Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold134
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: 811437
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
File 3 of 5
Found at i:371397 original size:2 final size:2
Alignment explanation
Indices: 371390--371431 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
371380 TCATATAAAC
371390 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
371432 GTGCTTGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:371624 original size:25 final size:24
Alignment explanation
Indices: 371593--371659 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 24
371583 TATTCATATT
371593 ATTTTTTGTGTTGTGTCATATTTTA
1 ATTTTTT-TGTTGTGTCATATTTTA
* *
371618 ATTTTTTTTGTCGTGTCATGTTTTA
1 A-TTTTTTTGTTGTGTCATATTTTA
*
371643 ACTTTTTT-TTGTGTCAT
1 ATTTTTTTGTTGTGTCAT
371660 GTCTGATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 8 0.22
24 6 0.16
25 17 0.46
26 6 0.16
ACGTcount: A:0.13, C:0.07, G:0.15, T:0.64
Consensus pattern (24 bp):
ATTTTTTTGTTGTGTCATATTTTA
Found at i:378580 original size:2 final size:2
Alignment explanation
Indices: 378567--378605 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
378557 TAAGTGTGGA
* * *
378567 AT AT AT AC AT AT AT AT AT AT AT AT AT AG AT AG AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
378606 CATAAAATGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (2 bp):
AT
Found at i:380821 original size:31 final size:30
Alignment explanation
Indices: 380747--380821 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 30
380737 AGCATGAAAA
380747 CAATTAGTGGCAATTTTGGTAAAGGATAAT
1 CAATTAGTGGCAATTTTGGTAAAGGATAAT
* *
380777 CAATTAAGGGGCAATTGTT-GTAAAGGTTAAAT
1 CAATT-AGTGGCAATT-TTGGTAAAGGAT-AAT
380809 -AATTGAGTGGCAA
1 CAATT-AGTGGCAA
380822 CTGTGGTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
30 5 0.13
31 28 0.74
32 5 0.13
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (30 bp):
CAATTAGTGGCAATTTTGGTAAAGGATAAT
Found at i:380868 original size:18 final size:19
Alignment explanation
Indices: 380845--380885 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
380835 AGAAAGAAAG
380845 GAAAGAG-AGAAAAAAAAA
1 GAAAGAGAAGAAAAAAAAA
*
380863 GAAAGAGAAGGAAAAAAAA
1 GAAAGAGAAGAAAAAAAAA
380882 GAAA
1 GAAA
380886 AAAATTTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (19 bp):
GAAAGAGAAGAAAAAAAAA
Found at i:381063 original size:19 final size:19
Alignment explanation
Indices: 381024--381063 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
381014 CTTTTATTCA
* * *
381024 TTTCGTATTATGTTATGTT
1 TTTCATATTATGTCATATT
381043 TTTCATATTATGTCATATT
1 TTTCATATTATGTCATATT
381062 TT
1 TT
381064 AATTATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.62
Consensus pattern (19 bp):
TTTCATATTATGTCATATT
Found at i:381970 original size:22 final size:23
Alignment explanation
Indices: 381930--381974 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
381920 TTTTAATAAT
* *
381930 TTTTATATATTTTATTTATATTA
1 TTTTATATATTATAATTATATTA
381953 TTTT-TATATTATAATTATATTA
1 TTTTATATATTATAATTATATTA
381975 CCGATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTATATATTATAATTATATTA
Found at i:381974 original size:11 final size:11
Alignment explanation
Indices: 381935--381974 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
381925 ATAATTTTTA
*
381935 TATATTTTATT
1 TATATTATATT
*
381946 TATATTATTTT
1 TATATTATATT
*
381957 TATATTATAAT
1 TATATTATATT
381968 TATATTA
1 TATATTA
381975 CCGATATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATATTATATT
Found at i:382465 original size:22 final size:22
Alignment explanation
Indices: 382440--382487 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 22
382430 TATAATTATA
* *
382440 TTTAAGATATTTTATATAT-AAT
1 TTTAA-ATATGTTATACATAAAT
382462 TTT-AATATGTTATACATAAAT
1 TTTAAATATGTTATACATAAAT
382483 TTTAA
1 TTTAA
382488 CACATTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 11 0.50
21 7 0.32
22 4 0.18
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (22 bp):
TTTAAATATGTTATACATAAAT
Found at i:382469 original size:20 final size:21
Alignment explanation
Indices: 382446--382487 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
382436 TATATTTAAG
* *
382446 ATATTTTATATAT-AATTTTA
1 ATATGTTATACATAAATTTTA
382466 ATATGTTATACATAAATTTTA
1 ATATGTTATACATAAATTTTA
382487 A
1 A
382488 CACATTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
ATATGTTATACATAAATTTTA
Found at i:382994 original size:33 final size:32
Alignment explanation
Indices: 382939--383003 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
382929 TGATATAATT
* *
382939 TTTAATATTTAATTAAAATTAAATATTTAAAA
1 TTTAATATTTAATTAAAATTAAAAAATTAAAA
*
382971 TTTATTATTTAGA-TAAATATTAAAAAATTAAAA
1 TTTAATATTTA-ATTAAA-ATTAAAAAATTAAAA
383004 ATAAATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (32 bp):
TTTAATATTTAATTAAAATTAAAAAATTAAAA
Found at i:383475 original size:2 final size:2
Alignment explanation
Indices: 383468--383499 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
383458 ACATTAATTC
383468 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
383500 TCATGTGTGT
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:385754 original size:24 final size:24
Alignment explanation
Indices: 385708--385757 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
385698 TTTGGTAAGA
*
385708 TTGATTTTCATTTAACTTGATAAT
1 TTGATTTTCATTTAACTTAATAAT
*
385732 TTGATTTTTATTTATA-TTAATAAT
1 TTGATTTTCATTTA-ACTTAATAAT
385756 TT
1 TT
385758 TGCTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (24 bp):
TTGATTTTCATTTAACTTAATAAT
Found at i:387302 original size:21 final size:21
Alignment explanation
Indices: 387260--387303 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
387250 ATTTCAACAA
* *
387260 GAAACAAGAGCCAACATTCAG
1 GAAACAAGAGACAACATCCAG
387281 GAAACAAG-GACAAGCATCCAG
1 GAAACAAGAGACAA-CATCCAG
387302 GA
1 GA
387304 TTTAGGCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.48, C:0.23, G:0.23, T:0.07
Consensus pattern (21 bp):
GAAACAAGAGACAACATCCAG
Found at i:391875 original size:5 final size:5
Alignment explanation
Indices: 391854--391898 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
391844 TGTTCATATC
391854 TTTTA TTGTTA -TTTA TTTTA TTTTA TTTTA CTTTTA TTTT- TTTTA
1 TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA
391899 GGCTGGTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
4 7 0.19
5 21 0.58
6 8 0.22
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:392543 original size:1 final size:1
Alignment explanation
Indices: 392539--392600 Score: 61
Period size: 1 Copynumber: 62.0 Consensus size: 1
392529 AAAAAGTTCT
** * * * * *
392539 AAAAAAAAAGTAAAAAAAAAAACAAAAAAAAAAGAAAAGAAAGAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
392601 GTGAAGATTT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.89, C:0.03, G:0.06, T:0.02
Consensus pattern (1 bp):
A
Found at i:392556 original size:14 final size:14
Alignment explanation
Indices: 392525--392600 Score: 59
Period size: 14 Copynumber: 5.5 Consensus size: 14
392515 TGGCAATTGT
***
392525 AAAAAAAAAGTTCT
1 AAAAAAAAAGTAAA
392539 AAAAAAAAAGTAAA
1 AAAAAAAAAGTAAA
*
392553 AAAAAAAACA-AAAA
1 AAAAAAAA-AGTAAA
392567 AAAAAGAAAAG-AAA
1 AAAAA-AAAAGTAAA
* *
392581 GAAAAAAAA-CAAA
1 AAAAAAAAAGTAAA
392594 AAAAAAA
1 AAAAAAA
392601 GTGAAGATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
13 13 0.25
14 35 0.67
15 4 0.08
ACGTcount: A:0.84, C:0.04, G:0.07, T:0.05
Consensus pattern (14 bp):
AAAAAAAAAGTAAA
Found at i:392600 original size:24 final size:25
Alignment explanation
Indices: 392539--392601 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
392529 AAAAAGTTCT
*
392539 AAAAAAAAAGTAAAA-AAA-AAAACA
1 AAAAAAAAAG-AAAAGAAAGAAAAAA
392563 AAAAAAAAAGAAAAGAAAGAAAAAA
1 AAAAAAAAAGAAAAGAAAGAAAAAA
*
392588 AACAAAAAA-AAAAG
1 AAAAAAAAAGAAAAG
392602 TGAAGATTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 4 0.11
24 18 0.51
25 13 0.37
ACGTcount: A:0.87, C:0.03, G:0.08, T:0.02
Consensus pattern (25 bp):
AAAAAAAAAGAAAAGAAAGAAAAAA
Found at i:392601 original size:29 final size:29
Alignment explanation
Indices: 392539--392601 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
392529 AAAAAGTTCT
392539 AAAAA-AAAAGTAAAAAAAAAAACAAAAA
1 AAAAAGAAAAGTAAAAAAAAAAACAAAAA
392567 AAAAAGAAAAG-AAAGAAAAAAAACAAAAA
1 AAAAAGAAAAGTAAA-AAAAAAAACAAAAA
392596 AAAAAG
1 AAAAAG
392602 TGAAGATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 8 0.24
29 25 0.76
ACGTcount: A:0.87, C:0.03, G:0.08, T:0.02
Consensus pattern (29 bp):
AAAAAGAAAAGTAAAAAAAAAAACAAAAA
Found at i:394571 original size:24 final size:25
Alignment explanation
Indices: 394520--394581 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
394510 GGAAGTTTGG
* *
394520 TAAGATTGATTTTCATTTAACTTGA
1 TAAGTTTGATTTTCATTTAACTTAA
*
394545 TAA-TTTGATTTTTATTTATA-TTAA
1 TAAGTTTGATTTTCATTTA-ACTTAA
*
394569 TAAGTTTGCTTTT
1 TAAGTTTGATTTT
394582 ATTAATCGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 19 0.61
25 12 0.39
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (25 bp):
TAAGTTTGATTTTCATTTAACTTAA
Found at i:395876 original size:20 final size:20
Alignment explanation
Indices: 395847--395886 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
395837 ATTTTTTTTA
395847 TCTTACTCAAACCTAAATTT
1 TCTTACTCAAACCTAAATTT
* *
395867 TCTTAGTCAAACCTATATTT
1 TCTTACTCAAACCTAAATTT
395887 CTATTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.42
Consensus pattern (20 bp):
TCTTACTCAAACCTAAATTT
Found at i:395937 original size:27 final size:25
Alignment explanation
Indices: 395880--395941 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
395870 TAGTCAAACC
*
395880 TATATTTCTATTTAAAAAATATTAA
1 TATATTTTTATTTAAAAAATATTAA
* *
395905 AATATTTTTATTTAAAAATATTATTTA
1 TATATTTTTATTTAAAAA-A-TATTAA
395932 TATATTTTTA
1 TATATTTTTA
395942 AAATTTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 16 0.52
26 1 0.03
27 14 0.45
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TATATTTTTATTTAAAAAATATTAA
Found at i:404657 original size:17 final size:17
Alignment explanation
Indices: 404635--404668 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
404625 AAAAATTAAT
404635 GCTTATTTTTTATATGC
1 GCTTATTTTTTATATGC
404652 GCTTATTTTTTATATGC
1 GCTTATTTTTTATATGC
404669 ATATTTGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.59
Consensus pattern (17 bp):
GCTTATTTTTTATATGC
Found at i:404673 original size:15 final size:15
Alignment explanation
Indices: 404633--404674 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
404623 AAAAAAATTA
404633 ATGCTTATTTTTTAT
1 ATGCTTATTTTTTAT
404648 ATGCGCTTATTTTTTAT
1 AT--GCTTATTTTTTAT
*
404665 ATGCATATTT
1 ATGCTTATTT
404675 GGAAAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.38
17 15 0.62
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.60
Consensus pattern (15 bp):
ATGCTTATTTTTTAT
Found at i:410154 original size:2 final size:2
Alignment explanation
Indices: 410147--410185 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
410137 ATGTTGTACT
410147 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
410186 TTTAATGTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:410387 original size:12 final size:11
Alignment explanation
Indices: 410349--410403 Score: 67
Period size: 12 Copynumber: 4.9 Consensus size: 11
410339 GTGGCTGAAT
*
410349 TATTTAAATTA
1 TATTTATATTA
*
410360 AATTTATATT-
1 TATTTATATTA
410370 TATTTATATCTA
1 TATTTATAT-TA
410382 TATTTATATTTA
1 TATTTATA-TTA
410394 TATTTATATT
1 TATTTATATT
410404 TTTATTTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
10 8 0.21
11 11 0.29
12 18 0.47
13 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTTATATTA
Found at i:410389 original size:22 final size:21
Alignment explanation
Indices: 410348--410394 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
410338 AGTGGCTGAA
410348 TTATTTAAATTAAATTTATAT
1 TTATTTAAATTAAATTTATAT
* *
410369 TTATTTATATCTATATTTATAT
1 TTATTTAAAT-TAAATTTATAT
410391 TTAT
1 TTAT
410395 ATTTATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTTAAATTAAATTTATAT
Found at i:410412 original size:6 final size:6
Alignment explanation
Indices: 410361--410410 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
410351 TTTAAATTAA
* *
410361 ATTTAT A-TT-T ATTTAT ATCTAT ATTTAT ATTTAT ATTTAT ATTTTT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT
410407 ATTT
1 ATTT
410411 TTGTATCATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
4 2 0.05
5 4 0.10
6 33 0.85
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTAT
Found at i:411521 original size:3 final size:3
Alignment explanation
Indices: 411513--411548 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
411503 ATCCGTATCT
411513 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
411549 AGAAGAATCA
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):
TAA
Found at i:411688 original size:11 final size:11
Alignment explanation
Indices: 411672--411696 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
411662 GAAAAGCTTG
411672 AATTTATTAAT
1 AATTTATTAAT
411683 AATTTATTAAT
1 AATTTATTAAT
411694 AAT
1 AAT
411697 AGAAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTTATTAAT
Found at i:411762 original size:22 final size:20
Alignment explanation
Indices: 411724--411763 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
411714 TAGATGAGGG
*
411724 AAATTTTAATAATTTTAATC
1 AAATTTTAATAAATTTAATC
411744 AAATATTTAATTAAATTTAA
1 AAAT-TTTAA-TAAATTTAA
411764 ATAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 5 0.29
22 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTTTAATAAATTTAATC
Found at i:412453 original size:6 final size:6
Alignment explanation
Indices: 412442--412485 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
412432 TTTAAATTAA
*
412442 ATTTAT ATTTAT ATTTAT A-TT-T ATTTAT ATCTAT ATTTAT ATTT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTT
412486 TCATATCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 2 0.06
5 4 0.12
6 28 0.82
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTAT
Found at i:412468 original size:16 final size:16
Alignment explanation
Indices: 412447--412481 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
412437 ATTAAATTTA
*
412447 TATTTATATTTATATT
1 TATTTATATCTATATT
412463 TATTTATATCTATATT
1 TATTTATATCTATATT
412479 TAT
1 TAT
412482 ATTTTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTTATATCTATATT
Found at i:412469 original size:22 final size:22
Alignment explanation
Indices: 412442--412485 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
412432 TTTAAATTAA
*
412442 ATTTATATTTATATTTATATTT
1 ATTTATATCTATATTTATATTT
412464 ATTTATATCTATATTTATATTT
1 ATTTATATCTATATTTATATTT
412486 TCATATCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTTATATCTATATTTATATTT
Found at i:412498 original size:20 final size:21
Alignment explanation
Indices: 412446--412492 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
412436 AATTAAATTT
* *
412446 ATATTTATATTTATATTTATTT
1 ATATCTATATTTATA-TTATTC
412468 ATATCTATATTTATATT-TTC
1 ATATCTATATTTATATTATTC
412488 ATATC
1 ATATC
412493 ATTATTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
21 2 0.09
22 14 0.61
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATCTATATTTATATTATTC
Found at i:412660 original size:11 final size:11
Alignment explanation
Indices: 412637--412678 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
412627 ATAATTTTTA
412637 ATAAAATAATTT
1 ATAAAA-AATTT
412649 ATAAAAAATTT
1 ATAAAAAATTT
* *
412660 ATAAACATTTT
1 ATAAAAAATTT
412671 A-AAAAAAT
1 ATAAAAAAT
412679 CACCCACCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 5 0.19
11 15 0.58
12 6 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAAAAAATTT
Found at i:414529 original size:18 final size:19
Alignment explanation
Indices: 414498--414537 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
414488 GAATTTACTC
414498 AAAAATCAAAATAAAATGA
1 AAAAATCAAAATAAAATGA
* *
414517 AAAAAT-AACATAAATTGA
1 AAAAATCAAAATAAAATGA
414535 AAA
1 AAA
414538 GTACTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.17
Consensus pattern (19 bp):
AAAAATCAAAATAAAATGA
Found at i:416583 original size:2 final size:2
Alignment explanation
Indices: 416576--416611 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
416566 ACATTGATTC
416576 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
416612 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:416616 original size:2 final size:2
Alignment explanation
Indices: 416611--416637 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
416601 TATATATATA
416611 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
416638 TTTTGTCTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:421517 original size:17 final size:16
Alignment explanation
Indices: 421490--421537 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
421480 GTCAAATCTT
421490 AATTAATTTTTAAATAAA
1 AATT-ATTTTTAAA-AAA
*
421508 AATTATTTTTTTAAAAA
1 AATTA-TTTTTAAAAAA
*
421525 ATTTATTTTTAAA
1 AATTATTTTTAAA
421538 CTTAATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 7 0.27
17 8 0.31
18 11 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTATTTTTAAAAAA
Found at i:421535 original size:15 final size:16
Alignment explanation
Indices: 421505--421537 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
421495 ATTTTTAAAT
*
421505 AAAAATTATTTTTTTA
1 AAAAATTATATTTTTA
421521 AAAAATT-TATTTTTA
1 AAAAATTATATTTTTA
421536 AA
1 AA
421538 CTTAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AAAAATTATATTTTTA
Found at i:427555 original size:19 final size:21
Alignment explanation
Indices: 427533--427571 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
427523 AATGAATTAG
427533 ATTTAT-ATA-TTTATATTTT
1 ATTTATGATATTTTATATTTT
*
427552 ATTTATGTTATTTTATATTT
1 ATTTATGATATTTTATATTT
427572 AGATTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (21 bp):
ATTTATGATATTTTATATTTT
Found at i:432900 original size:50 final size:50
Alignment explanation
Indices: 432692--432900 Score: 310
Period size: 50 Copynumber: 4.2 Consensus size: 50
432682 AGTTGTTGCC
* * * *
432692 ATTGTTGACTATCCTTCACCAACTTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAAGAGGTGGCCATA
* * *
432742 ATTGTTGATGATTCTTCACTAACCTTTGATAATAGAAAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAAGAGGTGGCCATA
* *
432792 ATTGTTGATGATTCTTCACTAACCTTTGACAATAGAAAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAAGAGGTGGCCATA
* **
432842 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAAGAGGTGGCCATA
432892 ATTGTTGAC
1 ATTGTTGAC
432901 TCTAAGTATA
Statistics
Matches: 146, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 146 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAAGAGGTGGCCATA
Found at i:437371 original size:50 final size:51
Alignment explanation
Indices: 437293--437512 Score: 268
Period size: 50 Copynumber: 4.2 Consensus size: 51
437283 AGTTGTTGCC
* *
437293 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGA-GAAGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGGAGGTGGCCATA
* * *
437343 ATTGTTGACGATTCTTCACTAACTTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGGAGGTGGCCATA
437393 ATTGTTGACTATTCTTCACCAACC-TTGACAATAGAGGGAGGTGGCCGGGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGA--GA--------GGAGGTGGCCATA
*
437453 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAG-GGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGGAGGTGGCCATA
437503 ATTGTTGACT
1 ATTGTTGACT
437513 CTAAGTATAT
Statistics
Matches: 147, Mismatches: 10, Indels: 26
0.80 0.05 0.14
Matches are distributed among these distances:
49 12 0.08
50 86 0.59
52 1 0.01
59 1 0.01
60 36 0.24
61 11 0.07
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (51 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGGAGGTGGCCATA
Found at i:437473 original size:60 final size:61
Alignment explanation
Indices: 437380--437499 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 61
437370 GACAATAGAA
*
437380 GGAGGTGGCCATAATTGTTGACTATTCTTCACCAACC-TTGACAATAGAGGGAGGTGGCCG
1 GGAGGTGGCCATAATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCG
437440 GGAGGTGGCCATAATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCC
1 GGAGGTGGCCATAATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCC
437500 ATAATTGTTG
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
60 36 0.62
61 22 0.38
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (61 bp):
GGAGGTGGCCATAATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCG
Found at i:438031 original size:15 final size:16
Alignment explanation
Indices: 438007--438039 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
437997 TTTACATACA
438007 AAAAATTAAAAAAATT
1 AAAAATTAAAAAAATT
438023 AAAAA-TAAAAAAATT
1 AAAAATTAAAAAAATT
438038 AA
1 AA
438040 TTTTTAACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATTAAAAAAATT
Found at i:441533 original size:25 final size:23
Alignment explanation
Indices: 441505--441550 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
441495 AATTTGATTG
441505 TTAATATTCATATAAAATAAATTTT
1 TTAATATT-ATATAAAA-AAATTTT
*
441530 TTAATATTATATTAAAAAATT
1 TTAATATTATATAAAAAAATT
441551 ATATAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAATATTATATAAAAAAATTTT
Found at i:442096 original size:21 final size:20
Alignment explanation
Indices: 442067--442118 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
442057 TATATGACAC
* *
442067 AAAATTAATCTCTTTATTACT
1 AAAAATAATATCTTTATT-CT
* *
442088 AAAAATAATATTTTTATTTT
1 AAAAATAATATCTTTATTCT
442108 AAAAATTAATA
1 AAAAA-TAATA
442119 ATTATAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAAATAATATCTTTATTCT
Found at i:442777 original size:10 final size:10
Alignment explanation
Indices: 442764--442788 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
442754 ATTTAATATT
442764 TTAATTTTTA
1 TTAATTTTTA
442774 TTAATTTTTA
1 TTAATTTTTA
442784 TTAAT
1 TTAAT
442789 ATAATACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTAATTTTTA
Found at i:443884 original size:25 final size:25
Alignment explanation
Indices: 443822--443891 Score: 99
Period size: 24 Copynumber: 2.8 Consensus size: 25
443812 AATAAAAATT
*
443822 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
443846 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
*
443871 AGCCTCC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
443892 CAAAGGAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 21 0.50
25 21 0.50
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:443937 original size:27 final size:27
Alignment explanation
Indices: 443876--443946 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
443866 AAACAAGCCT
* *
443876 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
443904 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
443931 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
443947 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:443949 original size:24 final size:24
Alignment explanation
Indices: 443824--443949 Score: 92
Period size: 24 Copynumber: 4.9 Consensus size: 24
443814 TAAAAATTAG
* *
443824 CCACCAATTTTGACAAACAACA-AG
1 CCACCATTTTTGACAAACAA-ATAA
* * *
443848 CCACCAATTTTGACAAATAAACAA
1 CCACCATTTTTGACAAACAAATAA
* * *
443872 GCCTCCATATTTGACAAATACAAAGGAAA
1 -CCACCATTTTTGAC-AA-ACAAA--TAA
443901 CCACCATTTTTGACAAACACAAAATAA
1 CCACCATTTTTGAC-AA-AC-AAATAA
443928 CCACCATTTTTGACAAACAAAT
1 CCACCATTTTTGACAAACAAAT
443950 GGGTGGCTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
23 1 0.01
24 24 0.29
25 13 0.15
26 4 0.05
27 20 0.24
28 17 0.20
29 5 0.06
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.21
Consensus pattern (24 bp):
CCACCATTTTTGACAAACAAATAA
Found at i:448478 original size:25 final size:25
Alignment explanation
Indices: 448416--448538 Score: 106
Period size: 24 Copynumber: 4.8 Consensus size: 25
448406 AATAAAAATT
*
448416 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
448440 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
*
448465 AGCCTCC-ATATTTGACAAATACAACGGA
1 AGCCACCAAT-TTTGACAAATA-AAC--A
* * * *
448493 AACCACCATTTTTGACAAACACAAAA
1 AGCCACCAATTTTGACAAATA-AACA
* *
448519 TAACCACCATTTTTGACAAA
1 -AGCCACCAATTTTGACAAA
448539 CAAATGGGTG
Statistics
Matches: 85, Mismatches: 7, Indels: 11
0.83 0.07 0.11
Matches are distributed among these distances:
24 21 0.25
25 21 0.25
26 4 0.05
27 19 0.22
28 19 0.22
29 1 0.01
ACGTcount: A:0.45, C:0.26, G:0.08, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:448509 original size:28 final size:26
Alignment explanation
Indices: 448418--448538 Score: 122
Period size: 25 Copynumber: 4.7 Consensus size: 26
448408 TAAAAATTAG
* *
448418 CCACCAATTTTGAC-AA-ACAACAAG
1 CCACCATTTTTGACAAATACAACAAA
* *
448442 CCACCAATTTTGACAAATA-AACAAG
1 CCACCATTTTTGACAAATACAACAAA
* *
448467 CCTCCATATTTGACAAATACAACGGAAA
1 CCACCATTTTTGACAAATACAAC--AAA
* *
448495 CCACCATTTTTGACAAACACAAAATAA
1 CCACCATTTTTGACAAATACAACA-AA
448522 CCACCATTTTTGACAAA
1 CCACCATTTTTGACAAA
448539 CAAATGGGTG
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
24 14 0.17
25 24 0.29
26 5 0.06
27 19 0.23
28 21 0.25
ACGTcount: A:0.45, C:0.26, G:0.07, T:0.21
Consensus pattern (26 bp):
CCACCATTTTTGACAAATACAACAAA
Found at i:448642 original size:2 final size:2
Alignment explanation
Indices: 448635--448660 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
448625 ACATTGATTC
448635 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
448661 GTGTGTGTGT
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:449924 original size:19 final size:20
Alignment explanation
Indices: 449885--449925 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
449875 GAATTCAAGA
* *
449885 TTTACATTTATTTTTATATG
1 TTTACATTTAATTTTACATG
449905 TTTACA-TTAATTTTACATG
1 TTTACATTTAATTTTACATG
449924 TT
1 TT
449926 AAATGCTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTACATTTAATTTTACATG
Found at i:450499 original size:15 final size:16
Alignment explanation
Indices: 450479--450509 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
450469 TTTAAAAATA
450479 TTAAAATATT-TTTAT
1 TTAAAATATTATTTAT
450494 TTAAAATATTATTTAT
1 TTAAAATATTATTTAT
450510 ATATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAAAATATTATTTAT
Found at i:450503 original size:23 final size:25
Alignment explanation
Indices: 450459--450504 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
450449 ACTCAAATTT
450459 ATATTTCTATTTTAAAAATATTAAA
1 ATATTTCTATTTTAAAAATATTAAA
*
450484 ATATTTTTA-TTT-AAAATATTA
1 ATATTTCTATTTTAAAAATATTA
450505 TTTATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 3 0.15
25 8 0.40
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
ATATTTCTATTTTAAAAATATTAAA
Found at i:454699 original size:12 final size:12
Alignment explanation
Indices: 454692--454718 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
454682 AATATATATT
454692 TATCTATATTTA
1 TATCTATATTTA
454704 TATCTATATTTA
1 TATCTATATTTA
454716 TAT
1 TAT
454719 TTTCATATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (12 bp):
TATCTATATTTA
Found at i:455196 original size:2 final size:2
Alignment explanation
Indices: 455189--455217 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
455179 ATTAGTAAAG
455189 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 A
455218 GCATAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:457571 original size:27 final size:27
Alignment explanation
Indices: 457529--457600 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 27
457519 TATTCATATT
*
457529 ATTTTTTGTAT-T-GTGTCATATTTTA
1 ATTTTTTTTATGTCGTGTCATATTTTA
*
457554 ATTTTTTTTATGTCGTGTCATGTTTTA
1 ATTTTTTTTATGTCGTGTCATATTTTA
* *
457581 ACTTTTTTTTGTGTCATGTC
1 A-TTTTTTTTATGTCGTGTC
457601 TGATATTGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
25 10 0.25
26 1 0.03
27 13 0.32
28 16 0.40
ACGTcount: A:0.15, C:0.08, G:0.14, T:0.62
Consensus pattern (27 bp):
ATTTTTTTTATGTCGTGTCATATTTTA
Found at i:457595 original size:28 final size:27
Alignment explanation
Indices: 457530--457600 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
457520 ATTCATATTA
* *
457530 TTTTTTGTATTGTGTCATATTTTAATT
1 TTTTTTGTGTCGTGTCATATTTTAATT
* *
457557 TTTTTTATGTCGTGTCATGTTTTAACTT
1 TTTTTTGTGTCGTGTCATATTTTAA-TT
*
457585 TTTTTTGTGTCATGTC
1 TTTTTTGTGTCGTGTC
457601 TGATATTGTC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.14, C:0.08, G:0.14, T:0.63
Consensus pattern (27 bp):
TTTTTTGTGTCGTGTCATATTTTAATT
Found at i:459452 original size:4 final size:4
Alignment explanation
Indices: 459438--459469 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
459428 AAATATTGCC
459438 TTTA TTTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTT
459470 TACTTCTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:460389 original size:15 final size:16
Alignment explanation
Indices: 460369--460401 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
460359 TAAGTAGCTT
460369 TTTTAT-AATATAAAA
1 TTTTATAAATATAAAA
*
460384 TTTTATAAATTTAAAA
1 TTTTATAAATATAAAA
460400 TT
1 TT
460402 CAAATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTATAAATATAAAA
Found at i:461588 original size:4 final size:4
Alignment explanation
Indices: 461579--461605 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
461569 CAAGGTACTT
461579 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
461606 TTTTGAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:463495 original size:16 final size:16
Alignment explanation
Indices: 463471--463513 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
463461 TATTAACAGT
463471 ATTTT-ATATATATAA
1 ATTTTGATATATATAA
*
463486 ATTTTGATATGA-ATAT
1 ATTTTGATAT-ATATAA
463502 ATTTTGATATAT
1 ATTTTGATATAT
463514 TCGTACATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 6 0.25
16 17 0.71
17 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
ATTTTGATATATATAA
Found at i:463760 original size:17 final size:15
Alignment explanation
Indices: 463737--463775 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
463727 AAAATTTTGA
463737 TATATTTATTTTATAT
1 TATATTT-TTTTATAT
463753 TA-ATATTTTTTATAT
1 TATAT-TTTTTTATAT
463768 TATATTTT
1 TATATTTT
463776 AATTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATATTTTTTTATAT
Found at i:463773 original size:27 final size:27
Alignment explanation
Indices: 463681--463776 Score: 76
Period size: 27 Copynumber: 3.6 Consensus size: 27
463671 ATATATTTTA
463681 TTTATATTAT-TTTTATATT-ATAATTAAT
1 TTTATATTATATTTTATATTAAT-ATT--T
* * * *
463709 TTTA-A-AATATTATATATAAAAATTT
1 TTTATATTATATTTTATATTAATATTT
*
463734 TGATATATT-TATTTTATATTAATATTT
1 T-TTATATTATATTTTATATTAATATTT
463761 TTTATATTATATTTTA
1 TTTATATTATATTTTA
463777 ATTTAAAAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 13
0.69 0.13 0.17
Matches are distributed among these distances:
25 2 0.04
26 10 0.19
27 35 0.67
28 5 0.10
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (27 bp):
TTTATATTATATTTTATATTAATATTT
Found at i:463782 original size:69 final size:68
Alignment explanation
Indices: 463674--463801 Score: 172
Period size: 69 Copynumber: 1.9 Consensus size: 68
463664 AATTATCATA
*
463674 TATTTTATTTATATTATTTTTATATTATAATTAATTTTAAAATATTATATATAAAAATTTTGATA
1 TATTTTATTTATATTATTTTTATATTATAATTAATTTTAAAAAATTAT-TATAAAAATTTTGATA
463739 TATT
65 TATT
* *
463743 TATTTTATATTA-A-TATTTTTTATATTATATTTTAA-TTTAAAAAATTATTATAAATATTT
1 TATTTTAT-TTATATTA-TTTTTATATTATA-ATTAATTTTAAAAAATTATTATAAAAATTT
463802 AATTTAAACT
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
68 12 0.23
69 34 0.64
70 7 0.13
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.59
Consensus pattern (68 bp):
TATTTTATTTATATTATTTTTATATTATAATTAATTTTAAAAAATTATTATAAAAATTTTGATAT
ATT
Found at i:464212 original size:16 final size:17
Alignment explanation
Indices: 464193--464228 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
464183 GCTATAAATC
*
464193 TTAAATCGATCAAA-AA
1 TTAAATCGATAAAATAA
464209 TTAAATCGATAAAATAA
1 TTAAATCGATAAAATAA
464226 TTA
1 TTA
464229 TTTTATTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.31
Consensus pattern (17 bp):
TTAAATCGATAAAATAA
Found at i:464803 original size:22 final size:22
Alignment explanation
Indices: 464775--464824 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
464765 ATATATATAT
*
464775 ATATATATATATGTATGTATGC
1 ATATATATATATATATGTATGC
464797 ATATATATATATATATGTATGC
1 ATATATATATATATATGTATGC
464819 ATATAT
1 ATATAT
464825 GTGTGTCTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (22 bp):
ATATATATATATATATGTATGC
Found at i:464822 original size:12 final size:12
Alignment explanation
Indices: 464788--464826 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
464778 TATATATATG
464788 TATGTATGCATA
1 TATGTATGCATA
*
464800 TATATAT--ATA
1 TATGTATGCATA
464810 TATGTATGCATA
1 TATGTATGCATA
464822 TATGT
1 TATGT
464827 GTGTCTGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.39
12 14 0.61
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (12 bp):
TATGTATGCATA
Found at i:464824 original size:2 final size:2
Alignment explanation
Indices: 464765--464812 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
464755 ACATTGATTC
* * **
464765 AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT GC 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
464807 AT AT AT
1 AT AT AT
464813 GTATGCATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (2 bp):
AT
Found at i:465123 original size:21 final size:21
Alignment explanation
Indices: 465084--465125 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
465074 TCTGTGGTAA
* **
465084 AGAGAGAAAGAAAGGAAAGAG
1 AGAGAGAAAAAAAAAAAAGAG
465105 AGAGAGAAAAAAAAAAAAGAG
1 AGAGAGAAAAAAAAAAAAGAG
465126 TACGAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (21 bp):
AGAGAGAAAAAAAAAAAAGAG
Found at i:465125 original size:17 final size:18
Alignment explanation
Indices: 465082--465138 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 18
465072 AATCTGTGGT
465082 AAAGAGAGAAAGAAAGGAAAG
1 AAAGAGAGAAA-AAA--AAAG
*
465103 AGAGAGAGAAAAAAAAA-
1 AAAGAGAGAAAAAAAAAG
465120 AAAGAGTACGAAAAAAAAA
1 AAAGAG-A-GAAAAAAAAA
465139 TTCATGTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 5 0.16
18 4 0.12
19 10 0.31
20 3 0.09
21 10 0.31
ACGTcount: A:0.72, C:0.02, G:0.25, T:0.02
Consensus pattern (18 bp):
AAAGAGAGAAAAAAAAAG
Found at i:467728 original size:16 final size:16
Alignment explanation
Indices: 467700--467735 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
467690 AAATCTTCAC
*
467700 TTTT-TTTTGTTTTTT
1 TTTTCTTTTCTTTTTT
467715 TTTTCTTTTCTTTTTT
1 TTTTCTTTTCTTTTTT
467731 TTTTC
1 TTTTC
467736 AATTGCCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (16 bp):
TTTTCTTTTCTTTTTT
Found at i:474520 original size:24 final size:24
Alignment explanation
Indices: 474493--474542 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
474483 AATAAAAGCA
474493 AAATTAT-AAATATAAATAAAAATC
1 AAATTATCAAAT-TAAATAAAAATC
* *
474517 AAATTATCAAGTTAAATGAAAATC
1 AAATTATCAAATTAAATAAAAATC
474541 AA
1 AA
474543 TCTTACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (24 bp):
AAATTATCAAATTAAATAAAAATC
Found at i:476003 original size:19 final size:21
Alignment explanation
Indices: 475976--476018 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
475966 CATATAATGA
475976 ATTAAATTTATG-TA-TTTAT
1 ATTAAATTTATGCTATTTTAT
*
475995 ATTATATTTATGCTATTTTAT
1 ATTAAATTTATGCTATTTTAT
476016 ATT
1 ATT
476019 TAAACTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
20 2 0.10
21 8 0.38
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (21 bp):
ATTAAATTTATGCTATTTTAT
Found at i:477073 original size:25 final size:25
Alignment explanation
Indices: 477040--477088 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
477030 ATGTTATACG
*
477040 TAGATTTTAATACATTTATTTTATA
1 TAGATTTTAACACATTTATTTTATA
*
477065 TAGATTTTAACACATTTGTTTTAT
1 TAGATTTTAACACATTTATTTTAT
477089 GTTAGTATGA
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:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (25 bp):
TAGATTTTAACACATTTATTTTATA
Found at i:477811 original size:13 final size:13
Alignment explanation
Indices: 477795--477831 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
477785 AGAGAAAAGG
477795 AAAAAAAAAAACA
1 AAAAAAAAAAACA
**
477808 AAAAAAAAATTCA
1 AAAAAAAAAAACA
477821 AAAAAAAAAAA
1 AAAAAAAAAAA
477832 GAATTAGAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.89, C:0.05, G:0.00, T:0.05
Consensus pattern (13 bp):
AAAAAAAAAAACA
Found at i:477823 original size:19 final size:18
Alignment explanation
Indices: 477801--477836 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
477791 AAGGAAAAAA
477801 AAAAACAAAAAAAAAATTC
1 AAAAA-AAAAAAAAAATTC
*
477820 AAAAAAAAAAAAGAATT
1 AAAAAAAAAAAAAAATT
477837 AGAATCATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.81, C:0.06, G:0.03, T:0.11
Consensus pattern (18 bp):
AAAAAAAAAAAAAAATTC
Found at i:478080 original size:2 final size:2
Alignment explanation
Indices: 478073--478117 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
478063 ACATTAATTC
478073 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
478115 AT A
1 AT A
478118 CATACGTGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:478559 original size:22 final size:21
Alignment explanation
Indices: 478529--478569 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
478519 AGTGAGAAGC
478529 TTTTCTAAATAAAAATATAATA
1 TTTTCTAAATAAAAA-ATAATA
*
478551 TTTTTTAAATAAAAAATAA
1 TTTTCTAAATAAAAAATAA
478570 AAAATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTTCTAAATAAAAAATAATA
Found at i:480132 original size:34 final size:34
Alignment explanation
Indices: 480065--480247 Score: 208
Period size: 34 Copynumber: 5.4 Consensus size: 34
480055 ACCTAATTTA
** * *
480065 TGTTGATTAAAT-GTTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * * *
480098 TATTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
480132 TGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
** *
480166 TGTTGATTAAATAAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
**
480200 TGTTGATTAAATGGGAGATTTGGTAAG-TTGTCAT
1 TGTTGATTAAATGGGAGATTTGGT-AGCTTACCAT
480234 TGTTGATTAAATGG
1 TGTTGATTAAATGG
480248 TGGTTTTTAC
Statistics
Matches: 128, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
33 11 0.09
34 115 0.90
35 2 0.02
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.42
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:480589 original size:19 final size:19
Alignment explanation
Indices: 480554--480597 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
480544 TGGTTGTCAA
*
480554 GGTACTATTTACATATACG
1 GGTACTATTCACATATACG
480573 GGTACTATTCA-AGTATACG
1 GGTACTATTCACA-TATACG
*
480592 GTTACT
1 GGTACT
480598 GTACACGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (19 bp):
GGTACTATTCACATATACG
Found at i:484729 original size:34 final size:34
Alignment explanation
Indices: 484660--484844 Score: 210
Period size: 34 Copynumber: 5.5 Consensus size: 34
484650 AAGTGGGAGA
** * *
484660 ATTGTTGATTAAAT-GTTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * * *
484693 ATTATTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
484727 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
484761 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * **
484795 ATTGTTAATTAAATGGAAGATTTGGTAGGTTGTC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
484829 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
484845 TGGTTTTTAC
Statistics
Matches: 129, Mismatches: 22, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
33 13 0.10
34 116 0.90
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.42
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:484817 original size:102 final size:101
Alignment explanation
Indices: 484660--484844 Score: 248
Period size: 102 Copynumber: 1.8 Consensus size: 101
484650 AAGTGGGAGA
* * * **
484660 ATTGTTGATTAAATGTTGATTTAGTAGTTTACCATTATTGATTAAATGGGTGATTTGGT-GGTTT
1 ATTGTTGATTAAATGTAGATTTAGTAGCTTACCATTATTAATTAAATGGAAGATTTGGTAGG-TT
484724 GCCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
65 GCCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
* *
484761 ATTGTTGATTAAATG-AGAAATTTGGTAGCTTACCATTGTTAATTAAATGGAAGATTTGGTAGGT
1 ATTGTTGATTAAATGTAG--ATTTAGTAGCTTACCATTATTAATTAAATGGAAGATTTGGTAGGT
* *
484825 TGTCATTGTTGATTAAATGG
64 TGCCATTGTTGACTAAATGG
484845 TGGTTTTTAC
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
100 1 0.01
101 15 0.21
102 54 0.75
103 2 0.03
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.42
Consensus pattern (101 bp):
ATTGTTGATTAAATGTAGATTTAGTAGCTTACCATTATTAATTAAATGGAAGATTTGGTAGGTTG
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:485219 original size:20 final size:20
Alignment explanation
Indices: 485194--485234 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
485184 AATTTTTTTA
*
485194 TTCTTACTCAAACCTATATT
1 TTCTTACTCAAAACTATATT
*
485214 TTCTTAGTCAAAACTATATT
1 TTCTTACTCAAAACTATATT
485234 T
1 T
485235 CTATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.02, T:0.46
Consensus pattern (20 bp):
TTCTTACTCAAAACTATATT
Found at i:485264 original size:25 final size:27
Alignment explanation
Indices: 485229--485290 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 27
485219 AGTCAAAACT
*
485229 ATATTTCTATTTAAAAA-A-TATTAAA
1 ATATTTTTATTTAAAAATATTATTAAA
* *
485254 ATATTTTTATTTAAAAATATTATTTAT
1 ATATTTTTATTTAAAAATATTATTAAA
485281 ATATTTTTAT
1 ATATTTTTAT
485291 AATTTAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 16 0.50
26 1 0.03
27 15 0.47
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (27 bp):
ATATTTTTATTTAAAAATATTATTAAA
Found at i:487718 original size:50 final size:50
Alignment explanation
Indices: 487638--487924 Score: 452
Period size: 50 Copynumber: 5.8 Consensus size: 50
487628 TATACTTAGA
* * * * * *
487638 GTCAACAATTTTGGTCACATTTCTCCATTGTCAAAAGTTGGTAAAGAATC
1 GTCAACAATTATGGTCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
487688 GTTAACAATTATGGTCACCTCTCTCTATTGTCAAAAGTTGGTGAAGAATC
1 GTCAACAATTATGGTCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
487738 GTCAACAATTATGGTCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGTCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
487788 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGTCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
487838 GTCAACAATTATGGTCACCTC-CTTCTATTGTCAAAGGTT-GTGAATAATC
1 GTCAACAATTATGGTCACCTCTC-TCTATTGTCAAAGGTTGGTGAAGAATC
*
487887 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGT
1 GTCAACAATTATGGTCACCTCTCTCTATTGTCAAAGGT
487925 ACTTTCCACC
Statistics
Matches: 223, Mismatches: 12, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
49 45 0.20
50 178 0.80
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (50 bp):
GTCAACAATTATGGTCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:488043 original size:13 final size:13
Alignment explanation
Indices: 488021--488053 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
488011 TAATTTACAC
488021 AAAA-AAAACAAT
1 AAAATAAAACAAT
488033 AAAATAAAACAAT
1 AAAATAAAACAAT
*
488046 AACATAAA
1 AAAATAAA
488054 TTTAAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAATAAAACAAT
Found at i:488510 original size:2 final size:2
Alignment explanation
Indices: 488503--488535 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
488493 ATGTTGTACT
488503 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
488536 TTTAATGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:490077 original size:2 final size:2
Alignment explanation
Indices: 490072--490111 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
490062 ACACACACAC
*
490072 AT AT AT AT AC 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
490112 GTAGATGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:490270 original size:16 final size:17
Alignment explanation
Indices: 490249--490280 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
490239 TATTTGCTTA
490249 ATTATTATAG-AAAAAT
1 ATTATTATAGTAAAAAT
490265 ATTATTATAGTAAAAA
1 ATTATTATAGTAAAAA
490281 AAAGGTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
ATTATTATAGTAAAAAT
Found at i:493690 original size:21 final size:22
Alignment explanation
Indices: 493652--493697 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
493642 ATCTGTTGAA
* **
493652 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
493673 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
493695 ACT
1 ACT
493698 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:496175 original size:20 final size:20
Alignment explanation
Indices: 496150--496188 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
496140 AAGAATTGAA
496150 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAT
496170 GAGGGATACAAGAGAGGGA
1 GAGGGATACAAGAGAGGGA
496189 AGAAGAAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.46, T:0.08
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAT
Found at i:497385 original size:6 final size:6
Alignment explanation
Indices: 497383--497415 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
497373 AATTTATATT
*
497383 TATCTA TATCTA TATCTA TATTTA TATCTA TAT
1 TATCTA TATCTA TATCTA TATCTA TATCTA TAT
497416 TTTCATATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (6 bp):
TATCTA
Found at i:498091 original size:18 final size:18
Alignment explanation
Indices: 498068--498124 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 18
498058 TGGTTAAATA
*
498068 TAAATATAAATGAATTAT
1 TAAATATAAATAAATTAT
* *
498086 TAAATAT-ATTAAATTTT
1 TAAATATAAATAAATTAT
498103 TAAATATAAATACAATATAT
1 TAAATATAAATA-AAT-TAT
498123 TA
1 TA
498125 TATGTATTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 14 0.45
18 10 0.32
19 3 0.10
20 4 0.13
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
TAAATATAAATAAATTAT
Found at i:498757 original size:2 final size:2
Alignment explanation
Indices: 498750--498785 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
498740 TTTACTACTG
498750 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
498786 AGATGAACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:499115 original size:28 final size:29
Alignment explanation
Indices: 499064--499122 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
499054 ATTTTAATCA
* * *
499064 AATATTTATTTAATTTAAATAAATTTATT
1 AATATTTATCTAATTTAAAAAAATTCATT
499093 AATATTTATCT-ATTTAAAAAAATTCATT
1 AATATTTATCTAATTTAAAAAAATTCATT
499121 AA
1 AA
499123 AATTAACCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 17 0.63
29 10 0.37
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.49
Consensus pattern (29 bp):
AATATTTATCTAATTTAAAAAAATTCATT
Found at i:499783 original size:34 final size:34
Alignment explanation
Indices: 499737--499921 Score: 250
Period size: 34 Copynumber: 5.5 Consensus size: 34
499727 GTAAAAACCA
* *
499737 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCAC
*
499771 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCAC
* **
499805 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCAC
*
499839 CCATTTAATCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCAC
* *
499873 CCATTTAATCAACAATGGTAAACTACTAAATCA-
1 CCATTTAATCAACAATGGTAACCTACCAAATCAC
499906 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
499922 TCTCCCACTT
Statistics
Matches: 133, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
33 20 0.15
34 108 0.81
35 5 0.04
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCAC
Found at i:499879 original size:102 final size:101
Alignment explanation
Indices: 499737--499921 Score: 300
Period size: 102 Copynumber: 1.8 Consensus size: 101
499727 GTAAAAACCA
* * *
499737 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCACCCATTTAATCAACAATGGTAAACCACCAAAT
499802 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTC
66 CA-CCATTTAATCAACAATGGTAAGCTACCAAATTTC
* *
499839 CCATTTAATCAACAATGGCAAACC-ACCAAATCACCCATTTAATCAACAATGGTAAACTACTAAA
1 CCATTTAATCAACAATGGC-AACCTACCAAATCACCCATTTAATCAACAATGGTAAACCACCAAA
499903 TCACCATTTAATCAACAAT
65 TCACCATTTAATCAACAAT
499922 TCTCCCACTT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
101 16 0.21
102 57 0.74
103 4 0.05
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (101 bp):
CCATTTAATCAACAATGGCAACCTACCAAATCACCCATTTAATCAACAATGGTAAACCACCAAAT
CACCATTTAATCAACAATGGTAAGCTACCAAATTTC
Found at i:504378 original size:34 final size:34
Alignment explanation
Indices: 504332--504514 Score: 246
Period size: 34 Copynumber: 5.4 Consensus size: 34
504322 GTAAAAACCA
* *
504332 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCAC
*
504366 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCAC
* **
504400 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCAC
*
504434 CCATTTAATCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCAC
* *
504468 CCATTTAATCAACAATGGTAAACTACTAAATCA-
1 CCATTTAATCAACAATGGTAACCTACCAAATCAC
504501 CCATTTAATCAACA
1 CCATTTAATCAACA
504515 TTAAAAACTG
Statistics
Matches: 131, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
33 18 0.14
34 108 0.82
35 5 0.04
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCAC
Found at i:504474 original size:102 final size:101
Alignment explanation
Indices: 504332--504514 Score: 296
Period size: 102 Copynumber: 1.8 Consensus size: 101
504322 GTAAAAACCA
* * *
504332 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCACCCATTTAATCAACAATGGTAAACCACCAAAT
504397 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTC
66 CA-CCATTTAATCAACAATGGTAAGCTACCAAATTTC
* *
504434 CCATTTAATCAACAATGGCAAACC-ACCAAATCACCCATTTAATCAACAATGGTAAACTACTAAA
1 CCATTTAATCAACAATGGC-AACCTACCAAATCACCCATTTAATCAACAATGGTAAACCACCAAA
504498 TCACCATTTAATCAACA
65 TCACCATTTAATCAACA
504515 TTAAAAACTG
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
101 14 0.19
102 57 0.76
103 4 0.05
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (101 bp):
CCATTTAATCAACAATGGCAACCTACCAAATCACCCATTTAATCAACAATGGTAAACCACCAAAT
CACCATTTAATCAACAATGGTAAGCTACCAAATTTC
Found at i:504829 original size:6 final size:6
Alignment explanation
Indices: 504818--504867 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
504808 TTTAAATTAA
*
504818 ATTTAT ATTTAT ATTTAT ATTTAT A-TT-T ATTTAT ATCTAT ATTTAT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT
504864 ATTT
1 ATTT
504868 TCATATCATT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 2 0.05
5 4 0.10
6 34 0.85
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTAT
Found at i:504850 original size:16 final size:16
Alignment explanation
Indices: 504818--504863 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
504808 TTTAAATTAA
504818 ATTTATATTTATATTTAT
1 ATTTATA-TT-TATTTAT
504836 ATTTATATTTATTTAT
1 ATTTATATTTATTTAT
*
504852 ATCTATATTTAT
1 ATTTATATTTAT
504864 ATTTTCATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 18 0.67
17 2 0.07
18 7 0.26
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTATATTTATTTAT
Found at i:504850 original size:22 final size:22
Alignment explanation
Indices: 504823--504867 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
504813 ATTAAATTTA
*
504823 TATTTATATTTATATTTATATT
1 TATTTATATCTATATTTATATT
504845 TATTTATATCTATATTTATATT
1 TATTTATATCTATATTTATATT
504867 T
1 T
504868 TCATATCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTTATATCTATATTTATATT
Found at i:504880 original size:20 final size:21
Alignment explanation
Indices: 504823--504874 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
504813 ATTAAATTTA
* *
504823 TATTTATATTTATATTTATATT
1 TATTCATATCTATATTTATA-T
*
504845 TATTTATATCTATATTTATAT
1 TATTCATATCTATATTTATAT
504866 T-TTCATATC
1 TATTCATATC
504875 ATTATTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 7 0.25
21 2 0.07
22 19 0.68
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTCATATCTATATTTATAT
Found at i:505042 original size:11 final size:11
Alignment explanation
Indices: 505019--505060 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
505009 ATAATTTTTA
505019 ATAAAATAATTT
1 ATAAAA-AATTT
505031 ATAAAAAATTT
1 ATAAAAAATTT
*
505042 ATAAAAATTTT
1 ATAAAAAATTT
505053 A-AAAAAAT
1 ATAAAAAAT
505061 CACCCACCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 6 0.21
11 16 0.57
12 6 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAAAAAATTT
Found at i:506919 original size:18 final size:19
Alignment explanation
Indices: 506891--506930 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
506881 GAATTTACTC
506891 AAAAATCAAAATAAAATGA
1 AAAAATCAAAATAAAATGA
*
506910 AAAAAT-AAAATAAATTGA
1 AAAAATCAAAATAAAATGA
506928 AAA
1 AAA
506931 GTACTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (19 bp):
AAAAATCAAAATAAAATGA
Found at i:513211 original size:12 final size:12
Alignment explanation
Indices: 513194--513224 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
513184 TTTTTCTTAC
513194 GTTATGTTTTAT
1 GTTATGTTTTAT
513206 GTTATGTTTTAT
1 GTTATGTTTTAT
513218 GTTATGT
1 GTTATGT
513225 AATTTTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.19, T:0.65
Consensus pattern (12 bp):
GTTATGTTTTAT
Found at i:513261 original size:10 final size:10
Alignment explanation
Indices: 513246--513289 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
513236 ACTTAAACTT
*
513246 ATAAATTTAA
1 ATAAATTAAA
513256 ATAAATTAAA
1 ATAAATTAAA
*
513266 ATTAAGATTTAA
1 A-TAA-ATTAAA
513278 ATAAATTAAA
1 ATAAATTAAA
513288 AT
1 AT
513290 TAAGATGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 17 0.59
11 6 0.21
12 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (10 bp):
ATAAATTAAA
Found at i:513277 original size:22 final size:22
Alignment explanation
Indices: 513250--513295 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
513240 AAACTTATAA
513250 ATTTAAATAAATTAAAATTAAG
1 ATTTAAATAAATTAAAATTAAG
513272 ATTTAAATAAATTAAAATTAAG
1 ATTTAAATAAATTAAAATTAAG
513294 AT
1 AT
513296 GTTTTAGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (22 bp):
ATTTAAATAAATTAAAATTAAG
Found at i:514119 original size:4 final size:4
Alignment explanation
Indices: 514110--514144 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
514100 CAAGGTACTT
514110 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
514145 GAGTTTCGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:515040 original size:50 final size:49
Alignment explanation
Indices: 514971--515152 Score: 292
Period size: 50 Copynumber: 3.7 Consensus size: 49
514961 AGTTGTTGTC
* *
514971 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGG-CATA
* *
515021 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCTATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGC-ATA
515071 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGG-CATA
*
515121 ATTGTTGACGATTCTTCACCAAACTTTGACAA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAA
515153 ATGTGGCCAT
Statistics
Matches: 124, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
49 1 0.01
50 122 0.98
51 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (49 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCATA
Found at i:519621 original size:50 final size:50
Alignment explanation
Indices: 519553--519684 Score: 194
Period size: 50 Copynumber: 2.6 Consensus size: 50
519543 AGTTGTTGTC
* *
519553 ATTGTTGACTA-TCATTCACCAACCTTTAACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
519603 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
519653 ATTATTGATAATTCTTCACCAACCTTTGACAA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAA
519685 ATGTGGCTAT
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
50 73 0.97
51 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (50 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:520330 original size:12 final size:12
Alignment explanation
Indices: 520313--520339 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
520303 TATATATTAT
520313 ATATATATAAAC
1 ATATATATAAAC
520325 ATATATATAAAC
1 ATATATATAAAC
520337 ATA
1 ATA
520340 AAATGAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATATATAAAC
Found at i:521236 original size:22 final size:22
Alignment explanation
Indices: 521221--521261 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
521211 TATTTATTTT
521221 ATGGATTTAATATATTAAATTG
1 ATGGATTTAATATATTAAATTG
*
521243 ATTGATTTAATA-A-TAAATT
1 ATGGATTTAATATATTAAATT
521262 TTTTAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (22 bp):
ATGGATTTAATATATTAAATTG
Found at i:521709 original size:30 final size:30
Alignment explanation
Indices: 521673--521739 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
521663 GCTTAGCCAA
521673 CTTTCATCCTTGCATCTGGTGGATATGTTC
1 CTTTCATCCTTGCATCTGGTGGATATGTTC
521703 CTTTCATCCTTGCATCTGGTGGATATGTTC
1 CTTTCATCCTTGCATCTGGTGGATATGTTC
521733 CTTTCAT
1 CTTTCAT
521740 GTTCTTCTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (30 bp):
CTTTCATCCTTGCATCTGGTGGATATGTTC
Found at i:527005 original size:27 final size:27
Alignment explanation
Indices: 526939--527009 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
526929 CCACCCTTTG
** *
526939 TTTGTCAAAAATAATGGTTACTTTGTG
1 TTTGTCAAAAATGGTGGTTACTTTGTA
* *
526966 TTTGTCAAAAATGGTGGTTTCTTTTTA
1 TTTGTCAAAAATGGTGGTTACTTTGTA
526993 TTTGTCAAAAATGGTGG
1 TTTGTCAAAAATGGTGG
527010 CATGTTGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.27, C:0.07, G:0.21, T:0.45
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTACTTTGTA
Done.