Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000851.1 Hibiscus syriacus cultivar Beakdansim tig00001644_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: 7304151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 31
Found at i:319220 original size:23 final size:23
Alignment explanation
Indices: 319166--319230 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
319156 AGGGACATTT
319166 TATATGGCACTTCGGTGCAACTC
1 TATATGGCACTTCGGTGCAACTC
** *
319189 T-TCGCGGCACTTCGGTGCAATTC
1 TAT-ATGGCACTTCGGTGCAACTC
*
319212 TATATGGCACATCGGTGCA
1 TATATGGCACTTCGGTGCA
319231 TTTATACGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 1 0.03
23 32 0.94
24 1 0.03
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.29
Consensus pattern (23 bp):
TATATGGCACTTCGGTGCAACTC
Found at i:321284 original size:19 final size:20
Alignment explanation
Indices: 321260--321304 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
321250 AAAAAGGCTC
*
321260 AATTTC-ACATTCTAACATG
1 AATTTCAACACTCTAACATG
*
321279 AATTTCAACACTCTAACATT
1 AATTTCAACACTCTAACATG
321299 AATTTC
1 AATTTC
321305 CATCATAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (20 bp):
AATTTCAACACTCTAACATG
Found at i:321745 original size:19 final size:20
Alignment explanation
Indices: 321718--321759 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
321708 CAATAACAAC
*
321718 AAAATCCATCATCAT-TTCAT
1 AAAATCCAT-AACATGTTCAT
321738 AAAA-CCATAACATGTTCAT
1 AAAATCCATAACATGTTCAT
321757 AAA
1 AAA
321760 CCCTAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 4 0.20
19 12 0.60
20 4 0.20
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAATCCATAACATGTTCAT
Found at i:323019 original size:29 final size:29
Alignment explanation
Indices: 322965--323024 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
322955 AGAAAAAATA
*
322965 AAGTTGGCACAGACTCCAAATAGAAAAAG
1 AAGTTGGCACAGAATCCAAATAGAAAAAG
*
322994 AAGTTGGCACAGAATCCTAAA-GGAAAAAG
1 AAGTTGGCACAGAATCC-AAATAGAAAAAG
323023 AA
1 AA
323025 AGGGGAGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 25 0.89
30 3 0.11
ACGTcount: A:0.50, C:0.15, G:0.22, T:0.13
Consensus pattern (29 bp):
AAGTTGGCACAGAATCCAAATAGAAAAAG
Found at i:323554 original size:26 final size:26
Alignment explanation
Indices: 323519--323575 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
323509 TTGACATGGA
*
323519 AAATTATCGGACAAGTACTAGTTCTG
1 AAATTATCGGACAAGTACTACTTCTG
323545 AAATTATCGGACAAGTACTACTTCTG
1 AAATTATCGGACAAGTACTACTTCTG
323571 AAATT
1 AAATT
323576 CTCCTTGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (26 bp):
AAATTATCGGACAAGTACTACTTCTG
Found at i:328389 original size:36 final size:36
Alignment explanation
Indices: 328339--328419 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 36
328329 TGGACCTTAA
* * *
328339 TAATCATCACTAGCAATTGCATGTATATCATGCATG
1 TAATCATCAATAGCAAGTACATGTATATCATGCATG
328375 TAATCATCAATAGCAAGTACATGTATATCATGCATG
1 TAATCATCAATAGCAAGTACATGTATATCATGCATG
328411 TAATCATCA
1 TAATCATCA
328420 TTATTGATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (36 bp):
TAATCATCAATAGCAAGTACATGTATATCATGCATG
Found at i:329304 original size:58 final size:56
Alignment explanation
Indices: 329228--329640 Score: 310
Period size: 51 Copynumber: 7.8 Consensus size: 56
329218 TTCAACAGTT
* * * *
329228 AACTTATTACTTATTTACACCAGTGGAATTTAACACATTATTCCAACAATGAGAATTG
1 AACTTATCACTGACTTACACCAGTGAAATTTAACACATTATTCCAACAAT-AGAA-TG
* * * * * *
329286 AACTTATCATTGACTTACACAAGTGAAATTGAACAAATTATTCCAGCAATGAGCTATG
1 AACTTATCACTGACTTACACCAGTGAAATTTAACACATTATTCCAACAAT-AG-AATG
* * *
329344 AACTTATCACTTACTTACACTAGTGAAATTGAACACATTATTCCAAC----G-ATG
1 AACTTATCACTGACTTACACCAGTGAAATTTAACACATTATTCCAACAATAGAATG
329395 AACTTATCAGC-GACTTACACCAGAT-AAATTTAACACATTATT----C--TAGTAATG
1 AACTTATCA-CTGACTTACACCAG-TGAAATTTAACACATTATTCCAACAATAG-AATG
*
329446 AAATTATCACTGACTTACACCAGTGAAATTTAACAC-TATATTCCAACAAT-GAAT-
1 AACTTATCACTGACTTACACCAGTGAAATTTAACACAT-TATTCCAACAATAGAATG
* **
329500 ---TTATCACTGACTTACACCAGTTAAATTTAACATGTTATTCCAACAAT----T-
1 AACTTATCACTGACTTACACCAGTGAAATTTAACACATTATTCCAACAATAGAATG
* * *
329548 AACTTATTACTGACTTACACCTGTTAAATTTAACGA-ATTATTCCAAC-----AATG
1 AACTTATCACTGACTTACACCAGTGAAATTTAAC-ACATTATTCCAACAATAGAATG
* * ** *
329599 AACTTATCACTTACTTATATTAGTGAAATTTAACATATTATT
1 AACTTATCACTGACTTACACCAGTGAAATTTAACACATTATT
329641 ATATCATCAG
Statistics
Matches: 299, Mismatches: 31, Indels: 57
0.77 0.08 0.15
Matches are distributed among these distances:
47 1 0.00
48 1 0.00
49 1 0.00
50 5 0.02
51 191 0.64
52 4 0.01
53 1 0.00
55 4 0.01
56 1 0.00
57 1 0.00
58 88 0.29
59 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (56 bp):
AACTTATCACTGACTTACACCAGTGAAATTTAACACATTATTCCAACAATAGAATG
Found at i:329397 original size:51 final size:51
Alignment explanation
Indices: 329341--329640 Score: 347
Period size: 51 Copynumber: 5.9 Consensus size: 51
329331 GCAATGAGCT
* * * *
329341 ATGAACTTATCACTTACTTACACTAGTGAAATTGAACACATTATTCCAACG
1 ATGAACTTATCACTGACTTACACCAGTGAAATTTAACACATTATTCCAACA
* **
329392 ATGAACTTATCAGC-GACTTACACCAGAT-AAATTTAACACATTATTCTAGTA
1 ATGAACTTATCA-CTGACTTACACCAG-TGAAATTTAACACATTATTCCAACA
*
329443 ATGAAATTATCACTGACTTACACCAGTGAAATTTAACAC-TATATTCCAACA
1 ATGAACTTATCACTGACTTACACCAGTGAAATTTAACACAT-TATTCCAACA
* * **
329494 ATGAATTTATCACTGACTTACACCAGTTAAATTTAACATGTTATTCCAACA
1 ATGAACTTATCACTGACTTACACCAGTGAAATTTAACACATTATTCCAACA
* * * *
329545 ATTAACTTATTACTGACTTACACCTGTTAAATTTAACGA-ATTATTCCAACA
1 ATGAACTTATCACTGACTTACACCAGTGAAATTTAAC-ACATTATTCCAACA
* * ** *
329596 ATGAACTTATCACTTACTTATATTAGTGAAATTTAACATATTATT
1 ATGAACTTATCACTGACTTACACCAGTGAAATTTAACACATTATT
329641 ATATCATCAG
Statistics
Matches: 214, Mismatches: 27, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
50 4 0.02
51 206 0.96
52 4 0.02
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (51 bp):
ATGAACTTATCACTGACTTACACCAGTGAAATTTAACACATTATTCCAACA
Found at i:329473 original size:25 final size:25
Alignment explanation
Indices: 329444--329526 Score: 78
Period size: 25 Copynumber: 3.3 Consensus size: 25
329434 ATTCTAGTAA
329444 TGAAATTATCACTGACTTACACCAG
1 TGAAATTATCACTGACTTACACCAG
* * * * *
329469 TGAAATTTAACACT-ATATTCCAACAA
1 TGAAA-TTATCACTGA-CTTACACCAG
*
329495 TGAATTTATCACTGACTTACACCAG
1 TGAAATTATCACTGACTTACACCAG
*
329520 TTAAATT
1 TGAAATT
329527 TAACATGTTA
Statistics
Matches: 42, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
25 24 0.57
26 18 0.43
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TGAAATTATCACTGACTTACACCAG
Found at i:329527 original size:26 final size:26
Alignment explanation
Indices: 329449--329579 Score: 74
Period size: 26 Copynumber: 5.1 Consensus size: 26
329439 AGTAATGAAA
*
329449 TTATCACTGACTTACACCAGTGAAAT
1 TTATCACTGACTTACACCAGTTAAAT
* * * * * *
329475 TTAACACT-ATATTCCAACA-ATGAAT
1 TTATCACTGA-CTTACACCAGTTAAAT
329500 TTATCACTGACTTACACCAGTTAAAT
1 TTATCACTGACTTACACCAGTTAAAT
* * * * *
329526 TTAACA-TGTTA-TTCCAACAATT-AAC
1 TTATCACTG--ACTTACACCAGTTAAAT
* *
329551 TTATTACTGACTTACACCTGTTAAAT
1 TTATCACTGACTTACACCAGTTAAAT
329577 TTA
1 TTA
329580 ACGAATTATT
Statistics
Matches: 72, Mismatches: 25, Indels: 16
0.64 0.22 0.14
Matches are distributed among these distances:
24 1 0.01
25 32 0.44
26 38 0.53
27 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.36
Consensus pattern (26 bp):
TTATCACTGACTTACACCAGTTAAAT
Found at i:333390 original size:19 final size:19
Alignment explanation
Indices: 333366--333402 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
333356 ACTTTTATAA
333366 TTCATTT-CATCTTCTTCCT
1 TTCATTTCCAT-TTCTTCCT
333385 TTCATTTCCATTTCTTCC
1 TTCATTTCCATTTCTTCC
333403 ATTTTTATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.11, C:0.32, G:0.00, T:0.57
Consensus pattern (19 bp):
TTCATTTCCATTTCTTCCT
Found at i:334440 original size:15 final size:15
Alignment explanation
Indices: 334420--334451 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
334410 GCAGTAGAGC
334420 TAAGAGTCACAACAA
1 TAAGAGTCACAACAA
334435 TAAGAGTCACAACAA
1 TAAGAGTCACAACAA
334450 TA
1 TA
334452 GCTCATTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.19, G:0.12, T:0.16
Consensus pattern (15 bp):
TAAGAGTCACAACAA
Found at i:341828 original size:16 final size:16
Alignment explanation
Indices: 341778--341832 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
341768 GACGAGTGAG
341778 ATAACAACTAGAAAC-
1 ATAACAACTAGAAACA
341793 ATAAACAA-T-G--ACA
1 AT-AACAACTAGAAACA
*
341806 GTAACAACTAGAAACA
1 ATAACAACTAGAAACA
341822 ATAACAACTAG
1 ATAACAACTAG
341833 GATTTAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
12 7 0.22
13 2 0.06
14 2 0.06
15 3 0.09
16 18 0.56
ACGTcount: A:0.58, C:0.18, G:0.09, T:0.15
Consensus pattern (16 bp):
ATAACAACTAGAAACA
Found at i:349416 original size:32 final size:32
Alignment explanation
Indices: 349380--349440 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
349370 CCATAGCCAG
349380 TATTGCATTCAA-ATAATACATAACAGAGTAAA
1 TATTGCATT-AAGATAATACATAACAGAGTAAA
* *
349412 TATTGCATTAAGATAATGCATATCAGAGT
1 TATTGCATTAAGATAATACATAACAGAGT
349441 TAGTGTCGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 2 0.08
32 24 0.92
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (32 bp):
TATTGCATTAAGATAATACATAACAGAGTAAA
Found at i:356502 original size:33 final size:33
Alignment explanation
Indices: 356437--356504 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 33
356427 TTCTTCAATG
* * * * *
356437 AACTAAATGCATGAATGAAGTAGTTTATTAAAT
1 AACTAAATGCATAAATGAACTACTTCACTAAAT
*
356470 AACTAAATGCATAAATGAACTACTTCCCTAAAT
1 AACTAAATGCATAAATGAACTACTTCACTAAAT
356503 AA
1 AA
356505 AATATATGCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.29
Consensus pattern (33 bp):
AACTAAATGCATAAATGAACTACTTCACTAAAT
Found at i:360382 original size:17 final size:17
Alignment explanation
Indices: 360353--360403 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
360343 TAAGAGTTAG
* *
360353 TTTAATAAATGAACTAT
1 TTTAATGAATGAACTAA
* *
360370 TTTGATGAATGAACCAA
1 TTTAATGAATGAACTAA
*
360387 TTTAATTAATGAACTAA
1 TTTAATGAATGAACTAA
360404 CTTTCTTCAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (17 bp):
TTTAATGAATGAACTAA
Found at i:364501 original size:17 final size:17
Alignment explanation
Indices: 364479--364531 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
364469 AATTAAGAGT
364479 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
364496 TAGTTTGATGAGTGAAC
1 TAGTTTAATAAATGAAC
* *
364513 CAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
364530 TA
1 TA
364532 ACTTTCTTCA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.36
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:375412 original size:17 final size:17
Alignment explanation
Indices: 375390--375444 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
375380 AATTAAGAGT
375390 TAGTTTAAGAAATGAAC
1 TAGTTTAAGAAATGAAC
** *
375407 TAGTTTAATTAATGAGC
1 TAGTTTAAGAAATGAAC
* *
375424 TAACTTTATGAAATGAAC
1 T-AGTTTAAGAAATGAAC
375442 TAG
1 TAG
375445 ATGCATAAAT
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (17 bp):
TAGTTTAAGAAATGAAC
Found at i:375456 original size:17 final size:17
Alignment explanation
Indices: 375434--375515 Score: 51
Period size: 17 Copynumber: 4.8 Consensus size: 17
375424 TAACTTTATG
375434 AAATGAACTAGATGCAT
1 AAATGAACTAGATGCAT
* * *
375451 AAATGAAGTAGCT-TACT
1 AAATGAACTAGATGCA-T
* *
375468 AAA-CAATCTAAATGCAT
1 AAATGAA-CTAGATGCAT
** * *
375485 AAATGAACTACTTCCCT
1 AAATGAACTAGATGCAT
375502 AAATGAACTAGATG
1 AAATGAACTAGATG
375516 ATTTAAATGC
Statistics
Matches: 45, Mismatches: 16, Indels: 8
0.65 0.23 0.12
Matches are distributed among these distances:
16 3 0.07
17 39 0.87
18 3 0.07
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (17 bp):
AAATGAACTAGATGCAT
Found at i:376635 original size:21 final size:21
Alignment explanation
Indices: 376611--376650 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
376601 CTCATTTTTA
376611 CTCTCAAT-TCTCTTTTCAATG
1 CTCTCAATGTCT-TTTTCAATG
376632 CTCTCAATGTCTTTTTCAA
1 CTCTCAATGTCTTTTTCAA
376651 CTCTCATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.20, C:0.28, G:0.05, T:0.47
Consensus pattern (21 bp):
CTCTCAATGTCTTTTTCAATG
Found at i:377804 original size:30 final size:30
Alignment explanation
Indices: 377770--377836 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
377760 ATGAAAGTAA
*
377770 TGGAAATGATATAATGAAGTTGAAGTGGAT
1 TGGAAATGATATAATAAAGTTGAAGTGGAT
377800 TGGAAATGATATAATAAAGTTGAAGTGGAT
1 TGGAAATGATATAATAAAGTTGAAGTGGAT
*
377830 TGTAAAT
1 TGGAAAT
377837 AAAAGAAGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (30 bp):
TGGAAATGATATAATAAAGTTGAAGTGGAT
Found at i:378695 original size:25 final size:25
Alignment explanation
Indices: 378658--378706 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
378648 ATGAACATCT
*
378658 TTGGTTTGAATGATTAAATCAGCCC
1 TTGGGTTGAATGATTAAATCAGCCC
*
378683 TTGGGTTGGATGATTAAATCAGCC
1 TTGGGTTGAATGATTAAATCAGCC
378707 TTGAATGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (25 bp):
TTGGGTTGAATGATTAAATCAGCCC
Found at i:378836 original size:15 final size:15
Alignment explanation
Indices: 378816--378851 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
378806 TCCATGCATG
* *
378816 AAATTCCCGTAATGA
1 AAATTCCAGCAATGA
378831 AAATTCCAGCAATGA
1 AAATTCCAGCAATGA
378846 AAATTC
1 AAATTC
378852 TAGCCTGCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.25
Consensus pattern (15 bp):
AAATTCCAGCAATGA
Found at i:379146 original size:17 final size:17
Alignment explanation
Indices: 379124--379195 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
379114 AATTAAGAGT
379124 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
379141 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
* *
379158 TAGTTTAATTAATGAGC
1 TAGTTTAATAAATGAAC
* *
379175 TAACTTTATTAAATGAAC
1 T-AGTTTAATAAATGAAC
379193 TAG
1 TAG
379196 ATGCATAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
17 31 0.70
18 13 0.30
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:379204 original size:17 final size:17
Alignment explanation
Indices: 379184--379266 Score: 53
Period size: 17 Copynumber: 4.9 Consensus size: 17
379174 CTAACTTTAT
379184 TAAATGAACTAGATGCA
1 TAAATGAACTAGATGCA
* * *
379201 TAAATGAAGTAGCT-TA
1 TAAATGAACTAGATGCA
* *
379217 CTAAAT-AATCTAAATACA
1 -TAAATGAA-CTAGATGCA
** * *
379235 TAAATGAACTATTTCCC
1 TAAATGAACTAGATGCA
379252 TAAATGAACTAGATG
1 TAAATGAACTAGATG
379267 ATATAAATGC
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
16 3 0.06
17 42 0.88
18 3 0.06
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (17 bp):
TAAATGAACTAGATGCA
Found at i:379345 original size:46 final size:46
Alignment explanation
Indices: 379278--379374 Score: 158
Period size: 46 Copynumber: 2.1 Consensus size: 46
379268 TATAAATGCA
* * *
379278 ATGCATGATTAAATGAACAACACGCTTTTTAAATGCAATGAATGTC
1 ATGCATGATTAAATGAACAACACACTTATTAAATGCAACGAATGTC
*
379324 ATGCATGATTACATGAACAACACACTTATTAAATGCAACGAATGTC
1 ATGCATGATTAAATGAACAACACACTTATTAAATGCAACGAATGTC
379370 ATGCA
1 ATGCA
379375 ACTAATAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (46 bp):
ATGCATGATTAAATGAACAACACACTTATTAAATGCAACGAATGTC
Found at i:397613 original size:14 final size:15
Alignment explanation
Indices: 397582--397614 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
397572 ATCATTTCAG
397582 AAAATATTATAAAATA
1 AAAATATTAT-AAATA
397598 AAAATATTAT-AATA
1 AAAATATTATAAATA
397612 AAA
1 AAA
397615 TCATATTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
16 10 0.59
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATATTATAAATA
Found at i:402317 original size:17 final size:17
Alignment explanation
Indices: 402285--402337 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
402275 AATTAAGAGT
*
402285 TAGTTTAATAAATGAAC
1 TAGTTTAATGAATGAAC
* *
402302 TATTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
* *
402319 CAGTTTAATTAATGAAC
1 TAGTTTAATGAATGAAC
402336 TA
1 TA
402338 ACTTTCTTCA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.38
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:406452 original size:16 final size:17
Alignment explanation
Indices: 406421--406472 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
406411 AATTAAGAGT
*
406421 TAGTTTAATAAATGAAC
1 TAGTTTAATGAATGAAC
*
406438 TAG-TTGATGAATGAAC
1 TAGTTTAATGAATGAAC
* *
406454 CAGTTTAATTAATGAAC
1 TAGTTTAATGAATGAAC
406471 TA
1 TA
406473 ACTTTCTTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:406469 original size:17 final size:17
Alignment explanation
Indices: 406422--406470 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
406412 ATTAAGAGTT
*
406422 AGTTTAATAAATGAACT
1 AGTTTAATAAATGAACC
* *
406439 AG-TTGATGAATGAACC
1 AGTTTAATAAATGAACC
*
406455 AGTTTAATTAATGAAC
1 AGTTTAATAAATGAAC
406471 TAACTTTCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (17 bp):
AGTTTAATAAATGAACC
Found at i:411983 original size:66 final size:66
Alignment explanation
Indices: 411861--412489 Score: 785
Period size: 66 Copynumber: 9.6 Consensus size: 66
411851 CATGACTTTT
* * * * *
411861 AAAGGTTTATATTTCAAGAGAAACTGT-T-TATAGAGATAAAATTTGTTTCAAGAGAAATAATCT
1 AAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCT
411924 C
66 C
* * * * * * *
411925 AAAGGTTTATTTTTCAAGCA-AAATTGTCTCAAGTGAAACAAAATTTGCTTCAATAGAAACAACC
1 AAAGGTTTATGTTTCAAG-AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATC
411989 TC
65 TC
*
411991 AAAGGTTTATGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCT
1 AAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCT
412056 C
66 C
* ** * *
412057 AAAGATTTATGTTTCAAGAGAAACTAACTCAAGAGAGACAAAATTTGCTTCAAGAGAAATAATCT
1 AAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCT
412122 C
66 C
* *
412123 AAAGGTTTATGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTT-TTTCCAAGAGAAAAAATC
1 AAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT-CAAGAGAAACAATC
412187 TC
65 TC
* * * * *
412189 AAAGGTTTATGTTTCAAAAGAAACTATCCCAA-A-AGAGAAAATTTGTTTTGAA-AGAAACAATC
1 AAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG-TTTCAAGAGAAACAATC
412251 TC
65 TC
* * * * * * *
412253 -TAGTGTTTATGTTTCAGGAGAAATTGTCTCAAGAGAGACAAAGTTTGTTTTAACATAAACAATC
1 AAAG-GTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATC
412317 TC
65 TC
* *
412319 AAAGGTTTATGTTTCAAGAGAAACTGTCTCAAAAGAGACGAAATTTGTTTCAAGAGAAACAATCT
1 AAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCT
412384 C
66 C
412385 AAAGG-TTATGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAAATTTGTTTC-AGCAGAAACAATC
1 AAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG-AGAAACAATC
412447 TC
65 TC
* * * * *
412449 AAAGTTTTCTATTTCAAGAGAAACTGTTTCAAGAGAAACAA
1 AAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
412490 TCTCAAAGGT
Statistics
Matches: 488, Mismatches: 62, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
63 4 0.01
64 94 0.19
65 73 0.15
66 315 0.65
67 2 0.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (66 bp):
AAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCT
C
Found at i:412047 original size:36 final size:36
Alignment explanation
Indices: 412000--412190 Score: 142
Period size: 36 Copynumber: 5.6 Consensus size: 36
411990 CAAAGGTTTA
*
412000 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAATTATCTCAAGAGAGACAAAATT
** *
412036 TGTTTCAAGAGAAACAATCTC-A-A-AG----ATTT
1 TGTTTCAAGAGAAATTATCTCAAGAGAGACAAAATT
* *
412065 ATGTTTCAAGAGAAACTAACTCAAGAGAGACAAAATT
1 -TGTTTCAAGAGAAATTATCTCAAGAGAGACAAAATT
* * *
412102 TGCTTCAAGAGAAATAATCTCAA-AG-G-----TTT
1 TGTTTCAAGAGAAATTATCTCAAGAGAGACAAAATT
*
412131 ATGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATT
1 -TGTTTCAAGAGAAATTATCTCAAGAGAGACAAAATT
**
412168 T-TTTCCAAGAGAAAAAATCTCAA
1 TGTTT-CAAGAGAAATTATCTCAA
412191 AGGTTTATGT
Statistics
Matches: 119, Mismatches: 19, Indels: 34
0.69 0.11 0.20
Matches are distributed among these distances:
29 5 0.04
30 39 0.33
31 3 0.03
32 2 0.02
33 4 0.03
34 2 0.02
35 6 0.05
36 53 0.45
37 5 0.04
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAATTATCTCAAGAGAGACAAAATT
Found at i:412330 original size:196 final size:195
Alignment explanation
Indices: 411861--412489 Score: 784
Period size: 196 Copynumber: 3.2 Consensus size: 195
411851 CATGACTTTT
* * * * *
411861 AAAGGTTTATATTTCAAGAGAAACTGT-T-TATAGAGATAAAATTTGTTTCAAGAGAAATAATCT
1 AAAGTTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATAATCT
* * * * * *
411924 CAAAGGTTTATTTTTCAAGCA-AAATTGTCTCAAGTGAAACAAAATTTGCTTCAATAGAAACAAC
66 CAAAGGTTTATGTTTCAAG-AGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAAT
* *
411988 CTCAAAGGTTTATGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAA
130 CTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAA-A-AGAGAAAATTTGTTTCAA-AGAAACAA
412053 TCTC
192 TCTC
* ** *
412057 AAAGATTTATGTTTCAAGAGAAACTAACTCAAGAGAGACAAAATTTGCTTCAAGAGAAATAATCT
1 AAAGTTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATAATCT
*
412122 CAAAGGTTTATGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTT-TTTCCAAGAGAAAAAAT
66 CAAAGGTTTATGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTT-CAAGAGAAACAAT
* * * *
412186 CTCAAAGGTTTATGTTTCAAAAGAAACTATCCCAAAAGAGAAAATTTGTTTTGAAAGAAACAATC
130 CTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAAAGAGAAAATTTG-TTTCAAAGAAACAATC
412251 TC
194 TC
* * * * * * * *
412253 -TAGTGTTTATGTTTCAGGAGAAATTGTCTCAAGAGAGACAAAGTTTGTTTTAACATAAACAATC
1 AAAGT-TTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATAATC
* * *
412317 TCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAAAGAGACGAAATTTGTTTCAAGAGAAACAAT
65 TCAAAGGTTTATGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAAT
* *
412382 CTCAAAGG-TTATGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAATTTGTTTCAGCAGAAACAAT
130 CTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAAAGAG-AAAATTTGTTTCA-AAGAAACAAT
412446 CTC
193 CTC
* * * *
412449 AAAGTTTTCTATTTCAAGAGAAACTGTTTCAAGAGAAACAA
1 AAAGTTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
412490 TCTCAAAGGT
Statistics
Matches: 373, Mismatches: 50, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
195 33 0.09
196 210 0.56
197 16 0.04
198 114 0.31
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (195 bp):
AAAGTTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATAATCT
CAAAGGTTTATGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATC
TCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAAAGAGAAAATTTGTTTCAAAGAAACAATCTC
Found at i:412375 original size:36 final size:35
Alignment explanation
Indices: 412328--412451 Score: 111
Period size: 36 Copynumber: 3.7 Consensus size: 35
412318 CAAAGGTTTA
**
412328 TGTTTCAAGAGAAACTGTCTCAAAAGAGACGAAATT
1 TGTTTCAAGAGAAACAATCTCAAAAGAGA-GAAATT
412364 TGTTTCAAGAGAAACAATCTC--AA-AG-G---TT
1 TGTTTCAAGAGAAACAATCTCAAAAGAGAGAAATT
** * *
412392 ATGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAATT
1 -TGTTTCAAGAGAAACAATCTCAAAAGAGAGAAATT
412428 TGTTTC-AGCAGAAACAATCTCAAA
1 TGTTTCAAG-AGAAACAATCTCAAA
412452 GTTTTCTATT
Statistics
Matches: 70, Mismatches: 9, Indels: 19
0.71 0.09 0.19
Matches are distributed among these distances:
28 2 0.03
29 19 0.27
31 2 0.03
32 2 0.03
33 2 0.03
34 4 0.06
35 18 0.26
36 21 0.30
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.26
Consensus pattern (35 bp):
TGTTTCAAGAGAAACAATCTCAAAAGAGAGAAATT
Found at i:412526 original size:45 final size:45
Alignment explanation
Indices: 412437--412526 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
412427 TTGTTTCAGC
* * *
412437 AGAAACAATCTCAAAGTTTTCTATTTCAAGAGAAACTGTTTCAAG
1 AGAAACAATCTCAAAGGTTTATATTTCAAGAGAAACTGTCTCAAG
*
412482 AGAAACAATCTCAAAGGTTTATGTCTT-AAG-GAAGACTGTCTCAAG
1 AGAAACAATCTCAAAGGTTTATAT-TTCAAGAGAA-ACTGTCTCAAG
412527 TGAGAAAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 3 0.08
45 34 0.87
46 2 0.05
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (45 bp):
AGAAACAATCTCAAAGGTTTATATTTCAAGAGAAACTGTCTCAAG
Found at i:417810 original size:24 final size:23
Alignment explanation
Indices: 417778--417830 Score: 88
Period size: 24 Copynumber: 2.3 Consensus size: 23
417768 AATTAAGTTT
*
417778 AAAAAAATTATGACTTTATTTTG
1 AAAAAAATTATGACTTTATTTGG
417801 AAAAACAATTATGACTTTATTTGG
1 AAAAA-AATTATGACTTTATTTGG
417825 AAAAAA
1 AAAAAA
417831 TTGGAGATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (23 bp):
AAAAAAATTATGACTTTATTTGG
Found at i:419480 original size:14 final size:14
Alignment explanation
Indices: 419461--419489 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
419451 CCCCGTAAGC
419461 TCTCCTCTCTTTTA
1 TCTCCTCTCTTTTA
419475 TCTCCTCTCTTTTA
1 TCTCCTCTCTTTTA
419489 T
1 T
419490 ATATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.34, G:0.00, T:0.59
Consensus pattern (14 bp):
TCTCCTCTCTTTTA
Found at i:420231 original size:3 final size:3
Alignment explanation
Indices: 420225--420259 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
420215 ATATTATTAA
*
420225 AAT AAT AAT AAT AAT AAT AAT -AT AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
420260 TAGTAATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:420236 original size:20 final size:20
Alignment explanation
Indices: 420222--420259 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
420212 TTAATATTAT
420222 TAAAATAATAATAATAATAA
1 TAAAATAATAATAATAATAA
* *
420242 TAATATAATGATAATAAT
1 TAAAATAATAATAATAAT
420260 TAGTAATGAA
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:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
TAAAATAATAATAATAATAA
Found at i:422505 original size:21 final size:22
Alignment explanation
Indices: 422472--422512 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
422462 TTAAATATTA
*
422472 TAAAGGAAGTATCGATACTCAT
1 TAAAGGAAGTATCAATACTCAT
422494 TAAAGG-AGTATCAATACTC
1 TAAAGGAAGTATCAATACTC
422513 CTTGTCCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (22 bp):
TAAAGGAAGTATCAATACTCAT
Found at i:426511 original size:23 final size:25
Alignment explanation
Indices: 426468--426521 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
426458 ACGATCGAAG
*
426468 TTAGTTATTTTGTCCA-C-GTGTTT
1 TTAGATATTTTGTCCAGCTGTGTTT
* *
426491 TTAGATATTTTGTCGAGGTGTGTTT
1 TTAGATATTTTGTCCAGCTGTGTTT
426516 TTAGAT
1 TTAGAT
426522 GGTGCTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 14 0.54
25 12 0.46
ACGTcount: A:0.17, C:0.07, G:0.22, T:0.54
Consensus pattern (25 bp):
TTAGATATTTTGTCCAGCTGTGTTT
Found at i:432614 original size:10 final size:10
Alignment explanation
Indices: 432599--432631 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
432589 CTAATATAAC
432599 CTATATGCAA
1 CTATATGCAA
432609 CTATATGCAA
1 CTATATGCAA
*
432619 CTAAATGCAA
1 CTATATGCAA
432629 CTA
1 CTA
432632 AAAATGCAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27
Consensus pattern (10 bp):
CTATATGCAA
Found at i:445044 original size:20 final size:21
Alignment explanation
Indices: 445016--445090 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 21
445006 TCTTGCGTTT
* *
445016 AGTATCGATATTGTTCTTAG-
1 AGTACCGATATTATTCTTAGA
*
445036 AGTACCGATATTTTTCTTTAGA
1 AGTACCGATATTATTC-TTAGA
* * *
445058 AGTATCGATATTATTCAT-GC
1 AGTACCGATATTATTCTTAGA
445078 AGTACCGATATTA
1 AGTACCGATATTA
445091 GTATTATAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 27 0.59
21 5 0.11
22 14 0.30
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (21 bp):
AGTACCGATATTATTCTTAGA
Found at i:453002 original size:26 final size:26
Alignment explanation
Indices: 452973--453025 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
452963 TAACATTGAA
* *
452973 ATTATGTTTATCT-TTGTTTGATTCAG
1 ATTATGATTAT-TATTGGTTGATTCAG
452999 ATTATGATTATTATTGGTTGATTCAG
1 ATTATGATTATTATTGGTTGATTCAG
453025 A
1 A
453026 CTGTGGATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.25, C:0.06, G:0.17, T:0.53
Consensus pattern (26 bp):
ATTATGATTATTATTGGTTGATTCAG
Found at i:463347 original size:26 final size:26
Alignment explanation
Indices: 463297--463347 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
463287 ACACTAAGTG
* * *
463297 TATTATGGTGGGCACGATCTTATGTT
1 TATTATGATGGGCACGACCTAATGTT
463323 TATTATGATGGGCACGACCTAATGT
1 TATTATGATGGGCACGACCTAATGT
463348 GTAGCGCTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (26 bp):
TATTATGATGGGCACGACCTAATGTT
Found at i:465501 original size:2 final size:2
Alignment explanation
Indices: 465494--465519 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
465484 ATGTAACATA
465494 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
465520 CTTAATTTTT
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:467093 original size:3 final size:3
Alignment explanation
Indices: 467079--467127 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
467069 ATGATATTGA
*
467079 AAG AAG ACG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
467126 AA
1 AA
467128 ATATGAGGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:468515 original size:23 final size:23
Alignment explanation
Indices: 468489--468572 Score: 107
Period size: 23 Copynumber: 3.7 Consensus size: 23
468479 CTCGTATAAA
*
468489 TGCACCAAAGTGCCACGTAGAAT
1 TGCACCTAAGTGCCACGTAGAAT
*
468512 TGCACCTAAGTGCCGCGTAGAAAT
1 TGCACCTAAGTGCCACGTAG-AAT
* *
468536 T-CACCTAAGTGCCGCGTAGAAA
1 TGCACCTAAGTGCCACGTAGAAT
*
468558 TGCACCGAAGTGCCA
1 TGCACCTAAGTGCCA
468573 TATAAGATGT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
22 3 0.06
23 47 0.87
24 4 0.07
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (23 bp):
TGCACCTAAGTGCCACGTAGAAT
Found at i:468563 original size:46 final size:46
Alignment explanation
Indices: 468481--468571 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
468471 CACCATAACT
* * *
468481 CGTATAAATGCACCAAAGTGCCACGTAGAATTGCACCTAAGTGCCG
1 CGTAGAAATGCACCAAAGTGCCACGTAGAAATGCACCGAAGTGCCG
* * *
468527 CGTAGAAATTCACCTAAGTGCCGCGTAGAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCAAAGTGCCACGTAGAAATGCACCGAAGTGCC
468572 ATATAAGATG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (46 bp):
CGTAGAAATGCACCAAAGTGCCACGTAGAAATGCACCGAAGTGCCG
Found at i:470060 original size:20 final size:20
Alignment explanation
Indices: 470035--470072 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
470025 CTTCAAAATA
*
470035 TTAATGCATTGATGCACCCC
1 TTAATGCATCGATGCACCCC
*
470055 TTAATGTATCGATGCACC
1 TTAATGCATCGATGCACC
470073 TTCAAAATTT
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:0.16, T:0.32
Consensus pattern (20 bp):
TTAATGCATCGATGCACCCC
Found at i:473272 original size:2 final size:2
Alignment explanation
Indices: 473265--473299 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
473255 ACATCCAAAC
473265 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
473300 ACATTTCCTT
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:473756 original size:23 final size:23
Alignment explanation
Indices: 473730--473795 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
473720 CACCACAACT
*
473730 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
473753 CGTAGAATTGTACCTAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
473776 TGTAGAAATGCACCGAAGTG
1 CGTAGAAATGCACCGAAGTG
473796 TCATATAAGA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:476515 original size:35 final size:35
Alignment explanation
Indices: 476472--476543 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
476462 GATATGGAAT
* *
476472 TGTTGTGGCGAAAGTTTGATG-AAATTGTAAAAGTA
1 TGTTGTGGCGAAAGTTT-AAGAAAATTATAAAAGTA
*
476507 TGTTGTGGCTAAAGTTTAAGAAAATTATAAAAGTA
1 TGTTGTGGCGAAAGTTTAAGAAAATTATAAAAGTA
476542 TG
1 TG
476544 CTAAAGTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 2 0.06
35 31 0.94
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (35 bp):
TGTTGTGGCGAAAGTTTAAGAAAATTATAAAAGTA
Found at i:487646 original size:21 final size:19
Alignment explanation
Indices: 487609--487658 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
487599 GTTGGAGGCA
*
487609 AACTTAAATTTAAGGGGATG-
1 AACTAAAATTTAAGGGG--GC
487629 AACTAAAATTTAAAGGGGGC
1 AACTAAAATTT-AAGGGGGC
487649 AACTAAAATT
1 AACTAAAATT
487659 CTAGGGGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 1 0.04
20 20 0.74
21 6 0.22
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (19 bp):
AACTAAAATTTAAGGGGGC
Found at i:492755 original size:22 final size:22
Alignment explanation
Indices: 492721--492780 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
492711 ATTCCCTTGG
492721 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTC-AA
492744 GGGGGAAT-GGTTCCCCTTCAA
1 GGGGGAATCGGTTCCCCTTCAA
* *
492765 GGGGGTATCGATTCCC
1 GGGGGAATCGGTTCCC
492781 TCTGCCCTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 9 0.26
22 17 0.50
23 8 0.24
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.23
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCCTTCAA
Found at i:506078 original size:14 final size:13
Alignment explanation
Indices: 506044--506100 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
506034 ATAATAAATG
*
506044 AAAATAAACGAAC
1 AAAATAAACAAAC
*
506057 ACAATAAACAAAC
1 AAAATAAACAAAC
506070 ATAAATAAACAACAC
1 A-AAATAAACAA-AC
*
506085 AAACACAAA-AAAC
1 AAA-ATAAACAAAC
506098 AAA
1 AAA
506101 TTTATTCGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
13 17 0.46
14 13 0.35
15 7 0.19
ACGTcount: A:0.72, C:0.19, G:0.02, T:0.07
Consensus pattern (13 bp):
AAAATAAACAAAC
Found at i:506088 original size:19 final size:18
Alignment explanation
Indices: 506064--506099 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
506054 AACACAATAA
*
506064 ACAAACATAAATAAACAAC
1 ACAAACACAAA-AAACAAC
506083 ACAAACACAAAAAACAA
1 ACAAACACAAAAAACAA
506100 ATTTATTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.72, C:0.22, G:0.00, T:0.06
Consensus pattern (18 bp):
ACAAACACAAAAAACAAC
Found at i:513374 original size:2 final size:2
Alignment explanation
Indices: 513369--513398 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
513359 GACATAAAAA
513369 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
513399 TTAAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:513519 original size:19 final size:19
Alignment explanation
Indices: 513504--513544 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
513494 AACATTAAAT
*
513504 TTAGTTAAATATATTATGA
1 TTAGTTAAATATATTATAA
* *
513523 TTAGTTATATATATTATGA
1 TTAGTTAAATATATTATAA
513542 TTA
1 TTA
513545 TAATAATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (19 bp):
TTAGTTAAATATATTATAA
Found at i:514405 original size:139 final size:141
Alignment explanation
Indices: 514137--514418 Score: 345
Period size: 139 Copynumber: 2.0 Consensus size: 141
514127 ATAGGAGTCA
* *
514137 TTTTTTACCTTATATAAATTGTAAATAATATTTTTATTGTCATATACAACTATACTTCTGTTGAA
1 TTTTTTACCTTATATAAATTGTAAATAATA--TTTA-T-TCATATACAACTATACTTATGTCGAA
* * * * * *
514202 AATTTTTAAAAATTATCTTTTTATCATATTTATGCATGTTGTATCTGTATTACGCGTGTGCGTAA
62 AACTTTTAAAAATTATCTTTTCAACATATTTATGCATGTTGTATATGTATTACGCATGTACGTAA
*
514267 TTTTTAATATAGAATC
127 CTTTTAAT-TAGAATC
* * *
514283 TTTTTTACCTTATATAAATTGTAAATAATA-TTA-TCATATACAAGTGTAGTTATGTCG-AAACT
1 TTTTTTACCTTATATAAATTGTAAATAATATTTATTCATATACAACTATACTTATGTCGAAAACT
* * * * *
514345 TTTAAAGATTCTCTTTTCAACGTATTTATGTATGTTGTATATGTATTATGCATGTACGTAACTTT
66 TTTAAAAATTATCTTTTCAACATATTTATGCATGTTGTATATGTATTACGCATGTACGTAACTTT
514410 TAATTAGAA
131 TAATTAGAA
514419 ACTCTATTCT
Statistics
Matches: 119, Mismatches: 17, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
138 5 0.04
139 62 0.52
140 19 0.16
143 3 0.03
146 30 0.25
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.47
Consensus pattern (141 bp):
TTTTTTACCTTATATAAATTGTAAATAATATTTATTCATATACAACTATACTTATGTCGAAAACT
TTTAAAAATTATCTTTTCAACATATTTATGCATGTTGTATATGTATTACGCATGTACGTAACTTT
TAATTAGAATC
Found at i:514822 original size:2 final size:2
Alignment explanation
Indices: 514815--514846 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
514805 ACAAATCTGA
514815 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
514847 GCGATTTACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:520626 original size:16 final size:16
Alignment explanation
Indices: 520605--520647 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
520595 CCGACCGAAT
520605 TTCACTATTCACAAAA
1 TTCACTATTCACAAAA
520621 TTCACTATTCACAAAA
1 TTCACTATTCACAAAA
520637 TTCACTATTCA
1 TTCACTATTCA
520648 TGTGAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
TTCACTATTCACAAAA
Found at i:521441 original size:3 final size:3
Alignment explanation
Indices: 521433--521468 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
521423 TCTACAAATG
521433 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
521469 TATTATATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:522375 original size:61 final size:61
Alignment explanation
Indices: 522280--522403 Score: 230
Period size: 61 Copynumber: 2.0 Consensus size: 61
522270 TACCCTAATT
* *
522280 TTCTCAATTAAAATCCCTAACCCTACTTTCAATCTCCAATTCTCCCTGTCTTCTCTGATTG
1 TTCTCAATTAAAATCCCTAACCCTACTTTCAATCTCCAATTCTCCCCGTCTTCTCTGACTG
522341 TTCTCAATTAAAATCCCTAACCCTACTTTCAATCTCCAATTCTCCCCGTCTTCTCTGACTG
1 TTCTCAATTAAAATCCCTAACCCTACTTTCAATCTCCAATTCTCCCCGTCTTCTCTGACTG
522402 TT
1 TT
522404 TCTATATCTC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.23, C:0.34, G:0.05, T:0.39
Consensus pattern (61 bp):
TTCTCAATTAAAATCCCTAACCCTACTTTCAATCTCCAATTCTCCCCGTCTTCTCTGACTG
Found at i:522476 original size:18 final size:18
Alignment explanation
Indices: 522453--522491 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
522443 GACAATACCC
522453 TCCATGAAAGGATCCTTG
1 TCCATGAAAGGATCCTTG
522471 TCCATGAAAGGATCCTTG
1 TCCATGAAAGGATCCTTG
522489 TCC
1 TCC
522492 CTAAGGATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (18 bp):
TCCATGAAAGGATCCTTG
Found at i:522499 original size:16 final size:17
Alignment explanation
Indices: 522453--522500 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
522443 GACAATACCC
522453 TCCATGAAAGGATCCTTG
1 TCCAT-AAAGGATCCTTG
522471 TCCATGAAAGGATCCTTG
1 TCCAT-AAAGGATCCTTG
*
522489 TCCCT-AAGGATC
1 TCCATAAAGGATC
522501 AAAACCTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 7 0.24
18 22 0.76
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (17 bp):
TCCATAAAGGATCCTTG
Found at i:523199 original size:16 final size:16
Alignment explanation
Indices: 523178--523210 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
523168 ACCAAAAGAT
523178 AAAAAAGAGGAACAAA
1 AAAAAAGAGGAACAAA
523194 AAAAAAGAGGAACAAA
1 AAAAAAGAGGAACAAA
523210 A
1 A
523211 CCGAACAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAGAGGAACAAA
Found at i:527709 original size:41 final size:41
Alignment explanation
Indices: 527637--527862 Score: 208
Period size: 41 Copynumber: 5.6 Consensus size: 41
527627 TGGCAACATG
* * * *
527637 CAATAGTTCATCATTCAACTTGATTCTATCATGGTAGCATA
1 CAATAATTCACCATTCAACTTAATTCAATCATGGTAGCATA
* ** *
527678 CAATAACTCACCATTTGA-TTCAATTCAATCATGGTAACATA
1 CAATAATTCACCATTCAACTT-AATTCAATCATGGTAGCATA
* * * * * * *
527719 CATTAGTTTATCATTCAACTTGATTCAATCATAGTAGCATG
1 CAATAATTCACCATTCAACTTAATTCAATCATGGTAGCATA
** * *
527760 CAATAATTCACCATTTGA-TTCAATTCAATTATGGAAGCATA
1 CAATAATTCACCATTCAACTT-AATTCAATCATGGTAGCATA
* * *
527801 CAATAGTTCATCATTCAACTTGATTCAATCATGGTAGCATA
1 CAATAATTCACCATTCAACTTAATTCAATCATGGTAGCATA
527842 CAAT-ATTCACCATTCAA-TTAA
1 CAATAATTCACCATTCAACTTAA
527863 ATTATATCAT
Statistics
Matches: 141, Mismatches: 40, Indels: 10
0.74 0.21 0.05
Matches are distributed among these distances:
39 3 0.02
40 15 0.11
41 119 0.84
42 4 0.03
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (41 bp):
CAATAATTCACCATTCAACTTAATTCAATCATGGTAGCATA
Found at i:527771 original size:82 final size:81
Alignment explanation
Indices: 527631--527855 Score: 353
Period size: 82 Copynumber: 2.8 Consensus size: 81
527621 CGATCTTGGC
* * *
527631 AACATGCAATAGTTCATCATTCAACTTGATTCTATCATGGTAGCATACAATAACTCACCATTTGA
1 AACATACAATAGTTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAATTCACCATTTGA
527696 TTCAATTCAATCATGG
66 TTCAATTCAATCATGG
* * * *
527712 TAACATACATTAGTTTATCATTCAACTTGATTCAATCATAGTAGCATGCAATAATTCACCATTTG
1 -AACATACAATAGTTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAATTCACCATTTG
*
527777 ATTCAATTCAATTATGG
65 ATTCAATTCAATCATGG
527794 AAGCATACAATAGTTCATCATTCAACTTGATTCAATCATGGTAGCATACAAT-ATTCACCATT
1 AA-CATACAATAGTTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAATTCACCATT
527856 CAATTAAATT
Statistics
Matches: 130, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
81 12 0.09
82 118 0.91
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.35
Consensus pattern (81 bp):
AACATACAATAGTTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAATTCACCATTTGA
TTCAATTCAATCATGG
Found at i:535789 original size:41 final size:41
Alignment explanation
Indices: 535744--536034 Score: 243
Period size: 41 Copynumber: 7.1 Consensus size: 41
535734 TAGCAACATG
* *
535744 CAATAGTTCATCATTTGATTTAATTCAATCATGGTAGCATA
1 CAATAGTTCATCATTCGATTCAATTCAATCATGGTAGCATA
* * *
535785 CAATAGTTCATCATTCAACTTGAA-TCTAT-ATGGTAGCATA
1 CAATAGTTCATCATTCGA-TTCAATTCAATCATGGTAGCATA
* * * *
535825 CAATAATTTATCATTTGATTCAATTCAATCATGGCAGCATA
1 CAATAGTTCATCATTCGATTCAATTCAATCATGGTAGCATA
* * ** *
535866 CAATAGTTCATCATTCAACTT-GATTTGATCATGGTAGCATG
1 CAATAGTTCATCATTCGA-TTCAATTCAATCATGGTAGCATA
* * *
535907 TAATAATTCACCATTCGATTCAATTCAATCATGG-ATGCATA
1 CAATAGTTCATCATTCGATTCAATTCAATCATGGTA-GCATA
* * ** * *
535948 CAATAGTTCATCATTCAACTT-GATTTGATTATGGTAGCATG
1 CAATAGTTCATCATTCGA-TTCAATTCAATCATGGTAGCATA
* * * * *
535989 CAAT-GATTCACCATTCAATTCAATTCATTCACGGTAGCAAA
1 CAATAG-TTCATCATTCGATTCAATTCAATCATGGTAGCATA
536030 CAATA
1 CAATA
536035 ACCAATTTAC
Statistics
Matches: 193, Mismatches: 46, Indels: 21
0.74 0.18 0.08
Matches are distributed among these distances:
39 4 0.02
40 35 0.18
41 145 0.75
42 9 0.05
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (41 bp):
CAATAGTTCATCATTCGATTCAATTCAATCATGGTAGCATA
Found at i:535939 original size:82 final size:81
Alignment explanation
Indices: 535740--536034 Score: 396
Period size: 82 Copynumber: 3.6 Consensus size: 81
535730 ATCTTAGCAA
* * * *
535740 CATGCAATAGTTCATCATTTGATTTAATTCAATCATGGTAGCATACAATAGTTCATCATTCAACT
1 CATGCAATAATTCACCATTCGATTCAATTCAATCATGGTAGCATACAATAGTTCATCATTCAACT
*
535805 TGAATCT-ATATGGTAG
66 TG-ATTTGATATGGTAG
* * * * *
535821 CATACAATAATTTATCATTTGATTCAATTCAATCATGGCAGCATACAATAGTTCATCATTCAACT
1 CATGCAATAATTCACCATTCGATTCAATTCAATCATGGTAGCATACAATAGTTCATCATTCAACT
535886 TGATTTGATCATGGTAG
66 TGATTTGAT-ATGGTAG
*
535903 CATGTAATAATTCACCATTCGATTCAATTCAATCATGG-ATGCATACAATAGTTCATCATTCAAC
1 CATGCAATAATTCACCATTCGATTCAATTCAATCATGGTA-GCATACAATAGTTCATCATTCAAC
535967 TTGATTTGATTATGGTAG
65 TTGATTTGA-TATGGTAG
* * * * *
535985 CATGCAATGATTCACCATTCAATTCAATTCATTCACGGTAGCAAACAATA
1 CATGCAATAATTCACCATTCGATTCAATTCAATCATGGTAGCATACAATA
536035 ACCAATTTAC
Statistics
Matches: 192, Mismatches: 17, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
80 3 0.02
81 65 0.34
82 122 0.64
83 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (81 bp):
CATGCAATAATTCACCATTCGATTCAATTCAATCATGGTAGCATACAATAGTTCATCATTCAACT
TGATTTGATATGGTAG
Found at i:539904 original size:26 final size:25
Alignment explanation
Indices: 539857--539961 Score: 78
Period size: 25 Copynumber: 4.2 Consensus size: 25
539847 GAGCAACAAC
*
539857 AAAAAAGAGAAG--ATAATGAAAATGA
1 AAAAAAGAGAAGAAAAAATGAAAA--A
539882 AAAAAAGAGAAGAAAAAAT-AAAAA
1 AAAAAAGAGAAGAAAAAATGAAAAA
* *
539906 AAGAAAAGGAGAAGAAAAAA--ACAAC
1 AA-AAAA-GAGAAGAAAAAATGAAAAA
*
539931 AAAAAAGA-AAGAAAAAAAGGAAAAA
1 AAAAAAGAGAAG-AAAAAATGAAAAA
*
539956 AGAAAA
1 AAAAAA
539962 CAGATCAAGT
Statistics
Matches: 67, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
22 3 0.04
23 8 0.12
24 7 0.10
25 29 0.43
26 16 0.24
27 4 0.06
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (25 bp):
AAAAAAGAGAAGAAAAAATGAAAAA
Found at i:539905 original size:8 final size:8
Alignment explanation
Indices: 539894--539961 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
539884 AAAAGAGAAG
*
539894 AAAAAATA
1 AAAAAAGA
539902 AAAAAAGA
1 AAAAAAGA
539910 AAAGGAGAAGA
1 AAA--A-AAGA
*
539921 AAAAAA-C
1 AAAAAAGA
*
539928 AACAAA-A
1 AAAAAAGA
*
539935 AAGAAAGA
1 AAAAAAGA
*
539943 AAAAAAGG
1 AAAAAAGA
539951 AAAAAAGA
1 AAAAAAGA
539959 AAA
1 AAA
539962 CAGATCAAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
7 10 0.21
8 29 0.60
9 1 0.02
10 1 0.02
11 7 0.15
ACGTcount: A:0.81, C:0.03, G:0.15, T:0.01
Consensus pattern (8 bp):
AAAAAAGA
Found at i:539945 original size:20 final size:20
Alignment explanation
Indices: 539917--539960 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
539907 AGAAAAGGAG
*
539917 AAGAAA-AAAACAA-CAAAA
1 AAGAAAGAAAAAAAGCAAAA
*
539935 AAGAAAGAAAAAAAGGAAAA
1 AAGAAAGAAAAAAAGCAAAA
539955 AAGAAA
1 AAGAAA
539961 ACAGATCAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 6 0.27
20 10 0.45
ACGTcount: A:0.82, C:0.05, G:0.14, T:0.00
Consensus pattern (20 bp):
AAGAAAGAAAAAAAGCAAAA
Found at i:541704 original size:57 final size:57
Alignment explanation
Indices: 541561--541737 Score: 250
Period size: 57 Copynumber: 3.1 Consensus size: 57
541551 CTAACCCGAG
* * *
541561 TATGACACATAAGGTCGTGCCCACCATCTGTACTAGTTATACTTTAGTGC-ATTCCTGAA
1 TATGACACATAAGGTCGTGCCCACCATATGCACTA---ATACTTTAGTGCAAATCCTGAA
*
541620 TATGACACATAAGGTTGTGCCCACCATATGCACTAATACTTTAGTGCAAATCCTGAA
1 TATGACACATAAGGTCGTGCCCACCATATGCACTAATACTTTAGTGCAAATCCTGAA
* *
541677 TATGACACATAAGGTCGTGTCCGCCATATGCACTAATACTTTAGTGCAAAT-CTCGAA
1 TATGACACATAAGGTCGTGCCCACCATATGCACTAATACTTTAGTGCAAATCCT-GAA
541734 TATG
1 TATG
541738 CAGTCTGCTG
Statistics
Matches: 109, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
56 14 0.13
57 63 0.58
59 32 0.29
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (57 bp):
TATGACACATAAGGTCGTGCCCACCATATGCACTAATACTTTAGTGCAAATCCTGAA
Found at i:543735 original size:13 final size:13
Alignment explanation
Indices: 543719--543773 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
543709 TATGTCATAA
*
543719 ATTTATGACGCAC
1 ATTTATGACGCGC
*
543732 ATTTATGACACGC
1 ATTTATGACGCGC
*
543745 ATTTATGATGCGC
1 ATTTATGACGCGC
*
543758 ATTTATGACGCTC
1 ATTTATGACGCGC
543771 ATT
1 ATT
543774 GCGAGTCATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:543851 original size:85 final size:85
Alignment explanation
Indices: 543745--543908 Score: 197
Period size: 85 Copynumber: 1.9 Consensus size: 85
543735 TATGACACGC
** * * *
543745 ATTTATGATGCGCATTTATGACGCT-CATTGCGAGTCATTGAAGCCCCCGTCA-TAAATAAAGAC
1 ATTTATGACACGCATGTATGAC-CTACATTGCGAGTCATTGAAGCACACGTCATTAAA-AAAGAC
* *
543808 GGCACACATTTGTGTGTCATAA
64 GACACACATTCGTGTGTCATAA
* * * *
543830 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCACACGTCATTAAAAAATATGA
1 ATTTATGACACGCATGTATGACCTACATTGCGAGTCATTGAAGCACACGTCATTAAAAAAGACGA
543895 CACACATTCGTGTG
66 CACACATTCGTGTG
543909 GCGTGATTGT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
84 1 0.02
85 61 0.92
86 4 0.06
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACCTACATTGCGAGTCATTGAAGCACACGTCATTAAAAAAGACGA
CACACATTCGTGTGTCATAA
Found at i:555397 original size:3 final size:3
Alignment explanation
Indices: 555382--555423 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
555372 ATTTAATTTA
*
555382 ATT ATT GTT ATT ATT ATT ATT ATT ATGT -TT ATT ATT AATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT -ATT AT
555424 AAATTACATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 1 0.03
3 29 0.85
4 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:558890 original size:31 final size:30
Alignment explanation
Indices: 558831--558893 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
558821 TTATCATTTG
*
558831 TACTAACTCATTTTTCTCTGGTGTTTGTGT
1 TACTAACTCATTTTTCTCTGGTGCTTGTGT
*
558861 TACTAACTCATTTTTTCTCAT-TTGCTTGTGT
1 TACTAACTCA-TTTTTCTC-TGGTGCTTGTGT
558892 TA
1 TA
558894 TTTTTCATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 10 0.34
31 18 0.62
32 1 0.03
ACGTcount: A:0.16, C:0.17, G:0.13, T:0.54
Consensus pattern (30 bp):
TACTAACTCATTTTTCTCTGGTGCTTGTGT
Found at i:562094 original size:29 final size:28
Alignment explanation
Indices: 562040--562100 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
562030 GAAAAAAAAA
*
562040 AAAAAAAAAAGCAAAAACAAGGAAAGAG
1 AAAAAAAAAAGCAAAAACAAGCAAAGAG
* *
562068 CAAAAAAAAAA-CAAAAATATGACAAAGAG
1 -AAAAAAAAAAGCAAAAACAAG-CAAAGAG
562097 AAAA
1 AAAA
562101 GACAATGAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.75, C:0.08, G:0.13, T:0.03
Consensus pattern (28 bp):
AAAAAAAAAAGCAAAAACAAGCAAAGAG
Found at i:562269 original size:101 final size:101
Alignment explanation
Indices: 562121--562323 Score: 388
Period size: 101 Copynumber: 2.0 Consensus size: 101
562111 CCCTTGACTC
*
562121 AAATGACGCATCGAGCTTCAAACCGTGAGATTGATCAAGCAGGATCACTTCACTCGAATATCATG
1 AAATGACGCATCGAGCTTCAAACCGTGAGATTGATCAAGCAGAATCACTTCACTCGAATATCATG
562186 GAACATCAAGAGAAAATAAATAACTCATACGAGCAG
66 GAACATCAAGAGAAAATAAATAACTCATACGAGCAG
*
562222 AAATGACGCATTGAGCTTCAAACCGTGAGATTGATCAAGCAGAATCACTTCACTCGAATATCATG
1 AAATGACGCATCGAGCTTCAAACCGTGAGATTGATCAAGCAGAATCACTTCACTCGAATATCATG
562287 GAACATCAAGAGAAAATAAATAACTCATACGAGCAG
66 GAACATCAAGAGAAAATAAATAACTCATACGAGCAG
562323 A
1 A
562324 TTCAAATTGA
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.20
Consensus pattern (101 bp):
AAATGACGCATCGAGCTTCAAACCGTGAGATTGATCAAGCAGAATCACTTCACTCGAATATCATG
GAACATCAAGAGAAAATAAATAACTCATACGAGCAG
Found at i:563233 original size:14 final size:15
Alignment explanation
Indices: 563214--563244 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
563204 AAGAAAAGAC
563214 AAATTT-ATGGGGCA
1 AAATTTGATGGGGCA
563228 AAATTTGATGGGGCA
1 AAATTTGATGGGGCA
563243 AA
1 AA
563245 GAAAACAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.39, C:0.06, G:0.29, T:0.26
Consensus pattern (15 bp):
AAATTTGATGGGGCA
Found at i:564807 original size:132 final size:133
Alignment explanation
Indices: 564495--564956 Score: 529
Period size: 132 Copynumber: 3.5 Consensus size: 133
564485 CCAGTCATCC
* *
564495 TCATCACATATGAGTCGTGTCATCCCCCGACCAAACCTCCTCATCATGTAGGAGCTGTGTCACCC
1 TCATCACATATGAGTCGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCTGTGTCACCC
*
564560 ATAGATAACCAGCAGT-CTCATCGA-GTACGAACTGAGTTATCACCCTTCCTAAAGATGGCAAAG
66 ATAGATAACCAGCAGTCCTCATC-ACGTAGGAACTGAGTTATCA--CTTCCTAAAGATGGCAAAG
564623 AACTCT
128 AACTCT
* * * * * * *
564629 TCATCAC--GT-A-T-GT-T-ATCCCCTGACCAGAACTCCTCATCACATAGGAGCCGCGTCAACC
1 TCATCACATATGAGTCGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCTGTGTCACCC
* * * * *
564687 TTAGATAACCAGTC-GTCCTCATCACGTAGGAGCCGTGTTATCA-TTCCTAAAGATGGCCAAGAA
66 ATAGATAACCAG-CAGTCCTCATCACGTAGGAACTGAGTTATCACTTCCTAAAGATGGCAAAGAA
564750 CTCT
130 CTCT
564754 TCATCACATATGAGTCGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCTGTGTCACCC
1 TCATCACATATGAGTCGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCTGTGTCACCC
* * *
564819 ATACATAACCAGCAGTCCTCATCGCGTAGGAACTGAGTTATCACCCTTCCTAAAGATGGCTAAGA
66 ATAGATAACCAGCAGTCCTCATCACGTAGGAACTGAGTTATCA--CTTCCTAAAGATGGCAAAGA
564884 ACTCT
129 ACTCT
* ** ** * *
564889 TCATCACGTATGAG-CAGTGTCATCCCTTGATTAGA--TCCTCATCACGTTGGAGTTGTGTCACC
1 TCATCACATATGAGTC-GTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCTGTGTCACC
*
564951 CTTAGA
65 CATAGA
564957 CGACCCGAAC
Statistics
Matches: 275, Mismatches: 38, Indels: 31
0.80 0.11 0.09
Matches are distributed among these distances:
125 30 0.11
127 51 0.19
128 23 0.08
129 3 0.01
130 3 0.01
131 3 0.01
132 74 0.27
133 29 0.11
134 8 0.03
135 51 0.19
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (133 bp):
TCATCACATATGAGTCGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCTGTGTCACCC
ATAGATAACCAGCAGTCCTCATCACGTAGGAACTGAGTTATCACTTCCTAAAGATGGCAAAGAAC
TCT
Found at i:564990 original size:43 final size:40
Alignment explanation
Indices: 564881--564995 Score: 103
Period size: 38 Copynumber: 2.9 Consensus size: 40
564871 AAGATGGCTA
**
564881 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTTGATT
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTTGACG
* **
564921 AG-A-TCCTCATCACGT-TGGAGTTGTGTCA-CCCTTAGACG
1 AGAACTCTTCATCACGTAT-GAGCAGTGTCATCCCTT-GACG
*
564959 ACCCGAACTCTTCATCACGTATGAGCAGTGTCGTCCC
1 A---GAACTCTTCATCACGTATGAGCAGTGTCATCCC
564996 CAACAACCAA
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
37 6 0.11
38 23 0.40
39 1 0.02
40 2 0.04
41 1 0.02
42 1 0.02
43 19 0.33
44 4 0.07
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (40 bp):
AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTTGACG
Found at i:565171 original size:3 final size:3
Alignment explanation
Indices: 565156--565205 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
565146 ATTTAATTTA
*
565156 ATT ATT GTT ATT ATT ATT ATT ATT ATT A-T ATT ATGT -TT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
565200 AATT AT
1 -ATT AT
565206 AAATTACATT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 3 0.07
3 34 0.83
4 4 0.10
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:569002 original size:2 final size:2
Alignment explanation
Indices: 568995--569037 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
568985 ACATAATACC
568995 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
569037 C
1 C
569038 CCCCCAAACC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:574149 original size:7 final size:8
Alignment explanation
Indices: 574132--574160 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
574122 TTGGTTGTTA
574132 TTTTTATT
1 TTTTTATT
574140 TTTTTATT
1 TTTTTATT
574148 TTTTTATT
1 TTTTTATT
574156 TTTTT
1 TTTTT
574161 GTACAACAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTATT
Found at i:578720 original size:20 final size:20
Alignment explanation
Indices: 578695--578734 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
578685 ATTTTGATAA
578695 AAAAAATGTTTTATTAAAAG
1 AAAAAATGTTTTATTAAAAG
578715 AAAAAATGTTTTATTAAAAG
1 AAAAAATGTTTTATTAAAAG
578735 CATATGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (20 bp):
AAAAAATGTTTTATTAAAAG
Found at i:580956 original size:19 final size:19
Alignment explanation
Indices: 580932--580976 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
580922 AAGGACACAA
580932 CAAGAAATGACTGAGGAAG
1 CAAGAAATGACTGAGGAAG
580951 CAAGAAATGACTGAGGAAG
1 CAAGAAATGACTGAGGAAG
580970 CAAGAAA
1 CAAGAAA
580977 GTTCCAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.51, C:0.11, G:0.29, T:0.09
Consensus pattern (19 bp):
CAAGAAATGACTGAGGAAG
Found at i:584892 original size:34 final size:34
Alignment explanation
Indices: 584854--584956 Score: 154
Period size: 34 Copynumber: 3.0 Consensus size: 34
584844 TCCTTCGGGT
*
584854 CATCAGTAAGTCTTCCGAACATGATGATCAAATC
1 CATCAGTAAGTCTTCCGAGCATGATGATCAAATC
584888 CATCAGTAAGTCTTCCGAGCATGATGATCAAATC
1 CATCAGTAAGTCTTCCGAGCATGATGATCAAATC
* * *
584922 CATC-GATAAGTCTTTCGAGCATGATGCTTAAATC
1 CATCAG-TAAGTCTTCCGAGCATGATGATCAAATC
584956 C
1 C
584957 TTTGGGCCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
33 1 0.02
34 63 0.98
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (34 bp):
CATCAGTAAGTCTTCCGAGCATGATGATCAAATC
Found at i:585286 original size:111 final size:111
Alignment explanation
Indices: 585112--585705 Score: 906
Period size: 111 Copynumber: 5.4 Consensus size: 111
585102 GAAGAAGTGA
* * * *
585112 AACA-ATCACTCTTTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCTGATT
1 AACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCCTAATT
* * *
585176 CAATGAATCAACTTTCCCAGATCTGATATTCCCTCAGAGGAAGCAT
66 CAATGAATCAACTTTCCCAGATCTGATATTCCCTCAGAGAAAGAAG
* * * * *
585222 AATAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTATCATGATT
1 AACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCCTAATT
* * *
585287 TAATGAATCAACTTTCCCAGATCTGATATTCCCTCAGAGTAAGCAG
66 CAATGAATCAACTTTCCCAGATCTGATATTCCCTCAGAGAAAGAAG
585333 AACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCCTAATT
1 AACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCCTAATT
585398 CAATGAATCAACTTTCCCAGATCTGATATTCCCTCAGAGAAAGAAG
66 CAATGAATCAACTTTCCCAGATCTGATATTCCCTCAGAGAAAGAAG
* * *
585444 AACATATCCCCCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCTAATT
1 AACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCCTAATT
585509 CAATGAATCAACTTTCCCAGATCTGATATTCCCTCAGAGAAAGAAG
66 CAATGAATCAACTTTCCCAGATCTGATATTCCCTCAGAGAAAGAAG
* * *
585555 AACATATCCCCCTCTTTCAAGATTTGATATTCCCTAAGTGACAGTGGAACAAGTCTACCCTAATT
1 AACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCCTAATT
* * **
585620 CAATGGATCAACTTTCCCA-ATATGATATTCCCTCAGA-AGAAGTGG
66 CAATGAATCAACTTTCCCAGATCTGATATTCCCTCAGAGA-AAGAAG
* * *
585665 AACACATCCCTCTCTTTCAAGATTTGATATTACATGAGTGA
1 AACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGA
585706 TAATAGAGCA
Statistics
Matches: 450, Mismatches: 32, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
109 1 0.00
110 60 0.13
111 389 0.86
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (111 bp):
AACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCCTAATT
CAATGAATCAACTTTCCCAGATCTGATATTCCCTCAGAGAAAGAAG
Found at i:588736 original size:20 final size:20
Alignment explanation
Indices: 588711--588751 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
588701 ATTTTGATAA
588711 AAAAATGTTTTATTAAAAGC
1 AAAAATGTTTTATTAAAAGC
588731 AAAAATGTTTTATTAAAAGC
1 AAAAATGTTTTATTAAAAGC
588751 A
1 A
588752 TCTGGTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (20 bp):
AAAAATGTTTTATTAAAAGC
Found at i:596245 original size:30 final size:29
Alignment explanation
Indices: 596162--596251 Score: 85
Period size: 30 Copynumber: 3.1 Consensus size: 29
596152 TTGGTATTCG
596162 GGTCGGA-TTTTTTTTAAATTT-GGGATC
1 GGTCGGATTTTTTTTTAAATTTCGGGATC
* * ***
596189 GGTAGTATTATTTTAAAAAAATTTCGGGATC
1 GGTCGGATT-TTTT-TTTAAATTTCGGGATC
*
596220 GGTCGGATTTTTTTTTAAGATTTCGGGTTC
1 GGTCGGATTTTTTTTTAA-ATTTCGGGATC
596250 GG
1 GG
596252 GTCTGTTCGG
Statistics
Matches: 47, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
27 5 0.11
28 1 0.02
29 6 0.13
30 22 0.47
31 13 0.28
ACGTcount: A:0.22, C:0.08, G:0.26, T:0.44
Consensus pattern (29 bp):
GGTCGGATTTTTTTTTAAATTTCGGGATC
Found at i:596300 original size:33 final size:33
Alignment explanation
Indices: 596256--596330 Score: 116
Period size: 32 Copynumber: 2.3 Consensus size: 33
596246 GTTCGGGTCT
* *
596256 GTTCGGGTTTTTTAAGTTTGATATTTGGGCCGG
1 GTTCGGGTTTTTTAAGTGTGATATTCGGGCCGG
*
596289 GTT-GGGTTTTTTAAGTGTGATATTCGGGTCGG
1 GTTCGGGTTTTTTAAGTGTGATATTCGGGCCGG
596321 GTTCGGGTTT
1 GTTCGGGTTT
596331 AGGGTGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 29 0.76
33 9 0.24
ACGTcount: A:0.11, C:0.08, G:0.36, T:0.45
Consensus pattern (33 bp):
GTTCGGGTTTTTTAAGTGTGATATTCGGGCCGG
Found at i:597244 original size:15 final size:15
Alignment explanation
Indices: 597210--597242 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
597200 TATTGACAAG
597210 TTTTATGTTAATATT
1 TTTTATGTTAATATT
*
597225 ATTTAT-TTAATATT
1 TTTTATGTTAATATT
597239 TTTT
1 TTTT
597243 TAAGAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTTATGTTAATATT
Found at i:597592 original size:21 final size:21
Alignment explanation
Indices: 597568--597614 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
597558 CCAAAGAAAG
**
597568 GATCCCTCGAGGAAAAGGGTC
1 GATCCCTCGAGGAAAAGAATC
* *
597589 GATCTCTCGATGAAAAGAATC
1 GATCCCTCGAGGAAAAGAATC
597610 GATCC
1 GATCC
597615 ATTCCCTTAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (21 bp):
GATCCCTCGAGGAAAAGAATC
Found at i:598973 original size:18 final size:17
Alignment explanation
Indices: 598919--598967 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
598909 TTGGACCCTT
* *
598919 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
598937 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
598955 AGTGCATTCGATG
1 AGTGCA-TCGATG
598968 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:599036 original size:46 final size:45
Alignment explanation
Indices: 598938--599043 Score: 142
Period size: 45 Copynumber: 2.3 Consensus size: 45
598928 GTGCACTAAG
* *
598938 AGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
* *
598983 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTC
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCAC
*
599029 AGTGCATCGGTGCAT
1 AGTGCATCGATGCAT
599044 GGTAAGTGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 29 0.54
46 22 0.41
47 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (45 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
Found at i:601241 original size:13 final size:13
Alignment explanation
Indices: 601213--601251 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
601203 TGGGCAATGT
*
601213 TTTGAAAA-ACTA
1 TTTGAAAATAATA
601225 TTTGAAAATAATA
1 TTTGAAAATAATA
*
601238 TTTGTAAATAATA
1 TTTGAAAATAATA
601251 T
1 T
601252 GTATAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:604667 original size:16 final size:15
Alignment explanation
Indices: 604641--604670 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
604631 TTAGCACATG
604641 CATTACAAATTTTAT
1 CATTACAAATTTTAT
604656 CATTATCAAATTTTA
1 CATTA-CAAATTTTA
604671 GTTTAGGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
CATTACAAATTTTAT
Found at i:607722 original size:65 final size:65
Alignment explanation
Indices: 607607--607769 Score: 188
Period size: 65 Copynumber: 2.5 Consensus size: 65
607597 GTGCACTATG
* * *
607607 AGTGCAATCGATGCATTAAGTGCATTCAATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGC
1 AGTGC-ATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATGG-
607671 T-
64 TA
* * ** *
607672 GGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTTAGTGCATCGGTGCATGGT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCAGAGTGCATCGATGCATGGT
607736 A
65 A
* *
607737 AGTGTATCGATGCATGAAATGCATTCGATGTTT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTT
607770 AATTTAATTC
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
64 23 0.27
65 58 0.69
66 3 0.04
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (65 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATGGTA
Found at i:610651 original size:18 final size:18
Alignment explanation
Indices: 610628--610663 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
610618 CATTAGACTC
610628 AGACATAA-ATTGAAATAA
1 AGACATAACATT-AAATAA
610646 AGACATAACATTAAATAA
1 AGACATAACATTAAATAA
610664 GACTCAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.22
Consensus pattern (18 bp):
AGACATAACATTAAATAA
Found at i:616074 original size:136 final size:134
Alignment explanation
Indices: 615810--616279 Score: 472
Period size: 140 Copynumber: 3.5 Consensus size: 134
615800 AAGAAGAGAT
* * * * * *
615810 ATCCC-TAATTTCCATTAAGATGATTATTTCCTATTATCCAATTGAAACGAA-GAAATATTGTCA
1 ATCCCTTAATTTTCATTAAGGTGATTATATCCTATT-TTCAATAGAAA-TAAGGAAATATTGTCA
* * * *
615873 --CC-TTTAAAAATTTAAGGAAATTAGGAGAAATGCACATTGTTTTTCTATTTCTAGTTGAAGAG
64 TTCCTTTTAAAAATTTAAGGAAATTAGGAGAAATGCACATTATTTTTCTATTTCCAATTAAAGAG
615935 GAAATA
129 GAAATA
* * *
615941 ATCGCTTAATTTTCATTAAGGTGATTATA-CCATATTCTTCAATTGAATTAAGGAAATATTGTCA
1 ATCCCTTAATTTTCATTAAGGTGATTATATCC-TATT-TTCAATAGAAATAAGGAAATATTGTCA
** * * * *
616005 TTCCTTCTTAAAAATTTGAA-GAAATTAGGATCAATGCACATAATTGTTATATTTCCAATCAAAG
64 TTCCTT-TTAAAAATTT-AAGGAAATTAGGAGAAATGCACATTATTTTTCTATTTCCAATTAAAG
*
616069 TGGAAATA
127 AGGAAATA
* *
616077 ATCCCTTAATTTTCATTAACGTGATTATTTTATTTCCTATTTTTAATAGAAATAAGGAAATATTG
1 ATCCCTTAATTTTCATTAAGGTGATTA---TA--TCCTATTTTCAATAGAAATAAGGAAATATTG
* *
616142 TCATTCCTTTTAAAAAATTTAAGGAAATTAGGAGAAATTCACATTATTTTTCTATTTCCAATTAC
61 TCATTCCTTTT-AAAAATTTAAGGAAATTAGGAGAAATGCACATTATTTTTCTATTTCCAATTAA
616207 AGAGGAAA-A
125 AGAGGAAATA
* * * * * * * *
616216 ATCTCTTAATTTTCCTCAAGGTGATTAT-TTCTCATTTTTAATTGAAATTAGAAAATATTGTCAT
1 ATCCCTTAATTTTCATTAAGGTGATTATATCCT-ATTTTCAATAGAAATAAGGAAATATTGTCAT
616280 CCATTCTATG
Statistics
Matches: 281, Mismatches: 41, Indels: 31
0.80 0.12 0.09
Matches are distributed among these distances:
131 8 0.03
132 45 0.16
133 3 0.01
134 30 0.11
135 1 0.00
136 77 0.27
137 2 0.01
139 30 0.11
140 79 0.28
141 4 0.01
142 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (134 bp):
ATCCCTTAATTTTCATTAAGGTGATTATATCCTATTTTCAATAGAAATAAGGAAATATTGTCATT
CCTTTTAAAAATTTAAGGAAATTAGGAGAAATGCACATTATTTTTCTATTTCCAATTAAAGAGGA
AATA
Found at i:645175 original size:21 final size:21
Alignment explanation
Indices: 645149--645262 Score: 122
Period size: 21 Copynumber: 5.4 Consensus size: 21
645139 TCGAGGGTTC
645149 TATGTGGTCCTTTGGGACATA
1 TATGTGGTCCTTTGGGACATA
* * * *
645170 TATGTGATCATTTAGAACATA
1 TATGTGGTCCTTTGGGACATA
*
645191 TATGAT-GTCCTTCGGGACATA
1 TATG-TGGTCCTTTGGGACATA
* * *
645212 TATTTGGTCCTTTAGAACATA
1 TATGTGGTCCTTTGGGACATA
* *
645233 TATGTGGTCCTTCGAGACATA
1 TATGTGGTCCTTTGGGACATA
645254 TATGTGGTC
1 TATGTGGTC
645263 ATTCGAGACA
Statistics
Matches: 73, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
20 1 0.01
21 71 0.97
22 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (21 bp):
TATGTGGTCCTTTGGGACATA
Found at i:645214 original size:42 final size:42
Alignment explanation
Indices: 645149--645265 Score: 173
Period size: 42 Copynumber: 2.8 Consensus size: 42
645139 TCGAGGGTTC
* *
645149 TATGTGGTCCTTTGGGACATATATGTGATCATTTAGAACATA
1 TATGTGGTCCTTCGGGACATATATGTGGTCATTTAGAACATA
* *
645191 TATGAT-GTCCTTCGGGACATATATTTGGTCCTTTAGAACATA
1 TATG-TGGTCCTTCGGGACATATATGTGGTCATTTAGAACATA
*
645233 TATGTGGTCCTTCGAGACATATATGTGGTCATT
1 TATGTGGTCCTTCGGGACATATATGTGGTCATT
645266 CGAGACATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
41 1 0.02
42 64 0.97
43 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (42 bp):
TATGTGGTCCTTCGGGACATATATGTGGTCATTTAGAACATA
Found at i:645273 original size:63 final size:63
Alignment explanation
Indices: 645153--645273 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 63
645143 GGGTTCTATG
* * * * *
645153 TGGTCCTTTGGGACATATATGTGATCATTTAGAACATATATGATGTCCTTCGGGACATATATT
1 TGGTCCTTTAGAACATATATGTGATCATTGAGAACATATATGATGTCATTCGAGACATATATT
* *
645216 TGGTCCTTTAGAACATATATGTGGTCCTTCGAG-ACATATATG-TGGTCATTCGAGACAT
1 TGGTCCTTTAGAACATATATGTGATCATT-GAGAACATATATGAT-GTCATTCGAGACAT
645274 TTCTACGTGG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
62 1 0.02
63 46 0.94
64 2 0.04
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (63 bp):
TGGTCCTTTAGAACATATATGTGATCATTGAGAACATATATGATGTCATTCGAGACATATATT
Found at i:654034 original size:18 final size:18
Alignment explanation
Indices: 654013--654051 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
654003 CTTTAACCTT
654013 ACAACACTTACCACGACA
1 ACAACACTTACCACGACA
* *
654031 ACAACATTTGCCACGACA
1 ACAACACTTACCACGACA
654049 ACA
1 ACA
654052 CCATTCATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.36, G:0.08, T:0.13
Consensus pattern (18 bp):
ACAACACTTACCACGACA
Found at i:677770 original size:13 final size:13
Alignment explanation
Indices: 677754--677796 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
677744 CTATGATGCG
*
677754 CATTTATGACAGA
1 CATTTATGACACA
*
677767 CATTTATGACACT
1 CATTTATGACACA
*
677780 CATTTATGACACG
1 CATTTATGACACA
677793 CATT
1 CATT
677797 GTGAGTCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.35
Consensus pattern (13 bp):
CATTTATGACACA
Found at i:693729 original size:6 final size:6
Alignment explanation
Indices: 693718--693830 Score: 85
Period size: 6 Copynumber: 18.8 Consensus size: 6
693708 CCATAATTGA
* * *
693718 AAAAAG AAAAAG --AAAT AAAAAG -AAAAG AAGAAAAG AGAGAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG -A-AAAAG AAAAAG AAAAAG
* *
693765 GAAAAG AATGAAATG -AAAAG AAAAAG GAAAAG AAAAA- AAAAAG AAAAAG
1 AAAAAG AA--AAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
693814 AAAAA- AATAAAG AAAAA
1 AAAAAG AA-AAAG AAAAA
693831 ATGATGAAAG
Statistics
Matches: 85, Mismatches: 10, Indels: 24
0.71 0.08 0.20
Matches are distributed among these distances:
4 3 0.04
5 13 0.15
6 56 0.66
7 3 0.04
8 9 0.11
9 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:693743 original size:5 final size:5
Alignment explanation
Indices: 693719--693817 Score: 53
Period size: 5 Copynumber: 18.8 Consensus size: 5
693709 CATAATTGAA
*
693719 AAAAG AAAAAG AAATA- AAAAG AAAAG --AAG AAAAG AGAGAG AAAAAGG
1 AAAAG -AAAAG AAA-AG AAAAG AAAAG AAAAG AAAAG A-AAAG -AAAA-G
* * *
693766 AAAAG -AATG AAATG AAAAG AAAAAGG AAAAG AAAAAA AAAAG AAAAAG
1 AAAAG AAAAG AAAAG AAAAG -AAAA-G AAAAG -AAAAG AAAAG -AAAAG
693814 AAAA
1 AAAA
693818 AAATAAAGAA
Statistics
Matches: 75, Mismatches: 6, Indels: 25
0.71 0.06 0.24
Matches are distributed among these distances:
3 3 0.04
4 4 0.05
5 33 0.44
6 32 0.43
7 3 0.04
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:693799 original size:17 final size:17
Alignment explanation
Indices: 693717--693829 Score: 72
Period size: 17 Copynumber: 6.7 Consensus size: 17
693707 ACCATAATTG
*
693717 AAAAAAGAAAAAG-AAA
1 AAAAAAGGAAAAGAAAA
*
693733 TAAAAA-GAAAAGAAGAA
1 AAAAAAGGAAAAGAA-AA
* * **
693750 AAGAGAGAGAAAA-AGGA
1 AAAAAAG-GAAAAGAAAA
* * *
693767 AAAGAATGAAATGAAAA
1 AAAAAAGGAAAAGAAAA
*
693784 GAAAAAGGAAAAGAAAA
1 AAAAAAGGAAAAGAAAA
*
693801 AAAAAAGAAAAAGAAAA
1 AAAAAAGGAAAAGAAAA
693818 AAATAAA-GAAAA
1 AAA-AAAGGAAAA
693830 AATGATGAAA
Statistics
Matches: 70, Mismatches: 21, Indels: 11
0.69 0.21 0.11
Matches are distributed among these distances:
15 5 0.07
16 10 0.14
17 46 0.66
18 4 0.06
19 5 0.07
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.04
Consensus pattern (17 bp):
AAAAAAGGAAAAGAAAA
Found at i:693839 original size:29 final size:29
Alignment explanation
Indices: 693718--693831 Score: 92
Period size: 29 Copynumber: 3.8 Consensus size: 29
693708 CCATAATTGA
*
693718 AAAAAGAAAAAGAAATAA-AAAGAAAAGAAG
1 AAAAAGAAAAAGAAA-AAGAAA-AAAAAAAG
* * *
693748 -AAAAGAGAGAGAAAAAGGAAAAGAATGAAATG
1 AAAAAGAAAAAGAAAAA-GAAAA-AA--AAAAG
*
693780 -AAAAGAAAAAGGAAAAGAAAAAAAAAAG
1 AAAAAGAAAAAGAAAAAGAAAAAAAAAAG
693808 AAAAAGAAAAA-AATAAAGAAAAAA
1 AAAAAGAAAAAGAA-AAAGAAAAAA
693832 TGATGAAAGA
Statistics
Matches: 68, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
28 7 0.10
29 33 0.49
30 7 0.10
31 5 0.07
32 16 0.24
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (29 bp):
AAAAAGAAAAAGAAAAAGAAAAAAAAAAG
Found at i:693863 original size:22 final size:19
Alignment explanation
Indices: 693822--693867 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 19
693812 AGAAAAAAAT
*
693822 AAAGAAAAAATGATGAAAG
1 AAAGAAAAAAAGATGAAAG
693841 AAAGAAAGAAAAGATGGATAAG
1 AAAGAAA-AAAAGAT-GA-AAG
693863 AAAGA
1 AAAGA
693868 TAAGGAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 6 0.26
21 2 0.09
22 8 0.35
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (19 bp):
AAAGAAAAAAAGATGAAAG
Found at i:696624 original size:22 final size:22
Alignment explanation
Indices: 696598--696648 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 22
696588 GAGGGAACCG
696598 ATTCCCCCCCAAGGGGGTGCCA
1 ATTCCCCCCCAAGGGGGTGCCA
*
696620 ATT-CCCCCCAAGGGGGTGCCG
1 ATTCCCCCCCAAGGGGGTGCCA
696641 ATTCCCCC
1 ATTCCCCC
696649 TGAATGGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.16, C:0.43, G:0.25, T:0.16
Consensus pattern (22 bp):
ATTCCCCCCCAAGGGGGTGCCA
Found at i:701563 original size:21 final size:21
Alignment explanation
Indices: 701492--701574 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
701482 ATATGGCAGA
* *
701492 GGGAATCGATACCCCCATGAAG
1 GGGAATCGATACCCCCCT-TAG
* * ** *
701514 GGGAACCGATTCCCCATTTGAAT
1 GGGAATCGATACCCCCCTT--AG
*
701537 GGGAATCGATTCCCCCCTTAG
1 GGGAATCGATACCCCCCTTAG
701558 GGGAATCGATACCCCCC
1 GGGAATCGATACCCCCC
701575 AAGGGTTCTG
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
21 17 0.35
22 14 0.29
23 17 0.35
ACGTcount: A:0.25, C:0.31, G:0.24, T:0.19
Consensus pattern (21 bp):
GGGAATCGATACCCCCCTTAG
Found at i:701579 original size:20 final size:21
Alignment explanation
Indices: 701492--701579 Score: 70
Period size: 23 Copynumber: 4.1 Consensus size: 21
701482 ATATGGCAGA
*
701492 GGGAATCGATACCCCCATGAAG
1 GGGAATCGATACCCCCCT-AAG
* * ** *
701514 GGGAACCGATTCCCCATTTGAAT
1 GGGAATCGATACCCC-CCT-AAG
* *
701537 GGGAATCGATTCCCCCCTTAG
1 GGGAATCGATACCCCCCTAAG
701558 GGGAATCGATACCCCCC-AAG
1 GGGAATCGATACCCCCCTAAG
701578 GG
1 GG
701580 TTCTGGATAT
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
20 4 0.08
21 17 0.32
22 14 0.26
23 18 0.34
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.18
Consensus pattern (21 bp):
GGGAATCGATACCCCCCTAAG
Found at i:712714 original size:19 final size:19
Alignment explanation
Indices: 712651--712721 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
712641 ATGCATTGGA
*
712651 CTATGAATTT-GAAATTAAA
1 CTATGAATTTAGAAA-TAAG
* *
712670 CTATGAATCTAAAAATAAG
1 CTATGAATTTAGAAATAAG
*
712689 TTATGAATTTAGAAATAAG
1 CTATGAATTTAGAAATAAG
* *
712708 CTCTGAATTGAGAA
1 CTATGAATTTAGAA
712722 TGAATTTTTG
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 39 0.93
20 3 0.07
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.32
Consensus pattern (19 bp):
CTATGAATTTAGAAATAAG
Found at i:712799 original size:13 final size:13
Alignment explanation
Indices: 712764--712807 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
712754 AAAATGTTAT
*
712764 ATGAAAATGAATG
1 ATGAAAATGAAAG
*
712777 -TGAAAGTGAAAG
1 ATGAAAATGAAAG
*
712789 ATGAAAATGAAAT
1 ATGAAAATGAAAG
712802 ATGAAA
1 ATGAAA
712808 GTTTTGAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (13 bp):
ATGAAAATGAAAG
Found at i:713342 original size:25 final size:23
Alignment explanation
Indices: 713314--713369 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
713304 GTTTTTTGTT
*
713314 TTAGATAAAAAAATTATATTTTTAA
1 TTAGATAAAAAAA-TAT-TTTTAAA
*
713339 TTAGAATAAAGAAATATTTTTAAA
1 TTAG-ATAAAAAAATATTTTTAAA
*
713363 TTGGATA
1 TTAGATA
713370 GTTTTTAGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 3 0.11
24 9 0.33
25 7 0.26
26 8 0.30
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (23 bp):
TTAGATAAAAAAATATTTTTAAA
Found at i:713930 original size:12 final size:12
Alignment explanation
Indices: 713913--713941 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
713903 TTCACAATTT
713913 TTCCTCAATTAA
1 TTCCTCAATTAA
713925 TTCCTCAATTAA
1 TTCCTCAATTAA
713937 TTCCT
1 TTCCT
713942 TAGGGCCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.45
Consensus pattern (12 bp):
TTCCTCAATTAA
Done.