Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
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: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 4 of 27
Found at i:451663 original size:2 final size:2
Alignment explanation
Indices: 451656--451684 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
451646 GCATGCTTAC
451656 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
451685 ATTCTGGATT
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:453348 original size:20 final size:20
Alignment explanation
Indices: 453325--453408 Score: 62
Period size: 20 Copynumber: 4.7 Consensus size: 20
453315 TAATTATATT
453325 TAAATTATTATATATTTATA
1 TAAATTATTATATATTTATA
453345 TAAATT-TTA-ATA--TAT-
1 TAAATTATTATATATTTATA
*
453360 T-AATAATT-TAT-TTTATA
1 TAAATTATTATATATTTATA
*
453377 TAAATT-TTAATATATTCATA
1 TAAATTATT-ATATATTTATA
*
453397 T-ATTTATTATAT
1 TAAATTATTATAT
453409 GTTATATTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 21
0.67 0.05 0.28
Matches are distributed among these distances:
14 3 0.06
15 5 0.10
16 6 0.12
17 3 0.06
18 6 0.12
19 13 0.26
20 14 0.28
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (20 bp):
TAAATTATTATATATTTATA
Found at i:453376 original size:32 final size:33
Alignment explanation
Indices: 453330--453404 Score: 116
Period size: 32 Copynumber: 2.2 Consensus size: 33
453320 ATATTTAAAT
453330 TATTATATATTTATATAAATTTTAATATATTAATA
1 TATT-TAT-TTTATATAAATTTTAATATATTAATA
*
453365 -ATTTATTTTATATAAATTTTAATATATTCATA
1 TATTTATTTTATATAAATTTTAATATATTAATA
453397 TATTTATT
1 TATTTATT
453405 ATATGTTATA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
32 25 0.66
33 10 0.26
34 3 0.08
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (33 bp):
TATTTATTTTATATAAATTTTAATATATTAATA
Found at i:453419 original size:17 final size:16
Alignment explanation
Indices: 453348--453421 Score: 51
Period size: 16 Copynumber: 4.5 Consensus size: 16
453338 ATTTATATAA
*
453348 ATTTTAATATATTAAT
1 ATTTTAATATATTCAT
* * * *
453364 AATTTATTTTATAT-AA
1 ATTTTAATATAT-TCAT
453380 ATTTTAATATATTCAT
1 ATTTTAATATATTCAT
* *
453396 ATATTTATTATATGTTAT
1 AT-TTTAATATAT-TCAT
453414 ATTTTAAT
1 ATTTTAAT
453422 TTTTTTTTGT
Statistics
Matches: 43, Mismatches: 11, Indels: 7
0.70 0.18 0.11
Matches are distributed among these distances:
15 1 0.02
16 22 0.51
17 15 0.35
18 5 0.12
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (16 bp):
ATTTTAATATATTCAT
Found at i:453808 original size:19 final size:18
Alignment explanation
Indices: 453784--453819 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
453774 TTTATAACTC
*
453784 TTAATATGAATATGAATTA
1 TTAATATCAATAT-AATTA
453803 TTAATATCAATATAATT
1 TTAATATCAATATAATT
453820 TAAAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (18 bp):
TTAATATCAATATAATTA
Found at i:455857 original size:2 final size:2
Alignment explanation
Indices: 455852--455900 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
455842 CCCTCCCCCC
* *
455852 CT CT CT CT TT CT CT CT C- CT -T CT CT CT CT CT CT CT CT CT TT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
455892 CT CT CT CT C
1 CT CT CT CT C
455901 CCCCAAATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:455867 original size:10 final size:10
Alignment explanation
Indices: 455852--455899 Score: 78
Period size: 10 Copynumber: 4.8 Consensus size: 10
455842 CCCTCCCCCC
455852 CTCTCTCTTT
1 CTCTCTCTTT
*
455862 CTCTCTCCTT
1 CTCTCTCTTT
*
455872 CTCTCTCTCT
1 CTCTCTCTTT
455882 CTCTCTCTTT
1 CTCTCTCTTT
455892 CTCTCTCT
1 CTCTCTCT
455900 CCCCCAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (10 bp):
CTCTCTCTTT
Found at i:456626 original size:27 final size:27
Alignment explanation
Indices: 456578--456676 Score: 71
Period size: 27 Copynumber: 3.6 Consensus size: 27
456568 AGATTATATA
456578 ATATAAATTATTAAAAT-A-TTAAAATTT
1 ATATAAA-TA-TAAAATAATTTAAAATTT
*
456605 ATATAAATATAAAATAATTT-AAATAT
1 ATATAAATATAAAATAATTTAAAATTT
* * *
456631 A-ATTATAACATAACATAATATATAAATATT
1 ATA-TA-AATATAAAATAATTTA-AAAT-TT
456661 ATATAAATATACAAAT
1 ATATAAATATA-AAAT
456677 TACTCAATCT
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
25 7 0.12
26 11 0.20
27 21 0.38
29 9 0.16
30 7 0.12
31 1 0.02
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (27 bp):
ATATAAATATAAAATAATTTAAAATTT
Found at i:456629 original size:16 final size:16
Alignment explanation
Indices: 456577--456632 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
456567 AAGATTATAT
*
456577 AATAT-AAATTATTAA
1 AATATAAAATTATTTA
*
456592 AATATTAAAATTTATATA
1 AATA-TAAAA-TTATTTA
*
456610 AATATAAAATAATTTA
1 AATATAAAATTATTTA
456626 AATATAA
1 AATATAA
456633 TTATAACATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
15 4 0.12
16 13 0.38
17 8 0.24
18 9 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATATAAAATTATTTA
Found at i:458951 original size:9 final size:10
Alignment explanation
Indices: 458927--458970 Score: 54
Period size: 10 Copynumber: 4.2 Consensus size: 10
458917 ATGATGTTTA
458927 AATTTTAATATT
1 AATTTT-AT-TT
458939 AATTTT-TTT
1 AATTTTATTT
458948 AATTTTATTT
1 AATTTTATTT
458958 AATTTTATATT
1 AATTTTAT-TT
458969 AA
1 AA
458971 AAAACAAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 8 0.27
10 12 0.40
11 4 0.13
12 6 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
AATTTTATTT
Found at i:459900 original size:2 final size:2
Alignment explanation
Indices: 459893--459919 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
459883 CTATCACATT
459893 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
459920 GTATGTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:460611 original size:2 final size:2
Alignment explanation
Indices: 460604--460639 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
460594 ATCAAAGGCT
460604 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
460640 GAAAAGGCAA
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:461056 original size:16 final size:15
Alignment explanation
Indices: 461035--461068 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
461025 AAAATTAGAA
*
461035 TTTTAAATTTTAAATT
1 TTTTAAATATT-AATT
461051 TTTTAAATATTAATT
1 TTTTAAATATTAATT
461066 TTT
1 TTT
461069 AAAAGTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTAAATATTAATT
Found at i:464413 original size:18 final size:19
Alignment explanation
Indices: 464390--464441 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
464380 TAGTATATAA
464390 TTAAATTAAAAATAAAT-T
1 TTAAATTAAAAATAAATAT
**
464408 TTAAA-TATTTAATAAATAT
1 TTAAATTA-AAAATAAATAT
*
464427 TTAAATGAAAAATAA
1 TTAAATTAAAAATAA
464442 TTTAATTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
17 2 0.08
18 12 0.46
19 11 0.42
20 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TTAAATTAAAAATAAATAT
Found at i:464455 original size:37 final size:37
Alignment explanation
Indices: 464375--464457 Score: 89
Period size: 37 Copynumber: 2.2 Consensus size: 37
464365 CATTTACCTC
* * *
464375 AAATTTAGTATATAATTAAATTAAAAATAAATTTTAA
1 AAATTTAATAAATAATTAAATGAAAAATAAATTTTAA
* *
464412 ATATTTAATAAATATTTAAATGAAAAAT-AA-TTTAA
1 AAATTTAATAAATAATTAAATGAAAAATAAATTTTAA
464447 TTAAATTTAAT
1 --AAATTTAAT
464458 TTGATAGTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
35 5 0.13
36 2 0.05
37 31 0.82
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.42
Consensus pattern (37 bp):
AAATTTAATAAATAATTAAATGAAAAATAAATTTTAA
Found at i:464651 original size:26 final size:27
Alignment explanation
Indices: 464609--464660 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
464599 GTTTGATTCA
464609 AGAAAATATTTTCTATTTT-TATTTTT
1 AGAAAATATTTTCTATTTTCTATTTTT
464635 AGAAAATAGTTTT-TATTTTCTATTTT
1 AGAAAATA-TTTTCTATTTTCTATTTT
464661 GAAAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.60
Consensus pattern (27 bp):
AGAAAATATTTTCTATTTTCTATTTTT
Found at i:466476 original size:38 final size:38
Alignment explanation
Indices: 466435--466578 Score: 189
Period size: 38 Copynumber: 3.8 Consensus size: 38
466425 TTGAATTAGT
* *
466435 TGACGGTTAGAGAATTCAATTTGAAATTGGTTAACGGT
1 TGACGGTTAGAGAATTCAATTTGAAATTGGTTGACGGC
* ***
466473 TGACGGTTAGAAAATTCAATTTGAAATTTACTGACGGC
1 TGACGGTTAGAGAATTCAATTTGAAATTGGTTGACGGC
* *
466511 TGACGGTTAGAGAATTCAATTTGAAATTGGTCGGCGGC
1 TGACGGTTAGAGAATTCAATTTGAAATTGGTTGACGGC
** *
466549 TGACGACTAGAGAATTCAATTTGGAATTGG
1 TGACGGTTAGAGAATTCAATTTGAAATTGG
466579 CCGGTGACTG
Statistics
Matches: 91, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 91 1.00
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.31
Consensus pattern (38 bp):
TGACGGTTAGAGAATTCAATTTGAAATTGGTTGACGGC
Found at i:466565 original size:76 final size:76
Alignment explanation
Indices: 466435--466576 Score: 212
Period size: 76 Copynumber: 1.9 Consensus size: 76
466425 TTGAATTAGT
* * **
466435 TGACGGTTAGAGAATTCAATTTGAAATTGGTTAACGGTTGACGGTTAGAAAATTCAATTTGAAAT
1 TGACGGTTAGAGAATTCAATTTGAAATTGGTCAACGGCTGACGACTAGAAAATTCAATTTGAAAT
466500 TTACTGACGGC
66 TTACTGACGGC
** * *
466511 TGACGGTTAGAGAATTCAATTTGAAATTGGTCGGCGGCTGACGACTAGAGAATTCAATTTGGAAT
1 TGACGGTTAGAGAATTCAATTTGAAATTGGTCAACGGCTGACGACTAGAAAATTCAATTTGAAAT
466576 T
66 T
466577 GGCCGGTGAC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 58 1.00
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (76 bp):
TGACGGTTAGAGAATTCAATTTGAAATTGGTCAACGGCTGACGACTAGAAAATTCAATTTGAAAT
TTACTGACGGC
Found at i:474066 original size:26 final size:26
Alignment explanation
Indices: 474010--474074 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
474000 ATTAGAATAC
* * *
474010 ATAATATT-TATAAAAATATTTTATT
1 ATAATATTATATATAAATAATATATT
474035 ATAATATTATATATAAATAATATACTT
1 ATAATATTATATATAAATAATATA-TT
*
474062 A-AATATTAAATAT
1 ATAATATTATATAT
474075 TATATAACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.24
26 23 0.68
27 3 0.09
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
ATAATATTATATATAAATAATATATT
Found at i:474088 original size:20 final size:20
Alignment explanation
Indices: 474065--474107 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
474055 TATACTTAAA
*
474065 TATTAAATATTATATAACAT
1 TATTAAATATAATATAACAT
** *
474085 TATTTGATATAATATAATAT
1 TATTAAATATAATATAACAT
474105 TAT
1 TAT
474108 AATACGAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TATTAAATATAATATAACAT
Found at i:480004 original size:22 final size:22
Alignment explanation
Indices: 479979--480059 Score: 66
Period size: 23 Copynumber: 3.7 Consensus size: 22
479969 CTTAATATTA
479979 TAATATTAAAATATTTTTATAT
1 TAATATTAAAATATTTTTATAT
*
480001 TAATATTTTAAATATTTTTA-A-
1 TAATA-TTAAAATATTTTTATAT
480022 -AAT-TATAAATATATATTTT-TAT
1 TAATAT-TAAA-ATAT-TTTTATAT
480044 TAATA-TAATAATATTT
1 TAATATTAA-AATATTT
480060 AATTTAATCA
Statistics
Matches: 48, Mismatches: 2, Indels: 19
0.70 0.03 0.28
Matches are distributed among these distances:
18 1 0.02
19 3 0.06
20 7 0.15
21 7 0.15
22 13 0.27
23 17 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TAATATTAAAATATTTTTATAT
Found at i:481057 original size:21 final size:24
Alignment explanation
Indices: 481028--481076 Score: 68
Period size: 21 Copynumber: 2.2 Consensus size: 24
481018 ACTTCACCAC
481028 ATATCTTATTTTT-TT-TAA-TTA
1 ATATCTTATTTTTATTATAACTTA
*
481049 ATATTTTATTTTTATTATAACTTA
1 ATATCTTATTTTTATTATAACTTA
481073 ATAT
1 ATAT
481077 GTCCTATTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 12 0.50
22 2 0.08
23 3 0.12
24 7 0.29
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (24 bp):
ATATCTTATTTTTATTATAACTTA
Found at i:482353 original size:20 final size:21
Alignment explanation
Indices: 482330--482370 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
482320 TTAAAAAATT
482330 ATTATATATTT-TATTTTTAA
1 ATTATATATTTATATTTTTAA
* *
482350 ATTATTTTTTTATATTTTTAA
1 ATTATATATTTATATTTTTAA
482371 TATAGATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTATATATTTATATTTTTAA
Found at i:482468 original size:14 final size:13
Alignment explanation
Indices: 482447--482541 Score: 53
Period size: 14 Copynumber: 7.5 Consensus size: 13
482437 TAGCGCTTCG
482447 TATTATATTTGATA
1 TATTATATTT-ATA
482461 -ATTTATATATTATA
1 TA-TTATAT-TTATA
482475 T-TTATAATTT-T-
1 TATTAT-ATTTATA
482486 TATTATA-TTATA
1 TATTATATTTATA
*
482498 -ATTATATTTAAAA
1 TATTATATTT-ATA
482511 TATTATATATT-T-
1 TATTATAT-TTATA
* *
482523 TATAATTTTTATA
1 TATTATATTTATA
482536 TATTAT
1 TATTAT
482542 TAATTTATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 27
0.66 0.05 0.28
Matches are distributed among these distances:
10 2 0.03
11 11 0.17
12 14 0.22
13 14 0.22
14 18 0.29
15 4 0.06
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (13 bp):
TATTATATTTATA
Found at i:482473 original size:21 final size:18
Alignment explanation
Indices: 482447--482500 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 18
482437 TAGCGCTTCG
482447 TATTATATTTGATAATTTAT
1 TATTATATTT-ATAATTT-T
482467 ATATTATATTTATAATTTT
1 -TATTATATTTATAATTTT
482486 TATTATA-TTATAATT
1 TATTATATTTATAATT
482501 ATATTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.24
18 7 0.21
19 1 0.03
20 7 0.21
21 10 0.30
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TATTATATTTATAATTTT
Found at i:482496 original size:23 final size:22
Alignment explanation
Indices: 482447--482541 Score: 90
Period size: 23 Copynumber: 4.3 Consensus size: 22
482437 TAGCGCTTCG
482447 TATTATATTTGATAA--TTTATA
1 TATTATATTT-ATAATTTTTATA
482468 TATTATATTTATAATTTTTATTA
1 TATTATATTTATAATTTTTA-TA
* * *
482491 TATTATAATTAT-A-TTTAAAA
1 TATTATATTTATAATTTTTATA
482511 TATTATATATTTTATAATTTTTATA
1 TA-T-TATA-TTTATAATTTTTATA
482536 TATTAT
1 TATTAT
482542 TAATTTATTT
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
20 7 0.12
21 15 0.25
22 9 0.15
23 20 0.33
24 2 0.03
25 7 0.12
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (22 bp):
TATTATATTTATAATTTTTATA
Found at i:482505 original size:29 final size:29
Alignment explanation
Indices: 482463--482529 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
482453 ATTTGATAAT
* *
482463 TTATATATTATATTTATAAT-TTTTATTATA
1 TTATA-ATTATATTTAAAATATTATA-TATA
*
482493 TTATAATTATATTTAAAATATTATATATT
1 TTATAATTATATTTAAAATATTATATATA
482522 TTATAATT
1 TTATAATT
482530 TTTATATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 24 0.73
30 9 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
TTATAATTATATTTAAAATATTATATATA
Found at i:482555 original size:18 final size:19
Alignment explanation
Indices: 482511--482556 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
482501 ATATTTAAAA
*
482511 TATTATATATTTTATAATT
1 TATTATATATTATATAATT
482530 T-TTATATATTAT-TAATT
1 TATTATATATTATATAATT
*
482547 TATTTTATAT
1 TATTATATAT
482557 AAATTTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.25
18 17 0.71
19 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTATATATTATATAATT
Found at i:483833 original size:16 final size:16
Alignment explanation
Indices: 483802--483844 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
483792 TTTAATATTT
*
483802 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATT-A
483819 ATAAAA-TTATAATTA
1 ATAAAATTTATAATTA
*
483834 ATAAATTTTAT
1 ATAAAATTTAT
483845 TTAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 11 0.48
17 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAAATTTATAATTA
Found at i:484381 original size:15 final size:16
Alignment explanation
Indices: 484356--484385 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
484346 ACATAAATTT
484356 TTTCTCTTTTTCTTTC
1 TTTCTCTTTTTCTTTC
484372 TTTC-CTTTTTCTTT
1 TTTCTCTTTTTCTTT
484386 TTTTTATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTCTTTTTCTTTC
Found at i:484776 original size:17 final size:18
Alignment explanation
Indices: 484754--484836 Score: 73
Period size: 19 Copynumber: 4.4 Consensus size: 18
484744 ATACTATTTT
484754 AAATATACAT-AAAATAA
1 AAATATACATAAAAATAA
484771 AAATATGACATAAAAATAATTA
1 AAATAT-ACATAAAAAT-A--A
*
484793 AAACATA-ATATAAAA-AA
1 AAATATACATA-AAAATAA
484810 TAAATATGACATAAAAATAA
1 -AAATAT-ACATAAAAATAA
484830 AAATATA
1 AAATATA
484837 TAAATATATA
Statistics
Matches: 54, Mismatches: 2, Indels: 19
0.72 0.03 0.25
Matches are distributed among these distances:
17 7 0.13
18 10 0.19
19 17 0.31
20 9 0.17
21 5 0.09
22 6 0.11
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (18 bp):
AAATATACATAAAAATAA
Found at i:484794 original size:23 final size:21
Alignment explanation
Indices: 484754--484837 Score: 69
Period size: 20 Copynumber: 4.3 Consensus size: 21
484744 ATACTATTTT
484754 AAATAT-ACAT-AAAAT-A-A
1 AAATATGACATAAAAATAATA
484771 AAATATGACATAAAAATAATTA
1 AAATATGACATAAAAATAA-TA
*
484793 AAACAT-A-ATATAAAA-AAT-
1 AAATATGACATA-AAAATAATA
484811 AAATATGACATAAAAATAA-A
1 AAATATGACATAAAAATAATA
484831 AATATAT
1 AA-ATAT
484838 AAATATATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
17 6 0.11
18 9 0.17
19 11 0.20
20 13 0.24
21 9 0.17
22 6 0.11
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (21 bp):
AAATATGACATAAAAATAATA
Found at i:484995 original size:11 final size:11
Alignment explanation
Indices: 484979--485047 Score: 50
Period size: 11 Copynumber: 5.7 Consensus size: 11
484969 ATTTTATTTT
484979 AATAATATAAA
1 AATAATATAAA
484990 AATAATATAAA
1 AATAATATAAA
*
485001 TATGATATTTATCAAA
1 -A--ATA-ATAT-AAA
*
485017 AA-ATATTTAAA
1 AATA-ATATAAA
485028 ATATAATATAAA
1 A-ATAATATAAA
485040 AATAATAT
1 AATAATAT
485048 GTATATGACA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
11 22 0.47
12 13 0.28
13 2 0.04
14 3 0.06
15 4 0.09
16 3 0.06
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (11 bp):
AATAATATAAA
Found at i:485126 original size:21 final size:19
Alignment explanation
Indices: 485083--485128 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
485073 ATAAAAATAT
*
485083 ATATAAAAAAATTATTAAT
1 ATATAAAAAAATTATTAAA
*
485102 ATATAAAAAATTTATATAAAA
1 ATATAAAAAAATTAT-T-AAA
485123 ATATAA
1 ATATAA
485129 TATTTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 14 0.61
20 1 0.04
21 8 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATATAAAAAAATTATTAAA
Found at i:485143 original size:32 final size:31
Alignment explanation
Indices: 485073--485143 Score: 72
Period size: 32 Copynumber: 2.2 Consensus size: 31
485063 ATATATACAT
* *
485073 ATAAAAATATATATAAAAAAATTATTAATAT
1 ATAAAAATATATATAAAAAAAATATTAATAA
* *
485104 ATAAAAAATTTATATAAAAATATAATATT-TTAA
1 AT-AAAAATATATATAAAAA-A-AATATTAATAA
485137 ATAAAAA
1 ATAAAAA
485144 ATAACATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
31 2 0.06
32 21 0.64
33 5 0.15
34 5 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (31 bp):
ATAAAAATATATATAAAAAAAATATTAATAA
Found at i:485210 original size:13 final size:12
Alignment explanation
Indices: 485182--485230 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
485172 GTTTTCTTTC
485182 TTTTCTTTTCCTTT
1 TTTTCTTTT-C-TT
485196 TTTTCTCTTTCTT
1 TTTTCT-TTTCTT
*
485209 TTTTCTTTCCTT
1 TTTTCTTTTCTT
485221 TCTTTCTTTT
1 T-TTTCTTTT
485231 TCGGCTGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 6 0.19
13 15 0.48
14 7 0.23
15 3 0.10
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTCTT
Found at i:485212 original size:16 final size:15
Alignment explanation
Indices: 485193--485232 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
485183 TTTCTTTTCC
485193 TTTTTTTCTCTTTCTT
1 TTTTTTTC-CTTTCTT
485209 TTTTCTTTCCTTTCTT
1 TTTT-TTTCCTTTCTT
*
485225 TCTTTTTC
1 TTTTTTTC
485233 GGCTGAACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 14 0.64
17 4 0.18
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTTCCTTTCTT
Found at i:485218 original size:26 final size:25
Alignment explanation
Indices: 485176--485232 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
485166 AATATGGTTT
*
485176 TCTTTCTTTTCTTTTCCTTTTTTTC
1 TCTTTCTTTTCTTTTCCTTTCTTTC
*
485201 TCTTTCTTTTTTCTTTCCTTTCTTTC
1 TCTTTCTTTTCT-TTTCCTTTCTTTC
*
485227 TTTTTC
1 TCTTTC
485233 GGCTGAACAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 11 0.39
26 17 0.61
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (25 bp):
TCTTTCTTTTCTTTTCCTTTCTTTC
Found at i:486064 original size:12 final size:12
Alignment explanation
Indices: 486049--486098 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
486039 TATAAATTAA
*
486049 TTAAAATAAATT
1 TTAAAATAATTT
**
486061 TT-AAATTTTTT
1 TTAAAATAATTT
486072 ATTAAAATAATTT
1 -TTAAAATAATTT
486085 TTAAAAT-ATTT
1 TTAAAATAATTT
486096 TTA
1 TTA
486099 TCACGTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 13 0.42
12 11 0.35
13 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTAAAATAATTT
Found at i:486078 original size:24 final size:26
Alignment explanation
Indices: 486048--486099 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
486038 ATATAAATTA
486048 ATTAAAATAAATTTT-AAAT-TTTTT
1 ATTAAAATAAATTTTAAAATATTTTT
*
486072 ATTAAAATAATTTTTAAAATATTTTT
1 ATTAAAATAAATTTTAAAATATTTTT
486098 AT
1 AT
486100 CACGTTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 14 0.56
25 4 0.16
26 7 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTAAAATAAATTTTAAAATATTTTT
Found at i:487152 original size:25 final size:25
Alignment explanation
Indices: 487123--487182 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
487113 AATAATAAAA
487123 AAAATTTAAATTTTATAATTTTATT
1 AAAATTTAAATTTTATAATTTTATT
* *
487148 AAAA-TAAAATTTTTATATTTTTATT
1 AAAATTTAAA-TTTTATAATTTTATT
*
487173 -ATATTTAAAT
1 AAAATTTAAAT
487183 AAAAATTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
AAAATTTAAATTTTATAATTTTATT
Found at i:487158 original size:30 final size:29
Alignment explanation
Indices: 487118--487198 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 29
487108 GTTAAAATAA
*
487118 TAAAA-AAAATTTAAATTTTATAATTTTAT
1 TAAAATAAAATTTAAATTTTAT-ATTATAT
*
487147 TAAAATAAAATTTTTATATTTT-TATTATAT
1 TAAAATAAAA--TTTAAATTTTATATTATAT
* *
487177 TTAAATAAAAATTCAAATTTTA
1 TAAAAT-AAAATTTAAATTTTA
487199 ATTGATACTC
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
29 13 0.31
30 15 0.36
31 5 0.12
32 9 0.21
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
TAAAATAAAATTTAAATTTTATATTATAT
Found at i:487376 original size:29 final size:30
Alignment explanation
Indices: 487305--487384 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
487295 GAATTAATTT
* *
487305 ATATAAAATTTTATTTAAGTATAAAATAAA
1 ATATAAAAATTTATTTAAATATAAAATAAA
* *
487335 AAATAAAAATTTATTTAAATATAAGA-AAA
1 ATATAAAAATTTATTTAAATATAAAATAAA
* *
487364 ATATAAAACTTTACTTAAATA
1 ATATAAAAATTTATTTAAATA
487385 AAATTAATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 21 0.49
30 22 0.51
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (30 bp):
ATATAAAAATTTATTTAAATATAAAATAAA
Found at i:487781 original size:19 final size:20
Alignment explanation
Indices: 487740--487781 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
487730 TATAAATTTT
*
487740 TTTTAAAAAAATAAATATTAA
1 TTTTAAAAAAAT-AATATCAA
*
487761 TTTTATAAAAAT-ATATCAA
1 TTTTAAAAAAATAATATCAA
487780 TT
1 TT
487782 CATTTAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.42
21 11 0.58
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TTTTAAAAAAATAATATCAA
Found at i:487786 original size:23 final size:22
Alignment explanation
Indices: 487715--487786 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 22
487705 TATGGAATCA
* *
487715 AATTTTTTAAATATATATAAATT
1 AATTTTATAAAAATATAT-AATT
** * *
487738 TTTTTTAAAAAAATAAAT-ATT
1 AATTTTATAAAAATATATAATT
487759 AATTTTATAAAAATATATCAATT
1 AATTTTATAAAAATATAT-AATT
*
487782 CATTT
1 AATTT
487787 AGAATAATAT
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
21 17 0.47
23 19 0.53
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTTTATAAAAATATATAATT
Found at i:487999 original size:5 final size:5
Alignment explanation
Indices: 487989--488016 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
487979 ACTTCATGCT
487989 TTTTC TTTTC TTTTC TTTTC TTTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTT
488017 ATCCAGCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:489655 original size:21 final size:21
Alignment explanation
Indices: 489629--489671 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
489619 CTGTATCTAT
489629 ATCATATCATTCAAGCATTGG
1 ATCATATCATTCAAGCATTGG
489650 ATCATATCATTCAAGCATTGG
1 ATCATATCATTCAAGCATTGG
489671 A
1 A
489672 CTATTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (21 bp):
ATCATATCATTCAAGCATTGG
Found at i:493302 original size:1 final size:1
Alignment explanation
Indices: 493296--493320 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
493286 GTCTTTTCCA
493296 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
493321 ACTTTTCTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:493648 original size:20 final size:20
Alignment explanation
Indices: 493625--493672 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 20
493615 ATTAATAAAA
493625 ATTTTAATATTTAATATTAT
1 ATTTTAATATTTAATATTAT
493645 A--TT--TA-TTAATATTAT
1 ATTTTAATATTTAATATTAT
493660 ATTTTAATTATTT
1 ATTTTAA-TATTT
493673 TATTCAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 11
0.67 0.00 0.33
Matches are distributed among these distances:
15 11 0.50
16 2 0.09
17 2 0.09
18 2 0.09
20 3 0.14
21 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTAATATTTAATATTAT
Found at i:493655 original size:15 final size:15
Alignment explanation
Indices: 493635--493663 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
493625 ATTTTAATAT
493635 TTAATATTATATTTA
1 TTAATATTATATTTA
493650 TTAATATTATATTT
1 TTAATATTATATTT
493664 TAATTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAATATTATATTTA
Found at i:494057 original size:22 final size:20
Alignment explanation
Indices: 494014--494076 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
494004 TTAAGTAAAA
494014 TTTTAAAATAATTATAATAT
1 TTTTAAAATAATTATAATAT
*
494034 TTTTAAAATAATATTTAA-AT
1 TTTTAAAATAAT-TATAATAT
* *
494054 ATTTAAATATTATTAATAATAT
1 TTTTAAA-ATAATT-ATAATAT
494076 T
1 T
494077 AAATATTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 21 0.62
21 11 0.32
22 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTAAAATAATTATAATAT
Found at i:494092 original size:19 final size:19
Alignment explanation
Indices: 494051--494088 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
494041 ATAATATTTA
494051 AATATTTAAATATTATTAAT
1 AATA-TTAAATATTATTAAT
494071 AATATTAAATATT-TTAAT
1 AATATTAAATATTATTAAT
494089 TAATTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 9 0.50
20 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATTAAATATTATTAAT
Found at i:494096 original size:27 final size:28
Alignment explanation
Indices: 494040--494097 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
494030 ATATTTTTAA
*
494040 AATAATATTTAAATATTTAAATATTATT
1 AATAATATTTAAATATTTAAATAATATT
*
494068 AATAATA-TTAAATATTTTAATTAAT-TT
1 AATAATATTTAAATA-TTTAAATAATATT
494095 AAT
1 AAT
494098 TTATTACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
AATAATATTTAAATATTTAAATAATATT
Found at i:495453 original size:22 final size:22
Alignment explanation
Indices: 495426--495503 Score: 94
Period size: 22 Copynumber: 3.8 Consensus size: 22
495416 ATTCGGTAAT
495426 TTTAAATATAATATAAAAATAA
1 TTTAAATATAATATAAAAATAA
**
495448 TTTAAATACGATA-AAAAAT-A
1 TTTAAATATAATATAAAAATAA
495468 --T-AATATAATATAAAAATAA
1 TTTAAATATAATATAAAAATAA
*
495487 TTTTAATATAATATAAA
1 TTTAAATATAATATAAA
495504 TATTATAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
17 7 0.15
18 7 0.15
19 1 0.02
20 1 0.02
21 7 0.15
22 24 0.51
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (22 bp):
TTTAAATATAATATAAAAATAA
Found at i:495474 original size:5 final size:5
Alignment explanation
Indices: 495464--495515 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
495454 TACGATAAAA
* * *
495464 AATAT AATAT AATAT AAAAAT AATTTT AATAT AATAT AA-AT ATTAT AATAT
1 AATAT AATAT AATAT -AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT
495515 A
1 A
495516 TCAAAATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 3 0.08
5 28 0.74
6 7 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:507313 original size:17 final size:17
Alignment explanation
Indices: 507291--507324 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
507281 TCATAATAAA
*
507291 ATGTTCCAAGTACATAT
1 ATGTTCCAAATACATAT
507308 ATGTTCCAAATACATAT
1 ATGTTCCAAATACATAT
507325 GCTGCATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (17 bp):
ATGTTCCAAATACATAT
Found at i:511755 original size:14 final size:14
Alignment explanation
Indices: 511736--511767 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
511726 TTTCAACAAT
*
511736 ATTTATTTTGGATA
1 ATTTATTTTGAATA
511750 ATTTATTTTGAATA
1 ATTTATTTTGAATA
511764 ATTT
1 ATTT
511768 TAAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (14 bp):
ATTTATTTTGAATA
Found at i:512351 original size:10 final size:10
Alignment explanation
Indices: 512336--512365 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
512326 AATTGATAAA
512336 ATATTATTTT
1 ATATTATTTT
512346 ATATTATTTT
1 ATATTATTTT
*
512356 ATTTTATTTT
1 ATATTATTTT
512366 TTTAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
ATATTATTTT
Found at i:512938 original size:25 final size:24
Alignment explanation
Indices: 512884--512939 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
512874 TAAATTAAAT
**
512884 TAAATTAAAATTATTATTTAATTA
1 TAAATTAAAATTATTATTTAAAAA
512908 TAAAATATAAAA-TATTATTATAAAAA
1 T-AAAT-TAAAATTATTATT-TAAAAA
512934 TAAATT
1 TAAATT
512940 TTAATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
24 2 0.07
25 15 0.56
26 10 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TAAATTAAAATTATTATTTAAAAA
Found at i:513156 original size:35 final size:33
Alignment explanation
Indices: 513102--513170 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 33
513092 CATACACATG
*
513102 TTATTTATTTTTATGTATATAAATATATTATATAT
1 TTATTTATTTTTATATATATAAATA-ATT-TATAT
*
513137 TTATTTAATTTTTA-ATATATTAATAATTTATAT
1 TTATTT-ATTTTTATATATATAAATAATTTATAT
513170 T
1 T
513171 AAATAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 6 0.19
34 3 0.10
35 15 0.48
36 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (33 bp):
TTATTTATTTTTATATATATAAATAATTTATAT
Found at i:513210 original size:18 final size:18
Alignment explanation
Indices: 513124--513220 Score: 68
Period size: 18 Copynumber: 5.8 Consensus size: 18
513114 ATGTATATAA
513124 ATATATTATATATT-TATT
1 ATATATT-TATATTATATT
* *
513142 -TA-ATTTTTAATATATT
1 ATATATTTATATTATATT
*
513158 A-ATAATTTATATTA-AAT
1 ATAT-ATTTATATTATATT
*
513175 A-AAATTTA-A-TAT-TT
1 ATATATTTATATTATATT
513189 ATATATTTATATTATATT
1 ATATATTTATATTATATT
*
513207 ATATATTTTTATTA
1 ATATATTTATATTA
513221 GATTTTTATA
Statistics
Matches: 61, Mismatches: 9, Indels: 18
0.69 0.10 0.20
Matches are distributed among these distances:
14 4 0.07
15 11 0.18
16 14 0.23
17 9 0.15
18 23 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATATATTTATATTATATT
Found at i:516125 original size:13 final size:14
Alignment explanation
Indices: 516109--516137 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
516099 TATTTATAAT
516109 AATTAT-TTTTTGA
1 AATTATGTTTTTGA
516122 AATTATGTTTTTGA
1 AATTATGTTTTTGA
516136 AA
1 AA
516138 AGTTTTAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
AATTATGTTTTTGA
Found at i:519907 original size:2 final size:2
Alignment explanation
Indices: 519900--519944 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
519890 CAACAACCAG
*
519900 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
519942 TA T
1 TA T
519945 GTGTGTGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:521021 original size:18 final size:18
Alignment explanation
Indices: 521000--521034 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
520990 TGTTTATTAA
521000 ATATATTTTAT-TTATATT
1 ATAT-TTTTATCTTATATT
521018 ATATTTTTATCTTATAT
1 ATATTTTTATCTTATAT
521035 CCAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
ATATTTTTATCTTATATT
Found at i:521108 original size:18 final size:18
Alignment explanation
Indices: 521085--521124 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
521075 TGGCTTGCTA
521085 GGAAGGTATTTTAATAGT
1 GGAAGGTATTTTAATAGT
521103 GGAAGGTATTTTAATAGT
1 GGAAGGTATTTTAATAGT
521121 GGAA
1 GGAA
521125 CTCTTAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (18 bp):
GGAAGGTATTTTAATAGT
Found at i:523308 original size:11 final size:11
Alignment explanation
Indices: 523288--523341 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
523278 ACACGACACG
523288 AAAA-ATAATA
1 AAAACATAATA
523298 AAAACATAATA
1 AAAACATAATA
*
523309 AATACA-ATATGA
1 AAAACATA-AT-A
523321 AAAA-ATAATA
1 AAAACATAATA
*
523331 AAAGCATAATA
1 AAAACATAATA
523342 CAATACAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
10 9 0.25
11 22 0.61
12 5 0.14
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (11 bp):
AAAACATAATA
Found at i:527911 original size:16 final size:16
Alignment explanation
Indices: 527886--527920 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
527876 AACACTGAGG
527886 GAAAAAAAAAAAAAAA
1 GAAAAAAAAAAAAAAA
* *
527902 GAAAAGAAAAGAAAAA
1 GAAAAAAAAAAAAAAA
527918 GAA
1 GAA
527921 GACAATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
GAAAAAAAAAAAAAAA
Found at i:528653 original size:15 final size:15
Alignment explanation
Indices: 528633--528718 Score: 106
Period size: 15 Copynumber: 5.9 Consensus size: 15
528623 CAGAGCTGCG
*
528633 GCAACAGCAGCAGCA
1 GCAACAACAGCAGCA
*
528648 GCAACAACAGCAACA
1 GCAACAACAGCAGCA
528663 GCAAC-A-AG-AGCA
1 GCAACAACAGCAGCA
*
528675 GCAACAACAGCAACA
1 GCAACAACAGCAGCA
*
528690 GCAACAAGAGCAGCA
1 GCAACAACAGCAGCA
*
528705 ACAACAACAGCAGC
1 GCAACAACAGCAGC
528719 TGCCGCGGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
12 8 0.13
13 3 0.05
14 3 0.05
15 46 0.77
ACGTcount: A:0.49, C:0.31, G:0.20, T:0.00
Consensus pattern (15 bp):
GCAACAACAGCAGCA
Found at i:528718 original size:27 final size:27
Alignment explanation
Indices: 528644--528710 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
528634 CAACAGCAGC
528644 AGCAGCAACAACAGCAACAGCAACAAG
1 AGCAGCAACAACAGCAACAGCAACAAG
528671 AGCAGCAACAACAGCAACAGCAACAAG
1 AGCAGCAACAACAGCAACAGCAACAAG
528698 AGCAGCAACAACA
1 AGCAGCAACAACA
528711 ACAGCAGCTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.52, C:0.30, G:0.18, T:0.00
Consensus pattern (27 bp):
AGCAGCAACAACAGCAACAGCAACAAG
Found at i:530035 original size:21 final size:21
Alignment explanation
Indices: 529977--530035 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
529967 CATATGCCTT
* *
529977 TGAGAAATCCCCATACGCTCG
1 TGAGAGATCCCCATATGCTCG
* * **
529998 TGATAGATCACTGTATGCTCG
1 TGAGAGATCCCCATATGCTCG
530019 TGAGAGATCCCCATATG
1 TGAGAGATCCCCATATG
530036 ATCGGAGTCA
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (21 bp):
TGAGAGATCCCCATATGCTCG
Found at i:535209 original size:2 final size:2
Alignment explanation
Indices: 535202--535235 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
535192 CTAGAGCTGT
535202 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
535236 AATTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:546384 original size:2 final size:2
Alignment explanation
Indices: 546364--546400 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
546354 TGATTTATTT
*
546364 TA TA -A TA TG TA TA -A 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
546401 GTATCTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:547966 original size:2 final size:2
Alignment explanation
Indices: 547959--547986 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
547949 AAAGAAAGAA
547959 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
547987 GATATCACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:548268 original size:2 final size:2
Alignment explanation
Indices: 548261--548305 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
548251 GGCAAAGGAA
548261 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
548303 AG A
1 AG A
548306 CTACCTCTTC
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:550130 original size:21 final size:21
Alignment explanation
Indices: 550075--550132 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
550065 AAAAGATGTA
* *
550075 TTTT-GATGAAATAATATATT
1 TTTTGGATGAAAAAATACATT
* *
550095 TGTTGGATG-AAAAATGCATT
1 TTTTGGATGAAAAAATACATT
550115 TTTTGGATGAAAAAATAC
1 TTTTGGATGAAAAAATAC
550133 TACTTTTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (21 bp):
TTTTGGATGAAAAAATACATT
Found at i:551867 original size:20 final size:20
Alignment explanation
Indices: 551842--551885 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
551832 AAATAGTGGC
551842 ATGAAAATTTTGACAAAGTT
1 ATGAAAATTTTGACAAAGTT
*
551862 ATGAAAATTTTGACAACGTT
1 ATGAAAATTTTGACAAAGTT
551882 ATGA
1 ATGA
551886 TGTCAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (20 bp):
ATGAAAATTTTGACAAAGTT
Found at i:553475 original size:20 final size:20
Alignment explanation
Indices: 553423--553476 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
553413 AAAATGTGTA
* *
553423 TTTAGATGAAATGATGTATTT
1 TTTAGATGAAA-AATGCATTT
* * *
553444 GTTGGATAAAAAATGCATTT
1 TTTAGATGAAAAATGCATTT
553464 TTTAGATGAAAAA
1 TTTAGATGAAAAA
553477 AATTTAACTT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.41, C:0.02, G:0.19, T:0.39
Consensus pattern (20 bp):
TTTAGATGAAAAATGCATTT
Found at i:554360 original size:20 final size:20
Alignment explanation
Indices: 554303--554361 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
554293 TAATAGTAAT
* *
554303 ATTACACAAATTTATTAT-A
1 ATTACATAAATATATTATCA
* *
554322 TTTACATAAA-ATTTTATCA
1 ATTACATAAATATATTATCA
554341 ATTACATAAATATATTATCA
1 ATTACATAAATATATTATCA
554361 A
1 A
554362 AAGGTAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 5 0.16
19 18 0.56
20 9 0.28
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTACATAAATATATTATCA
Found at i:554917 original size:20 final size:19
Alignment explanation
Indices: 554885--554947 Score: 74
Period size: 20 Copynumber: 3.3 Consensus size: 19
554875 TAAGAATTTT
554885 TATTA-AAATTACATAAAA
1 TATTATAAATTACATAAAA
* *
554903 TATTATCATATTACATATAAT
1 TATTAT-AAATTACATA-AAA
*
554924 TATTATAAATTATATAAAA
1 TATTATAAATTACATAAAA
554943 TATTA
1 TATTA
554948 CTTAAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
18 5 0.14
19 7 0.19
20 17 0.46
21 8 0.22
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (19 bp):
TATTATAAATTACATAAAA
Found at i:554944 original size:75 final size:76
Alignment explanation
Indices: 554865--555013 Score: 205
Period size: 75 Copynumber: 2.0 Consensus size: 76
554855 GAGCTATGTG
* *
554865 AAATATTGA-TTAAGAATTTT-TATTAAAATTACATAAAATATTATCA-TATTACATATAATTAT
1 AAATATT-ACTTAA-AATTTTATATTAAAATTACATAAAATATTACCATTATTACATATAAATAT
*
554927 TATAAATTATATA
64 TACAAATTATATA
* *
554940 AAATATTACTTAAAATTTTATATTAAAATTATATAAAATATTACCATTTTTACATATAAATATTA
1 AAATATTACTTAAAATTTTATATTAAAATTACATAAAATATTACCATTATTACATATAAATATTA
*
555005 CAAGTTATA
66 CAAATTATA
555014 CAAAGCGCCA
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
74 7 0.11
75 35 0.54
76 23 0.35
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (76 bp):
AAATATTACTTAAAATTTTATATTAAAATTACATAAAATATTACCATTATTACATATAAATATTA
CAAATTATATA
Found at i:555004 original size:40 final size:39
Alignment explanation
Indices: 554885--555013 Score: 115
Period size: 40 Copynumber: 3.4 Consensus size: 39
554875 TAAGAATTTT
* * *
554885 TATTA-AAATTACATAAAATATTATCATATTACATATAAT
1 TATTACAAATTATATAAAATATTA-CATTTTACATATAAA
* * * **
554924 TATTATAAATTATATAAAATATTAC--TTAAAAT-TTTA
1 TATTACAAATTATATAAAATATTACATTTTACATATAAA
554960 TATTA-AAATTATATAAAATATTACCATTTTTACATATAAA
1 TATTACAAATTATATAAAATATTA-CA-TTTTACATATAAA
*
555000 TATTACAAGTTATA
1 TATTACAAATTATA
555014 CAAAGCGCCA
Statistics
Matches: 71, Mismatches: 12, Indels: 12
0.75 0.13 0.13
Matches are distributed among these distances:
35 18 0.25
36 7 0.10
37 4 0.06
39 11 0.15
40 24 0.34
41 7 0.10
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (39 bp):
TATTACAAATTATATAAAATATTACATTTTACATATAAA
Found at i:555015 original size:22 final size:23
Alignment explanation
Indices: 554970--555015 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
554960 TATTAAAATT
* * *
554970 ATATAAAATATTACCATTTTTAC
1 ATATAAAATATTACAAGTTATAC
554993 ATAT-AAATATTACAAGTTATAC
1 ATATAAAATATTACAAGTTATAC
555015 A
1 A
555016 AAGCGCCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (23 bp):
ATATAAAATATTACAAGTTATAC
Found at i:556603 original size:2 final size:2
Alignment explanation
Indices: 556590--556635 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
556580 ATCAATTCAG
*
556590 AT AT AT AC 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
556632 AT AT
1 AT AT
556636 CAGGTCTTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:560307 original size:11 final size:12
Alignment explanation
Indices: 560286--560325 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
560276 CATGTTATAT
560286 TTTATATTATTA
1 TTTATATTATTA
*
560298 TTTA-ATTATTT
1 TTTATATTATTA
560309 TTTATA-TA-TA
1 TTTATATTATTA
560319 TTTATAT
1 TTTATAT
560326 CATATAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
10 7 0.29
11 12 0.50
12 5 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATATTATTA
Found at i:560309 original size:21 final size:21
Alignment explanation
Indices: 560283--560322 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
560273 TATCATGTTA
560283 TATTTTATAT-TATTATTTAAT
1 TATTTTATATATA-TATTTAAT
*
560304 TATTTTTTATATATATTTA
1 TATTTTATATATATATTTA
560323 TATCATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTTATATATATATTTAAT
Found at i:561974 original size:13 final size:13
Alignment explanation
Indices: 561942--561986 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
561932 TGAATTGAAA
*
561942 AGAGATACAAAAG
1 AGAGATACAAGAG
*
561955 AGGGATACAAGAG
1 AGAGATACAAGAG
* *
561968 ATAGATACAAGAA
1 AGAGATACAAGAG
561981 AGAGAT
1 AGAGAT
561987 GCATGAGAGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.56, C:0.07, G:0.27, T:0.11
Consensus pattern (13 bp):
AGAGATACAAGAG
Found at i:562121 original size:27 final size:27
Alignment explanation
Indices: 562083--562155 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
562073 ACAAGCTACA
*
562083 ATTTTTGACAAACAAAAAGGAACCACC
1 ATTTTTGACAAACAAAAAGGAACAACC
* * * *
562110 ATTTTTTACAAATATAAAGTAACAACC
1 ATTTTTGACAAACAAAAAGGAACAACC
*
562137 ATTTTTGACAAACACAAAG
1 ATTTTTGACAAACAAAAAG
562156 AGTGGCTTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.26
Consensus pattern (27 bp):
ATTTTTGACAAACAAAAAGGAACAACC
Found at i:563086 original size:27 final size:28
Alignment explanation
Indices: 563036--563110 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 28
563026 ACAAGTCATA
*
563036 ATTTTTTACAAAGA-AAAAGGAACTA-T
1 ATTTTTTACAAACACAAAAGGAACTACT
* *
563062 CATTTTTTACAAATACAAAA-TAACTACT
1 -ATTTTTTACAAACACAAAAGGAACTACT
*
563090 ATTTTTGACAAACACAAAAGG
1 ATTTTTTACAAACACAAAAGG
563111 TGACTTTTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 35 0.88
28 5 0.12
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.31
Consensus pattern (28 bp):
ATTTTTTACAAACACAAAAGGAACTACT
Found at i:565609 original size:21 final size:21
Alignment explanation
Indices: 565577--565624 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
565567 ATAGATTTTG
565577 ATATATTTATATATTTATATT-
1 ATATATTTATAT-TTTATATTC
*
565598 ATAT-TTTAATATTTTTTATTC
1 ATATATTT-ATATTTTATATTC
565619 ATATAT
1 ATATAT
565625 ATAACATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 10 0.43
21 12 0.52
22 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATATTTATATTTTATATTC
Found at i:569767 original size:17 final size:17
Alignment explanation
Indices: 569742--569774 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
569732 ATGTTGCTTA
569742 GACTCTTTTTTTTTTCG
1 GACTCTTTTTTTTTTCG
*
569759 GACTTTTTTTTTTTTC
1 GACTCTTTTTTTTTTC
569775 AAAGTGCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.15, G:0.09, T:0.70
Consensus pattern (17 bp):
GACTCTTTTTTTTTTCG
Found at i:571040 original size:52 final size:52
Alignment explanation
Indices: 570960--571064 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
570950 CTAAACCTGC
570960 AACAAAAAGTACAATTGAAAAAACCTAAGTTGAGCATGTTAGCAAGGAAATG
1 AACAAAAAGTACAATTGAAAAAACCTAAGTTGAGCATGTTAGCAAGGAAATG
*
571012 AACAAAAAGTACAATTGAAAAAAGCTAAGTTGAGCATGTTAGCAAGGAAATG
1 AACAAAAAGTACAATTGAAAAAACCTAAGTTGAGCATGTTAGCAAGGAAATG
571064 A
1 A
571065 CACGCTAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.50, C:0.10, G:0.20, T:0.19
Consensus pattern (52 bp):
AACAAAAAGTACAATTGAAAAAACCTAAGTTGAGCATGTTAGCAAGGAAATG
Found at i:576143 original size:30 final size:30
Alignment explanation
Indices: 576108--576176 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
576098 AATCTTTAAT
*
576108 TAAATAAGTCTTT-AAATTTTAACTTATATCC
1 TAAATAAAT-TTTGAAATTTTAACTTATA-CC
* *
576139 -AAATAAATTTTGAACTTTTAATTTATACC
1 TAAATAAATTTTGAAATTTTAACTTATACC
576168 TAAATAAAT
1 TAAATAAAT
576177 GTTTAACATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 5 0.15
30 28 0.85
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.43
Consensus pattern (30 bp):
TAAATAAATTTTGAAATTTTAACTTATACC
Found at i:576527 original size:24 final size:24
Alignment explanation
Indices: 576478--576532 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
576468 TAATTTAAAA
* *
576478 TTATATAATATAACAATATATCAT
1 TTATATAATATAACAATACAACAT
*
576502 TTATATAATATAA-TATACAACAAT
1 TTATATAATATAACAATACAAC-AT
*
576526 TTTTATA
1 TTATATA
576533 TTAAAAACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (24 bp):
TTATATAATATAACAATACAACAT
Found at i:577480 original size:2 final size:2
Alignment explanation
Indices: 577473--577515 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
577463 TGAGACAGTT
577473 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
577516 CTACTGAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:580802 original size:27 final size:27
Alignment explanation
Indices: 580752--580803 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
580742 TTTTTTTTTT
*
580752 TAATTTTAAGTTCAAACCTATTATTGG
1 TAATTTTAAGTTCAAACATATTATTGG
*
580779 TAATTTTAAGTTCAAACATGTTATT
1 TAATTTTAAGTTCAAACATATTATT
580804 AGTCTAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.46
Consensus pattern (27 bp):
TAATTTTAAGTTCAAACATATTATTGG
Found at i:580894 original size:22 final size:21
Alignment explanation
Indices: 580866--580909 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
580856 AATATTAAAA
580866 ATGTATTTT-TATATTAATATTT
1 ATGTATTTTATA-ATTAA-ATTT
580888 ATGTATTTTATAATTAAATTT
1 ATGTATTTTATAATTAAATTT
580909 A
1 A
580910 AATAAAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 14 0.67
23 2 0.10
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
ATGTATTTTATAATTAAATTT
Found at i:580898 original size:21 final size:22
Alignment explanation
Indices: 580866--580909 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
580856 AATATTAAAA
580866 ATGTATTTTTAT-ATTAATATTT
1 ATGTATTTTTATAATTAA-ATTT
580888 ATGTA-TTTTATAATTAAATTT
1 ATGTATTTTTATAATTAAATTT
580909 A
1 A
580910 AATAAAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (22 bp):
ATGTATTTTTATAATTAAATTT
Found at i:581006 original size:20 final size:21
Alignment explanation
Indices: 580960--581009 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
580950 CTAATCAAGC
*
580960 TAAATTTAAATATATATTATTT
1 TAAA-TTAAAAATATATTATTT
580982 T-AATTAAAAAT-TATTATTT
1 TAAATTAAAAATATATTATTT
581001 TAAATTAAA
1 TAAATTAAA
581010 TTAAATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 9 0.35
20 14 0.54
21 2 0.08
22 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATTAAAAATATATTATTT
Found at i:581017 original size:20 final size:20
Alignment explanation
Indices: 580960--581017 Score: 50
Period size: 20 Copynumber: 2.9 Consensus size: 20
580950 CTAATCAAGC
*
580960 TAAATTTAAATATATATTATTT
1 TAAA-TTAAAT-TAAATTATTT
580982 T-AATTAAA--AATTATTATTT
1 TAAATTAAATTAA--ATTATTT
581001 TAAATTAAATTAAATTA
1 TAAATTAAATTAAATTA
581018 ATCTAAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 12
0.70 0.02 0.28
Matches are distributed among these distances:
17 1 0.03
19 8 0.27
20 16 0.53
21 2 0.07
22 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAATTAAATTAAATTATTT
Found at i:581521 original size:15 final size:16
Alignment explanation
Indices: 581494--581523 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
581484 TTTAAATATG
581494 ATTATATAAATATAAT
1 ATTATATAAATATAAT
581510 ATTATA-AAATATAA
1 ATTATATAAATATAA
581524 AATACATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTATATAAATATAAT
Found at i:582023 original size:11 final size:11
Alignment explanation
Indices: 581982--582023 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
581972 ATTAAATATG
581982 TATTT-TTATT
1 TATTTATTATT
*
581992 T-TTTATTATA
1 TATTTATTATT
582002 TATTTATTATT
1 TATTTATTATT
*
582013 TATTTAATATT
1 TATTTATTATT
582024 AAAATGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 3 0.11
10 6 0.22
11 18 0.67
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TATTTATTATT
Found at i:582223 original size:17 final size:17
Alignment explanation
Indices: 582178--582250 Score: 64
Period size: 17 Copynumber: 4.4 Consensus size: 17
582168 TTAAATATAA
* *
582178 ATATATATTTTAAAA-T
1 ATATATATATAAAAATT
582194 ATATATA-ATAAAAATT
1 ATATATATATAAAAATT
*
582210 ATCA-ATATATAAAATTT
1 AT-ATATATATAAAAATT
*
582227 ATATAAATATAAAATATT
1 ATATATATATAAAA-ATT
582245 AT-TATA
1 ATATATA
582251 GAAATATATA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
15 5 0.11
16 14 0.30
17 23 0.50
18 4 0.09
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATATATATAAAAATT
Found at i:583114 original size:3 final size:3
Alignment explanation
Indices: 583106--583144 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
583096 AATTCTTATG
583106 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
583145 ATTTGTGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:584160 original size:16 final size:16
Alignment explanation
Indices: 584139--584199 Score: 59
Period size: 16 Copynumber: 3.4 Consensus size: 16
584129 TATATTTCAC
584139 ATATATAAAAATATAA
1 ATATATAAAAATATAA
584155 ATATATAAAAATAATTTTTTAA
1 ATATATAAAAAT-A-----TAA
*
584177 ATATATAAAAAAATAA
1 ATATATAAAAATATAA
584193 ATATATA
1 ATATATA
584200 TTTATATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
16 22 0.58
17 1 0.03
21 1 0.03
22 14 0.37
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATATAAAAATATAA
Found at i:584360 original size:18 final size:18
Alignment explanation
Indices: 584337--584376 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
584327 AATTTTTTTA
*
584337 AAATTAAAAAAAATTAAT
1 AAATTAAAAAAAATCAAT
**
584355 AAATTAAATCAAATCAAT
1 AAATTAAAAAAAATCAAT
584373 AAAT
1 AAAT
584377 ATTTTTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATTAAAAAAAATCAAT
Found at i:589337 original size:2 final size:2
Alignment explanation
Indices: 589330--589369 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
589320 GCAATAGACC
*
589330 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
589370 AGCTTTTTAA
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:589558 original size:2 final size:2
Alignment explanation
Indices: 589551--589587 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
589541 GAGTCCAAGG
589551 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 T
589588 GTTTTCCTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:592155 original size:5 final size:5
Alignment explanation
Indices: 592145--592177 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
592135 CGGCCTTCAA
592145 TTTCC TTTCC TTTCC TTTCCC TTTCC TTTCC TT
1 TTTCC TTTCC TTTCC TTT-CC TTTCC TTTCC TT
592178 CGATGTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTCC
Found at i:592169 original size:11 final size:11
Alignment explanation
Indices: 592145--592175 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
592135 CGGCCTTCAA
592145 TTTCCTTT-CC
1 TTTCCTTTCCC
592155 TTTCCTTTCCC
1 TTTCCTTTCCC
592166 TTTCCTTTCC
1 TTTCCTTTCC
592176 TTCGATGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTCCTTTCCC
Found at i:592694 original size:27 final size:28
Alignment explanation
Indices: 592649--592704 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
592639 ACCCAAATTT
* *
592649 AAATAATTATTGAATATAAAATAATAAA
1 AAATAATTATTAAAAATAAAATAATAAA
592677 AAAT-ATTATTAAAAATAAAATAATAAA
1 AAATAATTATTAAAAATAAAATAATAAA
592704 A
1 A
592705 CTTAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (28 bp):
AAATAATTATTAAAAATAAAATAATAAA
Found at i:600861 original size:45 final size:42
Alignment explanation
Indices: 600812--600905 Score: 102
Period size: 45 Copynumber: 2.2 Consensus size: 42
600802 TAAATTTATT
* *
600812 TTAAATTACTT-ATATTTATATTTATTATTTATA-ATTAATAAAATA
1 TTAAATTAATTAAT-TTTATA-TTAATATTTATATA-T-ATAAAA-A
*
600857 TTAAAATAATTAATTTTATATTAATATTTATATATATAAAAA
1 TTAAATTAATTAATTTTATATTAATATTTATATATATAAAAA
600899 TTAAATT
1 TTAAATT
600906 TAAATAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
42 7 0.16
43 6 0.14
44 12 0.28
45 16 0.37
46 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (42 bp):
TTAAATTAATTAATTTTATATTAATATTTATATATATAAAAA
Found at i:600916 original size:44 final size:45
Alignment explanation
Indices: 600826--600917 Score: 102
Period size: 44 Copynumber: 2.1 Consensus size: 45
600816 ATTACTTATA
* *
600826 TTTATATTTATTATTTATAATTAATAAAATATTAAAATAATTAAT
1 TTTATATTTAATATTTATAATTAATAAAATATTAAAATAATAAAT
*
600871 TTTATA-TTAATATTTAT-A-TATATAAAA-ATTAAATTTAAATAAAT
1 TTTATATTTAATATTTATAATTA-ATAAAATATTAAA-AT-AATAAAT
600915 TTT
1 TTT
600918 TTAAATTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
42 8 0.20
43 8 0.20
44 19 0.46
45 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (45 bp):
TTTATATTTAATATTTATAATTAATAAAATATTAAAATAATAAAT
Found at i:600954 original size:23 final size:20
Alignment explanation
Indices: 600917--600960 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 20
600907 AAATAAATTT
*
600917 TTTAAATTATTAAATATTAA
1 TTTAAATTATTAAATAATAA
600937 TTTAAATCTATTTCAAATAATAA
1 TTTAAAT-TA-TT-AAATAATAA
600960 T
1 T
600961 AAAATATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
21 2 0.10
22 2 0.10
23 9 0.45
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTAAATTATTAAATAATAA
Found at i:602641 original size:17 final size:16
Alignment explanation
Indices: 602615--602649 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
602605 ATAAATTTAA
*
602615 TTTTTTTAAACATATT
1 TTTTTTTAAAAATATT
602631 TTTTATTTAAAAATATT
1 TTTT-TTTAAAAATATT
602648 TT
1 TT
602650 AAAATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTTTTAAAAATATT
Found at i:608048 original size:15 final size:16
Alignment explanation
Indices: 608016--608056 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
608006 TGACTTAAAC
608016 CTAAAATGAATTGAAA
1 CTAAAATGAATTGAAA
608032 CTAAAAT-AATTTG-AA
1 CTAAAATGAA-TTGAAA
608047 CTTAAAATGA
1 C-TAAAATGA
608057 CATAAAATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.23
16 16 0.73
17 1 0.05
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.29
Consensus pattern (16 bp):
CTAAAATGAATTGAAA
Found at i:608271 original size:5 final size:5
Alignment explanation
Indices: 608261--608305 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
608251 TTTAAAATAT
*
608261 TTATA TTATA TTAATA TTAT- TT-T- TTATA TTTTA TTATA TTATA TT
1 TTATA TTATA TT-ATA TTATA TTATA TTATA TTATA TTATA TTATA TT
608306 TTAATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 3 0.09
4 3 0.09
5 24 0.69
6 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (5 bp):
TTATA
Found at i:608272 original size:30 final size:29
Alignment explanation
Indices: 608236--608313 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 29
608226 AGTCAATCAT
608236 TTATATTATATA-AATTTTAAAATATTTATA
1 TTATATTATATATAATTTT-AAATATTT-TA
* **
608266 TTATATTA-ATATTATTTTTTATATTTTA
1 TTATATTATATATAATTTTAAATATTTTA
*
608294 TTATATTATATTTTAATTTT
1 TTATATTATA-TATAATTTT
608314 TTATGTTATA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 10 0.25
29 10 0.25
30 20 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
TTATATTATATATAATTTTAAATATTTTA
Found at i:608286 original size:23 final size:22
Alignment explanation
Indices: 608260--608334 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 22
608250 TTTTAAAATA
*
608260 TTTATATTATATTAATATTATTT
1 TTTATATTATATT-ATATTATAT
*
608283 TTTATATTTTATTATATTATAT
1 TTTATATTATATTATATTATAT
* *
608305 TTTA-ATT-TTTTATGTTATAT
1 TTTATATTATATTATATTATAT
*
608325 TTAATATTAT
1 TTTATATTAT
608335 TATATCTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.31
21 6 0.13
22 13 0.29
23 12 0.27
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (22 bp):
TTTATATTATATTATATTATAT
Found at i:608313 original size:28 final size:28
Alignment explanation
Indices: 608257--608335 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
608247 AAATTTTAAA
608257 ATATTTATATTATATTAATATTATTTTTT
1 ATATTT-TATTATATTAATATTATTTTTT
* *
608286 ATATTTTATTATATTATATTTTAATTTTT
1 ATATTTTATTATATTA-ATATTATTTTTT
*
608315 -TATGTTA-TAT-TTAATATTATT
1 ATATTTTATTATATTAATATTATT
608336 ATATCTAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
25 6 0.14
26 3 0.07
27 3 0.07
28 16 0.36
29 16 0.36
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (28 bp):
ATATTTTATTATATTAATATTATTTTTT
Found at i:608317 original size:15 final size:14
Alignment explanation
Indices: 608277--608317 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
608267 TATATTAATA
608277 TTATTTTTTATATT
1 TTATTTTTTATATT
*
608291 TTATTATATTATATT
1 TTATT-TTTTATATT
608306 TTAATTTTTTAT
1 TT-ATTTTTTAT
608318 GTTATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 5 0.22
15 15 0.65
16 3 0.13
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTTTTTATATT
Done.