Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008979.1 Hibiscus syriacus cultivar Beakdansim tig00112339_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1115631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:313418 original size:30 final size:31
Alignment explanation
Indices: 313384--313452 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
313374 CTTCTAAAAC
*
313384 TTGCAATACGAT-TCCCAACATTTAGCCCT-T
1 TTGCAATACGATCCCCCAACATTTAG-CCTGT
* * *
313414 TTGCAATATGGTCCCCCAACATTTAGTCTGT
1 TTGCAATACGATCCCCCAACATTTAGCCTGT
313445 TTGCAATA
1 TTGCAATA
313453 TGGTCTCCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 12 0.36
31 21 0.64
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (31 bp):
TTGCAATACGATCCCCCAACATTTAGCCTGT
Found at i:313435 original size:31 final size:31
Alignment explanation
Indices: 313397--313457 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
313387 CAATACGATT
313397 CCCAACATTTAGCCCT-TTTGCAATATGGTCC
1 CCCAACATTTAG-CCTGTTTGCAATATGGTCC
*
313428 CCCAACATTTAGTCTGTTTGCAATATGGTC
1 CCCAACATTTAGCCTGTTTGCAATATGGTC
313458 TCCGACCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (31 bp):
CCCAACATTTAGCCTGTTTGCAATATGGTCC
Found at i:313746 original size:27 final size:27
Alignment explanation
Indices: 313708--313764 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
313698 TGGAGGTGCT
313708 GACTTGAATAAGGATCCATTGAGAGAA
1 GACTTGAATAAGGATCCATTGAGAGAA
*
313735 GACTTGAATAAGGGTCCATTGAGAGAA
1 GACTTGAATAAGGATCCATTGAGAGAA
313762 GAC
1 GAC
313765 CCGACCAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.21
Consensus pattern (27 bp):
GACTTGAATAAGGATCCATTGAGAGAA
Found at i:313774 original size:27 final size:27
Alignment explanation
Indices: 313717--313775 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
313707 TGACTTGAAT
* ** *
313717 AAGGATCCATTGAGAGAAGACTTGAAT
1 AAGGGTCCATTGAGAGAAGACCCGAAC
*
313744 AAGGGTCCATTGAGAGAAGACCCGACC
1 AAGGGTCCATTGAGAGAAGACCCGAAC
313771 AAGGG
1 AAGGG
313776 ACTATTGGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.17, G:0.31, T:0.15
Consensus pattern (27 bp):
AAGGGTCCATTGAGAGAAGACCCGAAC
Found at i:313782 original size:27 final size:27
Alignment explanation
Indices: 313723--313782 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
313713 GAATAAGGAT
** * *
313723 CCATTGAGAGAAGACTTGAATAAGGGT
1 CCATTGAGAGAAGACCCGAACAAGGGA
*
313750 CCATTGAGAGAAGACCCGACCAAGGGA
1 CCATTGAGAGAAGACCCGAACAAGGGA
*
313777 CTATTG
1 CCATTG
313783 GGACCATCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.18
Consensus pattern (27 bp):
CCATTGAGAGAAGACCCGAACAAGGGA
Found at i:315467 original size:30 final size:31
Alignment explanation
Indices: 315426--315483 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
315416 AACGGTCGGA
315426 GACCATATTGCAAA-CAACTAAATGTTGGGG
1 GACCATATTGCAAATCAACTAAATGTTGGGG
* **
315456 GACCATTTTGCAAATGGACTAAATGTTG
1 GACCATATTGCAAATCAACTAAATGTTG
315484 AGGAATTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (31 bp):
GACCATATTGCAAATCAACTAAATGTTGGGG
Found at i:316735 original size:19 final size:18
Alignment explanation
Indices: 316713--316756 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
316703 ATTTATTTTT
* *
316713 AAAATAAAAATATTTTTAA
1 AAAATAAAAAT-TCTATAA
*
316732 AAAATTAAAATTCTATAA
1 AAAATAAAAATTCTATAA
316750 AAAATAA
1 AAAATAA
316757 TTCATTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATAAAAATTCTATAA
Found at i:319533 original size:11 final size:11
Alignment explanation
Indices: 319517--319541 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
319507 TTTTAATTAA
319517 ATCCTTATTTT
1 ATCCTTATTTT
319528 ATCCTTATTTT
1 ATCCTTATTTT
319539 ATC
1 ATC
319542 TAATAAAAAT
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:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (11 bp):
ATCCTTATTTT
Found at i:321641 original size:20 final size:20
Alignment explanation
Indices: 321599--321641 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
321589 TAAAAAATTG
*
321599 AAAATGAAAACTATCTTCTA
1 AAAATGAAAACTATCTTCCA
*
321619 AAAATAGAAAA-TATTTTCCA
1 AAAAT-GAAAACTATCTTCCA
321639 AAA
1 AAA
321642 CTAAACATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAATGAAAACTATCTTCCA
Found at i:322867 original size:2 final size:2
Alignment explanation
Indices: 322860--322884 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
322850 AGAATAACTT
322860 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 T
322885 TGCAAGGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:326009 original size:18 final size:19
Alignment explanation
Indices: 325964--326010 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
325954 AATAAAATTA
325964 AAAAATATTTTTAGAAATGT
1 AAAAATATTTTTA-AAATGT
* *
325984 -AAATTATTTTT-TAATGT
1 AAAAATATTTTTAAAATGT
326001 AAAAATATTT
1 AAAAATATTT
326011 AGATGGTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 5 0.22
18 8 0.35
19 10 0.43
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (19 bp):
AAAAATATTTTTAAAATGT
Found at i:328122 original size:31 final size:31
Alignment explanation
Indices: 328086--328144 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
328076 AACTTAAAAG
* *
328086 AGTTTTGCAATATTGAGATTTAAATAATTTT
1 AGTTTTACAATATTGAAATTTAAATAATTTT
328117 AGTTTTACAATATTGAAATTTAAATAAT
1 AGTTTTACAATATTGAAATTTAAATAAT
328145 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (31 bp):
AGTTTTACAATATTGAAATTTAAATAATTTT
Found at i:328195 original size:22 final size:22
Alignment explanation
Indices: 328169--328211 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
328159 TAATAAATTA
328169 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
328191 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
328212 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:328220 original size:22 final size:22
Alignment explanation
Indices: 328171--328219 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
328161 ATAAATTATT
**
328171 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
328193 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
328216 TAAA
1 TAAA
328220 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:328223 original size:54 final size:54
Alignment explanation
Indices: 328159--328903 Score: 528
Period size: 54 Copynumber: 13.4 Consensus size: 54
328149 ACAACTACAA
328159 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*** * * *
328213 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATAC
328266 T-AT--A-T-TTTAAAATAAATCAATCCATATAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCC-----AT--A-T-TTTAAAATAAATCAATCCATAC
328324 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * **
328378 TAATAAATTATTTAAAATGAATCAATCCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** ** *
328435 TTTTAAAATAAAT-CAATCCATACAAATAAAT-TATTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
328490 TAATAAATTATTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAA-TC---C--AT--A-T-TTTAAAATAAATCAATCCATAC
** * ** * ** **
328553 TTTTAAAATAAAT-CAATCCATACAAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
328608 TAATAAATTATTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCCATAC
** * ** * ** **
328671 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
*
328726 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
328774 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
328828 TAATAAATTATTTAAAACAAATCAATCCATATTTTAAAATAAATCAATCCATAA
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
328882 TAATAAATTATTTAAAATAAAT
1 TAATAAATTATTTAAAATAAAT
328904 TATTTTAAAA
Statistics
Matches: 545, Mismatches: 85, Indels: 122
0.72 0.11 0.16
Matches are distributed among these distances:
48 48 0.09
49 5 0.01
50 7 0.01
51 1 0.00
52 3 0.01
53 5 0.01
54 267 0.49
55 32 0.06
56 21 0.04
57 22 0.04
58 29 0.05
59 2 0.00
60 4 0.01
61 1 0.00
62 11 0.02
63 37 0.07
64 50 0.09
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:328229 original size:32 final size:32
Alignment explanation
Indices: 328191--328903 Score: 559
Period size: 32 Copynumber: 25.4 Consensus size: 32
328181 CAATCCATAT
328191 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
328223 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* **
328253 --T--AATAAATCAATCTATA-TTTTAAA--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
328278 -------TAAATCAATCCATA-TAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
328302 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
328334 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
328356 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
328388 TTTAAAATGAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
328418 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
328436 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
328468 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
328500 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
328532 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
328554 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
328586 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
328618 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
328650 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
328672 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
328704 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
328734 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
328752 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
328784 TTTAAAATAAATCAAT---T-C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
328806 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
328838 TTTAAAACAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
328860 TTTAAAATAAATCAATCCATAATAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
328892 TTTAAAATAAAT
1 TTTAAAATAAAT
328904 TATTTTAAAA
Statistics
Matches: 565, Mismatches: 22, Indels: 188
0.73 0.03 0.24
Matches are distributed among these distances:
20 2 0.00
22 125 0.22
23 11 0.02
24 10 0.02
25 6 0.01
26 58 0.10
28 18 0.03
29 1 0.00
30 8 0.01
31 29 0.05
32 297 0.53
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:328264 original size:80 final size:80
Alignment explanation
Indices: 328174--328489 Score: 510
Period size: 80 Copynumber: 3.9 Consensus size: 80
328164 AATTATTTAA
328174 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
328239 CCATACAACTACAAT
66 CCATACAACTACAAT
*
328254 AATAAATCAATCTATATTTTAAAATAAATCAATCCATA-TAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
328318 CCATACTAA-TAAATTATTT
66 CCATAC-AACTACA--A--T
*
328337 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATGAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
328402 ATCCATACAACTACAAT
64 ATCCATACAACTACAAT
*
328419 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
328484 CTATAC
66 CCATAC
328490 TAATAAATTA
Statistics
Matches: 219, Mismatches: 8, Indels: 18
0.89 0.03 0.07
Matches are distributed among these distances:
79 35 0.16
80 107 0.49
81 1 0.00
82 1 0.00
83 1 0.00
84 1 0.00
85 39 0.18
86 34 0.16
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:328298 original size:22 final size:22
Alignment explanation
Indices: 328225--328298 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 22
328215 ATAAATTATT
*
328225 TAAAATAAATCAATCCATACAA
1 TAAAATAAATCAATCCATATAA
* **
328247 CTACAATAATAAATCAATCTATATTT
1 -T--AA-AATAAATCAATCCATATAA
328273 TAAAATAAATCAATCCATATAA
1 TAAAATAAATCAATCCATATAA
328295 TAAA
1 TAAA
328299 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
22 20 0.49
23 3 0.07
25 3 0.07
26 15 0.37
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:328360 original size:22 final size:22
Alignment explanation
Indices: 328334--328376 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
328324 TAATAAATTA
328334 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
328356 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
328377 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:328385 original size:22 final size:22
Alignment explanation
Indices: 328336--328384 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
328326 ATAAATTATT
**
328336 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
328358 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
328381 TAAA
1 TAAA
328385 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:328475 original size:14 final size:14
Alignment explanation
Indices: 328458--328543 Score: 64
Period size: 14 Copynumber: 5.6 Consensus size: 14
328448 CAATCCATAC
328458 AAATAAATTATTTA
1 AAATAAATTATTTA
*
328472 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
328489 CTAATAAATTATTTA
1 -AAATAAATTATTTA
*
328504 AAATAAATCAATTCATA
1 AAATAAAT-TATT--TA
*
328521 CTAATAAATTATTTA
1 -AAATAAATTATTTA
328536 AAATAAAT
1 AAATAAAT
328544 CAATCCATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
14 22 0.39
15 9 0.16
16 2 0.04
17 9 0.16
18 14 0.25
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:328558 original size:22 final size:22
Alignment explanation
Indices: 328532--328574 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
328522 TAATAAATTA
328532 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
328554 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
328575 CAAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:328567 original size:86 final size:86
Alignment explanation
Indices: 328468--328858 Score: 469
Period size: 86 Copynumber: 4.6 Consensus size: 86
328458 AAATAAATTA
* *
328468 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATTCATACTAATAAATTAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTAT
328533 TTAAAATAAATCAATCCATAT
66 TTAAAATAAATCAATCCATAT
*
328554 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTAT
*
328619 TTAAAATAAATCAATCCATACA
66 TTAAAATAAATCAATCCATA-T
** * ** * ** **
328641 AATAAATTATTTAAAATAAAT-C-AATCCA-TATTTTAAAATAAATCAATCCATACTAATAAATT
1 TTTAAAATAAAT-CAATCCATACTAATAAATTA-TTTAAAATAAATCAATCCATACTAATAAATT
*
328703 ATTTAAAATAAATCAATCCATACA
64 ATTTAAAATAAATCAATCCATA-T
** * * * *
328727 ACTACAAT-AATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTAT
*
328785 TTAAAATAAATCAATTCATAT
66 TTAAAATAAATCAATCCATAT
*
328806 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAACAAATCAATCCATA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
328859 TTTTAAAATA
Statistics
Matches: 265, Mismatches: 30, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
79 5 0.02
80 61 0.23
81 1 0.00
82 4 0.02
84 11 0.04
85 4 0.02
86 166 0.63
87 8 0.03
88 5 0.02
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (86 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATCCATAT
Found at i:328583 original size:22 final size:22
Alignment explanation
Indices: 328534--328582 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
328524 ATAAATTATT
***
328534 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATAAAA
328556 TAAAATAAATCAATCCATACAAA
1 TAAAATAAATCAATCCATA-AAA
328579 TAAA
1 TAAA
328583 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATAAAA
Found at i:328676 original size:22 final size:22
Alignment explanation
Indices: 328650--328692 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
328640 AAATAAATTA
328650 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
328672 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
328693 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:328701 original size:22 final size:22
Alignment explanation
Indices: 328652--328700 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
328642 ATAAATTATT
**
328652 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
328674 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
328697 TAAA
1 TAAA
328701 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:328757 original size:316 final size:305
Alignment explanation
Indices: 328160--328903 Score: 1198
Period size: 316 Copynumber: 2.4 Consensus size: 305
328150 CAACTACAAT
*
328160 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
1 AATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
*** * * * *
328225 TAAAATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C---TATA-T-TTTAAAATAAAT
66 TAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAAT
*
328283 CAATCCATATAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
130 CAATCCATATAATAAATTATTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCA
*
328348 ATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATGAATCAATCCATACAAC
195 ATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAAC
328413 TACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACA
260 TACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACA
*
328459 AATAAATTATTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATTCATACTA
1 AATAAATTATTTAAAATAAATCAA--T-T-C--AT--A-T-TTTAAAATAAATCAATCCATACTA
328524 ATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTT
56 ATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTT
328589 AAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAAATAAATTATTTA
121 AAAATAAATCAATCCATA-TAATAAATTATTTAAAATAAATCAATCCATACAAATAAATTATTTA
328654 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
185 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
*
328719 TCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACT
250 TCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACA
328775 AATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
1 AATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
*
328840 TAAAACAAATCAATCCATATTTTAAAATAAATCAATCCATA-ATAATAAATTATTTAAAATAAAT
66 TAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACA-AATAAATTATTTAAAATAAAT
328904 TATTTTAAAA
Statistics
Matches: 412, Mismatches: 14, Indels: 31
0.90 0.03 0.07
Matches are distributed among these distances:
299 24 0.06
301 1 0.00
303 1 0.00
305 3 0.01
306 94 0.23
307 2 0.00
308 7 0.02
309 61 0.15
310 3 0.01
312 1 0.00
313 4 0.01
314 2 0.00
315 21 0.05
316 188 0.46
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (305 bp):
AATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
TAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATC
AATCCATATAATAAATTATTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAA
TCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACT
ACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACA
Found at i:328781 original size:22 final size:23
Alignment explanation
Indices: 328706--328780 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
328696 ATAAATTATT
328706 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
328728 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
328754 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
328777 TAAA
1 TAAA
328781 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:328810 original size:22 final size:22
Alignment explanation
Indices: 328784--328826 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
328774 TAATAAATTA
*
328784 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
328806 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
328827 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:328835 original size:22 final size:22
Alignment explanation
Indices: 328786--328834 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
328776 ATAAATTATT
* **
328786 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
328808 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
328831 TAAA
1 TAAA
328835 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:328912 original size:15 final size:15
Alignment explanation
Indices: 328883--329101 Score: 215
Period size: 15 Copynumber: 13.5 Consensus size: 15
328873 AATCCATAAT
328883 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
328897 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
328912 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
328934 AATAATTTATTTTAA
1 AATAAATTATTTTAA
328949 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
328964 AATAAATAACCTTATTAA
1 AATAAATTA--TT-TTAA
328982 ATTATTTAAAATTATTTTAA
1 A--A--T-AAATTATTTTAA
* *
329002 AATTAATCCATATTTTAT
1 AATAAAT---TATTTTAA
*
329020 AATAAATTATTTTAT
1 AATAAATTATTTTAA
329035 AATAAATTATTTTAA
1 AATAAATTATTTTAA
329050 AATAAATTATTTTAA
1 AATAAATTATTTTAA
329065 AATAAATTATTTTAA
1 AATAAATTATTTTAA
329080 AATAAATTATTTTAA
1 AATAAATTATTTTAA
329095 AATAAAT
1 AATAAAT
329102 AACCTTATTA
Statistics
Matches: 176, Mismatches: 10, Indels: 37
0.79 0.04 0.17
Matches are distributed among these distances:
14 9 0.05
15 114 0.65
16 1 0.01
17 3 0.02
18 21 0.12
19 3 0.02
20 7 0.04
21 2 0.01
22 11 0.06
23 5 0.03
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:328929 original size:22 final size:22
Alignment explanation
Indices: 328838--328938 Score: 85
Period size: 22 Copynumber: 4.5 Consensus size: 22
328828 TAATAAATTA
*
328838 TTTAAAACAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
328860 TTTAAAATAAATCAATCCATAAT
1 TTTAAAATAAATCAATCCAT-AT
** * ** * **
328883 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCCA-TAT
328907 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
328929 TTTATAATAA
1 TTTAAAATAA
328939 TTTATTTTAA
Statistics
Matches: 58, Mismatches: 18, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
22 31 0.53
23 13 0.22
24 13 0.22
25 1 0.02
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:328953 original size:69 final size:66
Alignment explanation
Indices: 328829--328970 Score: 178
Period size: 69 Copynumber: 2.1 Consensus size: 66
328819 AATCCATACT
328829 AATAAATTATTTAAAACAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATAAATTA-T
1 AATAAATTATTTAAAACAAATCAATCCATATTTTAAAATAAATCAATCC--AA-AATAAATTATT
328893 TTAA
63 TTAA
* * * * * **
328897 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAATTATTTT
1 AATAAATTA-TTTAAAACAAATCAATCCATATTTTAAAATAAATCAATCCAAAATAAATTATTTT
328962 AA
65 AA
328964 AATAAAT
1 AATAAAT
328971 AACCTTATTA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
66 9 0.14
67 14 0.22
68 9 0.14
69 33 0.51
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (66 bp):
AATAAATTATTTAAAACAAATCAATCCATATTTTAAAATAAATCAATCCAAAATAAATTATTTTA
A
Found at i:337649 original size:22 final size:20
Alignment explanation
Indices: 337599--337661 Score: 56
Period size: 23 Copynumber: 2.9 Consensus size: 20
337589 ACATTACCTC
337599 AATTTGTTTGATTCTGATTG
1 AATTTGTTTGATTCTGATTG
*
337619 GATTCTGTTCTG-TATCTGATCTG
1 AATT-TGTT-TGAT-TCTGAT-TG
337642 AATTTGTTTTGATTTCTGAT
1 AATTTG-TTTGA-TTCTGAT
337662 ATCTCTGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
20 3 0.09
21 5 0.15
22 12 0.35
23 13 0.38
24 1 0.03
ACGTcount: A:0.17, C:0.10, G:0.19, T:0.54
Consensus pattern (20 bp):
AATTTGTTTGATTCTGATTG
Found at i:339140 original size:19 final size:20
Alignment explanation
Indices: 339053--339141 Score: 92
Period size: 19 Copynumber: 4.3 Consensus size: 20
339043 CGTGATTTTA
339053 AAAAATGTGTTGCGATAGT-
1 AAAAATGTGTTGCGATAGTG
* * *
339072 TAAAATGTGTCGCGAGAGTTTG
1 AAAAATGTGTTGCGATAG--TG
339094 AAAAACGTGTTGTTGCGATAGTG
1 AAAAA--TG-TGTTGCGATAGTG
339117 AAAAA-GTGTTGCGATAGTG
1 AAAAATGTGTTGCGATAGTG
339136 AAAAAT
1 AAAAAT
339142 CCAAAATAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
19 33 0.58
20 1 0.02
21 1 0.02
22 4 0.07
23 7 0.12
24 2 0.04
25 9 0.16
ACGTcount: A:0.36, C:0.07, G:0.28, T:0.29
Consensus pattern (20 bp):
AAAAATGTGTTGCGATAGTG
Found at i:339310 original size:49 final size:49
Alignment explanation
Indices: 339249--339408 Score: 214
Period size: 49 Copynumber: 3.2 Consensus size: 49
339239 TAAGATCTTA
*
339249 GTTTGAAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCTCAAGT
1 GTTTGCAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCTCAAGT
** *
339298 GTTTGCCTCAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCCCACA-T
1 GTTTGCAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCTCA-AGT
*
339347 AAGATAGTTGAAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCTCAAGT
1 --G-T--TTGCAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCTCAAGT
339401 GTTTGCAA
1 GTTTGCAA
339409 TGCTCAATCC
Statistics
Matches: 95, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
49 48 0.51
50 1 0.01
51 2 0.02
52 2 0.02
53 1 0.01
54 41 0.43
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.30
Consensus pattern (49 bp):
GTTTGCAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCTCAAGT
Found at i:339544 original size:6 final size:6
Alignment explanation
Indices: 339533--339559 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
339523 TCCCGTCTCG
339533 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
339560 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:339657 original size:19 final size:20
Alignment explanation
Indices: 339619--339659 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
339609 TTCTTAAGAA
339619 ATCGCAACGTGAACTTGGACT
1 ATCGCAACG-GAACTTGGACT
*
339640 ATCGCAAC-GAATTTGGACT
1 ATCGCAACGGAACTTGGACT
339659 A
1 A
339660 ACGTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
21 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (20 bp):
ATCGCAACGGAACTTGGACT
Found at i:339740 original size:20 final size:20
Alignment explanation
Indices: 339717--339816 Score: 96
Period size: 20 Copynumber: 5.0 Consensus size: 20
339707 ATAGTTAGAA
*
339717 TCGCATTACGATTTACATAT
1 TCGCATTGCGATTTACATAT
* *
339737 TCGCATTGCGATAGT-CAAAT
1 TCGCATTGCGAT-TTACATAT
*
339757 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* * *
339777 TCGCATTGCGATAGT-CAAAC
1 TCGCATTGCGAT-TTACATAT
*
339797 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
339817 ACTGATTTGC
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
19 2 0.03
20 58 0.94
21 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:339747 original size:40 final size:40
Alignment explanation
Indices: 339697--339816 Score: 179
Period size: 40 Copynumber: 3.0 Consensus size: 40
339687 TTTTGTATTA
* * * *
339697 TCGCGTTGCGATAGTTAGAA-TCGCATTACGATTTACATAT
1 TCGCATTGCGATAGTCA-AACTCGCGTTGCGATTTACATAT
*
339737 TCGCATTGCGATAGTCAAATTCGCGTTGCGATTTACATAT
1 TCGCATTGCGATAGTCAAACTCGCGTTGCGATTTACATAT
339777 TCGCATTGCGATAGTCAAACTCGCGTTGCGATTTACATAT
1 TCGCATTGCGATAGTCAAACTCGCGTTGCGATTTACATAT
339817 ACTGATTTGC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
39 2 0.03
40 72 0.97
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (40 bp):
TCGCATTGCGATAGTCAAACTCGCGTTGCGATTTACATAT
Found at i:344298 original size:24 final size:24
Alignment explanation
Indices: 344271--344355 Score: 98
Period size: 24 Copynumber: 3.5 Consensus size: 24
344261 TATATCAAAA
* * *
344271 ATCAAAACATAATTCAGGTCAAGT
1 ATCATAACAGAATCCAGGTCAAGT
* * *
344295 ATCAGATCAGAATCCAGGTCAAAT
1 ATCATAACAGAATCCAGGTCAAGT
* *
344319 ATCATATCAGAATCCAGGTCAGGT
1 ATCATAACAGAATCCAGGTCAAGT
344343 ATCATAACAGAAT
1 ATCATAACAGAAT
344356 TCAAATCGGA
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCATAACAGAATCCAGGTCAAGT
Found at i:348920 original size:24 final size:24
Alignment explanation
Indices: 348893--348950 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
348883 AACGGATATA
* *
348893 TCAAAAATCAAAACATAATTCAGG
1 TCAAATATCAAAACATAATCCAGG
* * *
348917 TCAAGTATCAGATCATAATCCAGG
1 TCAAATATCAAAACATAATCCAGG
348941 TCAAATATCA
1 TCAAATATCA
348951 TATCAGTATC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.47, C:0.19, G:0.10, T:0.24
Consensus pattern (24 bp):
TCAAATATCAAAACATAATCCAGG
Found at i:348955 original size:24 final size:24
Alignment explanation
Indices: 348906--348964 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
348896 AAAATCAAAA
* *
348906 CATAATTCAGGTCAAGTATCAGAT
1 CATAATCCAGGTCAAATATCAGAT
*
348930 CATAATCCAGGTCAAATATCATAT
1 CATAATCCAGGTCAAATATCAGAT
348954 CAGT-ATCCAGG
1 CA-TAATCCAGG
348965 CCAGGTATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 30 0.97
25 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (24 bp):
CATAATCCAGGTCAAATATCAGAT
Found at i:353601 original size:24 final size:24
Alignment explanation
Indices: 353574--353658 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
353564 TATATCAAAA
* * *
353574 ATCAAAACATAATTCAGGTCAAGT
1 ATCAGAACAGAATCCAGGTCAAGT
* * * *
353598 ATCAGATCATAATCCAAGTCAAAT
1 ATCAGAACAGAATCCAGGTCAAGT
* * *
353622 GTCAGATCAGAATCCAGGTCAGGT
1 ATCAGAACAGAATCCAGGTCAAGT
*
353646 ATCATAACAGAAT
1 ATCAGAACAGAAT
353659 TCAAATCTAA
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAGAACAGAATCCAGGTCAAGT
Found at i:358174 original size:2 final size:2
Alignment explanation
Indices: 358167--358224 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
358157 TTATTGATTC
358167 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
358209 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
358225 CAATTAACAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:369173 original size:90 final size:89
Alignment explanation
Indices: 369021--369193 Score: 283
Period size: 90 Copynumber: 1.9 Consensus size: 89
369011 ACATACCCTT
369021 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
* *
369086 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
* * * *
369110 TTATATCCAAGTTACCCTAATCTTATTGGGGATTTTATTATTTCAAATTAATTAAATTTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
369175 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
369194 TTCGGGATTA
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 28 0.36
90 49 0.64
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:376166 original size:15 final size:15
Alignment explanation
Indices: 376146--376177 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
376136 AAAATATTTC
*
376146 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
376161 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
376176 TT
1 TT
376178 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:381609 original size:31 final size:32
Alignment explanation
Indices: 381574--381634 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
381564 AGTCTATGCG
* *
381574 GCCCTGAGAT-CATTCTCGGGTAGGCCCCGCA
1 GCCCTAAGATGCATTCTCAGGTAGGCCCCGCA
* *
381605 GCCCTAAGATGTATTCTTAGGTAGGCCCCG
1 GCCCTAAGATGCATTCTCAGGTAGGCCCCG
381635 TGGCCCCGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 9 0.36
32 16 0.64
ACGTcount: A:0.18, C:0.31, G:0.28, T:0.23
Consensus pattern (32 bp):
GCCCTAAGATGCATTCTCAGGTAGGCCCCGCA
Found at i:383830 original size:2 final size:2
Alignment explanation
Indices: 383823--383872 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
383813 GAGTCAAATA
383823 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
383865 AT AT AT AT
1 AT AT AT AT
383873 CTCATTAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:383957 original size:25 final size:25
Alignment explanation
Indices: 383915--383994 Score: 124
Period size: 25 Copynumber: 3.2 Consensus size: 25
383905 GCGGGACTTT
383915 GAAAAGAAAATTTTAAAAGTGTTGTA
1 GAAAAG-AAATTTTAAAAGTGTTGTA
* *
383941 GAAAAGAATTTTTAAAAGTGTAGTA
1 GAAAAGAAATTTTAAAAGTGTTGTA
*
383966 GAAAAGAACTTTTAAAAGTGTTGTA
1 GAAAAGAAATTTTAAAAGTGTTGTA
383991 GAAA
1 GAAA
383995 TATTAGAGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 44 0.88
26 6 0.12
ACGTcount: A:0.49, C:0.01, G:0.20, T:0.30
Consensus pattern (25 bp):
GAAAAGAAATTTTAAAAGTGTTGTA
Found at i:384367 original size:23 final size:24
Alignment explanation
Indices: 384341--384392 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
384331 ATATATATAT
384341 ATATATATTATAAATAAAT-TGAA
1 ATATATATTATAAATAAATATGAA
* * *
384364 ATATA-ATTATTATTATATATGAA
1 ATATATATTATAAATAAATATGAA
384387 ATATAT
1 ATATAT
384393 CAATTTAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (24 bp):
ATATATATTATAAATAAATATGAA
Found at i:384961 original size:10 final size:11
Alignment explanation
Indices: 384938--384962 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
384928 TTTAGGTATC
384938 TTTTGAATATT
1 TTTTGAATATT
384949 TTTTGAATATT
1 TTTTGAATATT
384960 TTT
1 TTT
384963 AGAAACAAGA
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTGAATATT
Found at i:388047 original size:2 final size:2
Alignment explanation
Indices: 388040--388072 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
388030 TCTTAAAAGA
388040 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
388073 CACAAGCATG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:395636 original size:21 final size:21
Alignment explanation
Indices: 395562--395636 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
395552 AGATACAGTG
* * *
395562 GGTATCTATACTGGATAAACT
1 GGTATCCATACTAGATGAACT
* * **
395583 GGTGTCCATACCAGATGAGTT
1 GGTATCCATACTAGATGAACT
395604 GGTATCCATACTAGATGAACT
1 GGTATCCATACTAGATGAACT
*
395625 GATATCCATACT
1 GGTATCCATACT
395637 GAAGACTTGA
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (21 bp):
GGTATCCATACTAGATGAACT
Found at i:395649 original size:20 final size:21
Alignment explanation
Indices: 395606--395655 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
395596 GATGAGTTGG
*
395606 TATCCATACTAGATGAACTGA
1 TATCCATACTAGAAGAACTGA
395627 TATCCATACT-GAAG-ACTTGA
1 TATCCATACTAGAAGAAC-TGA
*
395647 TATCAATAC
1 TATCCATAC
395656 CCAAAGTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 14 0.54
21 10 0.38
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (21 bp):
TATCCATACTAGAAGAACTGA
Found at i:397624 original size:3 final size:3
Alignment explanation
Indices: 397616--397640 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
397606 GGAATAAAAG
397616 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
397641 TACTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:398414 original size:19 final size:19
Alignment explanation
Indices: 398386--398424 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
398376 ATTTATATTA
*
398386 TATTTGTATA-TATAATTTT
1 TATTTATATATTAT-ATTTT
398405 TATTTATATATTATATTTT
1 TATTTATATATTATATTTT
398424 T
1 T
398425 TTATTCTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
TATTTATATATTATATTTT
Found at i:398470 original size:17 final size:17
Alignment explanation
Indices: 398377--398470 Score: 51
Period size: 17 Copynumber: 5.8 Consensus size: 17
398367 TTCATTATTA
398377 TTTATATTATAT-TTG-
1 TTTATATTATATATTGT
* * * *
398392 TATATATAAT-TTTTAT
1 TTTATATTATATATTGT
398408 TTATATATTATAT-TT-T
1 TT-TATATTATATATTGT
398424 TTTAT-TCT-TATATTG-
1 TTTATAT-TATATATTGT
* *
398439 TTAATATGTAAATATTGT
1 TTTATAT-TATATATTGT
398457 TTTATATTATATAT
1 TTTATATTATATAT
398471 ATACACACAC
Statistics
Matches: 59, Mismatches: 10, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
14 5 0.08
15 20 0.34
16 6 0.10
17 21 0.36
18 7 0.12
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (17 bp):
TTTATATTATATATTGT
Found at i:402154 original size:2 final size:2
Alignment explanation
Indices: 402147--402208 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
402137 TAAGTTTTTC
402147 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
402189 AT AT -T AT AT -T AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
402209 ACTTTTACGT
Statistics
Matches: 57, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.05
2 54 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:402279 original size:51 final size:49
Alignment explanation
Indices: 402164--402280 Score: 112
Period size: 51 Copynumber: 2.3 Consensus size: 49
402154 TATATATATA
* *
402164 TATATATATATATATATATATATATATATTATATTATATTATATAACTTT
1 TATAT-TATTTATATATATATATATATATTATATTATATCATATAACTTT
* * *
402214 TACGTATTCA-TTATATATATATATATATTTTATATTTTATCATTCATTA-TTAT
1 TA--TATT-ATTTATATATATATATATATATTATATTATATCA-T-ATAACTT-T
402267 TATATTATTTATAT
1 TATATTATTTATAT
402281 TATTTTTGTA
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
50 3 0.05
51 39 0.71
52 7 0.13
53 6 0.11
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.56
Consensus pattern (49 bp):
TATATTATTTATATATATATATATATATTATATTATATCATATAACTTT
Found at i:402296 original size:26 final size:24
Alignment explanation
Indices: 402261--402330 Score: 63
Period size: 26 Copynumber: 2.8 Consensus size: 24
402251 TATCATTCAT
402261 TATTAT-TATATTATTTATATTAT-
1 TATTATATATATTATTTAT-TTATC
* * *
402284 TTTTGTATATATAACTTTTATTTATC
1 TATTATATATATTA--TTTATTTATC
402310 TATTATATATATTTATTTATT
1 TATTATATATA-TTATTTATT
402331 CTTATATTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
23 4 0.11
24 6 0.17
25 10 0.28
26 14 0.39
27 2 0.06
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (24 bp):
TATTATATATATTATTTATTTATC
Found at i:402338 original size:25 final size:25
Alignment explanation
Indices: 402237--402338 Score: 60
Period size: 25 Copynumber: 4.2 Consensus size: 25
402227 TATATATATA
* *
402237 TATATTTTATAT-TTTA-TCATTCAT
1 TATATTATATATATTTATTTATTC-T
*
402261 TATTATTATAT-TATTTATATTATTTT
1 TA-TATTATATATATTTAT-TTATTCT
*
402287 TGTA-TATATA-ACTTTTATTTA-TC-
1 TATATTATATATA--TTTATTTATTCT
402310 --TATTATATATATTTATTTATTCT
1 TATATTATATATATTTATTTATTCT
402333 TATATT
1 TATATT
402339 GTTAATATGT
Statistics
Matches: 60, Mismatches: 5, Indels: 25
0.67 0.06 0.28
Matches are distributed among these distances:
21 10 0.17
22 8 0.13
23 1 0.02
24 10 0.17
25 20 0.33
26 7 0.12
27 4 0.07
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (25 bp):
TATATTATATATATTTATTTATTCT
Found at i:403215 original size:3 final size:3
Alignment explanation
Indices: 403207--403231 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
403197 CAAACGTTAC
403207 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
403232 ACATTATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:406221 original size:60 final size:60
Alignment explanation
Indices: 406123--406243 Score: 181
Period size: 60 Copynumber: 2.0 Consensus size: 60
406113 AATTCAGGTA
* * * * *
406123 CGCTTTTTAGAAAAATAATAATGTTTAGGGGTCAAAATG-TCGAAATGTGAGAAGTGCTGT
1 CGCTATTTAGAAAAATAATAATCTTTAGAGGTCAAAATGCT-GAAATGAGAGAAGTACTGT
406183 CGCTATTTAGAAAAATAATAATCTTTAGAGGTCAAAATGCTGAAATGAGAGAAGTACTGT
1 CGCTATTTAGAAAAATAATAATCTTTAGAGGTCAAAATGCTGAAATGAGAGAAGTACTGT
406243 C
1 C
406244 TTAGATAGAC
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 54 0.98
61 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (60 bp):
CGCTATTTAGAAAAATAATAATCTTTAGAGGTCAAAATGCTGAAATGAGAGAAGTACTGT
Found at i:417061 original size:20 final size:20
Alignment explanation
Indices: 417000--417139 Score: 183
Period size: 20 Copynumber: 6.8 Consensus size: 20
416990 AGGGTGTCAA
417000 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
417021 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
417042 AGTGCATCCATGCACCCTGC
1 AGTGCATCCATGCACCCTGC
*
417062 AATGCATCCATGCACCCTGC
1 AGTGCATCCATGCACCCTGC
417082 AGTGCATCCATGCA-CCTGCCAC
1 AGTGCATCCATGCACCCTG---C
* * *
417104 TAGTGCATCAATGCACCATGT
1 -AGTGCATCCATGCACCCTGC
417125 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
417140 TCCATTTCGA
Statistics
Matches: 108, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.04
20 52 0.48
21 35 0.32
22 1 0.01
23 13 0.12
24 3 0.03
ACGTcount: A:0.23, C:0.38, G:0.19, T:0.21
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:417202 original size:21 final size:21
Alignment explanation
Indices: 417159--417202 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
417149 AATGAAATTA
* **
417159 GTGCATCGATGCACCCTGCCT
1 GTGCATCCATGCACCAAGCCT
*
417180 GTGCATCCATGCACCAAGGCT
1 GTGCATCCATGCACCAAGCCT
417201 GT
1 GT
417203 AACAGCTAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.18, C:0.34, G:0.25, T:0.23
Consensus pattern (21 bp):
GTGCATCCATGCACCAAGCCT
Found at i:420276 original size:21 final size:21
Alignment explanation
Indices: 420231--420347 Score: 165
Period size: 21 Copynumber: 5.9 Consensus size: 21
420221 TATATTTTCC
420231 AACAATTGGTATC--TTT-TT
1 AACAATTGGTATCTTTTTGTT
* *
420249 AATAATTGATATCTTTTTGTT
1 AACAATTGGTATCTTTTTGTT
420270 AACAATTGGTATCTTTTTGTT
1 AACAATTGGTATCTTTTTGTT
420291 AACAATTGGTATC--TTT-TT
1 AACAATTGGTATCTTTTTGTT
*
420309 AACAATTGATATCTTTTTGTT
1 AACAATTGGTATCTTTTTGTT
420330 AACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTT
420348 CATTAAACAT
Statistics
Matches: 87, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
18 25 0.29
19 3 0.03
20 6 0.07
21 53 0.61
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.52
Consensus pattern (21 bp):
AACAATTGGTATCTTTTTGTT
Found at i:420285 original size:39 final size:36
Alignment explanation
Indices: 420231--420347 Score: 117
Period size: 39 Copynumber: 3.0 Consensus size: 36
420221 TATATTTTCC
*
420231 AACAATTGGTATCTTTTTAATAATTGATATCTTTTTGTT
1 AACAATTGGTATCTTTTTAACAATTGATATC--TTT-TT
*
420270 AACAATTGGTATCTTTTTGTTAACAATTGGTATCTTTTT
1 AACAATTGGTATC--TTT-TTAACAATTGATATCTTTTT
* *
420309 AACAATTGATATCTTTTTGTTAACAATTGGTATCTTTTT
1 AACAATTGGTATC--TTT-TTAACAATTGATATCTTTTT
420348 CATTAAACAT
Statistics
Matches: 72, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
39 53 0.74
40 3 0.04
41 3 0.04
42 13 0.18
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.52
Consensus pattern (36 bp):
AACAATTGGTATCTTTTTAACAATTGATATCTTTTT
Found at i:420298 original size:60 final size:60
Alignment explanation
Indices: 420231--420347 Score: 225
Period size: 60 Copynumber: 1.9 Consensus size: 60
420221 TATATTTTCC
*
420231 AACAATTGGTATCTTTTTAATAATTGATATCTTTTTGTTAACAATTGGTATCTTTTTGTT
1 AACAATTGGTATCTTTTTAACAATTGATATCTTTTTGTTAACAATTGGTATCTTTTTGTT
420291 AACAATTGGTATCTTTTTAACAATTGATATCTTTTTGTTAACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTTAACAATTGATATCTTTTTGTTAACAATTGGTATCTTTTT
420348 CATTAAACAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.52
Consensus pattern (60 bp):
AACAATTGGTATCTTTTTAACAATTGATATCTTTTTGTTAACAATTGGTATCTTTTTGTT
Found at i:420438 original size:18 final size:19
Alignment explanation
Indices: 420409--420460 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
420399 TTTTGTTATA
420409 TCAAAAAGGGGGAGATTGT
1 TCAAAAAGGGGGAGATTGT
420428 TCAAAAAGGGGGAGATTGT
1 TCAAAAAGGGGGAGATTGT
420447 TCAAAAAGGGGGAG
1 TCAAAAAGGGGGAG
420461 CTTAACATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.38, C:0.06, G:0.38, T:0.17
Consensus pattern (19 bp):
TCAAAAAGGGGGAGATTGT
Found at i:420524 original size:21 final size:21
Alignment explanation
Indices: 420500--420540 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
420490 TGGTATATTT
420500 TTAACAATTGATATCCTTTTG
1 TTAACAATTGATATCCTTTTG
* *
420521 TTAACAATTGGTATCTTTTT
1 TTAACAATTGATATCCTTTT
420541 CATTGAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (21 bp):
TTAACAATTGATATCCTTTTG
Found at i:422587 original size:15 final size:15
Alignment explanation
Indices: 422547--422581 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
422537 TAAAGAAGAA
* *
422547 TAGACCATATAATAG
1 TAGACCAGATAACAG
422562 TAGACCAGATAACAG
1 TAGACCAGATAACAG
422577 TAGAC
1 TAGAC
422582 TTGATAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (15 bp):
TAGACCAGATAACAG
Found at i:429158 original size:30 final size:30
Alignment explanation
Indices: 429118--429272 Score: 143
Period size: 30 Copynumber: 5.2 Consensus size: 30
429108 CAAACACATG
* * *
429118 AGGACCAAAATAGCAAAAATGGAAACTTAA
1 AGGACTAAAATAGAAAAAATAGAAACTTAA
*
429148 AGGACTAAAATAGAAAAAACCA-AAACTTAA
1 AGGACTAAAATAGAAAAAA-TAGAAACTTAA
* * *
429178 AGGACTAAAATGGCATAAAA-AGAAATTTAA
1 AGGACTAAAATAG-AAAAAATAGAAACTTAA
* *
429208 AGGAATAAAATGGAAAAAATAGAAACTTAA
1 AGGACTAAAATAGAAAAAATAGAAACTTAA
* * * * * *
429238 AGGGCTAAAACAGTAAAAACAAAAACTGAA
1 AGGACTAAAATAGAAAAAATAGAAACTTAA
429268 AGGAC
1 AGGAC
429273 CTAATAAACA
Statistics
Matches: 102, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
29 6 0.06
30 91 0.89
31 5 0.05
ACGTcount: A:0.59, C:0.10, G:0.16, T:0.14
Consensus pattern (30 bp):
AGGACTAAAATAGAAAAAATAGAAACTTAA
Found at i:435517 original size:21 final size:21
Alignment explanation
Indices: 435491--435530 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
435481 CCCCCTTTGA
*
435491 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
435512 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
435531 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:440866 original size:131 final size:130
Alignment explanation
Indices: 440692--440958 Score: 344
Period size: 131 Copynumber: 2.0 Consensus size: 130
440682 ATCTTTAGGA
* * *
440692 AGGG-TGATAACACGGTTCCTACTCGATGAGGACGAGTGGTTATCT-AGGGTGACATG-GCTCCT
1 AGGGATGATAACACGATTCCTACTCAATGAGGACGAGTGGTTATCTAAGGGTG--ATGAACTCCT
* **
440754 ACGTGATGAGGAGGTCTGGTCGGGGGGATGACACGGTTCCTACGTGATGAGGACGACATGCCATC
64 ACGTGATGAGGAGGTATGGT-GGGGGGATGACACGGTTCCTACACGATGAGGACGACATGCCATC
440819 TTT
128 TTT
* * *
440822 AGGGATGATAACATGATTCCTACGT-AATGAGGACGATTGGTTATCTAAGGTTGATGCAACTCCT
1 AGGGATGATAACACGATTCCTAC-TCAATGAGGACGAGTGGTTATCTAAGGGTGATG-AACTCCT
* * *
440886 ACGTGATGAGGAGGTATGGTTGGGGGATGATACGGTTCCTACACGATGAGGACGGCATGCCATCT
64 ACGTGATGAGGAGGTATGGTGGGGGGATGACACGGTTCCTACACGATGAGGACGACATGCCATCT
440951 TT
129 TT
*
440953 AAGGAT
1 AGGGAT
440959 TTTGGTTTTA
Statistics
Matches: 119, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
130 7 0.06
131 82 0.69
132 30 0.25
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (130 bp):
AGGGATGATAACACGATTCCTACTCAATGAGGACGAGTGGTTATCTAAGGGTGATGAACTCCTAC
GTGATGAGGAGGTATGGTGGGGGGATGACACGGTTCCTACACGATGAGGACGACATGCCATCTTT
Found at i:441096 original size:35 final size:35
Alignment explanation
Indices: 441028--441097 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
441018 GACAAAATTC
***
441028 GTTTCAAGGGAAACGATATCAAAGATGTTTGTTTT
1 GTTTCAAGGGAAACGATATCAAAGATAAGTGTTTT
*
441063 GTTTCAAGGGAAAC-ATACTCAAATATAAGTGTTTT
1 GTTTCAAGGGAAACGATA-TCAAAGATAAGTGTTTT
441098 AAGAGAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 3 0.10
35 27 0.90
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (35 bp):
GTTTCAAGGGAAACGATATCAAAGATAAGTGTTTT
Found at i:442346 original size:13 final size:12
Alignment explanation
Indices: 442328--442358 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
442318 TATTTTGCTT
442328 TTTTTTTCTTTG
1 TTTTTTTCTTTG
442340 ATTTTTTTCTTTG
1 -TTTTTTTCTTTG
442353 TTTTTT
1 TTTTTT
442359 GTTTTTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.03, C:0.06, G:0.06, T:0.84
Consensus pattern (12 bp):
TTTTTTTCTTTG
Found at i:442347 original size:18 final size:19
Alignment explanation
Indices: 442342--442378 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
442332 TTTCTTTGAT
442342 TTTTTTCTTTGT-TTTTTG
1 TTTTTTCTTTGTCTTTTTG
442360 TTTTTTCTTTGATCTTTTT
1 TTTTTTCTTTG-TCTTTTT
442379 CTCTTTGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 1 0.06
20 5 0.29
ACGTcount: A:0.03, C:0.08, G:0.08, T:0.81
Consensus pattern (19 bp):
TTTTTTCTTTGTCTTTTTG
Found at i:446392 original size:3 final size:3
Alignment explanation
Indices: 446378--446424 Score: 60
Period size: 3 Copynumber: 15.3 Consensus size: 3
446368 TATGTAACAA
*
446378 AAT AATT AAT AAT AAT AAT AAT AAAT AAT AAT ATT AAT -AT AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
446424 A
1 A
446425 TTTTTGGTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 31 0.79
4 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:446399 original size:16 final size:16
Alignment explanation
Indices: 446378--446424 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
446368 TATGTAACAA
446378 AATAATTAATAATAAT
1 AATAATTAATAATAAT
*
446394 AATAATAAATAATAAT
1 AATAATTAATAATAAT
*
446410 ATTAATATAATAATA
1 AATAAT-TAATAATA
446425 TTTTTGGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 20 0.74
17 7 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATAATTAATAATAAT
Found at i:450862 original size:21 final size:21
Alignment explanation
Indices: 450838--450877 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
450828 ACATTAATAC
450838 GCGAAGATATTATAAGTCCGT
1 GCGAAGATATTATAAGTCCGT
450859 GCGAAGATATTATAAGTCC
1 GCGAAGATATTATAAGTCC
450878 ACGGACGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (21 bp):
GCGAAGATATTATAAGTCCGT
Found at i:463093 original size:22 final size:22
Alignment explanation
Indices: 463057--463119 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
463047 AGTCGAGGGT
* * *
463057 TACATATGTCCTTCGGGATATA
1 TACATAGGTCATTCGGGATACA
*
463079 TACATAGGTCTTTCGGG--ACA
1 TACATAGGTCATTCGGGATACA
463099 TACATGAGGTCATTCGGGATA
1 TACAT-AGGTCATTCGGGATA
463120 GATTTCACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
20 7 0.21
21 11 0.32
22 15 0.44
23 1 0.03
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (22 bp):
TACATAGGTCATTCGGGATACA
Found at i:463103 original size:20 final size:21
Alignment explanation
Indices: 463078--463117 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
463068 TTCGGGATAT
*
463078 ATACAT-AGGTCTTTCGGGAC
1 ATACATGAGGTCATTCGGGAC
463098 ATACATGAGGTCATTCGGGA
1 ATACATGAGGTCATTCGGGA
463118 TAGATTTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
ATACATGAGGTCATTCGGGAC
Found at i:465897 original size:21 final size:21
Alignment explanation
Indices: 465846--465898 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
465836 ATTATTACTA
*
465846 TCGCAATTCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
465867 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
465888 TCGCAATGCGA
1 TCGCAATGCGA
465899 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:465931 original size:21 final size:20
Alignment explanation
Indices: 465888--465961 Score: 112
Period size: 20 Copynumber: 3.6 Consensus size: 20
465878 TTTTCCCAAT
465888 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* *
465908 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
*
465929 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATAAGTAAA
465949 TCGCAATGCGAAT
1 TCGCAATGCGAAT
465962 CTGACTATCG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 31 0.63
21 18 0.37
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:466537 original size:20 final size:20
Alignment explanation
Indices: 466512--466549 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
466502 TAGCTTCGAG
466512 AATGACAATCGCAACGCGGA
1 AATGACAATCGCAACGCGGA
*
466532 AATGACTATCGCAACGCG
1 AATGACAATCGCAACGCG
466550 AAACCAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.26, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGACAATCGCAACGCGGA
Found at i:466629 original size:20 final size:20
Alignment explanation
Indices: 466565--466652 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
466555 AAAATCGCAA
466565 TGCGATTTTCATTT-CGCGT
1 TGCGATTTTCATTTCCGCGT
*
466584 TGCGA--TTC---T-CTCGT
1 TGCGATTTTCATTTCCGCGT
**
466598 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTTCCGCGT
*
466618 TGCGATTTTCA-TTCTCTCGT
1 TGCGATTTTCATTTC-CGCGT
466638 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
466653 AATCAAAAGA
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 9 0.16
20 28 0.51
21 3 0.05
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.45
Consensus pattern (20 bp):
TGCGATTTTCATTTCCGCGT
Found at i:468520 original size:94 final size:90
Alignment explanation
Indices: 468330--468541 Score: 318
Period size: 94 Copynumber: 2.3 Consensus size: 90
468320 TAGATTGCTT
* *
468330 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
1 AGTAAATTTGTTC-GTTGCTGCCAATTCTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
468395 GCCTTTTGTTTTGTCTTTTGGTTGAA
65 GCCTTTTGTTTTGTCTTTTGGTTGAA
*
468421 AGTAAATTTGTTCAGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTC-GTTGCTGCCAATTCTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
*
468486 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
61 ATTTGCCTTTTGTTTTGTCTTTTGGTTGAA
468515 AGTAAATTTGTTCGTTTGCTGCCAATT
1 AGTAAATTTGTTCG-TTGCTGCCAATT
468542 GAAACTATTC
Statistics
Matches: 111, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
91 33 0.30
93 4 0.04
94 49 0.44
95 25 0.23
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (90 bp):
AGTAAATTTGTTCGTTGCTGCCAATTCTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTTG
CCTTTTGTTTTGTCTTTTGGTTGAA
Found at i:469010 original size:21 final size:21
Alignment explanation
Indices: 468986--469052 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
468976 TCATTCCTCG
468986 AGAGTCCCCTCTCACCGTTCA
1 AGAGTCCCCTCTCACCGTTCA
* * * * *
469007 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCTCACCGTTCA
* *
469028 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCTCACCGTTCA
469049 AGAG
1 AGAG
469053 CTCGATTCAC
Statistics
Matches: 33, Mismatches: 12, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCTCACCGTTCA
Found at i:471149 original size:12 final size:12
Alignment explanation
Indices: 471132--471156 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
471122 TCTTCGGAGC
471132 CTTTTTCTTCTT
1 CTTTTTCTTCTT
471144 CTTTTTCTTCTT
1 CTTTTTCTTCTT
471156 C
1 C
471157 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:471369 original size:24 final size:23
Alignment explanation
Indices: 471331--471384 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
471321 CTGAAACATC
*
471331 ATCAAATCCGAGTATTGACCAAT
1 ATCAAATCCGAGTATTGACCAAG
*
471354 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAA-TCCGAGTATTGACCAAG
471378 ATCAAAT
1 ATCAAAT
471385 TTCGAATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (23 bp):
ATCAAATCCGAGTATTGACCAAG
Found at i:472149 original size:20 final size:20
Alignment explanation
Indices: 472128--472208 Score: 110
Period size: 20 Copynumber: 4.0 Consensus size: 20
472118 TCTATTATCT
*
472128 CGTTGCAATAGTCAGAATCT
1 CGTTGCAATAGTCAGAATCG
*
472148 CGTTGCAAAAGTCAGAATCG
1 CGTTGCAATAGTCAGAATCG
472168 CGTTGCGAA-AGTCAGAATCG
1 CGTTGC-AATAGTCAGAATCG
* *
472188 CGTTGCGATAGTCAGTATCG
1 CGTTGCAATAGTCAGAATCG
472208 C
1 C
472209 ATTACGATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
19 1 0.02
20 52 0.95
21 2 0.04
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (20 bp):
CGTTGCAATAGTCAGAATCG
Found at i:472253 original size:62 final size:62
Alignment explanation
Indices: 472184--472304 Score: 215
Period size: 62 Copynumber: 2.0 Consensus size: 62
472174 GAAAGTCAGA
* *
472184 ATCGCGTTGCGATAGTCAGTATCGCATTACGATTTTCCAAGTTCGTATTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTACGATTTTCCAAATTCGCATTGCGATTTTGTATT
*
472246 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCATTGCGATTTTGT
1 ATCGCGTTGCGATAGTCAGTATCGCATTACGATTTTCCAAATTCGCATTGCGATTTTGT
472305 TATTCGCATT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (62 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTACGATTTTCCAAATTCGCATTGCGATTTTGTATT
Found at i:472270 original size:20 final size:20
Alignment explanation
Indices: 472123--472278 Score: 100
Period size: 20 Copynumber: 7.7 Consensus size: 20
472113 GATTCTCTAT
* *
472123 TATCTCGTTGCAATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * * *
472143 AATCTCGTTGCAAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
472163 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
472183 AATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * **
472203 TATCGCATTACGATTTTCCAAG
1 TATCGCGTTGCGATAGT-C-AG
** * *
472225 T-TCGTATTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
472245 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
472265 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
472279 TTTCCAAATT
Statistics
Matches: 111, Mismatches: 19, Indels: 12
0.78 0.13 0.08
Matches are distributed among these distances:
19 3 0.03
20 83 0.75
21 19 0.17
22 3 0.03
23 3 0.03
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:472360 original size:21 final size:22
Alignment explanation
Indices: 472308--472360 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
472298 ATTTTGTTAT
472308 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
* **
472329 TCACAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
472350 TCGCATTGCGA
1 TCGCATTGCGA
472361 TAGTAATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:475793 original size:12 final size:12
Alignment explanation
Indices: 475759--475798 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
475749 AAACTTTATA
*
475759 TTATTTAATAAT
1 TTATTTAAAAAT
*
475771 ATATATTAAAAAT
1 TTAT-TTAAAAAT
475784 TTATTTAAAAAT
1 TTATTTAAAAAT
475796 TTA
1 TTA
475799 ATAATTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TTATTTAAAAAT
Found at i:476865 original size:113 final size:113
Alignment explanation
Indices: 476690--476907 Score: 339
Period size: 113 Copynumber: 1.9 Consensus size: 113
476680 GATTAATCTG
* *
476690 AATTGACATGTGTCGCACACCTGATTTTAGTAAGTGAGTCTCCCAACGGATATTTTTTGCATACA
1 AATTGACATGTGTCGCACACCTGATTTTACTAAGTGAGTCTCCCAACGGAGATTTTTTGCATACA
*
476755 CAATGACTCGAAATCGAGACATTAATTAAGCGATATCAAGCTAATCCA
66 CAATGACTCGAAATCAAGACATTAATTAAGCGATATCAAGCTAATCCA
* * *
476803 AATTGACATGTGTCGCACACCTGATTTTACTGAGTGAGTCTCCCTACAGG-GATTTTTTGCATAT
1 AATTGACATGTGTCGCACACCTGATTTTACTAAGTGAGTCTCCCAAC-GGAGATTTTTTGCATAC
* * *
476867 ACAATGATTCGAAATCAAGACTTTGATTAAGCGATATCAAG
65 ACAATGACTCGAAATCAAGACATTAATTAAGCGATATCAAG
476908 TTACATACTA
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
113 93 0.98
114 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (113 bp):
AATTGACATGTGTCGCACACCTGATTTTACTAAGTGAGTCTCCCAACGGAGATTTTTTGCATACA
CAATGACTCGAAATCAAGACATTAATTAAGCGATATCAAGCTAATCCA
Found at i:478162 original size:51 final size:52
Alignment explanation
Indices: 478067--478165 Score: 121
Period size: 51 Copynumber: 1.9 Consensus size: 52
478057 GTAATATTTT
* * * *
478067 ACATAATTAGGGGTTCATTTCTTTTATTTCGTCTGAGTTAAAAAAATAAAGA
1 ACATAAATAGGGGCTCATTTCTTTTATTTCGTCCGAGGTAAAAAAATAAAGA
* *
478119 ACATAAATA-GGGCTCATTTGTTTTATTTCGTCCCG-GGTCAAAAAATA
1 ACATAAATAGGGGCTCATTTCTTTTATTTCGT-CCGAGGTAAAAAAATA
478166 CCCAGAGCCG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
51 30 0.75
52 10 0.25
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (52 bp):
ACATAAATAGGGGCTCATTTCTTTTATTTCGTCCGAGGTAAAAAAATAAAGA
Found at i:478845 original size:17 final size:17
Alignment explanation
Indices: 478811--478844 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
478801 TTCCTTCACC
478811 TCTTTTGATCTTATTTT
1 TCTTTTGATCTTATTTT
*
478828 TCTTTTG-TTTTATTTT
1 TCTTTTGATCTTATTTT
478844 T
1 T
478845 TTAAAAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.76
Consensus pattern (17 bp):
TCTTTTGATCTTATTTT
Found at i:479880 original size:18 final size:19
Alignment explanation
Indices: 479847--479882 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
479837 TCATCTTATC
*
479847 TTTATCTTCTTTGTCTTTG
1 TTTATCTTCATTGTCTTTG
479866 TTTATCTT-ATTGTCTTT
1 TTTATCTTCATTGTCTTT
479883 ATCTTCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.08, C:0.14, G:0.08, T:0.69
Consensus pattern (19 bp):
TTTATCTTCATTGTCTTTG
Found at i:481529 original size:15 final size:15
Alignment explanation
Indices: 481504--481558 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
481494 TTTCAAACAA
481504 TTTATTGTTATATTAT
1 TTTATT-TTATATTAT
481520 TTTATTTTATATT-T
1 TTTATTTTATATTAT
* *
481534 TTAATATTATACTTAT
1 TTTATTTTATA-TTAT
481550 TTT-TTTTAT
1 TTTATTTTAT
481559 TTTTATCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 10 0.30
15 14 0.42
16 9 0.27
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTTATATTAT
Found at i:482307 original size:2 final size:2
Alignment explanation
Indices: 482300--482338 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
482290 ACATTAAAAT
482300 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
482339 GAAGCATAAG
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:483103 original size:38 final size:39
Alignment explanation
Indices: 483047--483173 Score: 120
Period size: 38 Copynumber: 3.3 Consensus size: 39
483037 TGGACACAAT
* *
483047 CTAAAATATTACTA-TCTTCTTAACATTTTCGGTT-GAAC
1 CTAAAATATTA-TATTCTTCATAACATTTTCGGTTCCAAC
* *
483085 CTAAAATGTTATATTCTTCATAA-AATTTCTGGTTTCCAAC
1 CTAAAATATTATATTCTTCATAACATTTTC-GG-TTCCAAC
* * *
483125 CGAAAATATTATATTCTTGATAACATTTTAGGTT-CAA-
1 CTAAAATATTATATTCTTCATAACATTTTCGGTTCCAAC
483162 CTGAAAATATTA
1 CT-AAAATATTA
483174 AGATATAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
37 8 0.11
38 32 0.44
39 4 0.05
40 25 0.34
41 4 0.05
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (39 bp):
CTAAAATATTATATTCTTCATAACATTTTCGGTTCCAAC
Found at i:484971 original size:60 final size:60
Alignment explanation
Indices: 484875--484987 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
484865 ATACTCGAGT
* * *
484875 GACTATTTTGTAACTTTTAATAGTTGAGAGATTCAATAAAGCAAT-TCACTATATTTGAGG
1 GACTATTTTGTAACTTTTAATAGTTCAGAGACTCAATAAAACAATATC-CTATATTTGAGG
*
484935 GACTATTTTGTAATTTTTAATAG-TCA-ATGTACTCAATAAAACAATATCCTATA
1 GACTATTTTGTAACTTTTAATAGTTCAGA-G-ACTCAATAAAACAATATCCTATA
484988 GCCGGAAGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
58 1 0.02
59 3 0.07
60 40 0.87
61 2 0.04
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (60 bp):
GACTATTTTGTAACTTTTAATAGTTCAGAGACTCAATAAAACAATATCCTATATTTGAGG
Found at i:490606 original size:2 final size:2
Alignment explanation
Indices: 490599--490645 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
490589 GGTTAATAGA
490599 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
490640 AT AT AT
1 AT AT AT
490646 TTAAACAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:490657 original size:21 final size:21
Alignment explanation
Indices: 490614--490657 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
490604 TATATATATA
* * *
490614 TATATATATATATATATATAT
1 TATATATATATATAAACAAAT
*
490635 TATATATATATTTAAACAAAT
1 TATATATATATATAAACAAAT
490656 TA
1 TA
490658 ATTAATATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TATATATATATATAAACAAAT
Found at i:492318 original size:13 final size:13
Alignment explanation
Indices: 492300--492327 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
492290 TTTTAATATT
492300 TTATTATTATTAA
1 TTATTATTATTAA
492313 TTATTATTATTAA
1 TTATTATTATTAA
492326 TT
1 TT
492328 TACATGCAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTATTATTAA
Found at i:493666 original size:2 final size:2
Alignment explanation
Indices: 493659--493766 Score: 170
Period size: 2 Copynumber: 56.0 Consensus size: 2
493649 GTGCACGTAC
493659 AT AT AT AT -T AT -T 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
493699 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
* *
493741 GT A- AT AT AT AT CT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
493767 GCATAACAGG
Statistics
Matches: 98, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
1 4 0.04
2 94 0.96
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
AT
Found at i:493917 original size:13 final size:13
Alignment explanation
Indices: 493891--493923 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
493881 CATATAAAAG
493891 TATTTATGAAGTT
1 TATTTATGAAGTT
493904 TATATTAT-AAGTT
1 TAT-TTATGAAGTT
493917 TATTTAT
1 TATTTAT
493924 TTTTTGTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 11 0.58
14 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (13 bp):
TATTTATGAAGTT
Found at i:494070 original size:2 final size:2
Alignment explanation
Indices: 494063--494098 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
494053 TGCATGGCTA
494063 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
494099 GTTAATGTTT
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:499029 original size:300 final size:300
Alignment explanation
Indices: 498487--499082 Score: 1111
Period size: 300 Copynumber: 2.0 Consensus size: 300
498477 AATATCAACT
*
498487 GAATTAAAAATTCTTTAAATGACTAGAGTTATAAATCTTTGAAAAAATGACAAGGTTGAAACCTG
1 GAATTAAAAATTCTTTAAATGACTAGAGTTATAAATCTTTGAAAAAATGACAAGGTTGAAACCTA
*
498552 ATAAAACAAGGACCTTGACTTTATCCATAGAAGATAAAATCGAACACCATACATTTTTATTGCAG
66 ATAAAACAAGGACCTTGACTTTATCCATAGAAGATAAAATCAAACACCATACATTTTTATTGCAG
*
498617 GGACCGATACAACCTTCTTTTATCATAAGAGAATGAACAATAGGCTTGGTATTCAGGTATGCATA
131 GGACCGATACAAACTTCTTTTATCATAAGAGAATGAACAATAGGCTTGGTATTCAGGTATGCATA
*
498682 GGAGCGGACAACATGGGGCATCTTTTGTGTATGATGTTACAAAACTAACTAGATCACACTTTTGT
196 GGAGCGGACAACATGGGGCATCTTTTGTGTATGATGTTACAAAACTAACTAGATCACACTTTTAT
498747 TGATGATGTTCAATGATGATTATGATCTTGACAGATAACC
261 TGATGATGTTCAATGATGATTATGATCTTGACAGATAACC
*
498787 GAATTAAAAATTCTTTAAATGACTAGAGTTATAAATCTTTGACAAAATGACAAGGTTGAAACCTA
1 GAATTAAAAATTCTTTAAATGACTAGAGTTATAAATCTTTGAAAAAATGACAAGGTTGAAACCTA
*
498852 ATAAAACAGGGACCTTGACTTTATCCATAGAAGATAAAATCAAACACCATACATTTTTATTGCAG
66 ATAAAACAAGGACCTTGACTTTATCCATAGAAGATAAAATCAAACACCATACATTTTTATTGCAG
* *
498917 GGACCGATACAAACTTCTTTTATCATAAGGGAATGAACAATAGGCTTGGTATTCAGGTGTGCATA
131 GGACCGATACAAACTTCTTTTATCATAAGAGAATGAACAATAGGCTTGGTATTCAGGTATGCATA
*
498982 GGAGCGGACAACATGGGGCATTTTTTGTGTATGATGTTACAAAACTAACTAGATCACACTTTTAT
196 GGAGCGGACAACATGGGGCATCTTTTGTGTATGATGTTACAAAACTAACTAGATCACACTTTTAT
499047 TGATGATGTTCAATGATGATTATGATCTTGACAGAT
261 TGATGATGTTCAATGATGATTATGATCTTGACAGAT
499083 GGAATAGTCG
Statistics
Matches: 287, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
300 287 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (300 bp):
GAATTAAAAATTCTTTAAATGACTAGAGTTATAAATCTTTGAAAAAATGACAAGGTTGAAACCTA
ATAAAACAAGGACCTTGACTTTATCCATAGAAGATAAAATCAAACACCATACATTTTTATTGCAG
GGACCGATACAAACTTCTTTTATCATAAGAGAATGAACAATAGGCTTGGTATTCAGGTATGCATA
GGAGCGGACAACATGGGGCATCTTTTGTGTATGATGTTACAAAACTAACTAGATCACACTTTTAT
TGATGATGTTCAATGATGATTATGATCTTGACAGATAACC
Found at i:501617 original size:18 final size:18
Alignment explanation
Indices: 501594--501637 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
501584 CGGTCAATAG
*
501594 CCGACCCGACCCGTTTAC
1 CCGACCCGACCCGTTGAC
*
501612 CCGACCCGACCTGTTGAC
1 CCGACCCGACCCGTTGAC
501630 CCGACCCG
1 CCGACCCG
501638 TTGACCGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.50, G:0.20, T:0.14
Consensus pattern (18 bp):
CCGACCCGACCCGTTGAC
Found at i:501630 original size:13 final size:13
Alignment explanation
Indices: 501614--501643 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
501604 CCGTTTACCC
*
501614 GACCCGACCTGTT
1 GACCCGACCCGTT
501627 GACCCGACCCGTT
1 GACCCGACCCGTT
501640 GACC
1 GACC
501644 GGTGATCGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:504023 original size:12 final size:11
Alignment explanation
Indices: 503998--504050 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
503988 CGTTACCTGA
*
503998 ATTCTGTTCTG
1 ATTCTGATCTG
504009 ATTCTGATCTGG
1 ATTCTGATCT-G
*
504021 ATTCTGTTCTG
1 ATTCTGATCTG
*
504032 ATATCTGATATG
1 AT-TCTGATCTG
504044 AATTCTG
1 -ATTCTG
504051 TTTTGATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 12 0.34
12 21 0.60
13 2 0.06
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.47
Consensus pattern (11 bp):
ATTCTGATCTG
Found at i:504064 original size:24 final size:24
Alignment explanation
Indices: 503995--504066 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
503985 ATACGTTACC
*
503995 TGAATTCTGTTCTGA-TTCTGATC
1 TGAATTCTGTTCTGATTTCTGATA
* *
504018 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
* *
504042 TGAATTCTGTTTTGATTTATGATA
1 TGAATTCTGTTCTGATTTCTGATA
504066 T
1 T
504067 CTCCGTTTAC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 14 0.34
24 27 0.66
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:505400 original size:34 final size:34
Alignment explanation
Indices: 505357--505443 Score: 156
Period size: 34 Copynumber: 2.6 Consensus size: 34
505347 GGTCATTAGG
505357 AAGTCTTCCGAGCATGATGATCAAATCCATCAGT
1 AAGTCTTCCGAGCATGATGATCAAATCCATCAGT
*
505391 AAGTCTTCCGAGCATGATGATCAAATCCATCTGT
1 AAGTCTTCCGAGCATGATGATCAAATCCATCAGT
*
505425 AAGTCTTTCGAGCATGATG
1 AAGTCTTCCGAGCATGATG
505444 CTTAAATTCT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.29
Consensus pattern (34 bp):
AAGTCTTCCGAGCATGATGATCAAATCCATCAGT
Found at i:505547 original size:79 final size:79
Alignment explanation
Indices: 505412--505579 Score: 223
Period size: 79 Copynumber: 2.1 Consensus size: 79
505402 GCATGATGAT
* * * * *
505412 CAAATCCATCTGTAAGTCTTTCGAGCATGATGCTTAAATTCTTTGGGCCATATTAAGCCTTCACC
1 CAAATCCATCAGTAAGTCTTCCGAGCATGACGATTAAAGTCTTTGGGCCATATTAAGCCTTCACC
**
505477 GAAGTGTAGTGAAG
66 GAAGACTAGTGAAG
*
505491 CAAATCCATCAGTAAG-CATTCCGAGCATGACGATT-AAGTCTTTCGGGCCATTTTAAGCCTTCA
1 CAAATCCATCAGTAAGTC-TTCCGAGCATGACGATTAAAGTCTTT-GGGCCATATTAAGCCTTCA
*
505554 CGGAAGACTAGTGAAG
64 CCGAAGACTAGTGAAG
505570 CAAATCCATC
1 CAAATCCATC
505580 TATCTGATAT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
78 8 0.10
79 70 0.90
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (79 bp):
CAAATCCATCAGTAAGTCTTCCGAGCATGACGATTAAAGTCTTTGGGCCATATTAAGCCTTCACC
GAAGACTAGTGAAG
Found at i:505775 original size:111 final size:110
Alignment explanation
Indices: 505581--506121 Score: 704
Period size: 111 Copynumber: 4.9 Consensus size: 110
505571 AAATCCATCT
* * * * *
505581 ATCTGATATTCCCTTTAGAAGAAGTGGAACATATCACTCTTTTTCAAGATTTGATATTCCCTGAG
1 ATCTGATATTCCC-TCAGAA-AAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAG
* * * *
505646 TAACAGCGGAACAAGTCTAGCTTGATTCAATGAATCAACTTTCCCAT
64 TGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTCCCAG
* * *
505693 ATCTGATATTCCCTCAGAGAAAGCAGAACAGATCCCTCTTTTTCAAGATTTGATATTCCCTGAGT
1 ATCTGATATTCCCTCAGA-AAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGT
* *
505758 GACAGCGGAACAAGTCTACCCTGATTCAATGGATCAACTTTCTCAG
65 GACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTCCCAG
** *
505804 ATCTGATATTCCCTCAGAAAAAATGAAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGT
1 ATCTGATATTCCCTCAG-AAAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGT
* * * *
505869 GACAGCGGAACAAGTCTACCCTTATTTAATAAATCAACTTTCCCAA
65 GACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTCCCAG
* * * * *
505915 ATTTGATATTCCCTTAGAGGAAGCGGAACATATCCTTCTCTTTCAAGATTTGATATTCCCTGAGT
1 ATCTGATATTCCCTCAGA-AAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGT
* * * *
505980 AACAGCGGAACAAGTCTACCCTGATTCAATGGATCAACATTCCTAG
65 GACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTCCCAG
* * * *
506026 ATCTGATATTCCCTTCAGAAGAAGCGGAACAAATTCCTATCTTCCAAGATTTGATATTCCTTGAG
1 ATCTGATATTCCC-TCAGAA-AAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAG
*
506091 TGACAGCGGAACAAGTCTACACTGATTCAAT
64 TGACAGCGGAACAAGTCTACCCTGATTCAAT
506122 CTTTCCTGAA
Statistics
Matches: 374, Mismatches: 50, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
110 1 0.00
111 287 0.77
112 86 0.23
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (110 bp):
ATCTGATATTCCCTCAGAAAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTG
ACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTCCCAG
Found at i:506008 original size:222 final size:224
Alignment explanation
Indices: 505581--506121 Score: 795
Period size: 222 Copynumber: 2.4 Consensus size: 224
505571 AAATCCATCT
* * * *
505581 ATCTGATATTCCCTTTAGAAGAAGTGGAACATATCACTCTTTTTCAAGATTTGATATTCCCTGAG
1 ATCTGATATTCCCTTCAGAAGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAG
* * * *
505646 TAACAGCGGAACAAGTCTA-GCTTGATTCAATGAATCAACTTTCCCATATCTGATATTCCCTCAG
66 TGACAGCGGAACAAGTCTACCCTTGATTCAATAAATCAACTTTCCCAAATCTGATATTCCCTCAG
* *
505710 AGAAAGCAGAACAGATCCCTCTTTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCT
131 AGAAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGCGGAACAAGTCT
*
505775 ACCCTGATTCAATGGATCAAC-TTTCTCAG
196 ACCCTGATTCAATGGATCAACATTCCT-AG
* * *
505804 ATCTGATATTCCC-TCAGAAAAAATGAAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAG
1 ATCTGATATTCCCTTCAGAAGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAG
* * *
505868 TGACAGCGGAACAAGTCTACCCTT-ATTTAATAAATCAACTTTCCCAAATTTGATATTCCCTTAG
66 TGACAGCGGAACAAGTCTACCCTTGATTCAATAAATCAACTTTCCCAAATCTGATATTCCCTCAG
* * * *
505932 AGGAAGCGGAACATATCCTTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGCGGAACAAGTCT
131 AGAAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGCGGAACAAGTCT
505997 ACCCTGATTCAATGGATCAACATTCCTAG
196 ACCCTGATTCAATGGATCAACATTCCTAG
* * * * *
506026 ATCTGATATTCCCTTCAGAAGAAGCGGAACAAATTCCTATCTTCCAAGATTTGATATTCCTTGAG
1 ATCTGATATTCCCTTCAGAAGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAG
*
506091 TGACAGCGGAACAAGTCTACAC-TGATTCAAT
66 TGACAGCGGAACAAGTCTACCCTTGATTCAAT
506122 CTTTCCTGAA
Statistics
Matches: 283, Mismatches: 31, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
222 193 0.68
223 90 0.32
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (224 bp):
ATCTGATATTCCCTTCAGAAGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAG
TGACAGCGGAACAAGTCTACCCTTGATTCAATAAATCAACTTTCCCAAATCTGATATTCCCTCAG
AGAAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGCGGAACAAGTCT
ACCCTGATTCAATGGATCAACATTCCTAG
Found at i:507693 original size:2 final size:2
Alignment explanation
Indices: 507686--507790 Score: 69
Period size: 2 Copynumber: 53.5 Consensus size: 2
507676 TTTAAGTAAT
*
507686 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGC TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
* * * * * *
507729 GTA TG TGA -A TA TA TA TC TA T- TT TA T- TA TC CA TA T- TA TG TA
1 -TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
507769 -A TA TA TA TA T- TA TA GTA TA TA T
1 TA TA TA TA TA TA TA TA -TA TA TA T
507791 GCATAACAGG
Statistics
Matches: 80, Mismatches: 13, Indels: 20
0.71 0.12 0.18
Matches are distributed among these distances:
1 6 0.08
2 69 0.86
3 5 0.06
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Done.