Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, 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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 22 of 32
Found at i:11304841 original size:21 final size:21
Alignment explanation
Indices: 11304793--11304908 Score: 88
Period size: 22 Copynumber: 5.4 Consensus size: 21
11304783 TTAACTACTG
* *
11304793 CGTGATTGGTTTTTAAGTATTA
1 CGTGATTGG-TTATAAGCATTA
** *
11304815 TATGATTGGTTATAAGCATTG
1 CGTGATTGGTTATAAGCATTA
* *
11304836 CGTGATTGGTTTTTAAGTATTA
1 CGTGATTGG-TTATAAGCATTA
** *
11304858 TATGATTGGTTATAAACATTA
1 CGTGATTGGTTATAAGCATTA
* * *
11304879 CGTGATTAGTTTTTAGGCATTA
1 CGTGATT-GGTTATAAGCATTA
11304901 CGTGATTG
1 CGTGATTG
11304909 ACTTTTAAGC
Statistics
Matches: 71, Mismatches: 21, Indels: 5
0.73 0.22 0.05
Matches are distributed among these distances:
21 31 0.44
22 40 0.56
ACGTcount: A:0.26, C:0.06, G:0.22, T:0.46
Consensus pattern (21 bp):
CGTGATTGGTTATAAGCATTA
Found at i:11304852 original size:43 final size:43
Alignment explanation
Indices: 11304791--11304893 Score: 179
Period size: 43 Copynumber: 2.4 Consensus size: 43
11304781 ACTTAACTAC
*
11304791 TGCGTGATTGGTTTTTAAGTATTATATGATTGGTTATAAGCAT
1 TGCGTGATTGGTTTTTAAGTATTATATGATTGGTTATAAACAT
11304834 TGCGTGATTGGTTTTTAAGTATTATATGATTGGTTATAAACAT
1 TGCGTGATTGGTTTTTAAGTATTATATGATTGGTTATAAACAT
* *
11304877 TACGTGATTAGTTTTTA
1 TGCGTGATTGGTTTTTA
11304894 GGCATTACGT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.48
Consensus pattern (43 bp):
TGCGTGATTGGTTTTTAAGTATTATATGATTGGTTATAAACAT
Found at i:11304914 original size:22 final size:22
Alignment explanation
Indices: 11304874--11304915 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
11304864 TGGTTATAAA
*
11304874 CATTACGTGATTAGTTTTTAGG
1 CATTACGTGATTAGCTTTTAGG
11304896 CATTACGTGATT-GACTTTTA
1 CATTACGTGATTAG-CTTTTA
11304916 AGCAATGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.24, C:0.12, G:0.19, T:0.45
Consensus pattern (22 bp):
CATTACGTGATTAGCTTTTAGG
Found at i:11304976 original size:23 final size:23
Alignment explanation
Indices: 11304935--11304978 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
11304925 TAAGTTACAC
* **
11304935 AATGCCTTACTAATTAGTCACGT
1 AATGACTTACTAACAAGTCACGT
11304958 AATGACTTACTAACAAGTCAC
1 AATGACTTACTAACAAGTCAC
11304979 ACAATACCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (23 bp):
AATGACTTACTAACAAGTCACGT
Found at i:11305061 original size:21 final size:21
Alignment explanation
Indices: 11305031--11305070 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11305021 AAGCAATGTC
*
11305031 CAAAGCCAGTCACGTAATATA
1 CAAAGCCAGTCACGCAATATA
* *
11305052 CAAAGTCAGTTACGCAATA
1 CAAAGCCAGTCACGCAATA
11305071 CCCAAAAACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (21 bp):
CAAAGCCAGTCACGCAATATA
Found at i:11306239 original size:61 final size:64
Alignment explanation
Indices: 11306172--11306313 Score: 175
Period size: 65 Copynumber: 2.2 Consensus size: 64
11306162 ATGAAAATTT
*
11306172 TATTAAAATTTTAATATG-ATTATTGAATTTTA-TT-TTTT-TTCTCTATTTTCACTTTGTGAAA
1 TATTAAAATTTTAATATGAATT-TTGAATTTTATTTATTTTATTCTCTATTTTCACTTTGTAAAA
* * * *
11306233 TATTAAAATTTTAATATGAATTTTTATTTTTATTTTATTTTATTCTCTATTTTCATTTTTTAAAA
1 TATTAAAATTTTAATATGAATTTTGAATTTTA-TTTATTTTATTCTCTATTTTCACTTTGTAAAA
* *
11306298 TACTAAAATATTAATA
1 TATTAAAATTTTAATA
11306314 ATTTATAATT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
61 26 0.38
62 3 0.04
63 2 0.03
64 4 0.06
65 34 0.49
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.58
Consensus pattern (64 bp):
TATTAAAATTTTAATATGAATTTTGAATTTTATTTATTTTATTCTCTATTTTCACTTTGTAAAA
Found at i:11309598 original size:55 final size:55
Alignment explanation
Indices: 11309501--11309605 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
11309491 TATTGAAAAA
* * * *
11309501 TATTATATGTTATATTGAAAATTTAGTTGTTACATGATATGTTGAAAAATATAAT
1 TATTATATATTATATTGAAAATTTAGTTATTACACGATATGTTAAAAAATATAAT
* * *
11309556 TATTCTATATTATGTTGAAGATTTAGTTATTACACG-TCATGTTAAAAAAT
1 TATTATATATTATATTGAAAATTTAGTTATTACACGAT-ATGTTAAAAAAT
11309606 TCAATTTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
54 1 0.02
55 41 0.98
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (55 bp):
TATTATATATTATATTGAAAATTTAGTTATTACACGATATGTTAAAAAATATAAT
Found at i:11323290 original size:340 final size:328
Alignment explanation
Indices: 11322615--11323351 Score: 946
Period size: 340 Copynumber: 2.2 Consensus size: 328
11322605 TAAAAAATAA
* * * *
11322615 ATAAATTATAATTTTTGTAATGTTAACACAAAATAGAAAGTAAGTATGTTTATATTTAAAGTATG
1 ATAAGTTATAATTTTTGTAATGCTAACACAAAATAGAAAGTAAATATGTTTATATTTAAAGTATA
*
11322680 TATACTAAAGGTATATCTATAATAGTAATTATATTCTTTATAAATTAACAAAATATATAAAGTAT
66 TATACTAAAAGTATATCTATAATAGTAATTATATTCTTTATAAATTAACAAAATATATAAAGTAT
* * * *
11322745 AAATTAAAAGACATTATAAGTTAATTAATAATCATAGTTTCATGAATTAATTTAATTAACTATAT
131 AAATTAAAAAACATTACAAGTTAATTAATAATCATAATTTCATGAATTAAATTAATTAACTATAT
* * * * *
11322810 GAGATTGTTCTTAATTGCATGAAATTAAAAAAAATAGCTAGGTTTCAAAACTATTCTAATCTTAT
196 GAGATTGTTCTTAATTACATGAAATTAAAAAAAATAACTAAGTTCCAAAACTATTCTAAACTTAT
* **
11322875 AACTTCTCTTTAGGTATATATTATAAGTTTATATAAATAAAGGTACATATATTATAATTAATAAT
261 AACTTCTCTTTAGATATATATTATAAGTTTATATAAATAAAAATACATATATTATAATTAATAAT
11322940 TTT
326 TTT
*
11322943 ATAAGTTATGATTTTTGTAACT-CTAACACAAAATAGAAAGTAAATATGTTTATATTTAAAGTAT
1 ATAAGTTATAATTTTTGTAA-TGCTAACACAAAATAGAAAGTAAATATGTTTATATTTAAAGTAT
* *
11323007 ATATACTAAAAGTATAT-TATAATAGTAATTATATTCTTTATAAATTAACACAATATATAGAGTA
65 ATATACTAAAAGTATATCTATAATAGTAATTATATTCTTTATAAATTAACAAAATATATAAAGTA
* *
11323071 TATCTATTAAAAAACATTACAAGTTAATTAATAATCATAATTTCATGAATTAAATTAATTAATTA
130 TA--AATTAAAAAACATTACAAGTTAATTAATAATCATAATTTCATGAATTAAATTAATTAACTA
* * * *
11323136 TATGCGTTTGTCTACCTTAATTACATGAAATT-AAAAAAATAATTAAGTTCCAATACTATTATAA
193 TATGAGATTGT-T--CTTAATTACATGAAATTAAAAAAAATAACTAAGTTCCAA-A--ACTAT--
* *
11323200 TCTCACAACTTGATAACTT-TTTTTAAGTATATATATTATAAGTTTATATAAATAAAAATATATA
250 TCT-A-AACTT-ATAACTTCTCTTT-AG-ATATATATTATAAGTTTATATAAATAAAAATACATA
11323264 TATTATAATTAATAATTTT
310 TATTATAATTAATAATTTT
* * * * ** * *
11323283 ATAAGTTATAATTTTTTTAAAG-TGAAC-CGAAAATAAAAAGTAAATGTAATTATATTAAAAGAA
1 ATAAGTTATAATTTTTGTAATGCT-AACAC-AAAATAGAAAGTAAATATGTTTATATTTAAAGTA
11323346 TATATA
64 TATATA
11323352 TAATAGTCAT
Statistics
Matches: 353, Mismatches: 37, Indels: 26
0.85 0.09 0.06
Matches are distributed among these distances:
327 47 0.13
328 73 0.21
329 65 0.18
330 1 0.00
331 17 0.05
332 17 0.05
334 4 0.01
336 3 0.01
337 1 0.00
338 8 0.02
339 11 0.03
340 106 0.30
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (328 bp):
ATAAGTTATAATTTTTGTAATGCTAACACAAAATAGAAAGTAAATATGTTTATATTTAAAGTATA
TATACTAAAAGTATATCTATAATAGTAATTATATTCTTTATAAATTAACAAAATATATAAAGTAT
AAATTAAAAAACATTACAAGTTAATTAATAATCATAATTTCATGAATTAAATTAATTAACTATAT
GAGATTGTTCTTAATTACATGAAATTAAAAAAAATAACTAAGTTCCAAAACTATTCTAAACTTAT
AACTTCTCTTTAGATATATATTATAAGTTTATATAAATAAAAATACATATATTATAATTAATAAT
TTT
Found at i:11343407 original size:20 final size:20
Alignment explanation
Indices: 11343379--11343417 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11343369 TCAGAAAGTG
* *
11343379 GGGGTGGAGGGGGTGGGGGA
1 GGGGAGGAGGAGGTGGGGGA
11343399 GGGGAGGAGGAGGTGGGGG
1 GGGGAGGAGGAGGTGGGGG
11343418 TGGTGGTGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.79, T:0.08
Consensus pattern (20 bp):
GGGGAGGAGGAGGTGGGGGA
Found at i:11348293 original size:18 final size:20
Alignment explanation
Indices: 11348270--11348316 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 20
11348260 TGAAAATATT
11348270 TAAATATTAATTAA-TAT-A
1 TAAATATTAATTAACTATAA
*
11348288 TTAATATTAATTAACTATAA
1 TAAATATTAATTAACTATAA
11348308 TAAATATTA
1 TAAATATTA
11348317 TAAAGAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 13 0.52
19 3 0.12
20 9 0.36
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATATTAATTAACTATAA
Found at i:11348300 original size:10 final size:10
Alignment explanation
Indices: 11348272--11348316 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
11348262 AAAATATTTA
11348272 AATATTAATT
1 AATATTAATT
11348282 AATA-T-ATT
1 AATATTAATT
11348290 AATATTAATT
1 AATATTAATT
*
11348300 AACTA-TAATA
1 AA-TATTAATT
11348310 AATATTA
1 AATATTA
11348317 TAAAGAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
8 7 0.23
9 4 0.13
10 17 0.57
11 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (10 bp):
AATATTAATT
Found at i:11348434 original size:23 final size:22
Alignment explanation
Indices: 11348408--11348478 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
11348398 AAAAGGTTTA
*
11348408 ATTATCTTTTAATACAAAATATT
1 ATTATATTTTAATA-AAAATATT
* *
11348431 ATTAAATTATAATAAAAATA-T
1 ATTATATTTTAATAAAAATATT
*
11348452 ATTTATATTTTGATAAAAAATATT
1 A-TTATATTTTAAT-AAAAATATT
11348476 ATT
1 ATT
11348479 TAATTATAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.05
22 15 0.38
23 20 0.51
24 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (22 bp):
ATTATATTTTAATAAAAATATT
Found at i:11348484 original size:45 final size:46
Alignment explanation
Indices: 11348380--11348497 Score: 157
Period size: 45 Copynumber: 2.6 Consensus size: 46
11348370 TTAATATTAG
* * * *
11348380 ATATTATTTAATTATAATAAAAGGTTTAATTATCTTTTAATACAAA
1 ATATTATTTAATTATAATAAAAGATATAATTATATTTTAATAAAAA
* * *
11348426 ATATTATTAAATTATAATAAAA-ATATATTTATATTTTGATAAAAA
1 ATATTATTTAATTATAATAAAAGATATAATTATATTTTAATAAAAA
*
11348471 ATATTATTTAATTATAGTAAAAGATAT
1 ATATTATTTAATTATAATAAAAGATAT
11348498 TTTGATTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 37 0.60
46 25 0.40
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (46 bp):
ATATTATTTAATTATAATAAAAGATATAATTATATTTTAATAAAAA
Found at i:11348491 original size:23 final size:23
Alignment explanation
Indices: 11348423--11348498 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
11348413 CTTTTAATAC
* *
11348423 AAAATATTATTAAATTATAAT-A
1 AAAATATTATTTAATTATAGTAA
*
11348445 AAAATA-TATTTATATT-TTGATAA
1 AAAATATTATTTA-ATTATAG-TAA
11348468 AAAATATTATTTAATTATAGTAA
1 AAAATATTATTTAATTATAGTAA
*
11348491 AAGATATT
1 AAAATATT
11348499 TTGATTTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
21 6 0.14
22 10 0.23
23 20 0.45
24 8 0.18
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
AAAATATTATTTAATTATAGTAA
Found at i:11348785 original size:32 final size:32
Alignment explanation
Indices: 11348748--11348809 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
11348738 TAATTTATAT
11348748 AATAATTATTCTT-TTAGTATTTTATTTTTTAA
1 AATAATTATT-TTATTAGTATTTTATTTTTTAA
**
11348780 AATAATTATTTTATTTTTATTTTATTTTTT
1 AATAATTATTTTATTAGTATTTTATTTTTT
11348810 TTGGGTGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 2 0.07
32 25 0.93
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (32 bp):
AATAATTATTTTATTAGTATTTTATTTTTTAA
Found at i:11351512 original size:23 final size:23
Alignment explanation
Indices: 11351471--11351514 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
11351461 GTAAAACAAG
11351471 CCTTCCACGCAACCATCTAGTCC
1 CCTTCCACGCAACCATCTAGTCC
* * *
11351494 CCTTCCCCGCCACCTTCTAGT
1 CCTTCCACGCAACCATCTAGT
11351515 TGGAGTAACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.16, C:0.50, G:0.09, T:0.25
Consensus pattern (23 bp):
CCTTCCACGCAACCATCTAGTCC
Found at i:11352707 original size:20 final size:21
Alignment explanation
Indices: 11352679--11352717 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
11352669 CTATTTGACG
11352679 TAAAATAAAAAT-ATAAAAAT
1 TAAAATAAAAATAATAAAAAT
* *
11352699 TAAATTAAATATAATAAAA
1 TAAAATAAAAATAATAAAA
11352718 GAATAAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAATAAAAATAATAAAAAT
Found at i:11356836 original size:34 final size:34
Alignment explanation
Indices: 11356789--11356856 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
11356779 TTTCCGGAGA
11356789 TAATTGAAAACTTGTATTACTCAGAAATATTTGT
1 TAATTGAAAACTTGTATTACTCAGAAATATTTGT
*
11356823 TAATT-AAAGACTTGTATTACTTAGAAATATTTGT
1 TAATTGAAA-ACTTGTATTACTCAGAAATATTTGT
11356857 GATTAAGTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 3 0.09
34 29 0.91
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (34 bp):
TAATTGAAAACTTGTATTACTCAGAAATATTTGT
Found at i:11361785 original size:2 final size:2
Alignment explanation
Indices: 11361780--11361808 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11361770 GTGTGTGTGT
11361780 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
11361809 CGCGAGAGCG
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:11363478 original size:29 final size:29
Alignment explanation
Indices: 11363445--11363593 Score: 116
Period size: 32 Copynumber: 5.3 Consensus size: 29
11363435 TTGAATATGA
11363445 CGTGTAACAACAATATTTTTTCAACATGG
1 CGTGTAACAACAATATTTTTTCAACATGG
* * * *
11363474 TGTGTAATAACAGTGTTTTTTTTTCAACATGG
1 CGTGTAACAACA---ATATTTTTTCAACATGG
*
11363506 CGTGTAACAAC--T-TTTTTTAAACATGG
1 CGTGTAACAACAATATTTTTTCAACATGG
* * *
11363532 CGTGT---AAC-ATGTTTTTT-TACATGA
1 CGTGTAACAACAATATTTTTTCAACATGG
* *
11363556 CGTGTAACAACAGTATTTTTTTAACATGG
1 CGTGTAACAACAATATTTTTTCAACATGG
*
11363585 TGTGTAACA
1 CGTGTAACA
11363594 GCCTAACCAT
Statistics
Matches: 96, Mismatches: 14, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
23 3 0.03
24 11 0.11
25 6 0.06
26 18 0.19
27 4 0.04
28 7 0.07
29 23 0.24
32 24 0.25
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (29 bp):
CGTGTAACAACAATATTTTTTCAACATGG
Found at i:11363528 original size:26 final size:25
Alignment explanation
Indices: 11363491--11363593 Score: 109
Period size: 26 Copynumber: 3.9 Consensus size: 25
11363481 TAACAGTGTT
11363491 TTTTTTTCAACATGGCGTGTAACAAC
1 TTTTTTT-AACATGGCGTGTAACAAC
**
11363517 TTTTTTTAAACATGGCGTGTAACATG
1 TTTTTTT-AACATGGCGTGTAACAAC
*
11363543 TTTTTTT-ACATGACGTGTAACAAC
1 TTTTTTTAACATGGCGTGTAACAAC
*
11363567 AGTATTTTTTTAACATGGTGTGTAACA
1 ----TTTTTTTAACATGGCGTGTAACA
11363594 GCCTAACCAT
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
24 14 0.22
26 30 0.47
28 7 0.11
29 13 0.20
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (25 bp):
TTTTTTTAACATGGCGTGTAACAAC
Found at i:11363594 original size:26 final size:26
Alignment explanation
Indices: 11363453--11363594 Score: 85
Period size: 26 Copynumber: 5.2 Consensus size: 26
11363443 GACGTGTAAC
* *
11363453 AACAATATTTTTTCAACATGGTGTGTAAT
1 AACAGTATTTTTTTAACATGGTGTG---T
* *
11363482 AACAGTGTTTTTTTTTCAACATGGCGTGT
1 AACA--GTATTTTTTT-AACATGGTGTGT
*
11363511 AACA--ACTTTTTTTAAACATGGCGTGT
1 AACAGTA-TTTTTTT-AACATGGTGTGT
* **
11363537 AACA-TGTTTTTTT-ACATGACGTGTAAC
1 AACAGTATTTTTTTAACATG--GTGT-GT
11363564 AACAGTATTTTTTTAACATGGTGTGT
1 AACAGTATTTTTTTAACATGGTGTGT
11363590 AACAG
1 AACAG
11363595 CCTAACCATG
Statistics
Matches: 90, Mismatches: 13, Indels: 23
0.71 0.10 0.18
Matches are distributed among these distances:
24 5 0.06
26 38 0.42
27 8 0.09
28 8 0.09
29 14 0.16
31 7 0.08
32 10 0.11
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (26 bp):
AACAGTATTTTTTTAACATGGTGTGT
Found at i:11363647 original size:43 final size:44
Alignment explanation
Indices: 11363586--11363752 Score: 185
Period size: 45 Copynumber: 3.8 Consensus size: 44
11363576 TTAACATGGT
* * *
11363586 GTGTAACAGCCTAACCATGACGTGTA-ATATGTTTGTATATGGC
1 GTGTAACAACCTAACCATGACGTGTACACATGTTTGTATATAGC
* * * * * *
11363629 GTGTAACAACTTAACCATGGCGTATCACACGTTTTTGTACATAGC
1 GTGTAACAACCTAACCATGACGTGT-ACACATGTTTGTATATAGC
* *
11363674 GTGTAACAACCTAACCATGACGTGTTACACTTTTTTGTATATAGC
1 GTGTAACAACCTAACCATGACGTG-TACACATGTTTGTATATAGC
* *
11363719 GTGTAACAACCTAACCATGGCGTTTA-ACATGTTT
1 GTGTAACAACCTAACCATGACGTGTACACATGTTT
11363753 CTGTAAACGG
Statistics
Matches: 103, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
43 27 0.26
44 3 0.03
45 72 0.70
46 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (44 bp):
GTGTAACAACCTAACCATGACGTGTACACATGTTTGTATATAGC
Found at i:11363679 original size:45 final size:45
Alignment explanation
Indices: 11363617--11363741 Score: 187
Period size: 45 Copynumber: 2.8 Consensus size: 45
11363607 GTGTAATATG
* *
11363617 TTTGTATATGGCGTGTAACAACTTAACCATGGCGTATCACACGTT
1 TTTGTATATAGCGTGTAACAACCTAACCATGGCGTATCACACGTT
* * * * *
11363662 TTTGTACATAGCGTGTAACAACCTAACCATGACGTGTTACACTTT
1 TTTGTATATAGCGTGTAACAACCTAACCATGGCGTATCACACGTT
11363707 TTTGTATATAGCGTGTAACAACCTAACCATGGCGT
1 TTTGTATATAGCGTGTAACAACCTAACCATGGCGT
11363742 TTAACATGTT
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (45 bp):
TTTGTATATAGCGTGTAACAACCTAACCATGGCGTATCACACGTT
Found at i:11363774 original size:27 final size:27
Alignment explanation
Indices: 11363736--11363791 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
11363726 AACCTAACCA
*
11363736 TGGCGTTTAACATGTTTCTGTAAACGG
1 TGGCGTGTAACATGTTTCTGTAAACGG
11363763 TGGCGTGTAACATGTTTCTGTAAACGG
1 TGGCGTGTAACATGTTTCTGTAAACGG
11363790 TG
1 TG
11363792 TGTAACATCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (27 bp):
TGGCGTGTAACATGTTTCTGTAAACGG
Found at i:11363799 original size:24 final size:25
Alignment explanation
Indices: 11363743--11363799 Score: 89
Period size: 27 Copynumber: 2.2 Consensus size: 25
11363733 CCATGGCGTT
11363743 TAACATGTTTCTGTAAACGGTGGCGTG
1 TAACATGTTTCTGTAAACGGT-G-GTG
11363770 TAACATGTTTCTGTAAACGGT-GTG
1 TAACATGTTTCTGTAAACGGTGGTG
11363794 TAACAT
1 TAACAT
11363800 CCTAGCATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 9 0.30
27 21 0.70
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (25 bp):
TAACATGTTTCTGTAAACGGTGGTG
Found at i:11364133 original size:25 final size:25
Alignment explanation
Indices: 11364059--11364217 Score: 123
Period size: 25 Copynumber: 6.4 Consensus size: 25
11364049 GTTTTGACGA
*
11364059 CTTGAT-T-TTGATCATGAACTAT-A
1 CTTGATATCTTGATCATGAACT-TCG
* * *
11364082 CTTGATATCTTAATCA-CAAATATCG
1 CTTGATATCTTGATCATGAACT-TCG
** * *
11364107 CTTGATATCTTGATTGTGGACTGCG
1 CTTGATATCTTGATCATGAACTTCG
*
11364132 CTT-AGTATCTTGATCATGAACTTTG
1 CTTGA-TATCTTGATCATGAACTTCG
** *
11364157 CTTGATATCTTGATTGTGGACTTCG
1 CTTGATATCTTGATCATGAACTTCG
*
11364182 C-TCAGTATCTTGATCATGAACTTCG
1 CTTGA-TATCTTGATCATGAACTTCG
11364207 CTTGATATCTT
1 CTTGATATCTT
11364218 CACTTCATAA
Statistics
Matches: 103, Mismatches: 25, Indels: 14
0.73 0.18 0.10
Matches are distributed among these distances:
23 6 0.06
24 9 0.09
25 83 0.81
26 5 0.05
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.42
Consensus pattern (25 bp):
CTTGATATCTTGATCATGAACTTCG
Found at i:11364142 original size:50 final size:50
Alignment explanation
Indices: 11364104--11364217 Score: 201
Period size: 50 Copynumber: 2.3 Consensus size: 50
11364094 ATCACAAATA
*
11364104 TCGCTTGATATCTTGATTGTGGACTGCGCTTAGTATCTTGATCATGAACT
1 TCGCTTGATATCTTGATTGTGGACTGCGCTCAGTATCTTGATCATGAACT
* *
11364154 TTGCTTGATATCTTGATTGTGGACTTCGCTCAGTATCTTGATCATGAACT
1 TCGCTTGATATCTTGATTGTGGACTGCGCTCAGTATCTTGATCATGAACT
11364204 TCGCTTGATATCTT
1 TCGCTTGATATCTT
11364218 CACTTCATAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.42
Consensus pattern (50 bp):
TCGCTTGATATCTTGATTGTGGACTGCGCTCAGTATCTTGATCATGAACT
Found at i:11364374 original size:10 final size:11
Alignment explanation
Indices: 11364346--11364378 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
11364336 GATGATGTAT
11364346 TTTTTAAAATTA
1 TTTTT-AAATTA
11364358 TTTTTAAATTA
1 TTTTTAAATTA
11364369 -TTTTAAATTA
1 TTTTTAAATTA
11364379 ATTAGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 6 0.29
12 5 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTTAAATTA
Found at i:11364677 original size:80 final size:80
Alignment explanation
Indices: 11364514--11364736 Score: 272
Period size: 80 Copynumber: 2.8 Consensus size: 80
11364504 AATTTGATTG
* * * * * *
11364514 TTATCTCTAAAATATCAT-AATCATTAGAGATAAATTAGATGACCAGTAATTAAATTTTAATTCG
1 TTATCTCTAAATTATCTTGATTTATTAGAGATAAATTAGATGACCAATAATTAAATTTTGA-TCG
* *
11364578 TTTAAAAATATGAATA
65 GTAAAAAATATGAATA
* *
11364594 TTATCTCTAAATTATCTTGATTTATTCAGAGATAAATTGGATGAACAATAATTAAATTTTGAT-G
1 TTATCTCTAAATTATCTTGATTTATT-AGAGATAAATTAGATGACCAATAATTAAATTTTGATCG
11364658 GTAAAAAATATGAATA
65 GTAAAAAATATGAATA
* * *
11364674 TTATCTCTAAATTACCTTGATTTATTTAAAG-TGAAATTAGATGACCGATAATTAAATTTTGAT
1 TTATCTCTAAATTATCTTGATTTA-TTAGAGAT-AAATTAGATGACCAATAATTAAATTTTGAT
11364737 TGGTCCAATT
Statistics
Matches: 124, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
79 1 0.01
80 84 0.68
81 8 0.06
82 31 0.25
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (80 bp):
TTATCTCTAAATTATCTTGATTTATTAGAGATAAATTAGATGACCAATAATTAAATTTTGATCGG
TAAAAAATATGAATA
Found at i:11365159 original size:33 final size:33
Alignment explanation
Indices: 11365116--11365241 Score: 118
Period size: 33 Copynumber: 4.0 Consensus size: 33
11365106 AAAACTATTC
*
11365116 GAAGAAGTATATTACAATACAACGATAATCTTA
1 GAAGAAGTATATTACAATAAAACGATAATCTTA
* * * *
11365149 GAAGATGTATATTGCAATAAAACTATAATCTTG
1 GAAGAAGTATATTACAATAAAACGATAATCTTA
* * * *
11365182 GAATAATTATATTGCAATAAAA--AT-GT-TT-
1 GAAGAAGTATATTACAATAAAACGATAATCTTA
* *
11365210 GAAGAAGTATATTGCAATAAAACTATAATCTT
1 GAAGAAGTATATTACAATAAAACGATAATCTT
11365242 GGAAAAATTA
Statistics
Matches: 77, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
28 20 0.26
29 2 0.03
30 3 0.04
31 3 0.04
32 2 0.03
33 47 0.61
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.33
Consensus pattern (33 bp):
GAAGAAGTATATTACAATAAAACGATAATCTTA
Found at i:11365991 original size:36 final size:35
Alignment explanation
Indices: 11365929--11366054 Score: 144
Period size: 36 Copynumber: 3.5 Consensus size: 35
11365919 CATTTGAAAA
* * *
11365929 ATGCTCTTTACAATAACACTTTTTGATCCATGAAGG
1 ATGCTCTTTATAATAACACTTGTTGATCCTTG-AGG
* * *
11365965 TTGCTTTTTATAATAACACTTGTTGATCTTTGGAGG
1 ATGCTCTTTATAATAACACTTGTTGATCCTT-GAGG
* * *
11366001 GTGCTCTTTATAATAACATTTGTTGATCCTTGTGG
1 ATGCTCTTTATAATAACACTTGTTGATCCTTGAGG
*
11366036 ATGCTTTTTATAATAACAC
1 ATGCTCTTTATAATAACAC
11366055 ACAATTTAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
35 19 0.25
36 55 0.73
37 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (35 bp):
ATGCTCTTTATAATAACACTTGTTGATCCTTGAGG
Found at i:11369288 original size:14 final size:14
Alignment explanation
Indices: 11369257--11369295 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
11369247 AATCAATATC
*
11369257 AATTAACT-AAATT
1 AATTAACTAAAAAT
11369270 AATTAACTAAAAAT
1 AATTAACTAAAAAT
*
11369284 AATTAACCAAAA
1 AATTAACTAAAA
11369296 TTAAAACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (14 bp):
AATTAACTAAAAAT
Found at i:11370426 original size:20 final size:20
Alignment explanation
Indices: 11370383--11370440 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
11370373 CTCCTACAAA
* * *
11370383 AACATAAAAATAAAAATAAAT
1 AACAT-AAAATAAACATTATT
*
11370404 AACATAAAATCAACATTATT
1 AACATAAAATAAACATTATT
*
11370424 AACTTAAAATAAACATT
1 AACATAAAATAAACATT
11370441 TAAATATAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
20 26 0.84
21 5 0.16
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (20 bp):
AACATAAAATAAACATTATT
Found at i:11375307 original size:77 final size:77
Alignment explanation
Indices: 11375180--11375325 Score: 276
Period size: 77 Copynumber: 1.9 Consensus size: 77
11375170 AGGACTAAGA
11375180 AAGTATGCTTATACAATTTAGTAAGAGCCCATGTCTTTCTCTGAGTACCATATGGATGTGTTGGA
1 AAGTATGCTTATACAATTTAGTAAGAGCCCATGTCTTTCTCTGAGTACCATATGGATGTGTTGGA
11375245 ACATTCATGCTT
66 ACATTCATGCTT
11375257 AAGTATGCTTATACAATTTAGTAAGAGCCTC-TGTCTTTCTCTGAGTACCATATGGATGTGTTGG
1 AAGTATGCTTATACAATTTAGTAAGAGCC-CATGTCTTTCTCTGAGTACCATATGGATGTGTTGG
11375321 AACAT
65 AACAT
11375326 CCGTGCTTGA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
77 67 0.99
78 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (77 bp):
AAGTATGCTTATACAATTTAGTAAGAGCCCATGTCTTTCTCTGAGTACCATATGGATGTGTTGGA
ACATTCATGCTT
Found at i:11375648 original size:25 final size:25
Alignment explanation
Indices: 11375602--11375991 Score: 207
Period size: 25 Copynumber: 15.2 Consensus size: 25
11375592 TGACAACTTG
* * *
11375602 ATCTTGATCAC-AAATTATACTTAAT
1 ATCTTGATCACGAACTT-CACTTGAT
*
11375627 ATCTTGATCATGAACTTCACTTGAT
1 ATCTTGATCACGAACTTCACTTGAT
* * **
11375652 ATCTTCGTTTCAATGGTCTTGACAACTTG--
1 ATCTT-G-ATC-ACGAACTT--C-ACTTGAT
11375681 ATCTTGATC-CTGAACTAT-ACTTGAT
1 ATCTTGATCAC-GAACT-TCACTTGAT
* **
11375706 ATCTTAATCATAAACTTCACTTGAT
1 ATCTTGATCACGAACTTCACTTGAT
* * *
11375731 ATTTTGATCACGAACTCCACTTGGT
1 ATCTTGATCACGAACTTCACTTGAT
* *
11375756 ATCTTGATCGCGGACTTTGCTGCCACTTGAT
1 ATCTTGATCACGAAC--T--T--CACTTGAT
* *
11375787 ATCTTGGTCATGAACTTCGA-TTGAT
1 ATCTTGATCACGAACTTC-ACTTGAT
** * ** *
11375812 ATCTTGGCCATGAACTTTGCTTGCT
1 ATCTTGATCACGAACTTCACTTGAT
* * *
11375837 ATCTTGATCACAAACTTCGCTTGTT
1 ATCTTGATCACGAACTTCACTTGAT
* * *
11375862 ATCTCGATCACGAACTTCGCTTGCT
1 ATCTTGATCACGAACTTCACTTGAT
* * * *
11375887 ATCTCGATCACAAACTTCGCTTGTT
1 ATCTTGATCACGAACTTCACTTGAT
* * *
11375912 ATCTCGATCACGAACTTCGCTTGCT
1 ATCTTGATCACGAACTTCACTTGAT
* * *
11375937 ATCTCGATCACGAACTTCGCTTGCT
1 ATCTTGATCACGAACTTCACTTGAT
* **
11375962 ATCTTGATCATGAACTTTGCTTGAT
1 ATCTTGATCACGAACTTCACTTGAT
11375987 ATCTT
1 ATCTT
11375992 CACGTTAGAA
Statistics
Matches: 294, Mismatches: 50, Indels: 42
0.76 0.13 0.11
Matches are distributed among these distances:
23 5 0.02
24 1 0.00
25 235 0.80
26 9 0.03
27 7 0.02
28 7 0.02
29 6 0.02
30 1 0.00
31 23 0.08
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.38
Consensus pattern (25 bp):
ATCTTGATCACGAACTTCACTTGAT
Found at i:11375686 original size:79 final size:79
Alignment explanation
Indices: 11375555--11375732 Score: 261
Period size: 79 Copynumber: 2.3 Consensus size: 79
11375545 TTGGTTTTGG
* *
11375555 TCATGAACTTCGCTTGATATCTTCGCTTTAAGGGTCTTGACAACTTGATCTTGATCAC-AAATTA
1 TCATGAACTTCACTTGATATCTTCGCTTTAAGGGTCTTGACAACTTGATCTTGATC-CTAAACTA
*
11375619 TACTTAATATCTTGA
65 TACTTAATATCTTAA
* *
11375634 TCATGAACTTCACTTGATATCTTCG-TTTCAATGGTCTTGACAACTTGATCTTGATCCTGAACTA
1 TCATGAACTTCACTTGATATCTTCGCTTT-AAGGGTCTTGACAACTTGATCTTGATCCTAAACTA
*
11375698 TACTTGATATCTTAA
65 TACTTAATATCTTAA
*
11375713 TCATAAACTTCACTTGATAT
1 TCATGAACTTCACTTGATAT
11375733 TTTGATCACG
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
78 4 0.04
79 86 0.96
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (79 bp):
TCATGAACTTCACTTGATATCTTCGCTTTAAGGGTCTTGACAACTTGATCTTGATCCTAAACTAT
ACTTAATATCTTAA
Found at i:11375853 original size:50 final size:50
Alignment explanation
Indices: 11375823--11375991 Score: 257
Period size: 50 Copynumber: 3.4 Consensus size: 50
11375813 TCTTGGCCAT
*
11375823 GAACTTTGCTTGCTATCTTGATCACAAACTTCGCTTGTTATCTCGATCAC
1 GAACTTCGCTTGCTATCTTGATCACAAACTTCGCTTGTTATCTCGATCAC
*
11375873 GAACTTCGCTTGCTATCTCGATCACAAACTTCGCTTGTTATCTCGATCAC
1 GAACTTCGCTTGCTATCTTGATCACAAACTTCGCTTGTTATCTCGATCAC
* * * * *
11375923 GAACTTCGCTTGCTATCTCGATCACGAACTTCGCTTGCTATCTTGATCAT
1 GAACTTCGCTTGCTATCTTGATCACAAACTTCGCTTGTTATCTCGATCAC
* *
11375973 GAACTTTGCTTGATATCTT
1 GAACTTCGCTTGCTATCTT
11375992 CACGTTAGAA
Statistics
Matches: 110, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 110 1.00
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (50 bp):
GAACTTCGCTTGCTATCTTGATCACAAACTTCGCTTGTTATCTCGATCAC
Found at i:11375903 original size:75 final size:75
Alignment explanation
Indices: 11375824--11375991 Score: 255
Period size: 75 Copynumber: 2.2 Consensus size: 75
11375814 CTTGGCCATG
* *
11375824 AACTTTGCTTGCTATCTTGATCACAAACTTCGCTTGTTATCTCGATCACGAACTTCGCTTGCTAT
1 AACTTTGCTTGATATCTTGATCACAAACTTCGCTTGCTATCTCGATCACGAACTTCGCTTGCTAT
11375889 CTCGATCACA
66 CTCGATCACA
* * * *
11375899 AACTTCGCTTGTTATCTCGATCACGAACTTCGCTTGCTATCTCGATCACGAACTTCGCTTGCTAT
1 AACTTTGCTTGATATCTTGATCACAAACTTCGCTTGCTATCTCGATCACGAACTTCGCTTGCTAT
* **
11375964 CTTGATCATG
66 CTCGATCACA
11375974 AACTTTGCTTGATATCTT
1 AACTTTGCTTGATATCTT
11375992 CACGTTAGAA
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 82 1.00
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.38
Consensus pattern (75 bp):
AACTTTGCTTGATATCTTGATCACAAACTTCGCTTGCTATCTCGATCACGAACTTCGCTTGCTAT
CTCGATCACA
Found at i:11376422 original size:82 final size:81
Alignment explanation
Indices: 11376336--11376519 Score: 262
Period size: 81 Copynumber: 2.3 Consensus size: 81
11376326 TTAAATGATT
* *
11376336 AATAATTAAATTTTGATTGGTCAAAAAATATGAATATTATCTCTAAATTACCTT-GATTTATTTA
1 AATAATTAAATTTTGATTGGT-AAAAAATATGAATATTATCTATAAATTA-CTTAAATTTATTTA
** * *
11376400 GAGGTAAATCGAATGACC
64 GAAATAAATCAAATAACC
*
11376418 AATAATTAAATTTTGATTAGTAAAAAATATGAATATTATCTATAAATTACTTAAATTTATTTAGA
1 AATAATTAAATTTTGATTGGTAAAAAATATGAATATTATCTATAAATTACTTAAATTTATTTAGA
* *
11376483 AATAAATTAAATAATC
66 AATAAATCAAATAACC
11376499 AATAATTAAATTTTGATTGGT
1 AATAATTAAATTTTGATTGGT
11376520 TCAATTTAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
80 3 0.03
81 68 0.75
82 20 0.22
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (81 bp):
AATAATTAAATTTTGATTGGTAAAAAATATGAATATTATCTATAAATTACTTAAATTTATTTAGA
AATAAATCAAATAACC
Found at i:11377800 original size:25 final size:25
Alignment explanation
Indices: 11377765--11377826 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
11377755 AAAGAAACAC
*
11377765 AGTCTAATGATACAATAATAGCCAA
1 AGTCTAATGATACAATAATACCCAA
* *
11377790 AGTCTAGTGATGCAATAATACCCAA
1 AGTCTAATGATACAATAATACCCAA
11377815 AGTCTAATGATA
1 AGTCTAATGATA
11377827 TCCAGGTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.26
Consensus pattern (25 bp):
AGTCTAATGATACAATAATACCCAA
Found at i:11383429 original size:2 final size:2
Alignment explanation
Indices: 11383422--11383446 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11383412 CTTAAGTATC
11383422 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 A
11383447 ACAATATTCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11385213 original size:17 final size:19
Alignment explanation
Indices: 11385191--11385231 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
11385181 AGGTAAAATT
*
11385191 ATAAAAAT-T-TTTTAAAA
1 ATAAAAATATATTATAAAA
11385208 ATAAAAATATATTATAAAA
1 ATAAAAATATATTATAAAA
11385227 ATAAA
1 ATAAA
11385232 TTATAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 1 0.05
19 12 0.57
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAAAATATATTATAAAA
Found at i:11385226 original size:13 final size:13
Alignment explanation
Indices: 11385208--11385239 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
11385198 TTTTTTAAAA
*
11385208 ATAAAAATATATT
1 ATAAAAATAAATT
11385221 ATAAAAATAAATT
1 ATAAAAATAAATT
11385234 ATAAAA
1 ATAAAA
11385240 TTTTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAAAATAAATT
Found at i:11385238 original size:43 final size:43
Alignment explanation
Indices: 11385186--11385271 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
11385176 ATAAGAGGTA
11385186 AAATTATAAAAATTTTTT-AAAAATAAAAATATATT-ATAAAAAT
1 AAATTATAAAAATTTTTTAAAAAATAAAAAT-TATTGA-AAAAAT
*
11385229 AAATTATAAAATTTTTTTAAAAAATAAAAATTATTGAAAAAAT
1 AAATTATAAAAATTTTTTAAAAAATAAAAATTATTGAAAAAAT
11385272 TTTAAAATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
43 27 0.68
44 13 0.32
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (43 bp):
AAATTATAAAAATTTTTTAAAAAATAAAAATTATTGAAAAAAT
Found at i:11391991 original size:20 final size:21
Alignment explanation
Indices: 11391959--11392002 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
11391949 TAAGATTGTT
11391959 AGAAATATTTGAGAAGAAAGA
1 AGAAATATTTGAGAAGAAAGA
11391980 AGAAAT-TTTGAGAAGAAAGA
1 AGAAATATTTGAGAAGAAAGA
11392000 AGA
1 AGA
11392003 GTGTGACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.18
Consensus pattern (21 bp):
AGAAATATTTGAGAAGAAAGA
Found at i:11405796 original size:21 final size:22
Alignment explanation
Indices: 11405767--11405810 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
11405757 GAGCGATTAA
11405767 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
11405788 TTTATGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
11405810 T
1 T
11405811 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:11410131 original size:19 final size:19
Alignment explanation
Indices: 11410103--11410149 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
11410093 TTTTAGAATC
11410103 TTTT-GTTCAAATGAATTG
1 TTTTAGTTCAAATGAATTG
11410121 TTTTAGTTCAAATGAATTG
1 TTTTAGTTCAAATGAATTG
11410140 TTTTAGTTCA
1 TTTTAGTTCA
11410150 GTGTAGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (19 bp):
TTTTAGTTCAAATGAATTG
Found at i:11413273 original size:19 final size:20
Alignment explanation
Indices: 11413251--11413293 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
11413241 CGATGATAGG
11413251 TAAAAAGAATATTTCA-AAA
1 TAAAAAGAATATTTCATAAA
* *
11413270 T-AAAATAATATTTTATAAA
1 TAAAAAGAATATTTCATAAA
11413289 TAAAA
1 TAAAA
11413294 TATTATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 12 0.60
19 5 0.25
20 3 0.15
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
TAAAAAGAATATTTCATAAA
Found at i:11413279 original size:18 final size:19
Alignment explanation
Indices: 11413253--11413300 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
11413243 ATGATAGGTA
*
11413253 AAAAGAATATTTCA-AAAT
1 AAAATAATATTTCATAAAT
*
11413271 AAAATAATATTTTATAAAT
1 AAAATAATATTTCATAAAT
*
11413290 AAAATATTATT
1 AAAATAATATT
11413301 AAAATATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAATAATATTTCATAAAT
Found at i:11413297 original size:16 final size:17
Alignment explanation
Indices: 11413276--11413318 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
11413266 AAAATAAAAT
11413276 AATATTTTATAAATA-A
1 AATATTTTATAAATATA
*
11413292 AATATTATTA-AAATATT
1 AATATT-TTATAAATATA
11413309 AATATTTTAT
1 AATATTTTAT
11413319 TTATTAGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATATTTTATAAATATA
Found at i:11416635 original size:21 final size:20
Alignment explanation
Indices: 11416606--11416649 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
11416596 AATGATAGCA
11416606 TCATACAAAGTCAAACAACTC
1 TCATACAAAGTCAAACAAC-C
* *
11416627 TCATTCAAAGTCAAGCAACC
1 TCATACAAAGTCAAACAACC
11416647 TCA
1 TCA
11416650 CTCCGAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.43, C:0.30, G:0.07, T:0.20
Consensus pattern (20 bp):
TCATACAAAGTCAAACAACC
Found at i:11423945 original size:21 final size:20
Alignment explanation
Indices: 11423920--11423963 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
11423910 TTAAATTAAG
11423920 TTATTTTAG-TTTAAGTTTACT
1 TTATTTT-GCTTTAA-TTTACT
11423941 TTATTTTGCTTTAATTTACT
1 TTATTTTGCTTTAATTTACT
11423961 TTA
1 TTA
11423964 CGAAGAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.64
Consensus pattern (20 bp):
TTATTTTGCTTTAATTTACT
Found at i:11426923 original size:20 final size:20
Alignment explanation
Indices: 11426891--11426940 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
11426881 AAAAACCTTT
*
11426891 TACATACATACATACATACA
1 TACATATATACATACATACA
*
11426911 TATATATATACATACATACA
1 TACATATATACATACATACA
11426931 TACATATATA
1 TACATATATA
11426941 TAACTGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (20 bp):
TACATATATACATACATACA
Found at i:11426926 original size:24 final size:24
Alignment explanation
Indices: 11426894--11426942 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
11426884 AACCTTTTAC
11426894 ATACATACATACATACATATATAT
1 ATACATACATACATACATATATAT
11426918 ATACATACATACATACATATATAT
1 ATACATACATACATACATATATAT
11426942 A
1 A
11426943 ACTGAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (24 bp):
ATACATACATACATACATATATAT
Found at i:11426942 original size:4 final size:4
Alignment explanation
Indices: 11426891--11426936 Score: 74
Period size: 4 Copynumber: 11.5 Consensus size: 4
11426881 AAAAACCTTT
* *
11426891 TACA TACA TACA TACA TACA TATA TATA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
11426937 TATATAACTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (4 bp):
TACA
Found at i:11429640 original size:2 final size:2
Alignment explanation
Indices: 11429633--11429682 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
11429623 TGAGTCTGTA
11429633 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
11429675 AT AT AT AT
1 AT AT AT AT
11429683 TAAAAGGTAC
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:11435477 original size:102 final size:102
Alignment explanation
Indices: 11435287--11435596 Score: 469
Period size: 102 Copynumber: 3.0 Consensus size: 102
11435277 TATTTACACT
*
11435287 TATTTCATTAAATAAAATTTAATACTTATTTTAAATGGATACGATTTTATATTATTTGTT-AATT
1 TATTTCAATAAATAAAATTTAATACTTATTTTAAATGGATACGATTTTATATTATTT-TTGAATT
* * * * *
11435351 AAATTAAAAGGAACAATGACAAAATTTTACTCATTAGA
65 AAATTAAAAAGTATAATGATAAAATTTTACTCATTAAA
* *
11435389 TATTTCAATAAATAAAATTTAGTATTTATTTTAAATGGATACGATTTTATATTATTTTTGAATTA
1 TATTTCAATAAATAAAATTTAATACTTATTTTAAATGGATACGATTTTATATTATTTTTGAATTA
* *
11435454 AATTAAAAAGTATAATGGTAAAATTTTACACATTAAA
66 AATTAAAAAGTATAATGATAAAATTTTACTCATTAAA
* * * *
11435491 TATTTCAATAAATAAAATTTACTACTTATTTTAAATGGATATGATTTTATATTATTATTGAATTC
1 TATTTCAATAAATAAAATTTAATACTTATTTTAAATGGATACGATTTTATATTATTTTTGAATTA
*
11435556 AATTAAAAAGTATAATGATAAAATTTTACTCAATAAA
66 AATTAAAAAGTATAATGATAAAATTTTACTCATTAAA
11435593 TATT
1 TATT
11435597 ATCTATAACT
Statistics
Matches: 189, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
101 2 0.01
102 187 0.99
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (102 bp):
TATTTCAATAAATAAAATTTAATACTTATTTTAAATGGATACGATTTTATATTATTTTTGAATTA
AATTAAAAAGTATAATGATAAAATTTTACTCATTAAA
Found at i:11435829 original size:175 final size:175
Alignment explanation
Indices: 11435432--11435842 Score: 462
Period size: 175 Copynumber: 2.4 Consensus size: 175
11435422 AATGGATACG
*
11435432 ATTTTATATTATTTTTGAATTAAATTAAAAAGTATAATGGTAAAATTTTACACATTAAATATTTC
1 ATTTTATATTATTTTTGAATTAAATTAAAAAGTATAATGATAAAATTTTACACATTAAATATTTC
* * ** * *
11435497 AATAAATAAAATTTACTACTTATTTTAAATGGATATGATTTTATATTATTATTGAATTCAATTAA
66 AATAAATAAAATCTAATACTTATTTTAAACAGATACGATTTTATATTATTATTGAATTAAATTAA
* *
11435562 AAAGTATAATGATAAAATTTTACTCAATAAATATTATCTATAACT
131 AAAGTATAATGATAAAATTTTACTCAATAAATATTATCAATAAAT
** * * * * * ** * * *
11435607 ACCTTA-CTTATTTTAAATGGATAAAATTATATA-T-TAA-CCTTAAATTTT-TA-TTTAACACT
1 ATTTTATATTATTTT---TGAATTAAATTAAAAAGTATAATGATAAAATTTTACACATTAA-A--
11435666 TATTTCAATAAATAAAATCTAATACTTATTTTAAACAGATACGATTTTATATTACTT-TTGAATT
60 TATTTCAATAAATAAAATCTAATACTTATTTTAAACAGATACGATTTTATATTA-TTATTGAATT
* *
11435730 AAATTAAAAAGTATAATGATAAAATTTTACTTATTAAATATT-TCAATACAAT
124 AAATTAAAAAGTATAATGATAAAATTTTACTCAATAAATATTATCAATA-AAT
* *
11435782 -TTTTATATTATTTTTGAATTAAATTAAAAAGTATAATGATAAAATTTTACTCTTTAAATAT
1 ATTTTATATTATTTTTGAATTAAATTAAAAAGTATAATGATAAAATTTTACACATTAAATAT
11435843 GATCTATTAC
Statistics
Matches: 188, Mismatches: 34, Indels: 29
0.75 0.14 0.12
Matches are distributed among these distances:
172 16 0.09
173 3 0.02
174 29 0.15
175 119 0.63
176 4 0.02
177 17 0.09
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.45
Consensus pattern (175 bp):
ATTTTATATTATTTTTGAATTAAATTAAAAAGTATAATGATAAAATTTTACACATTAAATATTTC
AATAAATAAAATCTAATACTTATTTTAAACAGATACGATTTTATATTATTATTGAATTAAATTAA
AAAGTATAATGATAAAATTTTACTCAATAAATATTATCAATAAAT
Found at i:11436020 original size:26 final size:27
Alignment explanation
Indices: 11435989--11436044 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 27
11435979 ACTCTTATCT
11435989 TTTTAT-TAT-ACTCAAATAAATTCTTA
1 TTTTATATATGACTCAAATAAATT-TTA
*
11436015 TTTTATGATTTGACTCAAATAAATTTTA
1 TTTTAT-ATATGACTCAAATAAATTTTA
11436043 TT
1 TT
11436045 GAACAAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 6 0.23
28 7 0.27
29 13 0.50
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.52
Consensus pattern (27 bp):
TTTTATATATGACTCAAATAAATTTTA
Found at i:11448532 original size:14 final size:14
Alignment explanation
Indices: 11448513--11448570 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
11448503 TAATGTTATA
11448513 ATTAAAATAAAAAT
1 ATTAAAATAAAAAT
11448527 ATTAAAATAAAATAT
1 ATTAAAATAAAA-AT
*
11448542 ATATAATATAAAAAT
1 AT-TAAAATAAAAAT
* *
11448557 -TAAAAATTAAAAT
1 ATTAAAATAAAAAT
11448570 A
1 A
11448571 AACTAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
13 9 0.24
14 13 0.35
15 6 0.16
16 9 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
ATTAAAATAAAAAT
Found at i:11448553 original size:30 final size:31
Alignment explanation
Indices: 11448519--11448590 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 31
11448509 TATAATTAAA
* * *
11448519 ATAAAAATATTAAAA-TAAAATATA-TATAAT
1 ATAAAAAT-TAAAAATTAAAATAAACTAAAAT
11448549 ATAAAAATTAAAAATTAAAATAAACTAAAAT
1 ATAAAAATTAAAAATTAAAATAAACTAAAAT
11448580 ATAAGAAATTA
1 ATAA-AAATTA
11448591 CAATTTATAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 5 0.14
30 16 0.44
31 9 0.25
32 6 0.17
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (31 bp):
ATAAAAATTAAAAATTAAAATAAACTAAAAT
Found at i:11448642 original size:14 final size:15
Alignment explanation
Indices: 11448512--11448702 Score: 60
Period size: 15 Copynumber: 12.9 Consensus size: 15
11448502 ATAATGTTAT
11448512 AATTAAAATAAAA-A
1 AATTAAAATAAAATA
*
11448526 TATTAAAATAAAATA
1 AATTAAAATAAAATA
* * *
11448541 TA-TATAATATAA-A
1 AATTAAAATAAAATA
11448554 AATTAAAAATTAAAATA
1 AATT-AAAA-TAAAATA
* * *
11448571 AACTAAAATATAAGA
1 AATTAAAATAAAATA
* **
11448586 AATTACAAT-TTATA
1 AATTAAAATAAAATA
**
11448600 CAA-TATAGGTAAAATA
1 -AATTA-AAATAAAATA
11448616 AATTAAAATAAAATA
1 AATTAAAATAAAATA
* *
11448631 TA-TAATAT-AAA-A
1 AATTAAAATAAAATA
* * *
11448643 AATT-ATATTAAAGA
1 AATTAAAATAAAATA
*
11448657 AATGAAAATAAAATA
1 AATTAAAATAAAATA
*
11448672 TA-TAAGATTATAATAATA
1 AATTAA-A--ATAA-AATA
*
11448690 AATGAAAATAAAA
1 AATTAAAATAAAA
11448703 AACATGACAT
Statistics
Matches: 128, Mismatches: 31, Indels: 35
0.66 0.16 0.18
Matches are distributed among these distances:
12 6 0.05
13 9 0.07
14 37 0.29
15 43 0.34
16 17 0.13
17 8 0.06
18 6 0.05
19 2 0.02
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (15 bp):
AATTAAAATAAAATA
Found at i:11448673 original size:34 final size:33
Alignment explanation
Indices: 11448621--11448702 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 33
11448611 AAATAAATTA
*
11448621 AAAT-AAAATATATAATATAAAAAATTATATTAAAG
1 AAATGAAAATA-A-AATATAAAAAATTATAAT-AAG
* * *
11448656 AAATGAAAATAAAATATATAAGATTATAATAAT
1 AAATGAAAATAAAATATAAAAAATTATAATAAG
11448689 AAATGAAAATAAAA
1 AAATGAAAATAAAA
11448703 AACATGACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
33 16 0.38
34 15 0.36
35 5 0.12
36 6 0.14
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (33 bp):
AAATGAAAATAAAATATAAAAAATTATAATAAG
Found at i:11453834 original size:20 final size:20
Alignment explanation
Indices: 11453809--11453858 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
11453799 TGTATACCTT
11453809 AAAATTTAT-CATATTAATAA
1 AAAATTTATACAT-TTAATAA
11453829 AAAA-TTATTACATTTAATAA
1 AAAATTTA-TACATTTAATAA
11453849 AAAATATTAT
1 AAAAT-TTAT
11453859 TCCAAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 3 0.12
20 16 0.62
21 4 0.15
22 3 0.12
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATTTATACATTTAATAA
Found at i:11455581 original size:15 final size:15
Alignment explanation
Indices: 11455561--11455593 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11455551 AGCAATTTTC
11455561 ATGCTATATTGCTGG
1 ATGCTATATTGCTGG
11455576 ATGCTATATTGCTGG
1 ATGCTATATTGCTGG
11455591 ATG
1 ATG
11455594 TTATGTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.12, G:0.27, T:0.39
Consensus pattern (15 bp):
ATGCTATATTGCTGG
Found at i:11459205 original size:12 final size:12
Alignment explanation
Indices: 11459188--11459225 Score: 67
Period size: 12 Copynumber: 3.1 Consensus size: 12
11459178 TCATAATGCT
11459188 ATAATTCTATAA
1 ATAATTCTATAA
11459200 ATAATTCTATAA
1 ATAATTCTATAA
11459212 ATAATTCTACTAA
1 ATAATTCTA-TAA
11459225 A
1 A
11459226 GGTTTTCGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 21 0.84
13 4 0.16
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAATTCTATAA
Found at i:11469047 original size:31 final size:31
Alignment explanation
Indices: 11469012--11469072 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
11469002 AAAATTACAT
11469012 ACCTACATATGTGACATAACATTATGAGATA
1 ACCTACATATGTGACATAACATTATGAGATA
11469043 ACCTACATATGTGACATAACATTATGAGAT
1 ACCTACATATGTGACATAACATTATGAGAT
11469073 TTTCAATCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (31 bp):
ACCTACATATGTGACATAACATTATGAGATA
Found at i:11483186 original size:2 final size:2
Alignment explanation
Indices: 11483179--11483208 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
11483169 TCTTTTCTCT
*
11483179 TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11483209 ATAAAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11483700 original size:15 final size:15
Alignment explanation
Indices: 11483677--11483707 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11483667 ACCCTTGCTT
11483677 ACCTCTAATGGTAGA
1 ACCTCTAATGGTAGA
*
11483692 ACCTTTAATGGTAGA
1 ACCTCTAATGGTAGA
11483707 A
1 A
11483708 AGAGACAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (15 bp):
ACCTCTAATGGTAGA
Found at i:11484739 original size:64 final size:64
Alignment explanation
Indices: 11484632--11484765 Score: 166
Period size: 64 Copynumber: 2.1 Consensus size: 64
11484622 TGCCCCCGAC
* * * *
11484632 AATTTTAAATTTTTATAACTTATCTTTATTTTTTGTGAGATTTTATAATTTTACCCTTATAA-A
1 AATTTTAAATTTTTATAACTTATCTTTATTTTTTATAAAATTTTATAATTTTACCCTTACAATA
* *
11484695 AATTTTAAAATATTTTA-AA-TATATTTTTATTTTTTATAAAATTTTATAATTTTATCCTTACAA
1 AATTTT-AAAT-TTTTATAACT-TATCTTTATTTTTTATAAAATTTTATAATTTTACCCTTACAA
11484758 TA
63 TA
11484760 AATTTT
1 AATTTT
11484766 TATTTAGTGA
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
63 7 0.11
64 42 0.69
65 12 0.20
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (64 bp):
AATTTTAAATTTTTATAACTTATCTTTATTTTTTATAAAATTTTATAATTTTACCCTTACAATA
Found at i:11487253 original size:3 final size:3
Alignment explanation
Indices: 11487245--11487273 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
11487235 CTTACTTACT
11487245 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11487274 CCCCTGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:11487851 original size:2 final size:2
Alignment explanation
Indices: 11487844--11487869 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11487834 GTGTTTGGTG
11487844 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
11487870 GAATGAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11491331 original size:11 final size:11
Alignment explanation
Indices: 11491315--11491353 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
11491305 AGTTATTATT
11491315 TTTTATAATAA
1 TTTTATAATAA
11491326 TTTTATAATAA
1 TTTTATAATAA
*
11491337 TTTCATAATAA
1 TTTTATAATAA
11491348 CTTTTA
1 -TTTTA
11491354 AATTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 21 0.84
12 4 0.16
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTATAATAA
Found at i:11509774 original size:31 final size:31
Alignment explanation
Indices: 11509737--11509796 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
11509727 ATATTGGTGA
*
11509737 AATTTTAAGCAACAATCAATAATACAATGTT
1 AATTTTAAACAACAATCAATAATACAATGTT
*
11509768 AATTTTAAACAACAATCAATAATGCAATG
1 AATTTTAAACAACAATCAATAATACAATG
11509797 CTACAATGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (31 bp):
AATTTTAAACAACAATCAATAATACAATGTT
Found at i:11510219 original size:20 final size:21
Alignment explanation
Indices: 11510195--11510245 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
11510185 AAGTTAAATA
11510195 AATTTATAAATTTATAA-AAT
1 AATTTATAAATTTATAATAAT
* *
11510215 TATTTAT-TATTTATAATAAT
1 AATTTATAAATTTATAATAAT
11510235 AATTTAATAAA
1 AATTT-ATAAA
11510246 AATTATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
19 8 0.33
20 13 0.54
21 2 0.08
22 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTTATAAATTTATAATAAT
Found at i:11510297 original size:59 final size:61
Alignment explanation
Indices: 11510232--11510345 Score: 180
Period size: 61 Copynumber: 1.9 Consensus size: 61
11510222 TATTTATAAT
*
11510232 AATAATTTAATAAAAA-TTATTTTAAGGATCTA-T-AAAAAATATATATAATATATTGCATC
1 AATAATTTAATAAAAATTTATTTTAAAG-TCTATTAAAAAAATATATATAATATATTGCATC
*
11510291 AATAATTTAATAAAAATTTATTTTAAAGTTTATTAAAAAAATATATATAATATAT
1 AATAATTTAATAAAAATTTATTTTAAAGTCTATTAAAAAAATATATATAATATAT
11510346 AAAATTTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
59 19 0.38
60 11 0.22
61 20 0.40
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (61 bp):
AATAATTTAATAAAAATTTATTTTAAAGTCTATTAAAAAAATATATATAATATATTGCATC
Found at i:11510763 original size:19 final size:20
Alignment explanation
Indices: 11510740--11510785 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
11510730 AATTTTATTT
*
11510740 TTTAAATAAAAAATTATATA
1 TTTAAATAAAAAATTAAATA
* *
11510760 -TTAATTAATAAATTAAATA
1 TTTAAATAAAAAATTAAATA
11510779 TTTAAAT
1 TTTAAAT
11510786 GTTAAATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTTAAATAAAAAATTAAATA
Found at i:11524321 original size:15 final size:16
Alignment explanation
Indices: 11524301--11524333 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
11524291 GATGATGTAA
11524301 TTATCATT-TTTTTCT
1 TTATCATTGTTTTTCT
11524316 TTATCATTGTTTTTCT
1 TTATCATTGTTTTTCT
11524332 TT
1 TT
11524334 TATTTTACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.73
Consensus pattern (16 bp):
TTATCATTGTTTTTCT
Found at i:11547477 original size:88 final size:88
Alignment explanation
Indices: 11547328--11547508 Score: 319
Period size: 88 Copynumber: 2.1 Consensus size: 88
11547318 AATGTCATCA
* *
11547328 ATATTCATCTCGTGTAATAATTGATGATATGGTGATGGCTGTAATGCTTTTGTCAACAAGTCTGC
1 ATATTCATCTCGTGTAATAATTGATGATATGGCGATGGCTGCAATGCTTTTGTCAACAAGTCTGC
11547393 AATATATGATTTAGTAAGAATAG
66 AATATATGATTTAGTAAGAATAG
*
11547416 ATATTCATCTCGTGTAATAATTGATGATATGGCGATGGTTGCAATGCTTTCT-TCAACAAGTCTG
1 ATATTCATCTCGTGTAATAATTGATGATATGGCGATGGCTGCAATGCTTT-TGTCAACAAGTCTG
11547480 CAATATATGATTTAGTAAGAATAG
65 CAATATATGATTTAGTAAGAATAG
11547504 ATATT
1 ATATT
11547509 GGTTCAACTA
Statistics
Matches: 89, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
88 88 0.99
89 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (88 bp):
ATATTCATCTCGTGTAATAATTGATGATATGGCGATGGCTGCAATGCTTTTGTCAACAAGTCTGC
AATATATGATTTAGTAAGAATAG
Found at i:11557834 original size:21 final size:22
Alignment explanation
Indices: 11557810--11557850 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
11557800 TGAAAATGAG
*
11557810 ATAAAAAAAT-ATTTTTTAAAC
1 ATAAAAAAATAATTTATTAAAC
*
11557831 ATAAAAGAATAATTTATTAA
1 ATAAAAAAATAATTTATTAA
11557851 TTATTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
ATAAAAAAATAATTTATTAAAC
Found at i:11558831 original size:45 final size:47
Alignment explanation
Indices: 11558775--11558873 Score: 139
Period size: 45 Copynumber: 2.1 Consensus size: 47
11558765 TAAAAATAAT
* *
11558775 AAAATGATAAAAATATTTTTTATTATAATTTAGTAA-A-ATTTATACC
1 AAAA-GATAAAAATATTCTTTATTATAATTTAATAATATATTTATACC
* *
11558821 AAAAGATAAAATTATTCTTTATTATAATTTAATAATATATTTATGCC
1 AAAAGATAAAAATATTCTTTATTATAATTTAATAATATATTTATACC
11558868 AAAAGA
1 AAAAGA
11558874 AGAAATTATC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
45 28 0.60
46 5 0.11
47 14 0.30
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (47 bp):
AAAAGATAAAAATATTCTTTATTATAATTTAATAATATATTTATACC
Found at i:11558880 original size:47 final size:47
Alignment explanation
Indices: 11558775--11558905 Score: 142
Period size: 47 Copynumber: 2.8 Consensus size: 47
11558765 TAAAAATAAT
* * *
11558775 AAAATGATAAAAATATTTTTTATTATAATTTAGTAA-A-ATTTATACC
1 AAAA-GATAAAATTATTCTTTATTATAATTTAATAATATATTTATACC
*
11558821 AAAAGATAAAATTATTCTTTATTATAATTTAATAATATATTTATGCC
1 AAAAGATAAAATTATTCTTTATTATAATTTAATAATATATTTATACC
* * * * *
11558868 AAAAGA-AGAAATTATCCTTGACTACAATTTCATAATAT
1 AAAAGATA-AAATTATTCTTTATTATAATTTAATAATAT
11558906 CTTCACAAGA
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
45 28 0.38
46 6 0.08
47 39 0.53
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (47 bp):
AAAAGATAAAATTATTCTTTATTATAATTTAATAATATATTTATACC
Found at i:11575774 original size:3 final size:3
Alignment explanation
Indices: 11575766--11575796 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
11575756 CCAATGAAAT
11575766 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
11575797 CTTCTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:11577985 original size:2 final size:2
Alignment explanation
Indices: 11577972--11578005 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
11577962 AATTAATGGG
* *
11577972 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11578006 CTAGGTCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:11584029 original size:41 final size:41
Alignment explanation
Indices: 11583984--11584223 Score: 131
Period size: 41 Copynumber: 6.0 Consensus size: 41
11583974 TTATTTATTT
11583984 TTATTTTATTTTTAAATATTAATATTTTATTTATAATTTAA
1 TTATTTTATTTTTAAATATTAATATTTTATTTATAATTTAA
** * * * * *
11584025 TTATTACATTATAAAATATCAATAATTTATTAATAATTTAA
1 TTATTTTATTTTTAAATATTAATATTTTATTTATAATTTAA
* * * * * *
11584066 --ATGTTA-TTCTGATTATTTATTATTTTATTT-T-ATTTTA
1 TTATTTTATTTTTAAATA-TTAATATTTTATTTATAATTTAA
* * * *
11584103 TT-TTTGAATATTTATAATATT-A-A-TTTATTTAAAATATGAA
1 TTATTT-TATTTTTA-AATATTAATATTTTATTTATAAT-TTAA
* * * * *
11584143 -TAATTGATAATTTAAATATTAATAGTGTATTTATAATTTAA
1 TTATTTTAT-TTTTAAATATTAATATTTTATTTATAATTTAA
* * *
11584184 TCATTAATATTTTCAAATATTAATATTTTATTTATAATTT
1 TTATT-TTATTTTTAAATATTAATATTTTATTTATAATTT
11584224 CAAAGTTATT
Statistics
Matches: 140, Mismatches: 43, Indels: 31
0.65 0.20 0.14
Matches are distributed among these distances:
37 12 0.09
38 8 0.06
39 25 0.18
40 14 0.10
41 41 0.29
42 38 0.27
43 2 0.01
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (41 bp):
TTATTTTATTTTTAAATATTAATATTTTATTTATAATTTAA
Found at i:11584286 original size:154 final size:155
Alignment explanation
Indices: 11583994--11584580 Score: 744
Period size: 154 Copynumber: 3.8 Consensus size: 155
11583984 TTATTTTATT
* * * * * * *
11583994 TTTAAATATTAATATTTTATTTATAATTTAATTAT-TACATTATAAAATATCAATAATTTATTAA
1 TTTAAATATTAATAGTGTATTTATAATTTAATCATCAACATTATAAAATATTAATATTTTATTTA
* *
11584058 TAATTT-AAATGTTATTCTGATTATTTATTATTTTATTTTATTTTATTTTTGAATATTTATAATA
66 TAATTTCAAATGTTATTATGATTATTTA-T-TTTTATTTTA--TTA-TTTT-AATATTAATAA-A
*
11584122 TTA-ATTTATTTAAAATATGAATAATTGATAA
124 TTATATTTATTTAAAATATGAATAATTGATCA
* * * *
11584153 TTTAAATATTAATAGTGTATTTATAATTTAATCATTAATATTTTCAAATATTAATATTTTATTTA
1 TTTAAATATTAATAGTGTATTTATAATTTAATCATCAACATTATAAAATATTAATATTTTATTTA
*
11584218 TAATTTCAAA-GTTATTATGATTATTTATTTTTATTTTA-TATTTTAAATATTAATAAGTTATAT
66 TAATTTCAAATGTTATTATGATTATTTATTTTTATTTTATTATTTT-AATATTAATAAATTATAT
11584281 TTATTTAAAATATGAATAATTGATCA
130 TTATTTAAAATATGAATAATTGATCA
* * * * *
11584307 TTTAAATATTAATAGTGTATTTATAATTTAATCATCAATATTTTCAAATATTAACATTTTGTTTA
1 TTTAAATATTAATAGTGTATTTATAATTTAATCATCAACATTATAAAATATTAATATTTTATTTA
*
11584372 TAATTTCAAA-GTTATTATGATTATTTATTTTTATTTTA-T-TTTTAATATTAATAATTTATATT
66 TAATTTCAAATGTTATTATGATTATTTATTTTTATTTTATTATTTTAATATTAATAAATTATATT
*
11584434 TATTT-AAATATTAATAATTGATCA
131 TATTTAAAATATGAATAATTGATCA
* * * *
11584458 TTTAAATATTTATAGTTTATTTAAAATTTAATCATCAACATTATAAAATAATAATATTTTATTTA
1 TTTAAATATTAATAGTGTATTTATAATTTAATCATCAACATTATAAAATATTAATATTTTATTTA
* * *
11584523 TGA-TTAAAATGTTATTATGATTTTTTATTTTTATTTTATTTTATTTTTAATATTAATA
66 TAATTTCAAATGTTATTATGATTATTTATTTTTATTTTA--TTA-TTTTAATATTAATA
11584581 GTTGATAATT
Statistics
Matches: 387, Mismatches: 32, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
150 5 0.01
151 103 0.27
152 23 0.06
153 7 0.02
154 143 0.37
155 2 0.01
156 14 0.04
158 10 0.03
159 33 0.09
160 44 0.11
161 3 0.01
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.55
Consensus pattern (155 bp):
TTTAAATATTAATAGTGTATTTATAATTTAATCATCAACATTATAAAATATTAATATTTTATTTA
TAATTTCAAATGTTATTATGATTATTTATTTTTATTTTATTATTTTAATATTAATAAATTATATT
TATTTAAAATATGAATAATTGATCA
Found at i:11584320 original size:22 final size:25
Alignment explanation
Indices: 11584259--11584320 Score: 67
Period size: 26 Copynumber: 2.6 Consensus size: 25
11584249 TATTTTATAT
* *
11584259 TTTAAATATTAATAAGTTATATTTA
1 TTTAAATATTAATAAGTTAGATTCA
*
11584284 TTTAAAATATGAATAA-TT-GA-TCA
1 TTT-AAATATTAATAAGTTAGATTCA
11584307 TTTAAATATTAATA
1 TTTAAATATTAATA
11584321 GTGTATTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
22 10 0.31
23 5 0.16
24 1 0.03
25 5 0.16
26 11 0.34
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (25 bp):
TTTAAATATTAATAAGTTAGATTCA
Found at i:11584443 original size:25 final size:26
Alignment explanation
Indices: 11584401--11584461 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
11584391 ATTATTTATT
*
11584401 TTTAT-TTTATTTTTAATATTAATAA
1 TTTATATTTATTTTAAATATTAATAA
11584426 TTTATATTTA-TTTAAATATTAATAA
1 TTTATATTTATTTTAAATATTAATAA
*
11584451 TTGATCATTTA
1 TTTAT-ATTTA
11584462 AATATTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 23 0.72
26 9 0.28
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (26 bp):
TTTATATTTATTTTAAATATTAATAA
Found at i:11584517 original size:151 final size:153
Alignment explanation
Indices: 11584084--11585084 Score: 899
Period size: 154 Copynumber: 6.6 Consensus size: 153
11584074 CTGATTATTT
* *
11584084 ATTATTT-TATTTTATTTTATTTTTGAATATTTATAATATTA-ATTTATTTAAAATATGAATAAT
1 ATTATTTAT-TTTTATTTTATTTTTAAATATTAATAAT-TTATATTTATTTAAAATATGAATAAT
* *
11584147 TGATAATTTAAATATTAATAGTGTATTTATAATTTAATCATTAATATTTTCAAATATTAATATTT
64 TGATCATTTAAATATTAATAGTGTATTTATAATTTAATCATCAATATTTTCAAATATTAATATTT
11584212 TATTTATAATTTCAAAGTTATTATG
129 TATTTATAATTTCAAAGTTATTATG
*
11584237 ATTATTTATTTTTATTTTATATTTTAAATATTAATAAGTTATATTTATTTAAAATATGAATAATT
1 ATTATTTATTTTTATTTTAT-TTTTAAATATTAATAATTTATATTTATTTAAAATATGAATAATT
*
11584302 GATCATTTAAATATTAATAGTGTATTTATAATTTAATCATCAATATTTTCAAATATTAACATTTT
65 GATCATTTAAATATTAATAGTGTATTTATAATTTAATCATCAATATTTTCAAATATTAATATTTT
*
11584367 GTTTATAATTTCAAAGTTATTATG
130 ATTTATAATTTCAAAGTTATTATG
*
11584391 ATTATTTATTTTTATTTTATTTTT-AATATTAATAATTTATATTTATTT-AAATATTAATAATTG
1 ATTATTTATTTTTATTTTATTTTTAAATATTAATAATTTATATTTATTTAAAATATGAATAATTG
* * * * * * *
11584454 ATCATTTAAATATTTATAGTTTATTTAAAATTTAATCATCAACATTATAAAATAATAATATTTTA
66 ATCATTTAAATATTAATAGTGTATTTATAATTTAATCATCAATATTTTCAAATATTAATATTTTA
* *
11584519 TTTATGA-TTAAAATGTTATTATG
131 TTTATAATTTCAAA-GTTATTATG
* * * * *
11584542 ATTTTTTATTTTTATTTTA-TTTT-ATTTTTAAT-ATTAATAGTTGATAATTT-AAATATTAAT-
1 ATTATTTATTTTTATTTTATTTTTAAATATTAATAATTTATA-TT--T-ATTTAAAATATGAATA
* *
11584602 ATT--TTATTTATAAT-TTAATCA-T-TAATTT-T--TTAAAT-AGT-AATATTTTC---T-TT-
62 ATTGATCATTTA-AATATTAAT-AGTGT-ATTTATAATTTAATCA-TCAATATTTTCAAATATTA
* * *
11584652 ATGATTTAAATGT-T-A-TT--ATGATTATT-T-
123 AT-ATTT-TATTTATAATTTCAAAG-TTATTATG
* * * * *
11584679 ATT-TTTA-TTTTAGTTTATTTTTGAGATATTAAT-ATTTATAATTTGTTTATAATATTAATAAT
1 ATTATTTATTTTTATTTTATTTTT-AAATATTAATAATTTAT-ATTTATTTAAAATATGAATAAT
* * * * * * **
11584741 TTATCATTTAAATATTAATAATTTTATTTGTAATTTAATAATTAAT-TTTAT-AAATGCTAATAT
64 TGATCATTTAAATATTAAT-AGTGTATTTATAATTTAATCATCAATATTT-TCAAATATTAATAT
* *
11584804 TTTATTTATAATTT-AAATGCTATTAGG
127 TTTATTTATAATTTCAAA-GTTATTATG
* *
11584831 ATTATTTATTTTCATTTTATTTTATTTTTTAAATATGAATAATTTATAATTTATTTAAAATATTA
1 ATTATTTA---T--TTTTATTTTA-TTTTTAAATATTAATAATTTAT-ATTTATTTAAAATATGA
* * * * * * * * * * * *
11584896 ATAATTGATCATTTAAACATTAATATTTTAATAATATTTTAATAATTAACATTATAAAATACTAA
59 ATAATTGATCATTTAAATATTAATAGTGTATTTATAATTTAATCATCAATATTTTCAAATATTAA
*
11584961 TATTTTATTTATAATTTCAATGTTATTATG
124 TATTTTATTTATAATTTCAAAGTTATTATG
* * * *
11584991 ATTATTTATTTATATTTTATTTTTAAAATATGAATAATTTATAATTTAGTTAAAATATTAATAAT
1 ATTATTTATTTTTATTTTATTTTT-AAATATTAATAATTTAT-ATTTATTTAAAATATGAATAAT
* * *
11585056 TGATCACTTAAATATTAATATTTTATTTA
64 TGATCATTTAAATATTAATAGTGTATTTA
11585085 CACATAAGCA
Statistics
Matches: 717, Mismatches: 74, Indels: 112
0.79 0.08 0.12
Matches are distributed among these distances:
135 12 0.02
136 18 0.03
137 6 0.01
138 18 0.03
139 19 0.03
140 5 0.01
141 7 0.01
142 6 0.01
143 13 0.02
144 5 0.01
146 11 0.02
147 12 0.02
148 3 0.00
149 9 0.01
150 38 0.05
151 108 0.15
152 30 0.04
153 43 0.06
154 148 0.21
155 73 0.10
157 1 0.00
159 39 0.05
160 91 0.13
161 2 0.00
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.55
Consensus pattern (153 bp):
ATTATTTATTTTTATTTTATTTTTAAATATTAATAATTTATATTTATTTAAAATATGAATAATTG
ATCATTTAAATATTAATAGTGTATTTATAATTTAATCATCAATATTTTCAAATATTAATATTTTA
TTTATAATTTCAAAGTTATTATG
Found at i:11584634 original size:41 final size:41
Alignment explanation
Indices: 11584408--11584977 Score: 167
Period size: 42 Copynumber: 13.8 Consensus size: 41
11584398 ATTTTTATTT
* *
11584408 TATTTTTAATATTAATAATTTATATTTATTTAAATATTAATAATTGA
1 TATTTTAAATATTAAT-ATTT-TATTTA--T-AAT-TTAATAATTAA
* * * * *
11584455 TCA-TTTAAATATTTATAGTTTATTTAAAATTTAATCATCAA
1 T-ATTTTAAATATTAATATTTTATTTATAATTTAATAATTAA
* * * *
11584496 CATTATAAAATAATAATATTTTATTTATGA-TTAA-AATGTTATTA
1 TATT-TTAAATATTAATATTTTATTTATAATTTAATAA--TTA--A
* * * * * * *
11584540 TGATTTTTTATTTTTATTTTATTTTATTTTTAATATTAATAGTTGA
1 T-A-TTTTAAATATTA--ATATTTTATTTATAAT-TTAATAATTAA
* *
11584586 TAATTTAAATATTAATATTTTATTTATAATTTAATCATTAA
1 TATTTTAAATATTAATATTTTATTTATAATTTAATAATTAA
* * * *
11584627 TTTTTTAAATAGTAATATTTTCTTTATGATTT-A-AATGT--
1 TATTTTAAATATTAATATTTTATTTATAATTTAATAAT-TAA
* * * * * ** *
11584665 TATTATGATTATTTAT-TTTTATTT-TAGTTT-ATTTTTGA
1 TATTTTAAATATTAATATTTTATTTATAATTTAATAATTAA
* * * * * *
11584703 GATATT-AATATTTATAATTTGTTTATAATATTAATAATTTA
1 TATTTTAAATATTAATATTTTATTTATAAT-TTAATAATTAA
*
11584744 TCA-TTTAAATATTAATAATTTTATTTGTAATTTAATAATTAA
1 T-ATTTTAAATATTAAT-ATTTTATTTATAATTTAATAATTAA
** **
11584786 T-TTTATAAATGCTAATATTTTATTTATAATTT-A-AA-TGC
1 TATTT-TAAATATTAATATTTTATTTATAATTTAATAATTAA
*** * * * **
11584824 TATTAGGATTATT--TATTTTCATTT-TATTTTATTTTTTAA
1 TATTTTAAATATTAATATTTT-ATTTATAATTTAATAATTAA
* * * * * *
11584863 -ATATGAATA-ATTTATAATTTATTTAAAATATTAATAATTGA
1 TATTTTAA-ATATTAATATTTTATTTATAAT-TTAATAATTAA
* * * *
11584904 TCA-TTTAAACATTAATATTTTAATAATATTTTAATAATTAA
1 T-ATTTTAAATATTAATATTTTATTTATAATTTAATAATTAA
* * *
11584945 CATTATAAAATACTAATATTTTATTTATAATTT
1 TATT-TTAAATATTAATATTTTATTTATAATTT
11584978 CAATGTTATT
Statistics
Matches: 367, Mismatches: 114, Indels: 89
0.64 0.20 0.16
Matches are distributed among these distances:
36 17 0.05
37 20 0.05
38 31 0.08
39 14 0.04
40 15 0.04
41 91 0.25
42 106 0.29
43 12 0.03
44 9 0.02
45 13 0.04
46 7 0.02
47 24 0.07
48 3 0.01
49 4 0.01
50 1 0.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (41 bp):
TATTTTAAATATTAATATTTTATTTATAATTTAATAATTAA
Found at i:11584683 original size:130 final size:130
Alignment explanation
Indices: 11584426--11584722 Score: 400
Period size: 130 Copynumber: 2.3 Consensus size: 130
11584416 ATATTAATAA
* * *
11584426 TTTATATTTA-TTTAAATATTAATAATTGATCATTTAAATATTTATAGTTTATTTAAAATTTAAT
1 TTTAT-TTTATTTTTAATATTAAT-ATTGATAATTTAAATATTAATAGTTTATTTAAAATTTAAT
*
11584490 CATCAACATTATAAAATAATAATATTTTATTTATGATTAAAATGTTATTATGATTTTTTATTTTT
64 CATCAACATTATAAAATAATAATATTTTATTTATGATTAAAATGTTATTATGATTATTTATTTTT
11584555 AT
129 AT
* *
11584557 TTTATTTTATTTTTAATATTAATAGTTGATAATTTAAATATTAATATTTTATTTATAATTTAATC
1 TTTATTTTATTTTTAATATTAATA-TTGATAATTTAAATATTAATAGTTTATTTAAAATTTAATC
* * * * * * *
11584622 ATTAA-TTTTTTAAATAGTAATATTTTCTTTATGATTTAAATGTTATTATGATTATTTATTTTTA
65 ATCAACATTATAAAATAATAATATTTTATTTATGATTAAAATGTTATTATGATTATTTATTTTTA
11584686 T
130 T
* *
11584687 TTTAGTTTATTTTTGAGATATTAATATTTATAATTT
1 TTTATTTTATTTTT-A-ATATTAATATTGATAATTT
11584723 GTTTATAATA
Statistics
Matches: 147, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
130 71 0.48
131 67 0.46
132 9 0.06
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (130 bp):
TTTATTTTATTTTTAATATTAATATTGATAATTTAAATATTAATAGTTTATTTAAAATTTAATCA
TCAACATTATAAAATAATAATATTTTATTTATGATTAAAATGTTATTATGATTATTTATTTTTAT
Found at i:11584891 original size:27 final size:26
Alignment explanation
Indices: 11584854--11584910 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
11584844 ATTTTATTTT
*
11584854 ATTT-TTTAAATATGAATAATTTATA
1 ATTTATTTAAATATGAATAATTGATA
* *
11584879 ATTTATTTAAAATATTAATAATTGATC
1 ATTTATTT-AAATATGAATAATTGATA
11584906 ATTTA
1 ATTTA
11584911 AACATTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 4 0.15
26 3 0.11
27 20 0.74
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (26 bp):
ATTTATTTAAATATGAATAATTGATA
Found at i:11584932 original size:11 final size:11
Alignment explanation
Indices: 11584916--11584941 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11584906 ATTTAAACAT
11584916 TAATATTTTAA
1 TAATATTTTAA
11584927 TAATATTTTAA
1 TAATATTTTAA
11584938 TAAT
1 TAAT
11584942 TAACATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TAATATTTTAA
Found at i:11584976 original size:160 final size:157
Alignment explanation
Indices: 11584562--11585084 Score: 687
Period size: 159 Copynumber: 3.3 Consensus size: 157
11584552 TTTATTTTAT
** * * *
11584562 TTTATTTTTAATATTAATAGTTGATAATTTAAATATTAATATTTTATTTATAATTTAATCATTAA
1 TTTATTTAAAATATTAATAATTGATCATTTAAATATTAATATTTTATTTATAATTTAATAATTAA
* * * * *
11584627 TTTTTTAAATAGTAATATTTTCTTTATGATTTAAATGTTATTATGATTATTTATTTTTATTTTAG
66 -TTTATAAATACTAATATTTTATTTATAATTTAAATGTTATTATGATTATTTA-TTTTATTTTAT
* * *
11584692 TTTATTTTTGAGATATTAAT-ATTTATAA
129 TTTATTTTTAAAATATGAATAATTTATAA
* * * *
11584720 TTTGTTTATAATATTAATAATTTATCATTTAAATATTAATAATTTTATTTGTAATTTAATAATTA
1 TTTATTTAAAATATTAATAATTGATCATTTAAATATTAAT-ATTTTATTTATAATTTAATAATTA
* * *
11584785 ATTTTATAAATGCTAATATTTTATTTATAATTTAAATGCTATTAGGATTATTTATTTTCATTTTA
65 A-TTTATAAATACTAATATTTTATTTATAATTTAAATGTTATTATGATTATTTATTTT-ATTTTA
*
11584850 TTTTATTTTTTAAATATGAATAATTTATAA
128 TTTTATTTTTAAAATATGAATAATTTATAA
* * * *
11584880 TTTATTTAAAATATTAATAATTGATCATTTAAACATTAATATTTTAATAATATTTTAATAATTAA
1 TTTATTTAAAATATTAATAATTGATCATTTAAATATTAATATTTTATTTATAATTTAATAATTAA
* *
11584945 CATTATAAAATACTAATATTTTATTTATAATTTCAATGTTATTATGATTATTTA-TTTA---TAT
66 -TTTAT-AAATACTAATATTTTATTTATAATTTAAATGTTATTATGATTATTTATTTTATTTTAT
11585006 TTTATTTTTAAAATATGAATAATTTATAA
129 TTTATTTTTAAAATATGAATAATTTATAA
* *
11585035 TTTAGTTAAAATATTAATAATTGATCACTTAAATATTAATATTTTATTTA
1 TTTATTTAAAATATTAATAATTGATCATTTAAATATTAATATTTTATTTA
11585085 CACATAAGCA
Statistics
Matches: 323, Mismatches: 38, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
155 76 0.24
158 40 0.12
159 120 0.37
160 87 0.27
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (157 bp):
TTTATTTAAAATATTAATAATTGATCATTTAAATATTAATATTTTATTTATAATTTAATAATTAA
TTTATAAATACTAATATTTTATTTATAATTTAAATGTTATTATGATTATTTATTTTATTTTATTT
TATTTTTAAAATATGAATAATTTATAA
Found at i:11585245 original size:22 final size:20
Alignment explanation
Indices: 11585169--11585247 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 20
11585159 AATTATAAAA
11585169 TATATATATTAATATTTTATT
1 TATA-ATATTAATATTTTATT
*
11585190 TATAAT-TTAATCATTAATATT
1 TATAATATTAAT-ATT-TTATT
*
11585211 TTTAAATATTAATATTTTATT
1 TAT-AATATTAATATTTTATT
11585232 TAATAATTATTAATAT
1 T-ATAA-TATTAATAT
11585248 GGGTAGGATT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
19 5 0.10
20 5 0.10
21 17 0.35
22 16 0.33
23 5 0.10
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (20 bp):
TATAATATTAATATTTTATT
Found at i:11593035 original size:4 final size:4
Alignment explanation
Indices: 11593020--11593123 Score: 65
Period size: 4 Copynumber: 26.0 Consensus size: 4
11593010 ATAATTTTTA
*
11593020 TAAT TAAAT TAAT TAAGT T--T TAAA TAAT TAAAT TAAT TAAT TAA- -AAT
1 TAAT T-AAT TAAT TAA-T TAAT TAAT TAAT T-AAT TAAT TAAT TAAT TAAT
* * ** *
11593067 TAGT TTA- TAAT TATAT TAGC TAAT TATT TAAT TAAT TAAAT TAAT TAAT
1 TAAT TAAT TAAT TA-AT TAAT TAAT TAAT TAAT TAAT T-AAT TAAT TAAT
*
11593116 TACT TAAT
1 TAAT TAAT
11593124 ATTAATCACA
Statistics
Matches: 76, Mismatches: 14, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
2 4 0.05
3 2 0.03
4 52 0.68
5 18 0.24
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:11593060 original size:13 final size:13
Alignment explanation
Indices: 11593020--11593117 Score: 69
Period size: 13 Copynumber: 7.5 Consensus size: 13
11593010 ATAATTTTTA
11593020 TAATTAAATTAAT
1 TAATTAAATTAAT
*
11593033 TAAGTT---TTAAA
1 TAA-TTAAATTAAT
11593044 TAATTAAATTAAT
1 TAATTAAATTAAT
*
11593057 TAATTAAAATTAGTTT
1 TAATT-AAATTA--AT
* **
11593073 ATAATTATATTAGC
1 -TAATTAAATTAAT
*
11593087 TAATT-ATTTAAT
1 TAATTAAATTAAT
11593099 TAATTAAATTAAT
1 TAATTAAATTAAT
11593112 TAATTA
1 TAATTA
11593118 CTTAATATTA
Statistics
Matches: 65, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
10 2 0.03
11 7 0.11
12 8 0.12
13 29 0.45
14 8 0.12
16 6 0.09
17 5 0.08
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (13 bp):
TAATTAAATTAAT
Found at i:11594052 original size:15 final size:16
Alignment explanation
Indices: 11594020--11594054 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
11594010 TAATTAAATA
11594020 TTATCAAAAAATAGAT
1 TTATCAAAAAATAGAT
11594036 TTATCAAAAAATA-AT
1 TTATCAAAAAATAGAT
11594051 TTAT
1 TTAT
11594055 ATATTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (16 bp):
TTATCAAAAAATAGAT
Found at i:11597371 original size:91 final size:92
Alignment explanation
Indices: 11597199--11597379 Score: 283
Period size: 91 Copynumber: 2.0 Consensus size: 92
11597189 CGAGTCCACT
* **
11597199 TCGACCCTTGTATCTCTCATGGAACTTTACATCAATGAAGATCTAGGTCTGGTTTGATACCAAAT
1 TCGACCCTCGTATCTCTCATGGAACTCCACATCAATGAAGATCTAGGTCTGGTTTGATACCAAAT
* *
11597264 CTCACGAGTCGGAACTTAAGTCTAATC
66 CTCACGAGCCGAAACTTAAGTCTAATC
**
11597291 TCGA-CCTCGTATCTCTCATGGGGCTCCACATCAATGAAGATCTAGGTCTGGTTTGATACCAAAT
1 TCGACCCTCGTATCTCTCATGGAACTCCACATCAATGAAGATCTAGGTCTGGTTTGATACCAAAT
*
11597355 CTCACGGGCCGAAACTTAAGTCTAA
66 CTCACGAGCCGAAACTTAAGTCTAA
11597380 ACTTGTGCAG
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
91 77 0.95
92 4 0.05
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (92 bp):
TCGACCCTCGTATCTCTCATGGAACTCCACATCAATGAAGATCTAGGTCTGGTTTGATACCAAAT
CTCACGAGCCGAAACTTAAGTCTAATC
Found at i:11597779 original size:24 final size:25
Alignment explanation
Indices: 11597747--11597793 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
11597737 AACAATTTTT
*
11597747 TTAAGATATTAAAAATT-TTATTTA
1 TTAAAATATTAAAAATTATTATTTA
*
11597771 TTAAAATATTTAAAATTATTATT
1 TTAAAATATTAAAAATTATTATT
11597794 AGTATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TTAAAATATTAAAAATTATTATTTA
Found at i:11602001 original size:20 final size:20
Alignment explanation
Indices: 11601976--11602014 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
11601966 AAATGTGGAA
11601976 CACTTGCACATTTTACTGTG
1 CACTTGCACATTTTACTGTG
11601996 CACTTGCACATTTTACTGT
1 CACTTGCACATTTTACTGT
11602015 ACACCCAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.41
Consensus pattern (20 bp):
CACTTGCACATTTTACTGTG
Found at i:11615437 original size:18 final size:19
Alignment explanation
Indices: 11615384--11615446 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 19
11615374 ATCTCCTTAC
11615384 TTACTCTTAAAAATAAAATA
1 TTACT-TTAAAAATAAAATA
*
11615404 TTAATATTTTAAAAATAAAA-A
1 -T--TACTTTAAAAATAAAATA
*
11615425 TTACTTTATAAATAAAATA
1 TTACTTTAAAAATAAAATA
11615444 TTA
1 TTA
11615447 ATATTTATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 14 0.39
19 4 0.11
20 1 0.03
21 2 0.06
22 12 0.33
23 3 0.08
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
TTACTTTAAAAATAAAATA
Found at i:11615455 original size:21 final size:21
Alignment explanation
Indices: 11615394--11615510 Score: 87
Period size: 22 Copynumber: 5.4 Consensus size: 21
11615384 TTACTCTTAA
*
11615394 AAATAAAATATTAATATTTTAA
1 AAATAAAATATTAATA-TTTAT
*
11615416 AAATAAAA-ATT-A-CTTTAT
1 AAATAAAATATTAATATTTAT
11615434 AAATAAAATATTAATATTTAT
1 AAATAAAATATTAATATTTAT
* * *
11615455 ATGAGAAATTATTAATATTATAAAT
1 A-AATAAAATATTAATATT-T--AT
* *
11615480 AAATATAAATTATTAATACTTAA
1 AAATA-AAA-TATTAATATTTAT
11615503 AAATAAAA
1 AAATAAAA
11615511 AATAAAAATA
Statistics
Matches: 75, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
18 12 0.16
19 3 0.04
20 2 0.03
21 9 0.12
22 25 0.33
23 7 0.09
24 2 0.03
25 6 0.08
26 9 0.12
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
AAATAAAATATTAATATTTAT
Found at i:11615636 original size:27 final size:28
Alignment explanation
Indices: 11615606--11615664 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
11615596 TACTAATATT
* * *
11615606 TAAAGTATCAATTTTTAATATTT-TAAA
1 TAAAGTATAAATTATTAATATTTAAAAA
*
11615633 TAAATTATAAATTATTAATATTTAAAAA
1 TAAAGTATAAATTATTAATATTTAAAAA
11615661 TAAA
1 TAAA
11615665 ATATTTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (28 bp):
TAAAGTATAAATTATTAATATTTAAAAA
Found at i:11615667 original size:15 final size:16
Alignment explanation
Indices: 11615649--11615680 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
11615639 ATAAATTATT
11615649 AATA-TTTAAAAATAA
1 AATATTTTAAAAATAA
11615664 AATATTTTAAAAATAA
1 AATATTTTAAAAATAA
11615680 A
1 A
11615681 TAATCATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATATTTTAAAAATAA
Found at i:11615706 original size:27 final size:26
Alignment explanation
Indices: 11615660--11615710 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
11615650 ATATTTAAAA
11615660 ATAAAATATTTTAAAAATAAATAATC
1 ATAAAATATTTTAAAAATAAATAATC
*
11615686 ATAATAATA-TTTAAATTATAAATAA
1 ATAA-AATATTTTAAA-AATAAATAA
11615711 AACATTAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
ATAAAATATTTTAAAAATAAATAATC
Found at i:11617532 original size:75 final size:78
Alignment explanation
Indices: 11617431--11617602 Score: 192
Period size: 75 Copynumber: 2.3 Consensus size: 78
11617421 AGTTGCACAC
**
11617431 CTTATCAC-TTTCTCTGCATTAATATTAGTATAGTATTAGCATT-AGCAACATATTTA-TTTTAT
1 CTTATCACTTTTCTCTGCATTAATATTAGTATAGTATTAGCATTAAGCAACATAGCTATTTTTAT
*
11617493 TAGCAAGCATCAA
66 TACCAAGCATCAA
* * * * * * * * *
11617506 CTTATCACTTTTTTC-GTATTAGTATTAGTGTAGTATTGGTATTAATCTATATAGCTATTTTTAT
1 CTTATCACTTTTCTCTGCATTAATATTAGTATAGTATTAGCATTAAGCAACATAGCTATTTTTAT
11617570 TACCAAGCATCAA
66 TACCAAGCATCAA
*
11617583 CTTATCAC-TTTCTTTGCATT
1 CTTATCACTTTTCTCTGCATT
11617603 TTAACTGTTT
Statistics
Matches: 78, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
75 31 0.40
76 17 0.22
77 30 0.38
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (78 bp):
CTTATCACTTTTCTCTGCATTAATATTAGTATAGTATTAGCATTAAGCAACATAGCTATTTTTAT
TACCAAGCATCAA
Found at i:11620123 original size:58 final size:59
Alignment explanation
Indices: 11620003--11620135 Score: 187
Period size: 58 Copynumber: 2.3 Consensus size: 59
11619993 TTCAATCCCT
* * *
11620003 TTTAAGCTTAAATTTTGGAATTAGTATTTTTTCTTTAACCCAAATTCTTAGATCGTTTGG
1 TTTAA-CTTAAATTTTGAAATTAGTATTTTTTCTTTAACCCAAATTCTTAGATCCTTGGG
* *
11620063 TTTAACTTAAATTTTGAAATTATTATTTTTTC-TTAATCCAAATTCTTAGATCCTTGGG
1 TTTAACTTAAATTTTGAAATTAGTATTTTTTCTTTAACCCAAATTCTTAGATCCTTGGG
* *
11620121 TTTGACTTATATTTT
1 TTTAACTTAAATTTT
11620136 TTCCTTAACC
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 36 0.55
59 25 0.38
60 5 0.08
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (59 bp):
TTTAACTTAAATTTTGAAATTAGTATTTTTTCTTTAACCCAAATTCTTAGATCCTTGGG
Found at i:11620174 original size:45 final size:44
Alignment explanation
Indices: 11620086--11620175 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
11620076 TTGAAATTAT
* * *
11620086 TATTTTTTCTTAATCCAAATTCTTAGATCCTTGGGTTTGACTTA
1 TATTTTTTCTTAACCCAAATTCCTAGATCATTGGGTTTGACTTA
*
11620130 TATTTTTTCCTTAACCCAAATTCCTAGATCATTTGGTTCT-ACTTA
1 TATTTTTT-CTTAACCCAAATTCCTAGATCATTGGGTT-TGACTTA
11620175 T
1 T
11620176 CTCAACTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
44 8 0.20
45 31 0.77
46 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.09, T:0.49
Consensus pattern (44 bp):
TATTTTTTCTTAACCCAAATTCCTAGATCATTGGGTTTGACTTA
Found at i:11620366 original size:136 final size:136
Alignment explanation
Indices: 11620120--11620367 Score: 329
Period size: 136 Copynumber: 1.8 Consensus size: 136
11620110 AGATCCTTGG
* *
11620120 GTTTGACTTATATTTTTTCCTTAACCCAAATTCCTAGATCATTTGGTTCTACTTATCTCAACTCT
1 GTTTGACTTATATTTTTTCCTTAACCCAAATTCCTAGATCATTTGATTCGACTTATCTCAACTCT
* *
11620185 TTAAATTTTTATAACAACTATAAAACGTGTATTTTCAGTTAAAAAAATAACCTGAATTCCTAAAT
66 TTAAATTTTTATAACAACTACAAAACGTGCATTTTCAGTTAAAAAAATAACCTGAATTCCTAAAT
11620250 CATTTA
131 CATTTA
* * ** * *
11620256 GTTTGACTTATATTTTTTCCTTAATCCAAATTCTTAGATTGTTTGATTCGACTTATCTTAATTCT
1 GTTTGACTTATATTTTTTCCTTAACCCAAATTCCTAGATCATTTGATTCGACTTATCTCAACTCT
* * * * * *
11620321 TTCAATTTTTAT-AGAACTGCATAAGGTGCATGTTT-AGTTAGAAAAAT
66 TTAAATTTTTATAACAACTACAAAACGTGCAT-TTTCAGTTAAAAAAAT
11620368 TATAAAGACA
Statistics
Matches: 95, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
135 24 0.25
136 71 0.75
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.44
Consensus pattern (136 bp):
GTTTGACTTATATTTTTTCCTTAACCCAAATTCCTAGATCATTTGATTCGACTTATCTCAACTCT
TTAAATTTTTATAACAACTACAAAACGTGCATTTTCAGTTAAAAAAATAACCTGAATTCCTAAAT
CATTTA
Found at i:11626316 original size:31 final size:30
Alignment explanation
Indices: 11626237--11626325 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 30
11626227 TAAACTTAGA
* *
11626237 TTTTATGT-TTCATCAAAATGTTAGATTTAG
1 TTTT-TGTATTCATCAAAATATTAGATTAAG
* * *
11626267 TTTTTGTATTCTACCAAAACATTTGATTAAG
1 TTTTTGTATTC-ATCAAAATATTAGATTAAG
11626298 TTTTTGTACTTCATCAAAATATTAGATT
1 TTTTTGTA-TTCATCAAAATATTAGATT
11626326 TAACCCCTCT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
29 3 0.06
30 7 0.15
31 35 0.73
32 3 0.06
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (30 bp):
TTTTTGTATTCATCAAAATATTAGATTAAG
Found at i:11627040 original size:26 final size:23
Alignment explanation
Indices: 11627011--11627070 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 23
11627001 AAGTCGTAAT
11627011 TGTTGGAAAAAACCAACAATGGTGAC
1 TGTT-GAAAAAA-C-ACAATGGTGAC
* *
11627037 TGTTTGAAACAAACACAATTGTGTC
1 TG-TTGAAA-AAACACAATGGTGAC
11627062 TGTTGAAAA
1 TGTTGAAAA
11627071 GAGGCACCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
23 1 0.03
24 6 0.20
25 11 0.37
26 7 0.23
27 5 0.17
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (23 bp):
TGTTGAAAAAACACAATGGTGAC
Found at i:11627957 original size:20 final size:20
Alignment explanation
Indices: 11627919--11627959 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
11627909 TATGGTTGTG
* *
11627919 TCCTCCATTATAGATAAACT
1 TCCTCCATCATAGAAAAACT
*
11627939 TCCTCCATCATGGAAAAACT
1 TCCTCCATCATAGAAAAACT
11627959 T
1 T
11627960 TAAAAGAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (20 bp):
TCCTCCATCATAGAAAAACT
Found at i:11642667 original size:3 final size:3
Alignment explanation
Indices: 11642659--11642685 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11642649 ACTACAGCCC
11642659 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
11642686 GAAAGTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:11644975 original size:51 final size:51
Alignment explanation
Indices: 11644896--11644993 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
11644886 GCGGGGCTCT
11644896 CATCTGTCGTTCAGAAAAAAGATCGGTTCAGAAAATT-AGATAAAAAGGCC
1 CATCTGTCGTTCAGAAAAAAGATCGGTTCAGAAAATTAAGATAAAAAGGCC
* * * *
11644946 CATCTGTTGTTTAGGAAAAAAGATTGGTTCAGACAATTAAAGATAAAA
1 CATCTGTCGTTCA-GAAAAAAGATCGGTTCAGAAAATT-AAGATAAAA
11644994 GCTTAAAAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
50 11 0.27
51 22 0.54
53 8 0.20
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26
Consensus pattern (51 bp):
CATCTGTCGTTCAGAAAAAAGATCGGTTCAGAAAATTAAGATAAAAAGGCC
Found at i:11646381 original size:27 final size:27
Alignment explanation
Indices: 11646350--11646402 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
11646340 AAAATAAGTA
11646350 ATTTTATTAATTATTA-ATTATTTTTAT
1 ATTTTATTAATTATTATA-TATTTTTAT
* *
11646377 ATTTTTTTAATTCTTATATATTTTTA
1 ATTTTATTAATTATTATATATTTTTA
11646403 ATATAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (27 bp):
ATTTTATTAATTATTATATATTTTTAT
Found at i:11648287 original size:2 final size:2
Alignment explanation
Indices: 11648280--11648319 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
11648270 GTTCCTACTC
11648280 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
11648320 TTATTTTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:11649828 original size:9 final size:9
Alignment explanation
Indices: 11649780--11649838 Score: 59
Period size: 9 Copynumber: 6.6 Consensus size: 9
11649770 GCCTCCACCG
*
11649780 AAAGATGGT
1 AAAGATGGA
*
11649789 AAGGATGGCA
1 AAAGATGG-A
11649799 AAA-ATGGA
1 AAAGATGGA
11649807 AAAGA-GGA
1 AAAGATGGA
11649815 GAAAGATGGA
1 -AAAGATGGA
*
11649825 AAAGATGCA
1 AAAGATGGA
11649834 AAAGA
1 AAAGA
11649839 AAGGAAGGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 7 0.17
9 30 0.71
10 5 0.12
ACGTcount: A:0.54, C:0.03, G:0.32, T:0.10
Consensus pattern (9 bp):
AAAGATGGA
Found at i:11649849 original size:27 final size:27
Alignment explanation
Indices: 11649789--11649864 Score: 66
Period size: 27 Copynumber: 2.8 Consensus size: 27
11649779 GAAAGATGGT
* *
11649789 AAGGATGGCAAAAATGGAAAAGAGGAG
1 AAGGATGGCAAAAATGCAAAAGAAGAG
*
11649816 AAAGATGG-AAAAGATGCAAAAGAA-AGG
1 AAGGATGGCAAAA-ATGCAAAAGAAGA-G
* *
11649843 AAGGATGCCAAGAATGACAAAA
1 AAGGATGGCAAAAATG-CAAAA
11649865 ATTCAACTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
26 5 0.13
27 26 0.67
28 8 0.21
ACGTcount: A:0.55, C:0.07, G:0.30, T:0.08
Consensus pattern (27 bp):
AAGGATGGCAAAAATGCAAAAGAAGAG
Done.