGTTTGCAT
* *
392678 GGTATCGATA-TCATCCTTAG
1 GGTATCGATACTCACCCTTAC
392698 GGTATCGATACT-ACCCTTAC
1 GGTATCGATACTCACCCTTAC
*
392718 AGTATCGATAC
1 GGTATCGATAC
392729 CTCTTCAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (21 bp):
GGTATCGATACTCACCCTTAC
Found at i:395274 original size:81 final size:84
Alignment explanation
Indices: 395162--395380 Score: 247
Period size: 85 Copynumber: 2.6 Consensus size: 84
395152 AAGAAGGAAT
* *
395162 AAATCAACAAAAAATTACGAA-TTAGCTTCCTTTA-AA-AAGGAGTAAGATCT-TCTCCTGATTT
1 AAATCAA-AAAAAATTAC-AACTTAGCGTCCTTTAGAAGAAGAAGTAAGAT-TGTCTCCTGATTT
* *
395223 -ACAT-TTTTAG-GAGAATGAGC
63 GACATATTTCAGAG-GAATGAGA
* *
395243 AAAT-AAATAGAAAATTACAACTTTGCGTCCTTCAGAAGAAGAAGTAAGATTGTCTCCTGATTTG
1 AAATCAAA-A-AAAATTACAACTTAGCGTCCTTTAGAAGAAGAAGTAAGATTGTCTCCTGATTTG
**
395307 GTATATTTCAGAGGAATGAGA
64 ACATATTTCAGAGGAATGAGA
395328 AAATCAAAAAAATATTACAACTTAGCGTCCTTTAGAAGAAGAAGTAAGATTGT
1 AAATCAAAAAAA-ATTACAACTTAGCGTCCTTTAGAAGAAGAAGTAAGATTGT
395381 AACATCCCAA
Statistics
Matches: 117, Mismatches: 10, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
79 1 0.01
80 5 0.04
81 22 0.19
82 3 0.03
83 22 0.19
84 5 0.04
85 55 0.47
86 4 0.03
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (84 bp):
AAATCAAAAAAAATTACAACTTAGCGTCCTTTAGAAGAAGAAGTAAGATTGTCTCCTGATTTGAC
ATATTTCAGAGGAATGAGA
Found at i:397214 original size:32 final size:32
Alignment explanation
Indices: 397173--397234 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
397163 GAGTCGAGGG
*
397173 TTACCTATGTCCTTCGGGACATATGGACAGGA
1 TTACCTATGTCATTCGGGACATATGGACAGGA
397205 TTACCTATGTCATTCGGGACATATGGACAG
1 TTACCTATGTCATTCGGGACATATGGACAG
397235 TTATCTATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (32 bp):
TTACCTATGTCATTCGGGACATATGGACAGGA
Found at i:401438 original size:29 final size:31
Alignment explanation
Indices: 401355--401448 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 31
401345 AAGAGTCGAG
*
401355 GGTTACCTATGTCCTTCGGGACATAT-GACA
1 GGTTACCTATGTTCTTCGGGACATATGGACA
401385 GGATTACCTATG-TCATTCGGGACAT-TGGACA
1 GG-TTACCTATGTTC-TTCGGGACATATGGACA
* * *
401416 -GTTACCTATGTTCTTCAGAACATATGGATA
1 GGTTACCTATGTTCTTCGGGACATATGGACA
401446 GGT
1 GGT
401449 CCTTCGAGAC
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
29 17 0.31
30 12 0.22
31 25 0.46
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (31 bp):
GGTTACCTATGTTCTTCGGGACATATGGACA
Found at i:404442 original size:2 final size:2
Alignment explanation
Indices: 404435--404506 Score: 105
Period size: 2 Copynumber: 37.5 Consensus size: 2
404425 ACGTATCCAT
* *
404435 TA TA TA TA TA TA TA TA TA TA -A TA TT TA CA TA T- TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
404474 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 T
404507 TAATTTCATG
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
1 3 0.05
2 60 0.95
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:410303 original size:35 final size:33
Alignment explanation
Indices: 410264--410331 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 33
410254 TTTATTATTT
*
410264 TAATATCATT-TTAATAAAAATATTAATTATTAAAG
1 TAATAT-ATTATT-ATAAAAAAATTAATT-TTAAAG
410299 TAATATATTAATTATAAAAAAATTAATTTTAAA
1 TAATATATT-ATTATAAAAAAATTAATTTTAAA
410332 TAGATTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 8 0.27
35 20 0.67
36 2 0.07
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (33 bp):
TAATATATTATTATAAAAAAATTAATTTTAAAG
Found at i:410348 original size:21 final size:22
Alignment explanation
Indices: 410320--410372 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
410310 TTATAAAAAA
*
410320 ATTA-ATTTTAAATAGATTTA-T
1 ATTATATTTTAAATA-ATATAGT
*
410341 -TTATATTTTTAATAATATAGT
1 ATTATATTTTAAATAATATAGT
410362 ATTATATTTTA
1 ATTATATTTTA
410373 TTGTTATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 7 0.27
21 10 0.38
22 9 0.35
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
ATTATATTTTAAATAATATAGT
Found at i:410386 original size:27 final size:28
Alignment explanation
Indices: 410331--410394 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
410321 TTAATTTTAA
*
410331 ATAG-ATT-TATTTATATTTTTAATAAT
1 ATAGTATTATATTTATATTGTTAATAAT
410357 ATAGTATTATATTT-TATTGTT-ATAATT
1 ATAGTATTATATTTATATTGTTAATAA-T
*
410384 ATATTATTATA
1 ATAGTATTATA
410395 ATATATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 8 0.24
27 20 0.61
28 5 0.15
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (28 bp):
ATAGTATTATATTTATATTGTTAATAAT
Found at i:410463 original size:21 final size:22
Alignment explanation
Indices: 410406--410464 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
410396 TATATAATAT
* *
410406 TATACTATTA-TTTTAATAATA
1 TATAATATTATTTTTAATAAAA
410427 TATAATA--ATTTATTAATAAAA
1 TATAATATTATTT-TTAATAAAA
410448 T-TAATATTATTTTTAAT
1 TATAATATTATTTTTAAT
410465 TTCATAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
19 1 0.03
20 7 0.22
21 20 0.62
22 4 0.12
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATAATATTATTTTTAATAAAA
Found at i:410642 original size:22 final size:22
Alignment explanation
Indices: 410563--410649 Score: 83
Period size: 22 Copynumber: 4.0 Consensus size: 22
410553 TTAAAATTTT
*
410563 AATAA-TAATATTATTTTAATA
1 AATAATTAATATAATTTTAATA
*
410584 AATAAGTAATATAA--TTAAT-
1 AATAATTAATATAATTTTAATA
* * *
410603 AATAAATTATTCTCATTTTAATA
1 AAT-AATTAATATAATTTTAATA
410626 AATAATTAATATAATTTATAATA
1 AATAATTAATATAATTT-TAATA
410649 A
1 A
410650 TTTTATTTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
19 3 0.06
20 12 0.23
21 5 0.10
22 23 0.44
23 9 0.17
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (22 bp):
AATAATTAATATAATTTTAATA
Found at i:410650 original size:19 final size:19
Alignment explanation
Indices: 410557--410651 Score: 59
Period size: 21 Copynumber: 4.7 Consensus size: 19
410547 TAATTTTTAA
410557 AATTT-TAATAA-TAATATT
1 AATTTATAATAATTAATA-T
* *
410575 ATTTTAATAAATAAGTAATAT
1 AATTT-AT-AATAATTAATAT
* * *
410596 AATTAATAATAAATTATTCT
1 AATTTATAAT-AATTAATAT
*
410616 CATTTTAATAAATAATTAATAT
1 -AATTT-AT-AATAATTAATAT
410638 AATTTATAATAATT
1 AATTTATAATAATT
410652 TTATTTTAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 15
0.69 0.13 0.18
Matches are distributed among these distances:
18 4 0.07
19 10 0.17
20 11 0.19
21 16 0.28
22 14 0.24
23 3 0.05
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (19 bp):
AATTTATAATAATTAATAT
Found at i:410680 original size:82 final size:81
Alignment explanation
Indices: 410520--410680 Score: 193
Period size: 81 Copynumber: 2.0 Consensus size: 81
410510 TCTTTAAAAT
* ** **
410520 ATAATAAATATTCTTATTTTAATATTCTAATTTTTAAAATTTTAATAATAATATTATTTTAATAA
1 ATAATAAATATTCTCATTTTAATATAATAATTAATAAAATTTTAATAATAATATTATTTTAATAA
*
410585 ATAAGTAATATAATTA
66 ATAAATAATATAATTA
* *
410601 ATAATAAATTATTCTCATTTTAATA-AATAATTAATATAA-TTT-ATAATAATTTTATTTTAATA
1 ATAATAAA-TATTCTCATTTTAATATAATAATTAATAAAATTTTAATAATAATATTATTTTAATA
410663 AACTATAATAATCATAAT
65 AA-TA-AATAAT-ATAAT
410681 ATTTTTATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
79 21 0.31
80 5 0.07
81 22 0.32
82 20 0.29
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.48
Consensus pattern (81 bp):
ATAATAAATATTCTCATTTTAATATAATAATTAATAAAATTTTAATAATAATATTATTTTAATAA
ATAAATAATATAATTA
Found at i:410757 original size:20 final size:22
Alignment explanation
Indices: 410717--410757 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
410707 AATATTTTAA
410717 TAATACTATTAAATGAATTATTC
1 TAATACTATTAAA-GAATTATTC
410740 TAATACT-TTAAA-AATTAT
1 TAATACTATTAAAGAATTAT
410758 ATTGTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
22 5 0.28
23 7 0.39
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (22 bp):
TAATACTATTAAAGAATTATTC
Found at i:412197 original size:13 final size:13
Alignment explanation
Indices: 412181--412210 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
412171 CTTAATTACG
412181 AAAATTAAAAATT
1 AAAATTAAAAATT
*
412194 AAAATTAAAATTT
1 AAAATTAAAAATT
412207 AAAA
1 AAAA
412211 ACCCGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:413364 original size:3 final size:3
Alignment explanation
Indices: 413338--413404 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
413328 TGACCCACAA
* *
413338 AAT AAT TAT ATT ATAT AA- AAT AAT AAT AAT AAT AAT AAT AAGT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
* * *
413384 TAT TAT AAT AAA AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
413405 TTTTTTAAGC
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 4 0.08
3 43 0.83
4 5 0.10
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:414413 original size:20 final size:21
Alignment explanation
Indices: 414370--414420 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
414360 TAATAAAACG
*
414370 TTAATTAATTATTAATTTTCA
1 TTAATAAATTATTAATTTTCA
* *
414391 TTAATAAATTA-TCATTTTGA
1 TTAATAAATTATTAATTTTCA
414411 TTAA-AAATTA
1 TTAATAAATTA
414421 AATGTTGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 6 0.22
20 11 0.41
21 10 0.37
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (21 bp):
TTAATAAATTATTAATTTTCA
Found at i:414502 original size:16 final size:16
Alignment explanation
Indices: 414481--414530 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
414471 TATTATATCT
414481 TTTATTGATTGTCGCA
1 TTTATTGATTGTCGCA
* *
414497 TTTATT-A-TAT--CT
1 TTTATTGATTGTCGCA
414509 TTTATTGATTGTCGCA
1 TTTATTGATTGTCGCA
414525 TTTATT
1 TTTATT
414531 TTTTTATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
12 7 0.27
13 1 0.04
14 4 0.15
15 1 0.04
16 13 0.50
ACGTcount: A:0.20, C:0.10, G:0.12, T:0.58
Consensus pattern (16 bp):
TTTATTGATTGTCGCA
Found at i:414544 original size:24 final size:28
Alignment explanation
Indices: 414471--414530 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
414461 AAAAATTAAA
414471 TATTATATCTTTTATTGATTGTCGCATT
1 TATTATATCTTTTATTGATTGTCGCATT
414499 TATTATATCTTTTATTGATTGTCGCATT
1 TATTATATCTTTTATTGATTGTCGCATT
414527 TATT
1 TATT
414531 TTTTTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.58
Consensus pattern (28 bp):
TATTATATCTTTTATTGATTGTCGCATT
Found at i:418013 original size:2 final size:2
Alignment explanation
Indices: 418006--418040 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
417996 ATCATAAATT
418006 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
418041 ATTTATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 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):
TA
Found at i:418519 original size:12 final size:12
Alignment explanation
Indices: 418502--418526 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
418492 ATTTTTTTAT
418502 TACATAGAAAAC
1 TACATAGAAAAC
418514 TACATAGAAAAC
1 TACATAGAAAAC
418526 T
1 T
418527 CTAAATACTA
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:0.56, C:0.16, G:0.08, T:0.20
Consensus pattern (12 bp):
TACATAGAAAAC
Found at i:425071 original size:29 final size:28
Alignment explanation
Indices: 425028--425088 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 28
425018 GCAATTGATC
*
425028 AGGGCCCCAATTTTTTTGTATTTATAATT
1 AGGGCCCCAA-TTTTTTATATTTATAATT
425057 AGGGCCCCCAA-TTTTTATATTTATAATT
1 AGGG-CCCCAATTTTTTATATTTATAATT
425085 AGGG
1 AGGG
425089 TTCCTAACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 20 0.67
29 4 0.13
30 6 0.20
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (28 bp):
AGGGCCCCAATTTTTTATATTTATAATT
Found at i:425619 original size:20 final size:20
Alignment explanation
Indices: 425555--425620 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
425545 TTTCATGCTA
425555 GGTCTCAAGACCAACTTTTT
1 GGTCTCAAGACCAACTTTTT
*
425575 TGTCTCAAGACCAACTTTTT
1 GGTCTCAAGACCAACTTTTT
* *
425595 TGTCTCAAGACCAACTTTCT
1 GGTCTCAAGACCAACTTTTT
425615 GGTCTC
1 GGTCTC
425621 GATACCAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.36
Consensus pattern (20 bp):
GGTCTCAAGACCAACTTTTT
Found at i:425628 original size:20 final size:20
Alignment explanation
Indices: 425556--425612 Score: 114
Period size: 20 Copynumber: 2.9 Consensus size: 20
425546 TTCATGCTAG
425556 GTCTCAAGACCAACTTTTTT
1 GTCTCAAGACCAACTTTTTT
425576 GTCTCAAGACCAACTTTTTT
1 GTCTCAAGACCAACTTTTTT
425596 GTCTCAAGACCAACTTT
1 GTCTCAAGACCAACTTT
425613 CTGGTCTCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (20 bp):
GTCTCAAGACCAACTTTTTT
Found at i:435689 original size:15 final size:15
Alignment explanation
Indices: 435669--435788 Score: 179
Period size: 15 Copynumber: 8.0 Consensus size: 15
435659 TAATAAGGTT
*
435669 ATTTATTTTAAAATA
1 ATTTATTATAAAATA
*
435684 ATTTATTTTAAAATA
1 ATTTATTATAAAATA
435699 ATTTATTATAAAATA
1 ATTTATTATAAAATA
* *
435714 ATTTATTTTGAAATA
1 ATTTATTATAAAATA
435729 ATTTATTATAAAATA
1 ATTTATTATAAAATA
435744 ATTTATTATAAAATA
1 ATTTATTATAAAATA
435759 ATTTACTT-TAAAATA
1 ATTTA-TTATAAAATA
*
435774 AATTATTATAAAATA
1 ATTTATTATAAAATA
435789 TGGATTGATT
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
14 2 0.02
15 93 0.96
16 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (15 bp):
ATTTATTATAAAATA
Found at i:435728 original size:45 final size:45
Alignment explanation
Indices: 435669--435788 Score: 204
Period size: 45 Copynumber: 2.7 Consensus size: 45
435659 TAATAAGGTT
*
435669 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTATAAAATA
*
435714 ATTTATTTTGAAATAATTTATTATAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTATAAAATA
* *
435759 ATTTACTTTAAAATAAATTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
435789 TGGATTGATT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (45 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATTTATTATAAAATA
Found at i:435801 original size:22 final size:22
Alignment explanation
Indices: 435776--435829 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
435766 TTAAAATAAA
*
435776 TTATTATAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
435798 TTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
435820 TTATTTTAAA
1 TTATTTTAAA
435830 TAATTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
TTATTTTAAAATATGGATTGAT
Found at i:435849 original size:54 final size:54
Alignment explanation
Indices: 435787--436718 Score: 492
Period size: 54 Copynumber: 16.7 Consensus size: 54
435777 TATTATAAAA
435787 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
*
435841 TATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT-G
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAG
435889 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTTAT
1 TATGGATTGATTTA-TTT---TAA---A--A-TATGGATTGATTTATTTT-AAATA---ATTTAT
435954 T--
52 TAG
* ** * * * *
435955 TAT---TTTAAATAATTTATTATTATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAG
*
436007 TATGGATTGATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT-G
1 TAT-G---GATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAG
* * * * * *
436059 TATGGATTGATTTATTTT-AAATA---ATTTA-TTAGTATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTA-TTTTAAATAATTTA--TT--AG
*
436113 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTA-TTT---TAA---A--A-TATGGATTGATTTATTTTAAATAATTTATTAG
* *
436177 TATGGATTGATTTATTTTAAAATATGGATTAATTTA--TT--AT--TGTAGTT-G
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAG
** * * ** * * *
436225 TATGGATTGATTTATTTT-AAATAATTTATTAGTATGTA-TTGATTTATTTTA-AAA
1 TATGGATTGATTTATTTTAAAAT-ATGGATT-G-ATTTATTTTAAATAATTTATTAG
436279 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTA-TTT---TAA---A--A-TATGGATTGATTTATTTTAAATAATTTATTAG
*
436343 TATGGATTTATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
*
436397 TATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
* *
436451 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTA-TTT---TAA---A--A-TATGGATTGATTTATTTTAAATAATTTATTAG
* *
436515 TATGGATTGATTTATTTTAAAATATGGATTAATTTA--TT--AT--TGTAGTT-G
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAG
* * **
436563 TATGAATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATTATGGATT-G
1 TATGGATTGATTTATTTT-AA-AA--TA-T-G---G-ATTGATTTATTTTAAATAATTTATTAG
** * ** * * *
436626 -ATTTATTTTAAATAATTTATTATTATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAG
*
436681 TATGGATTGATTTATTTTAAAATATAGATTGATTTATT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT
436719 ATTGTAGTTG
Statistics
Matches: 688, Mismatches: 78, Indels: 224
0.69 0.08 0.23
Matches are distributed among these distances:
43 3 0.00
44 4 0.01
46 1 0.00
47 9 0.01
48 81 0.12
49 11 0.02
50 22 0.03
51 4 0.01
52 21 0.03
53 9 0.01
54 247 0.36
55 27 0.04
56 5 0.01
57 6 0.01
58 43 0.06
59 14 0.02
60 15 0.02
61 1 0.00
62 15 0.02
63 38 0.06
64 82 0.12
65 3 0.00
66 5 0.01
67 2 0.00
68 17 0.02
69 3 0.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:435855 original size:18 final size:18
Alignment explanation
Indices: 435832--435879 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
435822 ATTTTAAATA
*
435832 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
435850 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
435872 ATTTATTA
1 ATTTATTA
435880 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:435946 original size:22 final size:22
Alignment explanation
Indices: 435921--435963 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
435911 AATTTATTAG
435921 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
435943 TATGGATTTATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
435964 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:435969 original size:14 final size:14
Alignment explanation
Indices: 435952--436005 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
435942 ATATGGATTT
435952 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
435966 ATTTATTATTATGGATTG
1 ATTTATT-TTA---AATA
435984 ATTTATTTTAAATA
1 ATTTATTTTAAATA
435998 ATTTATTT
1 ATTTATTT
436006 GTATGGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.53
15 3 0.09
17 3 0.09
18 9 0.28
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:435969 original size:18 final size:18
Alignment explanation
Indices: 435948--436005 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
435938 TAAAATATGG
435948 ATTTATTTATTTTAAATA
1 ATTTATTTATTTTAAATA
*
435966 ATTTA-TTA--TT--ATGG
1 ATTTATTTATTTTAAAT-A
*
435980 ATTGATTTATTTTAAATA
1 ATTTATTTATTTTAAATA
435998 ATTTATTT
1 ATTTATTT
436006 GTATGGATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
13 2 0.07
14 4 0.13
15 5 0.17
17 5 0.17
18 12 0.40
19 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
ATTTATTTATTTTAAATA
Found at i:435988 original size:32 final size:32
Alignment explanation
Indices: 435943--436701 Score: 524
Period size: 32 Copynumber: 24.7 Consensus size: 32
435933 TATTTTAAAA
* *
435943 TATGGATTTATTTATTTTAAATAATTTATTAT
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
435975 TATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
* * *
436007 TATGGATTGATTGA-TTT--AT--TTTA-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
436033 TATGGATTGATTTA--TT--AT--TGTAGTT-G
1 TATGGATTGATTTATTTTAAATAATTTA-TTAG
436059 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
436091 TATGAATTGATTTA-TTT---TAA---A--A-
1 TATGGATTGATTTATTTTAAATAATTTATTAG
436113 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
436145 TATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
* *
436177 TATGGATTGATTTATTTTAAAATATGGATTAATTTAT
1 TATGGATTGATTTATTTT-AAATA---ATTTA-TTAG
* * *
436214 TATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
1 TA-TGGA-TTG-AT--TTA------TTTTAAATAATTTATTAG
*
436257 TATGTATTGATTTA-TTT---TAA---A--A-
1 TATGGATTGATTTATTTTAAATAATTTATTAG
436279 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
436311 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
436343 TATGGATTTATTTA-TTT---TAA---A--A-
1 TATGGATTGATTTATTTTAAATAATTTATTAG
436365 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
436397 TATGAATTGATTTA-TTT---TAA---A--A-
1 TATGGATTGATTTATTTTAAATAATTTATTAG
436419 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
436451 TATGAATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
436483 TATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
**
436515 TATGGATTGATTTATTTTAAA-ATATGGATTA-
1 TATGGATTGATTTATTTTAAATA-ATTTATTAG
** * *
436546 -ATTTATT-ATTGTAGTTGTATGAATTGATTTATT--
1 TATGGATTGATT-TA-TT-T-T-AAATAATTTATTAG
* * * * * *
436579 T-T-AAATAATTTATTAGTATGAATTGATTTATTTTAAAT
1 TATGGATTGATTTATT--T-T-AAATAATTTA--TT--AG
*
436617 TATGGATTGATTTATTTTAAATAATTTATTAT
1 TATGGATTGATTTATTTTAAATAATTTATTAG
436649 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
436681 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
436702 ATATAGATTG
Statistics
Matches: 594, Mismatches: 50, Indels: 166
0.73 0.06 0.20
Matches are distributed among these distances:
22 52 0.09
23 16 0.03
25 11 0.02
26 39 0.07
27 4 0.01
28 14 0.02
29 9 0.02
30 9 0.02
31 26 0.04
32 327 0.55
33 10 0.02
34 11 0.02
36 12 0.02
37 5 0.01
38 6 0.01
39 4 0.01
40 13 0.02
41 3 0.01
42 5 0.01
43 5 0.01
44 4 0.01
47 5 0.01
48 4 0.01
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:436116 original size:22 final size:22
Alignment explanation
Indices: 436091--436133 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
436081 AATTTATTAG
436091 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
436113 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
436134 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:436273 original size:22 final size:22
Alignment explanation
Indices: 436257--436299 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
436247 AATTTATTAG
*
436257 TATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
436279 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
436300 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Done.