Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 31 of 93
Found at i:12320441 original size:70 final size:70
Alignment explanation
Indices: 12320356--12320505 Score: 239
Period size: 70 Copynumber: 2.1 Consensus size: 70
12320346 GTAACGCCAC
* * * *
12320356 TCCATATTTACTACTAACTGGAGTTAATATCTAATAGC-CACGCGATTCTAAATCTTAACGGTTC
1 TCCATATTTAATACTAACGGGAGTCAATATCTAATA-CTCACGCGATTCTAAATCTTAACAGTTC
12320420 ACGCGA
65 ACGCGA
*
12320426 TCCATATTTAATACTAACGGGAGTCAATATCTAATACTCACGCGATTCTCAATCTTAACAGTTCA
1 TCCATATTTAATACTAACGGGAGTCAATATCTAATACTCACGCGATTCTAAATCTTAACAGTTCA
12320491 CGCGA
66 CGCGA
12320496 TCCATATTTA
1 TCCATATTTA
12320506 CTAATCACAC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
69 1 0.01
70 73 0.99
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (70 bp):
TCCATATTTAATACTAACGGGAGTCAATATCTAATACTCACGCGATTCTAAATCTTAACAGTTCA
CGCGA
Found at i:12322757 original size:23 final size:23
Alignment explanation
Indices: 12322725--12322785 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 23
12322715 TTATCACATG
*
12322725 AATGAATACAAAGAATAATATGTA
1 AATG-ATACAAAGAATAATATGGA
12322749 AATGATACAACAAAGAATAATATGGA
1 AATGAT---ACAAAGAATAATATGGA
12322775 AATGATACAAA
1 AATGATACAAA
12322786 ATAATGTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
23 7 0.21
24 4 0.12
26 22 0.67
ACGTcount: A:0.59, C:0.07, G:0.13, T:0.21
Consensus pattern (23 bp):
AATGATACAAAGAATAATATGGA
Found at i:12322763 original size:26 final size:26
Alignment explanation
Indices: 12322732--12322784 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
12322722 ATGAATGAAT
*
12322732 ACAAAGAATAATATGTAAATGATACA
1 ACAAAGAATAATATGGAAATGATACA
12322758 ACAAAGAATAATATGGAAATGATACA
1 ACAAAGAATAATATGGAAATGATACA
12322784 A
1 A
12322785 AATAATGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.58, C:0.08, G:0.13, T:0.21
Consensus pattern (26 bp):
ACAAAGAATAATATGGAAATGATACA
Found at i:12324385 original size:24 final size:24
Alignment explanation
Indices: 12324357--12324474 Score: 134
Period size: 24 Copynumber: 5.0 Consensus size: 24
12324347 ACATCACTCA
12324357 CTGGATCTCCAACTGCATTGACTG
1 CTGGATCTCCAACTGCATTGACTG
* * *
12324381 CTGGATCTCTAACTGCATTAACTA
1 CTGGATCTCCAACTGCATTGACTG
* * * *
12324405 C---ATCTGCATCTGCATTGCCCG
1 CTGGATCTCCAACTGCATTGACTG
12324426 CTGGATCTCCAACTGCATTGACTG
1 CTGGATCTCCAACTGCATTGACTG
* *
12324450 TTGGATCTCCAATTGCATTGACTG
1 CTGGATCTCCAACTGCATTGACTG
12324474 C
1 C
12324475 ATCTGCATCT
Statistics
Matches: 74, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
21 14 0.19
24 60 0.81
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (24 bp):
CTGGATCTCCAACTGCATTGACTG
Found at i:12324441 original size:69 final size:69
Alignment explanation
Indices: 12324357--12324485 Score: 213
Period size: 69 Copynumber: 1.9 Consensus size: 69
12324347 ACATCACTCA
*
12324357 CTGGATCTCCAACTGCATTGACTGCTGGATCTCTAACTGCATTAACTACATCTGCATCTGCATTG
1 CTGGATCTCCAACTGCATTGACTGCTGGATCTCCAACTGCATTAACTACATCTGCATCTGCATTG
12324422 CCCG
66 CCCG
* * * *
12324426 CTGGATCTCCAACTGCATTGACTGTTGGATCTCCAATTGCATTGACTGCATCTGCATCTG
1 CTGGATCTCCAACTGCATTGACTGCTGGATCTCCAACTGCATTAACTACATCTGCATCTG
12324486 TATATTCATC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 55 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.32
Consensus pattern (69 bp):
CTGGATCTCCAACTGCATTGACTGCTGGATCTCCAACTGCATTAACTACATCTGCATCTGCATTG
CCCG
Found at i:12326414 original size:23 final size:21
Alignment explanation
Indices: 12326369--12326432 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 21
12326359 AATTTCCTAC
* *
12326369 AACAATAGTCACGCAATGCCT
1 AACATTAGTCACGCAATGACT
*
12326390 AATCAATTAGTCACGCAATTACT
1 AA-C-ATTAGTCACGCAATGACT
*
12326413 AACATTAAATCACGCAATGA
1 AACATT-AGTCACGCAATGA
12326433 TTTATAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 5 0.14
22 13 0.37
23 17 0.49
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.23
Consensus pattern (21 bp):
AACATTAGTCACGCAATGACT
Found at i:12327020 original size:19 final size:20
Alignment explanation
Indices: 12326996--12327033 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12326986 ACGAATAATA
12326996 ACCACT-CCAAAAGGCTCCT
1 ACCACTGCCAAAAGGCTCCT
*
12327015 ACCACTGCCAAAATGCTCC
1 ACCACTGCCAAAAGGCTCC
12327034 GAAGTTGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.32, C:0.42, G:0.11, T:0.16
Consensus pattern (20 bp):
ACCACTGCCAAAAGGCTCCT
Found at i:12335446 original size:23 final size:23
Alignment explanation
Indices: 12335416--12335495 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 23
12335406 GCCATGTTAG
* * *
12335416 ATATGCTCACGATGTCGTTTCAC
1 ATATGCTCACCATGACGTGTCAC
12335439 ATATGCTCACCATGACGTGTCAC
1 ATATGCTCACCATGACGTGTCAC
* *
12335462 AT-T-CTCA-CACTGGCATGTCAC
1 ATATGCTCACCA-TGACGTGTCAC
*
12335483 ATATTCTCACCAT
1 ATATGCTCACCAT
12335496 TTTGCCTCAC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
20 2 0.04
21 15 0.31
22 2 0.04
23 27 0.56
24 2 0.04
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.31
Consensus pattern (23 bp):
ATATGCTCACCATGACGTGTCAC
Found at i:12335646 original size:23 final size:23
Alignment explanation
Indices: 12335618--12335679 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
12335608 ACTTATTCTT
12335618 ACCATGAT-GTATCACACATTCCC
1 ACCATG-TCGTATCACACATTCCC
* *
12335641 ATCATGTCGTGTCACACATTCCC
1 ACCATGTCGTATCACACATTCCC
* *
12335664 ACCATGCCGTTTCACA
1 ACCATGTCGTATCACA
12335680 AACTTTAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 1 0.03
23 32 0.97
ACGTcount: A:0.26, C:0.35, G:0.11, T:0.27
Consensus pattern (23 bp):
ACCATGTCGTATCACACATTCCC
Found at i:12337192 original size:18 final size:18
Alignment explanation
Indices: 12337166--12337216 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
12337156 TTTTGAATAG
* *
12337166 TTATGTTTGTTCAAATTA-
1 TTATATTTGTTCAAA-CAC
*
12337184 TTATATTTGTTGAAACAC
1 TTATATTTGTTCAAACAC
*
12337202 TTATATTTATTCAAA
1 TTATATTTGTTCAAA
12337217 ATGTTGTCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (18 bp):
TTATATTTGTTCAAACAC
Found at i:12346797 original size:3 final size:3
Alignment explanation
Indices: 12346785--12346821 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
12346775 CTTGCAAATG
*
12346785 ATA A-A ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
12346822 TCATGATGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:12346871 original size:4 final size:4
Alignment explanation
Indices: 12346864--12346915 Score: 56
Period size: 4 Copynumber: 13.0 Consensus size: 4
12346854 TATATATATG
12346864 AAAT AAAT AAAT AAA- ATAAT -AAT AAA- ATAAT AAAT AAAT AAAT AAAAT
1 AAAT AAAT AAAT AAAT A-AAT AAAT AAAT A-AAT AAAT AAAT AAAT -AAAT
12346912 AAAT
1 AAAT
12346916 GGAACAATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
3 5 0.12
4 32 0.76
5 5 0.12
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:12346889 original size:11 final size:11
Alignment explanation
Indices: 12346873--12346913 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
12346863 GAAATAAATA
12346873 AATAAAATAAT
1 AATAAAATAAT
12346884 AATAAAATAAT
1 AATAAAATAAT
12346895 AA-ATAAAT-A-
1 AATA-AAATAAT
12346904 AATAAAATAA
1 AATAAAATAA
12346914 ATGGAACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
9 6 0.22
10 4 0.15
11 17 0.63
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:12357360 original size:21 final size:21
Alignment explanation
Indices: 12357325--12357364 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
12357315 AAAAATTCAA
12357325 ATTAGATAAAAAATATAATTT
1 ATTAGATAAAAAATATAATTT
12357346 ATTAG-TAAAATAATATAAT
1 ATTAGATAAAA-AATATAAT
12357365 GGGGTTGGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
ATTAGATAAAAAATATAATTT
Found at i:12368199 original size:14 final size:14
Alignment explanation
Indices: 12368180--12368209 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12368170 ACAACTTATC
12368180 TATAAAAAAAAATT
1 TATAAAAAAAAATT
*
12368194 TATAAAAATAAATT
1 TATAAAAAAAAATT
12368208 TA
1 TA
12368210 CCAAACAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TATAAAAAAAAATT
Found at i:12376872 original size:22 final size:22
Alignment explanation
Indices: 12376847--12376893 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
12376837 CAATTAGTTA
* *
12376847 TTAGATATTACATTACTGGTTT
1 TTAGACATTACATCACTGGTTT
**
12376869 TTAGACATTGTATCACTGGTTT
1 TTAGACATTACATCACTGGTTT
12376891 TTA
1 TTA
12376894 AGTATTGCGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.49
Consensus pattern (22 bp):
TTAGACATTACATCACTGGTTT
Found at i:12376974 original size:22 final size:22
Alignment explanation
Indices: 12376934--12376975 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12376924 GTTACTTAAT
*
12376934 CATTGCATGATTGGCTTTTAGG
1 CATTGCATGATTGACTTTTAGG
* *
12376956 CATTGCGTGATTGATTTTTA
1 CATTGCATGATTGACTTTTA
12376976 AGCAATACCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.12, G:0.24, T:0.45
Consensus pattern (22 bp):
CATTGCATGATTGACTTTTAGG
Found at i:12377044 original size:23 final size:23
Alignment explanation
Indices: 12376986--12377060 Score: 96
Period size: 23 Copynumber: 3.3 Consensus size: 23
12376976 AGCAATACCT
12376986 AAGTCACGTAATGCCTTACTAAC
1 AAGTCACGTAATGCCTTACTAAC
* * * *
12377009 TAGTTATGCAATGCCTTACTAAC
1 AAGTCACGTAATGCCTTACTAAC
* *
12377032 AAGTCACATAATGTCTTACTAAC
1 AAGTCACGTAATGCCTTACTAAC
12377055 AAGTCA
1 AAGTCA
12377061 TGAATGTCTA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (23 bp):
AAGTCACGTAATGCCTTACTAAC
Found at i:12377203 original size:22 final size:22
Alignment explanation
Indices: 12377171--12377229 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
12377161 GTCAGTCACG
* *
12377171 CAATGCTTAAAAATTAGTAACA
1 CAATGCCTAAAAACTAGTAACA
* *
12377193 CAATGCCTAAAAACTAGTTATA
1 CAATGCCTAAAAACTAGTAACA
*
12377215 CAATGCCCAAAAACT
1 CAATGCCTAAAAACT
12377230 GATTACGTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.24
Consensus pattern (22 bp):
CAATGCCTAAAAACTAGTAACA
Found at i:12377455 original size:61 final size:59
Alignment explanation
Indices: 12377356--12377472 Score: 139
Period size: 60 Copynumber: 1.9 Consensus size: 59
12377346 ACTCAAAATA
12377356 CTCAAACGTTTTTCTTCATATATCAAAAATAACTCAAAAGTGCTTAAAAATGCTTAAAACG
1 CTCAAACGTTTTTCTTCATATATCAAAAATAACTCAAAA-TGC-TAAAAATGCTTAAAACG
* * * * *
12377417 CTCAAAGGTTTTT-TTTATGTATTAAAAACT-ACTCCAAAATGCTCAAAATGCTTAAA
1 CTCAAACGTTTTTCTTCATATATCAAAAA-TAACT-CAAAATGCTAAAAATGCTTAAA
12377473 CATTTTTCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
59 13 0.27
60 18 0.37
61 18 0.37
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (59 bp):
CTCAAACGTTTTTCTTCATATATCAAAAATAACTCAAAATGCTAAAAATGCTTAAAACG
Found at i:12379350 original size:29 final size:28
Alignment explanation
Indices: 12379318--12379461 Score: 164
Period size: 29 Copynumber: 5.0 Consensus size: 28
12379308 AAATATTTGA
* *
12379318 TCTTGTCTAAATTTGAGACAAATATGTAT
1 TCTTGTCTAAA-TTAAGACAAATATGTTT
*
12379347 TCTTGTCTAGATTAAGACAAAAAATAT-TTT
1 TCTTGTCTAAATTAAGAC---AAATATGTTT
* *
12379377 TCTTGTCTTAAATTAAGACAAACATATTT
1 TCTTGTC-TAAATTAAGACAAATATGTTT
12379406 TCTTGTCTAAATTAAGACCAAATATGTTT
1 TCTTGTCTAAATTAAGA-CAAATATGTTT
* *
12379435 TCTTATCTAAATTAAGACAAACATGTT
1 TCTTGTCTAAATTAAGACAAATATGTT
12379462 AAAGCTGTCA
Statistics
Matches: 100, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
28 30 0.30
29 45 0.45
30 9 0.09
31 16 0.16
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAATATGTTT
Found at i:12379398 original size:59 final size:58
Alignment explanation
Indices: 12379296--12379460 Score: 208
Period size: 59 Copynumber: 2.8 Consensus size: 58
12379286 TTTTGTCTGT
* * *
12379296 AATTAAGACAAAAAATATTTGATCTTGTCTAAATTTGAGACAAATATGTATTCTTGTCTA
1 AATTAAGACAAAAAATATTT-TTCTTGTCTAAA-TTAAGACAAACATGTATTCTTGTCTA
* * *
12379356 GATTAAGACAAAAAATATTTTTCTTGTCTTAAATTAAGACAAACATATTTTCTTGTCTA
1 AATTAAGACAAAAAATATTTTTCTTGTC-TAAATTAAGACAAACATGTATTCTTGTCTA
* *
12379415 AATTAAGAC--CAAATATGTTTTCTTATCTAAATTAAGACAAACATGT
1 AATTAAGACAAAAAATAT-TTTTCTTGTCTAAATTAAGACAAACATGT
12379461 TAAAGCTGTC
Statistics
Matches: 93, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
57 24 0.26
58 9 0.10
59 37 0.40
60 23 0.25
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.38
Consensus pattern (58 bp):
AATTAAGACAAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGTATTCTTGTCTA
Found at i:12379438 original size:88 final size:90
Alignment explanation
Indices: 12379288--12379455 Score: 236
Period size: 88 Copynumber: 1.9 Consensus size: 90
12379278 AAGACAACTT
* *
12379288 TTGTCTGTAATTAAGACAAAAAATATTTGATCTTGTCTAAATTTGAGACAAATATGTATTCTTGT
1 TTGTCTGTAATTAAGACAAAAAATATTT-ATCTTGTCTAAATTTAAGACAAATATGTATTCTTAT
*
12379353 CTAGATTAAGACAAAAAATATTTTTC
65 CTAAATTAAGACAAAAAATATTTTTC
* *
12379379 TTGTCT-TAAATTAAGAC-AAACATATTT-TCTTGTCTAAA-TTAAGACCAAATATGTTTTCTTA
1 TTGTCTGT-AATTAAGACAAAAAATATTTATCTTGTCTAAATTTAAGA-CAAATATGTATTCTTA
12379440 TCTAAATTAAGACAAA
64 TCTAAATTAAGACAAA
12379456 CATGTTAAAG
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
87 5 0.07
88 40 0.57
90 10 0.14
91 15 0.21
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (90 bp):
TTGTCTGTAATTAAGACAAAAAATATTTATCTTGTCTAAATTTAAGACAAATATGTATTCTTATC
TAAATTAAGACAAAAAATATTTTTC
Found at i:12388822 original size:24 final size:24
Alignment explanation
Indices: 12388780--12388826 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
12388770 ATCTGTGAGT
*
12388780 AAAATTTATTTAAACATATATTTAA
1 AAAATTCATTTAAACATAT-TTTAA
*
12388805 AAAATTCATTT-AATATATTTTA
1 AAAATTCATTTAAACATATTTTA
12388827 TTATATTCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 6 0.30
25 10 0.50
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
AAAATTCATTTAAACATATTTTAA
Found at i:12393860 original size:2 final size:2
Alignment explanation
Indices: 12393853--12393879 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12393843 AAACGCTTAA
12393853 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 A
12393880 GTCTTTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12393941 original size:20 final size:20
Alignment explanation
Indices: 12393916--12393955 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
12393906 CCGACAACAA
*
12393916 AAAAGGTTTGGGAGAGCTAG
1 AAAAGGTTCGGGAGAGCTAG
12393936 AAAAGGTTCGGGAGAGCTAG
1 AAAAGGTTCGGGAGAGCTAG
12393956 TCAAATCCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.40, T:0.17
Consensus pattern (20 bp):
AAAAGGTTCGGGAGAGCTAG
Found at i:12394336 original size:8 final size:8
Alignment explanation
Indices: 12394323--12394392 Score: 61
Period size: 8 Copynumber: 8.4 Consensus size: 8
12394313 GGTTAAGAAG
12394323 AAAGAAAA
1 AAAGAAAA
12394331 AAAGAAAAGA
1 AAAG-AAA-A
12394341 AGAAGAGAAA
1 A-AAGA-AAA
*
12394351 AAAGAGAA
1 AAAGAAAA
12394359 AAAGAAAA
1 AAAGAAAA
* *
12394367 GAAGAAGA
1 AAAGAAAA
*
12394375 AAA-ATAA
1 AAAGAAAA
12394382 AAAGAAAA
1 AAAGAAAA
12394390 AAA
1 AAA
12394393 AAATAACTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
7 5 0.10
8 27 0.55
9 7 0.14
10 5 0.10
11 5 0.10
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (8 bp):
AAAGAAAA
Found at i:12394353 original size:23 final size:23
Alignment explanation
Indices: 12394324--12394389 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
12394314 GTTAAGAAGA
12394324 AAGAA-AAAAAG-AAAAGAAGAAG
1 AAGAAGAAAAAGAAAAAGAA-AAG
12394346 -AGAA-AAAAGAGAAAAAGAAAAG
1 AAGAAGAAAA-AGAAAAAGAAAAG
*
12394368 AAGAAGAAAAATAAAAAGAAAA
1 AAGAAGAAAAAGAAAAAGAAAA
12394390 AAAAAATAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
21 8 0.21
22 5 0.13
23 22 0.56
24 4 0.10
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (23 bp):
AAGAAGAAAAAGAAAAAGAAAAG
Found at i:12394355 original size:28 final size:28
Alignment explanation
Indices: 12394318--12394378 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
12394308 TGGAGGGTTA
*
12394318 AGAAGAAAGAAAAAAAGAAAAGAAGAAG
1 AGAAAAAAGAAAAAAAGAAAAGAAGAAG
*
12394346 AGAAAAAAGAGAAAAAGAAAAGAAGAAG
1 AGAAAAAAGAAAAAAAGAAAAGAAGAAG
12394374 A-AAAA
1 AGAAAA
12394379 TAAAAAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 4 0.13
28 27 0.87
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (28 bp):
AGAAAAAAGAAAAAAAGAAAAGAAGAAG
Found at i:12394375 original size:31 final size:27
Alignment explanation
Indices: 12394323--12394395 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 27
12394313 GGTTAAGAAG
12394323 AAAGAAAAAAAGAAAAGAAGAAGAGAA-AA
1 AAAGAAAAAAA-AAAAGAAGAA-A-AATAA
12394352 AAGAGAAAAAGAAAAGAAGAAGAAAAATAA
1 AA-AGAAAAA-AAAA-AAGAAGAAAAATAA
12394382 AAAGAAAAAAAAAA
1 AAAGAAAAAAAAAA
12394396 TAACTAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
27 1 0.03
28 4 0.10
29 11 0.28
30 14 0.35
31 10 0.25
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (27 bp):
AAAGAAAAAAAAAAAGAAGAAAAATAA
Found at i:12394389 original size:28 final size:28
Alignment explanation
Indices: 12394329--12394395 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
12394319 GAAGAAAGAA
* *
12394329 AAAAAGAAAAGAAGAAGAGAAAAAAGAG
1 AAAAAGAAAAGAAGAAGAAAAAAAAAAG
12394357 AAAAAGAAAAGAAGAAGAAAAATAAAAAG
1 AAAAAGAAAAGAAGAAGAAAAA-AAAAAG
*
12394386 AAAAAAAAAA
1 AAAAAGAAAA
12394396 TAACTAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
28 21 0.60
29 14 0.40
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (28 bp):
AAAAAGAAAAGAAGAAGAAAAAAAAAAG
Found at i:12405691 original size:34 final size:34
Alignment explanation
Indices: 12405653--12405719 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
12405643 TTGTCTTTCA
12405653 CTTTACAAATCACTTCTATCTTATCAAGCCTTTG
1 CTTTACAAATCACTTCTATCTTATCAAGCCTTTG
12405687 CTTTACAAATCACTTCTATCTTATCAAGCCTTT
1 CTTTACAAATCACTTCTATCTTATCAAGCCTTT
12405720 CCCTTCTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.27, C:0.27, G:0.04, T:0.42
Consensus pattern (34 bp):
CTTTACAAATCACTTCTATCTTATCAAGCCTTTG
Found at i:12407106 original size:2 final size:2
Alignment explanation
Indices: 12407099--12407154 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
12407089 CAAAACATTA
*
12407099 AT AT AT AT AT AT AT AT AT AT NT 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
12407141 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
12407155 TGCCTGGATA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12410535 original size:401 final size:402
Alignment explanation
Indices: 12409754--12410544 Score: 1221
Period size: 401 Copynumber: 2.0 Consensus size: 402
12409744 TACACTTTGC
* *
12409754 CAACCAAAACTTGTTAGCAACTCTGAAACTATCTTTTTTCTTAACCAATTTAGCAAGTTACTTCT
1 CAACCAAAACTTGTTAGCAACTCTGAAACTATCTTTTTTCATAACCAATTTAGCAAGTTAATTCT
* * * * *
12409819 AACCTGATTGTATATTGTTATTCATATTAGTGGTCTTCCTGTATCTGCAGCCTCTGAAAGCATAT
66 AACATGATTGTATACTGTTATTCATATTAGAGGTCTGCCTGTATCTGCAGCCTCTGAAAGCACAT
* * * * *
12409884 GTAGAGTTGCCAGCATGCACAAATAATTTTAATCTGATTCGCGTGCTCTAATAAGTATGCATATG
131 ATAGAGTTGCCAACATGCACAAATAATGTCAATCTGATTCGCATGCTCTAATAAGTATGCATATG
* * *
12409949 AACAACCTGATATATAGAAACTAATCAACAATTTATCTGGAGCAGAATGTGCTTAATTTTTTGGA
196 AACAACCTGATATATAGAAACTAATCAACAATTTATCTGGAACAGAATGTGCTTAATTTTTCGCA
12410014 GGTGCCTCAGACAAATATAACTTTTCATCAGGTCTGCCAACACGTTATCCTTACCTTGTGCACTA
261 GGTGCCTCAGACAAATATAACTTTTCATCAGGTCTGCCAACACGTTATCCTTACCTTGTGCACTA
* *
12410079 TTTCTATTACAAGCATTTTCCCCTTTATTTTGAGTCTTGTATTTTTCCCTTTCCCCACTTTACCC
326 TCTCTATTACAAGCATTTTACCCTTTATTTTGAGTCTTGTATTTTTCCCTTTCCCCACTTTACCC
12410144 TTTACATGCTAA
391 TTTACATGCTAA
* * * *
12410156 CAACCAGAACTTGTTAGCTACTC-GAAACTATCTTTTTTCATAATCAATTT-GCCAAGTTAATTG
1 CAACCAAAACTTGTTAGCAACTCTGAAACTATCTTTTTTCATAACCAATTTAG-CAAGTTAATTC
12410219 TAACATGATTGTATACTGTTATTCATATTAGAGGTCTGCCTGTATCTGCAGCCTCTGAAAGCACA
65 TAACATGATTGTATACTGTTATTCATATTAGAGGTCTGCCTGTATCTGCAGCCTCTGAAAGCACA
* * * * *
12410284 TATAGAGTTGCCAACATGCGCAAATAATGTCAATCTGATTCTCATGCTCTAATAAGTGTGTATGT
130 TATAGAGTTGCCAACATGCACAAATAATGTCAATCTGATTCGCATGCTCTAATAAGTATGCATAT
* *
12410349 GAGCAACCTGATACT-TAGAAACTAATCAACAATTTATTTGGAACAGAATGTGCTTAATTTTTCG
195 GAACAACCTGATA-TATAGAAACTAATCAACAATTTATCTGGAACAGAATGTGCTTAATTTTTCG
* *
12410413 CAGGTGCCTCAGACCAATATAACTTTTCATCAGGTCTGCCAACACGTTATTCTTACCTTGTGCAC
259 CAGGTGCCTCAGACAAATATAACTTTTCATCAGGTCTGCCAACACGTTATCCTTACCTTGTGCAC
* * * *
12410478 TATCTCTGTTACATGC-TTTTACCCTTTATTTTGAGTCTTGTATTTTTTTCTTTTCCCCACTTTA
324 TATCTCTATTACAAGCATTTTACCCTTTATTTTGAGTCTTGTA-TTTTTCCCTTTCCCCACTTTA
12410542 CCC
388 CCC
12410545 AAAGACTTGG
Statistics
Matches: 352, Mismatches: 34, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
400 26 0.07
401 304 0.86
402 22 0.06
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (402 bp):
CAACCAAAACTTGTTAGCAACTCTGAAACTATCTTTTTTCATAACCAATTTAGCAAGTTAATTCT
AACATGATTGTATACTGTTATTCATATTAGAGGTCTGCCTGTATCTGCAGCCTCTGAAAGCACAT
ATAGAGTTGCCAACATGCACAAATAATGTCAATCTGATTCGCATGCTCTAATAAGTATGCATATG
AACAACCTGATATATAGAAACTAATCAACAATTTATCTGGAACAGAATGTGCTTAATTTTTCGCA
GGTGCCTCAGACAAATATAACTTTTCATCAGGTCTGCCAACACGTTATCCTTACCTTGTGCACTA
TCTCTATTACAAGCATTTTACCCTTTATTTTGAGTCTTGTATTTTTCCCTTTCCCCACTTTACCC
TTTACATGCTAA
Found at i:12428639 original size:22 final size:22
Alignment explanation
Indices: 12428578--12428642 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
12428568 AGTTTTGATG
* * *
12428578 GTTTTTAGGCATTACGTAACTA
1 GTTTTTAAGTATTACGTGACTA
* *
12428600 ATTTTTATGTATTACGTGACTA
1 GTTTTTAAGTATTACGTGACTA
*
12428622 GTTTTTAAGTATTGCGTGACT
1 GTTTTTAAGTATTACGTGACT
12428643 TGTTGATATA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.46
Consensus pattern (22 bp):
GTTTTTAAGTATTACGTGACTA
Found at i:12428664 original size:23 final size:23
Alignment explanation
Indices: 12428632--12428681 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
12428622 GTTTTTAAGT
* *
12428632 ATTGCGTGACTTGTTGATATAGC
1 ATTGCATGACTGGTTGATATAGC
*
12428655 ATTGCATGACTGGTTGATATGGC
1 ATTGCATGACTGGTTGATATAGC
12428678 ATTG
1 ATTG
12428682 TGTGATTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (23 bp):
ATTGCATGACTGGTTGATATAGC
Found at i:12429904 original size:22 final size:22
Alignment explanation
Indices: 12429879--12429927 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
12429869 GATAAAAGGC
* *
12429879 ATTGTGAGACTAGATTTTAGGA
1 ATTGCGAGACGAGATTTTAGGA
* *
12429901 ATTGCGTGACGAGGTTTTAGGA
1 ATTGCGAGACGAGATTTTAGGA
12429923 ATTGC
1 ATTGC
12429928 TTGACTAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.08, G:0.31, T:0.35
Consensus pattern (22 bp):
ATTGCGAGACGAGATTTTAGGA
Found at i:12429932 original size:22 final size:21
Alignment explanation
Indices: 12429893--12429971 Score: 86
Period size: 22 Copynumber: 3.6 Consensus size: 21
12429883 TGAGACTAGA
12429893 TTTTAGGAATTGCGTGACGAGG
1 TTTTAGGAATTGCGTGACGA-G
* *
12429915 TTTTAGGAATTGCTTGACTAG
1 TTTTAGGAATTGCGTGACGAG
* *
12429936 TTTGTAGGCATTGCGTGACTGAT
1 TTT-TAGGAATTGCGTGAC-GAG
*
12429959 TTTTAGTAATTGC
1 TTTTAGGAATTGC
12429972 ATTGCTTTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
21 4 0.09
22 39 0.83
23 4 0.09
ACGTcount: A:0.22, C:0.10, G:0.28, T:0.41
Consensus pattern (21 bp):
TTTTAGGAATTGCGTGACGAG
Found at i:12429950 original size:44 final size:44
Alignment explanation
Indices: 12429886--12429971 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
12429876 GGCATTGTGA
12429886 GACTAGATTTTAGGAATTGCGTGAC-GAGGTTTTAGGAATTGCTT
1 GACTAGATTTTAGGAATTGCGTGACTGA-GTTTTAGGAATTGCTT
* * *
12429930 GACTAG-TTTGTAGGCATTGCGTGACTGATTTTTAGTAATTGC
1 GACTAGATTT-TAGGAATTGCGTGACTGAGTTTTAGGAATTGC
12429972 ATTGCTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 3 0.08
44 32 0.86
45 2 0.05
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.38
Consensus pattern (44 bp):
GACTAGATTTTAGGAATTGCGTGACTGAGTTTTAGGAATTGCTT
Found at i:12430801 original size:22 final size:22
Alignment explanation
Indices: 12430776--12430817 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
12430766 AAGGATTAAG
*
12430776 TGAATGGATATTATGCATTGTA
1 TGAATGGATATTAAGCATTGTA
12430798 TGAATGGATATTAAGCATTG
1 TGAATGGATATTAAGCATTG
12430818 CGTGTCTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (22 bp):
TGAATGGATATTAAGCATTGTA
Found at i:12431077 original size:22 final size:22
Alignment explanation
Indices: 12431025--12431078 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
12431015 CTTTGTAAGC
12431025 ATTGCGTGACTAGTTGTTATGT
1 ATTGCGTGACTAGTTGTTATGT
*
12431047 ATT-CTGTGACTTGTTGTTATGT
1 ATTGC-GTGACTAGTTGTTATGT
12431069 ATTGCGTGAC
1 ATTGCGTGAC
12431079 GTTGGGCCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 1 0.03
22 27 0.93
23 1 0.03
ACGTcount: A:0.17, C:0.11, G:0.26, T:0.46
Consensus pattern (22 bp):
ATTGCGTGACTAGTTGTTATGT
Found at i:12438444 original size:40 final size:37
Alignment explanation
Indices: 12438388--12438483 Score: 102
Period size: 40 Copynumber: 2.5 Consensus size: 37
12438378 ATCTAGCTCA
* *
12438388 TGTGCATCCCCTCACATTGTGCACATAGCCGAAGTCATCG
1 TGTGCATCCCC-CACATCGTGCACA-AGCAG-AGTCATCG
* *
12438428 TGTGCATCCCTCCACATCGTGCACAATCAGTGTCATCG
1 TGTGCATCCC-CCACATCGTGCACAAGCAGAGTCATCG
*
12438466 TGTACATCCCCCCACATC
1 TGTGCAT-CCCCCACATC
12438484 ATGTACACGG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
38 20 0.41
39 6 0.12
40 22 0.45
41 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (37 bp):
TGTGCATCCCCCACATCGTGCACAAGCAGAGTCATCG
Found at i:12439352 original size:42 final size:41
Alignment explanation
Indices: 12439278--12439419 Score: 178
Period size: 42 Copynumber: 3.4 Consensus size: 41
12439268 ACGGCTTATG
* *
12439278 CGCATATAGCCAGGTCAGCAACGACTTATGTGCACT-CTCACT
1 CGCACATAGCCAGGTCAGCAAAG-CTTATGTGCACTCCT-ACT
* * *
12439320 CACACATAGCCGGGTCAGCAATAGCTTGTGTGCACTCCTACT
1 CGCACATAGCCAGGTCAGCAA-AGCTTATGTGCACTCCTACT
* *
12439362 CGCACATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACT
1 CGCACATAGCCAGGTCAGCAA-AGCTTATGTGCACTCCTACT
12439404 CGCACATAGCCAGGTC
1 CGCACATAGCCAGGTC
12439420 CAAATCAACA
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
42 85 0.97
43 3 0.03
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22
Consensus pattern (41 bp):
CGCACATAGCCAGGTCAGCAAAGCTTATGTGCACTCCTACT
Found at i:12443279 original size:18 final size:19
Alignment explanation
Indices: 12443258--12443305 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
12443248 GTTACGAGTG
*
12443258 AAAAGAATATTTTA-AAAT
1 AAAATAATATTTTATAAAT
* *
12443276 AAAATATTATTTTATGAAT
1 AAAATAATATTTTATAAAT
12443295 AAAATAATATT
1 AAAATAATATT
12443306 AAAATATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:12445808 original size:18 final size:19
Alignment explanation
Indices: 12445787--12445834 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
12445777 GTTACGAGTG
*
12445787 AAAAGAATATTTTA-AAAT
1 AAAATAATATTTTATAAAT
* *
12445805 AAAATATTATTTTATGAAT
1 AAAATAATATTTTATAAAT
12445824 AAAATAATATT
1 AAAATAATATT
12445835 AAAATATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:12447065 original size:23 final size:23
Alignment explanation
Indices: 12447039--12447121 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 23
12447029 TACCTGAAGC
** *
12447039 CATGCAATACCATATCAAATAGT
1 CATGCAATTTCATATCAACTAGT
** *
12447062 CATGTTATTTCATATTAACTAGT
1 CATGCAATTTCATATCAACTAGT
*
12447085 CACGCAATTTCATATCAACTAGT
1 CATGCAATTTCATATCAACTAGT
**
12447108 CATGTGATTTCATA
1 CATGCAATTTCATA
12447122 CACACCATTC
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (23 bp):
CATGCAATTTCATATCAACTAGT
Found at i:12447986 original size:22 final size:21
Alignment explanation
Indices: 12447947--12447987 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12447937 CCTAGGTGGA
**
12447947 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGAAAAAAGTGTG
12447968 AAAATTCAAGAAAACAAGTG
1 AAAATTCAAGAAAA-AAGTG
12447988 AAAAAAGGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.54, C:0.07, G:0.22, T:0.17
Consensus pattern (21 bp):
AAAATTCAAGAAAAAAGTGTG
Found at i:12447992 original size:21 final size:20
Alignment explanation
Indices: 12447945--12447992 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
12447935 ACCCTAGGTG
**
12447945 GAAAAATTCAAGGGAAAAGT
1 GAAAAATTCAAGAAAAAAGT
*
12447965 GTGAAAATTCAAGAAAACAAGT
1 G-AAAAATTCAAGAAAA-AAGT
12447987 GAAAAA
1 GAAAAA
12447993 AGGTAAGATT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 16 0.73
22 5 0.23
ACGTcount: A:0.58, C:0.06, G:0.21, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAGAAAAAAGT
Found at i:12450518 original size:18 final size:18
Alignment explanation
Indices: 12450487--12450521 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12450477 ACATATTAGG
*
12450487 AAAAAGAATAAACAAATT
1 AAAAAAAATAAACAAATT
*
12450505 AAAAAAAATTAACAAAT
1 AAAAAAAATAAACAAAT
12450522 CACGCTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.17
Consensus pattern (18 bp):
AAAAAAAATAAACAAATT
Found at i:12451890 original size:27 final size:27
Alignment explanation
Indices: 12451852--12451904 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
12451842 AAGCTTGGAG
12451852 TAGATGCAATTACCTAATTTATGCCAA
1 TAGATGCAATTACCTAATTTATGCCAA
*
12451879 TAGATGCAATTACCTGATTTATGCCA
1 TAGATGCAATTACCTAATTTATGCCA
12451905 CCTGCCTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (27 bp):
TAGATGCAATTACCTAATTTATGCCAA
Found at i:12452180 original size:24 final size:24
Alignment explanation
Indices: 12452153--12452206 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
12452143 GCATTGACTG
12452153 CATTGCCCACTAGATCTCCAACTA
1 CATTGCCCACTAGATCTCCAACTA
*** *
12452177 CATTGCCTGTTGGATCTCCAACTA
1 CATTGCCCACTAGATCTCCAACTA
12452201 CATTGC
1 CATTGC
12452207 ATGCATATGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.33, G:0.13, T:0.30
Consensus pattern (24 bp):
CATTGCCCACTAGATCTCCAACTA
Found at i:12454435 original size:23 final size:23
Alignment explanation
Indices: 12454403--12454447 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
12454393 CTTGAACCAT
12454403 ATTCACGCAATGACCTATCAACC
1 ATTCACGCAATGACCTATCAACC
*
12454426 ATTCATGCAATGACCTATCAAC
1 ATTCACGCAATGACCTATCAAC
12454448 TAGTCATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.31, G:0.09, T:0.24
Consensus pattern (23 bp):
ATTCACGCAATGACCTATCAACC
Found at i:12454454 original size:23 final size:23
Alignment explanation
Indices: 12454409--12454459 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
12454399 CCATATTCAC
*
12454409 GCAATGACCTATCAACCATTCAT
1 GCAATGACCTATCAACCAGTCAT
*
12454432 GCAATGACCTATCAACTAGTCAT
1 GCAATGACCTATCAACCAGTCAT
*
12454455 ACAAT
1 GCAAT
12454460 ACTAAACCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.27, G:0.10, T:0.25
Consensus pattern (23 bp):
GCAATGACCTATCAACCAGTCAT
Found at i:12460293 original size:2 final size:2
Alignment explanation
Indices: 12460286--12460326 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
12460276 NNNNNNNNTA
12460286 AT AT AT AT A- 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
12460327 TTCATTTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12462207 original size:2 final size:2
Alignment explanation
Indices: 12462200--12462232 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12462190 CTAAGTTAAC
*
12462200 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12462233 AAGAGAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12463372 original size:2 final size:2
Alignment explanation
Indices: 12463365--12463431 Score: 111
Period size: 2 Copynumber: 34.0 Consensus size: 2
12463355 ATACTTTGAG
12463365 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
12463407 AT AT AT A- AT AT AT -T NAT AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT
12463432 GGTCTTTGTC
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.03
2 59 0.95
3 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12465483 original size:29 final size:29
Alignment explanation
Indices: 12465419--12465483 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
12465409 TATTTTTAAT
*
12465419 TTAAAAAAATTAAAAATATAATGACAAAA
1 TTAATAAAATTAAAAATATAATGACAAAA
12465448 TTCAATAAAATT-AAAATATAATGACAAAAA
1 TT-AATAAAATTAAAAATATAATGAC-AAAA
12465478 TTAATA
1 TTAATA
12465484 TTAAATCATA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 19 0.58
30 14 0.42
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (29 bp):
TTAATAAAATTAAAAATATAATGACAAAA
Found at i:12467970 original size:22 final size:22
Alignment explanation
Indices: 12467956--12467999 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12467946 AAAAATTTAT
*
12467956 TTAAATTTTCTTAAATAGTTTG
1 TTAAATTTTCTTAAATAATTTG
* *
12467978 TTAAGTTTTCTTAAATAGTTTG
1 TTAAATTTTCTTAAATAATTTG
12468000 GTTTTGAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.55
Consensus pattern (22 bp):
TTAAATTTTCTTAAATAATTTG
Found at i:12478507 original size:26 final size:27
Alignment explanation
Indices: 12478420--12478509 Score: 98
Period size: 26 Copynumber: 3.5 Consensus size: 27
12478410 TATTTTAATT
*
12478420 ATAATTTTACTATAAGAAGTGGAT-GA
1 ATAATTTTACCATAAGAAGTGGATAGA
* * **
12478446 ATAATTTTATCATCAGAA-TCTA-AGA
1 ATAATTTTACCATAAGAAGTGGATAGA
*
12478471 ATAATTTTACCATTAGAAGTGGATAG-
1 ATAATTTTACCATAAGAAGTGGATAGA
12478497 ATAATTTTACCAT
1 ATAATTTTACCAT
12478510 CAAAAGTTGA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
25 20 0.38
26 30 0.58
27 2 0.04
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (27 bp):
ATAATTTTACCATAAGAAGTGGATAGA
Found at i:12480047 original size:21 final size:21
Alignment explanation
Indices: 12480023--12480063 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12480013 TTTTTTCTTT
12480023 TATATATTATATTTATTTTCA
1 TATATATTATATTTATTTTCA
* * *
12480044 TATATGTTGTTTTTATTTTC
1 TATATATTATATTTATTTTC
12480064 TTCTTTTTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (21 bp):
TATATATTATATTTATTTTCA
Found at i:12480785 original size:42 final size:42
Alignment explanation
Indices: 12480754--12480840 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
12480744 ACCATGTCCC
12480754 CCACCACCACCATAACCTCCTCCATGTCCGCCACCGCCGCCA
1 CCACCACCACCATAACCTCCTCCATGTCCGCCACCGCCGCCA
*
12480796 CCGCCACCACCATAACCTCCTCCATGTCCGCCACCGCCGCCA
1 CCACCACCACCATAACCTCCTCCATGTCCGCCACCGCCGCCA
12480838 CCA
1 CCA
12480841 TAACCTCCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.21, C:0.57, G:0.10, T:0.11
Consensus pattern (42 bp):
CCACCACCACCATAACCTCCTCCATGTCCGCCACCGCCGCCA
Found at i:12480860 original size:42 final size:42
Alignment explanation
Indices: 12480754--12480861 Score: 135
Period size: 42 Copynumber: 2.6 Consensus size: 42
12480744 ACCATGTCCC
* *
12480754 CCACCACCACCATAACCTCCTCCATGTCCGCCACCGCCGCCA
1 CCACAACCACCATAACCGCCTCCATGTCCGCCACCGCCGCCA
* * *
12480796 CCGCCACCACCATAACCTCCTCCATGTCCGCCACCGCCGCCA
1 CCACAACCACCATAACCGCCTCCATGTCCGCCACCGCCGCCA
* * **
12480838 CCATAACCTCCATGTCCGCCTCCA
1 CCACAACCACCATAACCGCCTCCA
12480862 CCGCCCCATC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.20, C:0.56, G:0.10, T:0.14
Consensus pattern (42 bp):
CCACAACCACCATAACCGCCTCCATGTCCGCCACCGCCGCCA
Found at i:12480863 original size:33 final size:33
Alignment explanation
Indices: 12480787--12480866 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 33
12480777 ATGTCCGCCA
12480787 CCGCCGCCACCGCCACCACCATAACCTCCTCCATGT
1 CCGCC-CCACCGCCACCACCATAA-C-CCTCCATGT
*
12480823 CCG--CCACCGCCGCCACCATAA-CCTCCATGT
1 CCGCCCCACCGCCACCACCATAACCCTCCATGT
12480853 CCGCCTCCACCGCC
1 CCGCC-CCACCGCC
12480867 CCATCCACCC
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
30 12 0.30
33 25 0.62
36 3 0.08
ACGTcount: A:0.17, C:0.57, G:0.12, T:0.12
Consensus pattern (33 bp):
CCGCCCCACCGCCACCACCATAACCCTCCATGT
Found at i:12486410 original size:2 final size:2
Alignment explanation
Indices: 12486403--12486463 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
12486393 TTTCTATAAC
12486403 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
*
12486445 AT AT AC AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
12486464 CATACATACA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12486571 original size:43 final size:43
Alignment explanation
Indices: 12486500--12486626 Score: 184
Period size: 43 Copynumber: 3.0 Consensus size: 43
12486490 CCCTCCACAC
* ** *
12486500 TCAGCTCATGTGCACTTCC-TGCTCGCACATAGCCGGGTCATCA
1 TCAGCTCATGTGCACTCCCACACT-GCACATAGCTGGGTCATCA
12486543 TCAGCTCATGTGCACTCCCACACTGCACATAGCTGGGTCATCA
1 TCAGCTCATGTGCACTCCCACACTGCACATAGCTGGGTCATCA
* *
12486586 TCAACTCATGTGCACTCCTACACTGCACATAGCTGGGTCAT
1 TCAGCTCATGTGCACTCCCACACTGCACATAGCTGGGTCAT
12486627 TATTATCACA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
43 75 0.97
44 2 0.03
ACGTcount: A:0.22, C:0.34, G:0.19, T:0.25
Consensus pattern (43 bp):
TCAGCTCATGTGCACTCCCACACTGCACATAGCTGGGTCATCA
Found at i:12499670 original size:19 final size:19
Alignment explanation
Indices: 12499646--12499683 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12499636 ACTTCTAAAT
12499646 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
*
12499665 CTCAAATCATACTCTAATA
1 CTCAAATCATACTCCAATA
12499684 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:12502773 original size:57 final size:57
Alignment explanation
Indices: 12502709--12502821 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 57
12502699 TACACTTGAT
* * * *
12502709 TTACTGTAATGTTGAAGTGGTGTCTTTGA-TTTCTGTTTAGTTTAACCTCTTTTAAAA
1 TTACTGTAATGTTGAAGTGGTGTATCTAATTTTC-ATTTAGTTTAACCTCTTTTAAAA
12502766 TTACTGTAATGTTGAAGTGGTGTATCTAATTTTCATTTAGTTTAACCTCTTTTAAA
1 TTACTGTAATGTTGAAGTGGTGTATCTAATTTTCATTTAGTTTAACCTCTTTTAAA
12502822 GTTTAGTAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
57 47 0.92
58 4 0.08
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.49
Consensus pattern (57 bp):
TTACTGTAATGTTGAAGTGGTGTATCTAATTTTCATTTAGTTTAACCTCTTTTAAAA
Found at i:12511078 original size:1 final size:1
Alignment explanation
Indices: 12511072--12511101 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
12511062 TTAATCTGGG
*
12511072 TTTTTTTTTTTGTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12511102 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:12518399 original size:2 final size:2
Alignment explanation
Indices: 12518392--12518424 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12518382 TTAATAATTG
*
12518392 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12518425 GTCTGATCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12518992 original size:80 final size:76
Alignment explanation
Indices: 12518856--12519004 Score: 253
Period size: 80 Copynumber: 1.9 Consensus size: 76
12518846 TAAGTAATTC
12518856 AATTATTTCAAACCTATATATATATAGAGAGAGAGAGAGAGAGAGAGAGGCTATAATTTAGCTCT
1 AATTATTTCAAACCTATATATATATAGAGAGAGAGAGAGAGAGAGAGAGGCTATAATTTAGCTCT
12518921 TCATNAATTACT
66 TCAT-AATTACT
*
12518933 AATTAATTTCTAACCTAACTATATATATAGAGAGAGAGAGAGAGAGAGAGAGGCTATAATTTAGC
1 AATT-ATTTCAAACCT-A-TATATATATAGAGAGAGAGAGAGAGAGAGAGAGGCTATAATTTAGC
12518998 TCTTCAT
63 TCTTCAT
12519005 TACCACCTGG
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
77 4 0.06
78 10 0.15
79 1 0.01
80 53 0.78
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (76 bp):
AATTATTTCAAACCTATATATATATAGAGAGAGAGAGAGAGAGAGAGAGGCTATAATTTAGCTCT
TCATAATTACT
Found at i:12536106 original size:18 final size:18
Alignment explanation
Indices: 12536070--12536107 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
12536060 ATGTAAGATC
*
12536070 ATATTTTATTTAATTCTA
1 ATATTTTATTTAATGCTA
12536088 ATATTTTAATTT-ATGCTA
1 ATATTTT-ATTTAATGCTA
12536106 AT
1 AT
12536108 GAGTAGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (18 bp):
ATATTTTATTTAATGCTA
Found at i:12549822 original size:14 final size:14
Alignment explanation
Indices: 12549803--12549836 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
12549793 TGATAAAAAT
12549803 ATAAAATAATTTAA
1 ATAAAATAATTTAA
*
12549817 ATAAAATAATTTAT
1 ATAAAATAATTTAA
12549831 ATAAAA
1 ATAAAA
12549837 ATTATACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAAAATAATTTAA
Found at i:12550351 original size:23 final size:25
Alignment explanation
Indices: 12550310--12550358 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
12550300 ACTGAACAAA
* *
12550310 AAAATTATTGTAAAGATAAAATTAT
1 AAAATTATTGTAAAAATAAAAGTAT
12550335 AAAATT-TT-TAAAAATAAAAGTAT
1 AAAATTATTGTAAAAATAAAAGTAT
12550358 A
1 A
12550359 TTATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 14 0.64
24 2 0.09
25 6 0.27
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (25 bp):
AAAATTATTGTAAAAATAAAAGTAT
Found at i:12557645 original size:7 final size:7
Alignment explanation
Indices: 12557623--12557680 Score: 68
Period size: 7 Copynumber: 8.6 Consensus size: 7
12557613 TATGTTTGAA
12557623 TTATTA-
1 TTATTAT
*
12557629 TTATTTT
1 TTATTAT
*
12557636 TTATCAT
1 TTATTAT
12557643 TTATTAT
1 TTATTAT
12557650 TTATTAT
1 TTATTAT
12557657 TTATTAT
1 TTATTAT
12557664 TTATT-T
1 TTATTAT
12557670 ATTATT-T
1 -TTATTAT
12557677 TTAT
1 TTAT
12557681 CAAGTAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
6 10 0.22
7 36 0.78
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (7 bp):
TTATTAT
Found at i:12567656 original size:39 final size:42
Alignment explanation
Indices: 12567600--12567681 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
12567590 ACGTACACGT
* *
12567600 ACACGTTTAATACACGTG-T-A-ACACGACACGACACGATTA
1 ACACGTTTAATAAACGTGTTAATACACGACACGACACAATTA
* *
12567639 ACACGTTTATTAAACGTGTTAATATACGACACGACACAATTA
1 ACACGTTTAATAAACGTGTTAATACACGACACGACACAATTA
12567681 A
1 A
12567682 TAACACGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 16 0.44
40 1 0.03
41 1 0.03
42 18 0.50
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.24
Consensus pattern (42 bp):
ACACGTTTAATAAACGTGTTAATACACGACACGACACAATTA
Found at i:12567696 original size:9 final size:9
Alignment explanation
Indices: 12567682--12567713 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
12567672 ACACAATTAA
12567682 TAACACGTT
1 TAACACGTT
*
12567691 TAACACGAT
1 TAACACGTT
12567700 TAACACGTT
1 TAACACGTT
12567709 TAACA
1 TAACA
12567714 TGATTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (9 bp):
TAACACGTT
Found at i:12567705 original size:18 final size:18
Alignment explanation
Indices: 12567682--12567720 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
12567672 ACACAATTAA
12567682 TAACACGTTTAACACGAT
1 TAACACGTTTAACACGAT
*
12567700 TAACACGTTTAACATGAT
1 TAACACGTTTAACACGAT
12567718 TAA
1 TAA
12567721 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (18 bp):
TAACACGTTTAACACGAT
Found at i:12567720 original size:9 final size:9
Alignment explanation
Indices: 12567682--12567720 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
12567672 ACACAATTAA
*
12567682 TAACACGTT
1 TAACACGAT
12567691 TAACACGAT
1 TAACACGAT
*
12567700 TAACACGTT
1 TAACACGAT
*
12567709 TAACATGAT
1 TAACACGAT
12567718 TAA
1 TAA
12567721 ATAAAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (9 bp):
TAACACGAT
Found at i:12570602 original size:18 final size:17
Alignment explanation
Indices: 12570558--12570605 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
12570548 TTTACTCAAT
* * *
12570558 TTTAATTTTTTTTATTT
1 TTTAATTTATATTATTA
12570575 TTTAATTTATATTATTA
1 TTTAATTTATATTATTA
12570592 TTTATATTTATATT
1 TTTA-ATTTATATT
12570606 TTTTAATACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 18 0.67
18 9 0.33
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTAATTTATATTATTA
Found at i:12573796 original size:72 final size:74
Alignment explanation
Indices: 12573675--12573850 Score: 191
Period size: 73 Copynumber: 2.4 Consensus size: 74
12573665 AGAACCGACT
* * * **
12573675 TAGTCAACCAAGATG-TGAGTTAGTCGACTAAATGCTTTCTGCCAAAATCT-GGACTTCAAGACA
1 TAGTCGACCAAGAAGATGAGTTAGTCGACTAAATGCTTTCTACCAAAATCTAGGACCACAAGACA
*
12573738 GAACCAACC
66 AAACCAACC
* * * *
12573747 TAGTCGATCAAGAA-ATGAGTTAGTCGACTAAATGCTCTT-TACCAGAATCTATGACCAGAAGAC
1 TAGTCGACCAAGAAGATGAGTTAGTCGACTAAATGCT-TTCTACCAAAATCTAGGACCACAAGAC
*
12573810 AAAACCAACT
65 AAAACCAACC
* *
12573820 TAGTTGACCAAGAAGA-AAGTTAGTCGACTAA
1 TAGTCGACCAAGAAGATGAGTTAGTCGACTAA
12573851 GAGCTTTTTG
Statistics
Matches: 86, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
72 41 0.48
73 44 0.51
74 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.23
Consensus pattern (74 bp):
TAGTCGACCAAGAAGATGAGTTAGTCGACTAAATGCTTTCTACCAAAATCTAGGACCACAAGACA
AAACCAACC
Found at i:12578566 original size:24 final size:25
Alignment explanation
Indices: 12578518--12578568 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
12578508 TTGGAAAAGC
*
12578518 ATTTCCAACGAAAATTTTGTGGGAA
1 ATTTCCAACGAAAATTCTGTGGGAA
* *
12578543 ATTTCCAACG-GAATTCTGTTGGAA
1 ATTTCCAACGAAAATTCTGTGGGAA
12578567 AT
1 AT
12578569 GCTTCTCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (25 bp):
ATTTCCAACGAAAATTCTGTGGGAA
Found at i:12582545 original size:33 final size:33
Alignment explanation
Indices: 12582503--12582620 Score: 112
Period size: 33 Copynumber: 3.6 Consensus size: 33
12582493 ATCAAAATCC
*
12582503 AAATTATTTACTAAATATATTTATATGTTTACA
1 AAATTATTTACTAAATATGTTTATATGTTTACA
* * **** *
12582536 AAATTATTTACCAAATATGTTCATAAAAAT-CT
1 AAATTATTTACTAAATATGTTTATATGTTTACA
* * * *
12582568 AAATAATTTATTAAATATGTTTTTATGTTTACC
1 AAATTATTTACTAAATATGTTTATATGTTTACA
*
12582601 AAAGTATTTACTAAATATGT
1 AAATTATTTACTAAATATGT
12582621 CCACATCATT
Statistics
Matches: 63, Mismatches: 21, Indels: 2
0.73 0.24 0.02
Matches are distributed among these distances:
32 22 0.35
33 41 0.65
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (33 bp):
AAATTATTTACTAAATATGTTTATATGTTTACA
Found at i:12582565 original size:65 final size:65
Alignment explanation
Indices: 12582491--12582620 Score: 179
Period size: 65 Copynumber: 2.0 Consensus size: 65
12582481 TTTGTCTGCA
* * *
12582491 TCATCAAAATCCAAATTATTTACTAAATATATTTATATGTTTACAAAATTATTTACCAAATATGT
1 TCATAAAAATCCAAATAATTTACTAAATATATTTATATGTTTACAAAAGTATTTACCAAATATGT
* * * * * *
12582556 TCATAAAAATCTAAATAATTTATTAAATATGTTTTTATGTTTACCAAAGTATTTACTAAATATGT
1 TCATAAAAATCCAAATAATTTACTAAATATATTTATATGTTTACAAAAGTATTTACCAAATATGT
12582621 CCACATCATT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (65 bp):
TCATAAAAATCCAAATAATTTACTAAATATATTTATATGTTTACAAAAGTATTTACCAAATATGT
Found at i:12584390 original size:24 final size:24
Alignment explanation
Indices: 12584363--12584408 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
12584353 AACGCATGGC
12584363 TGATTATGT-AACAGAACATGTGGT
1 TGATTATGTGAACA-AACATGTGGT
*
12584387 TGATTATGTGACCAAACATGTG
1 TGATTATGTGAACAAACATGTG
12584409 ACAAAGTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.33
Consensus pattern (24 bp):
TGATTATGTGAACAAACATGTGGT
Found at i:12585262 original size:23 final size:23
Alignment explanation
Indices: 12585236--12585314 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
12585226 TTTTAGAGTT
*
12585236 TGTGAAACGGAATGGTGGGAATG
1 TGTGACACGGAATGGTGGGAATG
12585259 TGTGACAC-GACATGGTGGGAATG
1 TGTGACACGGA-ATGGTGGGAATG
** * *
12585282 TGTGACACGTCATGGTGAGAATA
1 TGTGACACGGAATGGTGGGAATG
*
12585305 TGTGAGACGG
1 TGTGACACGG
12585315 GTGTGACACA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
22 2 0.04
23 45 0.96
ACGTcount: A:0.28, C:0.10, G:0.39, T:0.23
Consensus pattern (23 bp):
TGTGACACGGAATGGTGGGAATG
Found at i:12585437 original size:23 final size:23
Alignment explanation
Indices: 12585340--12585457 Score: 76
Period size: 23 Copynumber: 5.1 Consensus size: 23
12585330 GTATAGAGTT
*
12585340 TGTGACACGGCATGGTG-GCAATG
1 TGTGACACGGCAAGGTGAG-AATG
* * * * *
12585363 TGTGACATGTCATGGTGAAAATA
1 TGTGACACGGCAAGGTGAGAATG
* * * * *
12585386 TGTGACATGGTAGGGTTTAGAGTG
1 TGTGACACGGCAAGG-TGAGAATG
* *
12585410 TGTGACACGTCAAGGTGATAATG
1 TGTGACACGGCAAGGTGAGAATG
* *
12585433 TGTGAGACGGCACGGTGAGAATG
1 TGTGACACGGCAAGGTGAGAATG
12585456 TG
1 TG
12585458 ACAGGGGTGT
Statistics
Matches: 71, Mismatches: 22, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
23 56 0.79
24 15 0.21
ACGTcount: A:0.26, C:0.11, G:0.36, T:0.26
Consensus pattern (23 bp):
TGTGACACGGCAAGGTGAGAATG
Found at i:12585676 original size:104 final size:103
Alignment explanation
Indices: 12585410--12585678 Score: 326
Period size: 104 Copynumber: 2.6 Consensus size: 103
12585400 GTTTAGAGTG
* * *
12585410 TGTGACACGTCAAGGTGATAATGTGTGAGACGGCACGGTGAG-A-ATGTGACAGGGGTGTGACAC
1 TGTGACACGACAGGGTGATAATGTGTGAGACGGCACGGTGAGAATATGTGACACGGGTGTGACAC
** ** *
12585473 GGTAGGGTTTAGAGTGTGTGACATGCCATGGTCAAACA
66 GACAGGGTTTAGAGTGTGTGACACACCATGGGCAAACA
* * * * * * *
12585511 TGTGACACGGCAGGGTTATAATGTGTGAAACAGCACAGTGATAATGTGTGACACGGGTGTGACAC
1 TGTGACACGACAGGGTGATAATGTGTGAGACGGCACGGTGAGAATATGTGACACGGGTGTGACAC
** **
12585576 GACAGGGTTTAGAGTGTGTGACACACCATGGAGGGAATT
66 GACAGGGTTTAGAGTGTGTGACACACCATGG-GCAAACA
* *
12585615 TGTGACGCGACAGGGTGATAATGTGTGAGACGGCACGGTGAGAATATGTGACACGAGTGTGACA
1 TGTGACACGACAGGGTGATAATGTGTGAGACGGCACGGTGAGAATATGTGACACGGGTGTGACA
12585679 TGGCAAGGTC
Statistics
Matches: 138, Mismatches: 27, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
101 35 0.25
102 1 0.01
103 45 0.33
104 57 0.41
ACGTcount: A:0.28, C:0.14, G:0.36, T:0.22
Consensus pattern (103 bp):
TGTGACACGACAGGGTGATAATGTGTGAGACGGCACGGTGAGAATATGTGACACGGGTGTGACAC
GACAGGGTTTAGAGTGTGTGACACACCATGGGCAAACA
Found at i:12585923 original size:81 final size:81
Alignment explanation
Indices: 12585768--12585926 Score: 192
Period size: 81 Copynumber: 2.0 Consensus size: 81
12585758 ACAGTGTCAT
* * * *** * *
12585768 AATGTGTGAAACGGCACAGTGATAATGTGTGACACGGGTGTGACACGGTAGGGTTTAGACTGTGT
1 AATGTGTGAAACGGCACAATGAGAATATGTGACACGGGTGTGACACAACAGCGTTTAGACTGTGG
12585833 GACACGCCATGGTGAA
66 GACACGCCATGGTGAA
* ** * *
12585849 AATGTGTGAGACGGCACAATGAGAATATGTGGGACGGGTGTGACACAACAGCGTTTAGAGTTTGG
1 AATGTGTGAAACGGCACAATGAGAATATGTGACACGGGTGTGACACAACAGCGTTTAGACTGTGG
*
12585914 GACATGCCATGGT
66 GACACGCCATGGT
12585927 CAGATGTGTG
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
81 64 1.00
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23
Consensus pattern (81 bp):
AATGTGTGAAACGGCACAATGAGAATATGTGACACGGGTGTGACACAACAGCGTTTAGACTGTGG
GACACGCCATGGTGAA
Found at i:12585939 original size:22 final size:23
Alignment explanation
Indices: 12585914--12585970 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
12585904 TAGAGTTTGG
12585914 GACATGCCATGG-TCAG-ATGTGT
1 GACATGCCATGGCT-AGAATGTGT
* *
12585936 GACATGGCATGGCTTGAATGTGT
1 GACATGCCATGGCTAGAATGTGT
*
12585959 GACACGCCATGG
1 GACATGCCATGG
12585971 GTTTAATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 12 0.41
23 17 0.59
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (23 bp):
GACATGCCATGGCTAGAATGTGT
Found at i:12585960 original size:23 final size:23
Alignment explanation
Indices: 12585930--12585991 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
12585920 CCATGGTCAG
* *
12585930 ATGTGTGACATGGCATGGCTTGA
1 ATGTGTGACACGCCATGGCTTGA
* *
12585953 ATGTGTGACACGCCATGGGTTTA
1 ATGTGTGACACGCCATGGCTTGA
*
12585976 ATATGTGACACGCCAT
1 ATGTGTGACACGCCAT
12585992 AGTGTGAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (23 bp):
ATGTGTGACACGCCATGGCTTGA
Found at i:12586492 original size:55 final size:55
Alignment explanation
Indices: 12586403--12586895 Score: 489
Period size: 55 Copynumber: 9.0 Consensus size: 55
12586393 CGTCTGCATA
* * * *
12586403 TGGCGTGTTGTGGGTTAACTGG-TTTTTAAGATTTTTAGCATGTCATGGCTGTTCT
1 TGGCGTGTTGTGGGTTAACTGGATTTTT-TGATTTTTAGCGTGTCACGGCTGTTCC
* * *
12586458 TGGCATGTTGTGGGTTAACTGGTTTTTTTGATTTTTAGTAG-GTCACGGCTGTTCC
1 TGGCGTGTTGTGGGTTAACTGGATTTTTTGATTTTTAG-CGTGTCACGGCTGTTCC
* * *
12586513 TGACGTGTAGTGGGTTAACTGGATTTTTTGGTTTTT-GACGTGTCACGGCTGTTCC
1 TGGCGTGTTGTGGGTTAACTGGATTTTTTGATTTTTAG-CGTGTCACGGCTGTTCC
* * * * * * * *
12586568 TGGCCTATTGTGGGTTAACTAGATTTTTTGGTTTTTGGTGTGTCACAGTTGTTCC
1 TGGCGTGTTGTGGGTTAACTGGATTTTTTGATTTTTAGCGTGTCACGGCTGTTCC
* * *
12586623 TGGTGTGTTGTGGGTTAACTGAATTTTTT-AGTTTTT-GACGTGTCACGGCTATTCC
1 TGGCGTGTTGTGGGTTAACTGGATTTTTTGA-TTTTTAG-CGTGTCACGGCTGTTCC
* * *
12586678 TGGCATGTTGTGGGTAAACTGG-TTTTTTGAGTTTTTAGCGTGTCACAGCTGTTCC
1 TGGCGTGTTGTGGGTTAACTGGATTTTTTGA-TTTTTAGCGTGTCACGGCTGTTCC
* * * * * * *
12586733 TAGCGTGTTGTGGGTTAACTGAATTTTTGGATTTTTGGCATGTGACTGCTGTTCC
1 TGGCGTGTTGTGGGTTAACTGGATTTTTTGATTTTTAGCGTGTCACGGCTGTTCC
* * * * * *
12586788 TAGCGTGTTGTGGGTTAACTAG-TTTTTTGGGTTTTTAGCGTGTGACGGTTGTTCT
1 TGGCGTGTTGTGGGTTAACTGGATTTTTT-GATTTTTAGCGTGTCACGGCTGTTCC
* * * *
12586843 TGACGTGTTGTGGGTTAACTGGGTTTTTGTG-TTTTTAGTGTGTCACAGCTGTT
1 TGGCGTGTTGTGGGTTAACTGGATTTTT-TGATTTTTAGCGTGTCACGGCTGTT
12586896 GGTGTAACGA
Statistics
Matches: 364, Mismatches: 62, Indels: 24
0.81 0.14 0.05
Matches are distributed among these distances:
54 14 0.04
55 329 0.90
56 20 0.05
57 1 0.00
ACGTcount: A:0.13, C:0.12, G:0.30, T:0.45
Consensus pattern (55 bp):
TGGCGTGTTGTGGGTTAACTGGATTTTTTGATTTTTAGCGTGTCACGGCTGTTCC
Found at i:12586980 original size:31 final size:31
Alignment explanation
Indices: 12586940--12587028 Score: 115
Period size: 31 Copynumber: 2.9 Consensus size: 31
12586930 GTCACGACAC
* * *
12586940 TAATATGCATGGTGTGTCACGACATTTGACT
1 TAATATGCATGGCGTGTTACAACATTTGACT
* * * *
12586971 TGATATGCATGACGTGTTACAAAATTTTACT
1 TAATATGCATGGCGTGTTACAACATTTGACT
12587002 TAATATGCATGGCGTGTTACAACATTT
1 TAATATGCATGGCGTGTTACAACATTT
12587029 ATTTATTTCT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (31 bp):
TAATATGCATGGCGTGTTACAACATTTGACT
Found at i:12589369 original size:81 final size:81
Alignment explanation
Indices: 12589284--12589470 Score: 236
Period size: 81 Copynumber: 2.3 Consensus size: 81
12589274 GGGATGTGAC
12589284 CCTTCAATCAGAT-GAT-GCTGAAGGAGTCCATGTTCCTGAGGCTGATTCGGTTATCAATGCATC
1 CCTTCAATC-GATCG-TGGCTGAAGGAGTCCATGTTCCTGAGGCTGATTCGGTTATCAATGCATC
*
12589347 TGCGGGAGGGGAGGGGGA
64 TGCGGGAGGGGAAGGGGA
* ** * *
12589365 CCTTCACTCTCTCGTGGCTGAAGGAGTCCATGTTCTTGAGGCTGATTCGGTTATCGATGCATCTG
1 CCTTCAATCGATCGTGGCTGAAGGAGTCCATGTTCCTGAGGCTGATTCGGTTATCAATGCATCTG
* *
12589430 TGGGAGGGGAAGGTGA
66 CGGGAGGGGAAGGGGA
* *
12589446 CCTTCACTC-ACTCGTGGTTGAAGGA
1 CCTTCAATCGA-TCGTGGCTGAAGGA
12589471 CAACATCTTC
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
80 2 0.02
81 91 0.98
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.27
Consensus pattern (81 bp):
CCTTCAATCGATCGTGGCTGAAGGAGTCCATGTTCCTGAGGCTGATTCGGTTATCAATGCATCTG
CGGGAGGGGAAGGGGA
Found at i:12591064 original size:86 final size:86
Alignment explanation
Indices: 12590909--12591329 Score: 549
Period size: 86 Copynumber: 4.9 Consensus size: 86
12590899 ATCAATTTTG
** * *
12590909 TGCCGTGTCA-CCCACAAGACTATAACAAGTCAGCGTGTTAGGCCATAAGTCTGCATGCACTCAG
1 TGCCGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCATAAGTCTGCATGCACTCAG
*
12590973 CGTGTCACCACAATTGGTTCC
66 CGTGTCACCACAATTGGTCCC
* * * **
12590994 TGCCATGTCACCCCACAAGACTGCAACAACTCAGCGTGTCACGCCAGAAGTCTGCATTTACTCAG
1 TGCCGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCATAAGTCTGCATGCACTCAG
* * *
12591059 TGTGTCACCACGATTGGGCCC
66 CGTGTCACCACAATTGGTCCC
* * * * *
12591080 TACCGTGTCACCCCACAAGATTGCAACAAGTCAGTGTGTCATGCCATAAGTCTGCATGCACTTAG
1 TGCCGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCATAAGTCTGCATGCACTCAG
12591145 CGTGTCACCACAATTGG-CCC
66 CGTGTCACCACAATTGGTCCC
* * * * * *
12591165 TTGTCGTGTCACCCCACAAGATTGCAACAAGTCAACGTGTCACGCCAGAAGTCTACATTCACTCA
1 -TGCCGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCATAAGTCTGCATGCACTCA
* *
12591230 GCATGTCACCACGATTGGTCCC
65 GCGTGTCACCACAATTGGTCCC
* * * *
12591252 TGCTGTGTCACCTCACAAGACTGCAACAAGTCAGCGTGTCACACCATAAGTCTGCATGCATTCAG
1 TGCCGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCATAAGTCTGCATGCACTCAG
12591317 CGTGTCACCACAA
66 CGTGTCACCACAA
12591330 GATGTCATTC
Statistics
Matches: 285, Mismatches: 48, Indels: 5
0.84 0.14 0.01
Matches are distributed among these distances:
85 12 0.04
86 270 0.95
87 3 0.01
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (86 bp):
TGCCGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCATAAGTCTGCATGCACTCAG
CGTGTCACCACAATTGGTCCC
Found at i:12591615 original size:19 final size:19
Alignment explanation
Indices: 12591578--12591616 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12591568 AATAAATTTC
*
12591578 TTTTTTTATATAATGAGTA
1 TTTTTTTATATAATAAGTA
12591597 TTTTTTTATATTAA-AAGTA
1 TTTTTTTATA-TAATAAGTA
12591616 T
1 T
12591617 AAATCTATAA
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:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (19 bp):
TTTTTTTATATAATAAGTA
Found at i:12591811 original size:15 final size:14
Alignment explanation
Indices: 12591768--12591815 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
12591758 ATATATTTTT
12591768 TAAATTA-AAAATA
1 TAAATTATAAAATA
* *
12591781 TAAATTCATGACATA
1 TAAATT-ATAAAATA
12591796 TAAATTATATAAATA
1 TAAATTATA-AAATA
12591811 TAAAT
1 TAAAT
12591816 AAAAGTGCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 6 0.21
14 3 0.11
15 19 0.68
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (14 bp):
TAAATTATAAAATA
Found at i:12595306 original size:31 final size:31
Alignment explanation
Indices: 12595266--12595499 Score: 326
Period size: 31 Copynumber: 7.5 Consensus size: 31
12595256 TCATTATGTT
* *
12595266 ACACACCATGCATATAACGTAAAATGTGGTA
1 ACACGCCATGCATATAACGTAAAATGTTGTA
*
12595297 ACACGCCATGCATATAACGTAAAATGTTTTA
1 ACACGCCATGCATATAACGTAAAATGTTGTA
*
12595328 ACACGCCATGCATATAACGTAAAATGTTTTA
1 ACACGCCATGCATATAACGTAAAATGTTGTA
12595359 ACACGCCATGCATATAACGTAAAATGTTGTA
1 ACACGCCATGCATATAACGTAAAATGTTGTA
* * *
12595390 ACACACCATGCATGTAACGTAAAATGTGGTA
1 ACACGCCATGCATATAACGTAAAATGTTGTA
*
12595421 ACACGCCATGCATATAACATAAAATG-TGATA
1 ACACGCCATGCATATAACGTAAAATGTTG-TA
* * * * *
12595452 ACATGCCATGAATATAACATTAAATATTGTA
1 ACACGCCATGCATATAACGTAAAATGTTGTA
*
12595483 ACACGACATGCATATAA
1 ACACGCCATGCATATAA
12595500 TCAATGTCGT
Statistics
Matches: 183, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
30 1 0.01
31 180 0.98
32 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (31 bp):
ACACGCCATGCATATAACGTAAAATGTTGTA
Found at i:12595833 original size:63 final size:63
Alignment explanation
Indices: 12595730--12595850 Score: 181
Period size: 63 Copynumber: 1.9 Consensus size: 63
12595720 ACAACCCGAT
* *
12595730 GACGATGGTGCTCAACAGAGAGTTGACAGAGCTCATACAGTTCAGAGA-TCTGAGAGAGCTGAC
1 GACGATGGTGCTCAACAGAGAGTTGACAGAGCTCAGACAGTTCAAAGAGT-TGAGAGAGCTGAC
* * *
12595793 GACGATGGTGCTCAACAGAGAGTTGGCAGAGTTGAGACAGTTCAAAGAGTTGAGAGAG
1 GACGATGGTGCTCAACAGAGAGTTGACAGAGCTCAGACAGTTCAAAGAGTTGAGAGAG
12595851 AAAGATGATC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
63 51 0.98
64 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.33, T:0.19
Consensus pattern (63 bp):
GACGATGGTGCTCAACAGAGAGTTGACAGAGCTCAGACAGTTCAAAGAGTTGAGAGAGCTGAC
Found at i:12596407 original size:30 final size:30
Alignment explanation
Indices: 12596371--12596432 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
12596361 ATGTTCAATC
12596371 AAGCTTTTACATTATCATTTTAAGTCAAAT
1 AAGCTTTTACATTATCATTTTAAGTCAAAT
* * * *
12596401 AAGCTTTTATATTTTTATTTTGAGTCAAAT
1 AAGCTTTTACATTATCATTTTAAGTCAAAT
12596431 AA
1 AA
12596433 CCTCTCATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (30 bp):
AAGCTTTTACATTATCATTTTAAGTCAAAT
Found at i:12599630 original size:2 final size:2
Alignment explanation
Indices: 12599619--12599732 Score: 119
Period size: 2 Copynumber: 58.0 Consensus size: 2
12599609 CTGTTATGAA
12599619 AT AT -T 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
* * * * * * *
12599660 AT AT AT GT AT GT AT GT TT AGT -T CT -T CAT TT AN AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT -AT AT AT AT AT AT AT AT
12599701 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
12599733 GTATTTATAA
Statistics
Matches: 95, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
1 4 0.04
2 89 0.94
3 2 0.02
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12603237 original size:2 final size:2
Alignment explanation
Indices: 12603230--12603293 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
12603220 AATGGCTTTC
* *
12603230 CT CT CT CT TT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12603272 CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
12603294 NNNNNNNNNN
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:12603372 original size:2 final size:2
Alignment explanation
Indices: 12603365--12603407 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
12603355 NNNNNNNNNN
12603365 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12603407 T
1 T
12603408 GCGTTTTATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12607947 original size:29 final size:30
Alignment explanation
Indices: 12607906--12607971 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
12607896 ACTAATACTT
*
12607906 TTTTTAT-TTTTTATTAT-ATTC-AATCAAA
1 TTTTTATATTTTTATTATAAATCGAAT-AAA
*
12607934 TTTTTATATTTTTATTTTAAATCGAATAAA
1 TTTTTATATTTTTATTATAAATCGAATAAA
12607964 TTTTTATA
1 TTTTTATA
12607972 ATTAATGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 7 0.21
29 9 0.27
30 14 0.42
31 3 0.09
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTTTATATTTTTATTATAAATCGAATAAA
Found at i:12609148 original size:22 final size:22
Alignment explanation
Indices: 12609123--12609180 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
12609113 TCATATGTAA
*
12609123 ATTTTATTTTCTACTTGTCAT-G
1 ATTTTATTTTCTACTTAT-ATGG
*
12609145 ATTTTCATTTTTCT-GTTATATGG
1 ATTTT-A-TTTTCTACTTATATGG
12609168 ATTTTATTTTCTA
1 ATTTTATTTTCTA
12609181 TGATTTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
21 6 0.20
22 8 0.27
23 10 0.33
24 6 0.20
ACGTcount: A:0.19, C:0.10, G:0.09, T:0.62
Consensus pattern (22 bp):
ATTTTATTTTCTACTTATATGG
Found at i:12618877 original size:22 final size:22
Alignment explanation
Indices: 12618806--12618871 Score: 114
Period size: 22 Copynumber: 3.0 Consensus size: 22
12618796 AACAAAGTAA
12618806 AGAGAAGAAAGAAGGATCGAGT
1 AGAGAAGAAAGAAGGATCGAGT
*
12618828 AGAGAAGGAAGAAGGATCGAGT
1 AGAGAAGAAAGAAGGATCGAGT
*
12618850 AGAGAAGAAAGAAGAATCGAGT
1 AGAGAAGAAAGAAGGATCGAGT
12618872 TAAGAAATCT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.50, C:0.05, G:0.36, T:0.09
Consensus pattern (22 bp):
AGAGAAGAAAGAAGGATCGAGT
Found at i:12623410 original size:22 final size:21
Alignment explanation
Indices: 12623362--12623410 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
12623352 ACAGAGTAGA
12623362 AAGAAGAAAGAAAGATCGAGT
1 AAGAAGAAAGAAAGATCGAGT
*
12623383 AGAGAAGGAAA-AATGATCGAGTT
1 A-AGAA-GAAAGAAAGATCGAG-T
12623406 AAGAA
1 AAGAA
12623411 ATCTGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 1 0.04
22 17 0.71
23 6 0.25
ACGTcount: A:0.55, C:0.04, G:0.29, T:0.12
Consensus pattern (21 bp):
AAGAAGAAAGAAAGATCGAGT
Found at i:12632880 original size:117 final size:116
Alignment explanation
Indices: 12632734--12632965 Score: 351
Period size: 117 Copynumber: 2.0 Consensus size: 116
12632724 TCATTTTTCA
* * *
12632734 TATTTTTCAACAATCAACCTCCTCTATAATGCATTTTCATCATTAAC-ATAATGCCACCACCATT
1 TATTTTTCAACAATCAACCTCCTCCATAATGCATTTTCATCACT-ACTATAACGCCACCACCATT
12632798 TTAG-AAGGAAAGTCAAGTTTTTATGTTTAAGGCTTGAGATCCCCAAACCACCT
65 TT-GCAAGGAAAGTCAAG-TTTTATGTTTAAGGCTTGAGATCCCCAAACCACCT
* * *
12632851 TATTTTTCAACAATCAACCTCCTCCATAATGCATTTTCATCACTACTGTACCGCCACCATCATTT
1 TATTTTTCAACAATCAACCTCCTCCATAATGCATTTTCATCACTACTATAACGCCACCACCATTT
* *
12632916 TGCAAGGAAAGTCAAGTTTTATGTTTAAGGCTTTAGATCCCTAAACCACC
66 TGCAAGGAAAGTCAAGTTTTATGTTTAAGGCTTGAGATCCCCAAACCACC
12632966 AAATCTTTTG
Statistics
Matches: 105, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
116 35 0.33
117 70 0.67
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.33
Consensus pattern (116 bp):
TATTTTTCAACAATCAACCTCCTCCATAATGCATTTTCATCACTACTATAACGCCACCACCATTT
TGCAAGGAAAGTCAAGTTTTATGTTTAAGGCTTGAGATCCCCAAACCACCT
Found at i:12643633 original size:40 final size:40
Alignment explanation
Indices: 12643585--12643665 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
12643575 CATAAAATCA
12643585 AATCAATTTCATCTCACCCACACATTGCCTCAAAAAATTT
1 AATCAATTTCATCTCACCCACACATTGCCTCAAAAAATTT
12643625 AATCAATTTCATCTCACCCACACATTGCCTCAAAAAATTT
1 AATCAATTTCATCTCACCCACACATTGCCTCAAAAAATTT
12643665 A
1 A
12643666 CTCCATTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.38, C:0.30, G:0.02, T:0.30
Consensus pattern (40 bp):
AATCAATTTCATCTCACCCACACATTGCCTCAAAAAATTT
Found at i:12655119 original size:109 final size:109
Alignment explanation
Indices: 12654928--12655132 Score: 261
Period size: 109 Copynumber: 1.9 Consensus size: 109
12654918 TATAATAAAG
* ** *
12654928 TGATTCATGCCTTGACTTGTAACATCAGTAAGAAGATGGAAGCTTTGACGTGTAATATCTAGTGT
1 TGATTCATGCCTTGAATTGTAACATCAGTAAGAAGAAAGAAGCTTTGACGTGTAATATCTAGTGC
* * ** *
12654993 TAACATTTCGTTTGTAAAGCTTTGGCCTTGGCATGTAATATCTA
66 TAACATCTAGCATGTAAAGCTTTGGCATTGGCATGTAATATCTA
* * **
12655037 TGATTCATGCCTT-AATGTGTAATATCCGTAAGAAGAAAGAAGCTTTGGTGTGTAATATCT-GAT
1 TGATTCATGCCTTGAAT-TGTAACATCAGTAAGAAGAAAGAAGCTTTGACGTGTAATATCTAG-T
12655100 GCTAACATCTAGCATGTAAAGCTTTGGCATTGG
64 GCTAACATCTAGCATGTAAAGCTTTGGCATTGG
12655133 TGTGCGACAT
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
108 3 0.04
109 78 0.96
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (109 bp):
TGATTCATGCCTTGAATTGTAACATCAGTAAGAAGAAAGAAGCTTTGACGTGTAATATCTAGTGC
TAACATCTAGCATGTAAAGCTTTGGCATTGGCATGTAATATCTA
Found at i:12657668 original size:25 final size:26
Alignment explanation
Indices: 12657620--12657669 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
12657610 TTTTTATTTT
* *
12657620 TTTCTTTTTCTTTTCTTTCTTGCCCA
1 TTTCTTTCTCTTTTCTTTCCTGCCCA
12657646 TTTCTTTCTC-TTTCTTTCCTGCCC
1 TTTCTTTCTCTTTTCTTTCCTGCCC
12657670 CTTCTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.02, C:0.32, G:0.04, T:0.62
Consensus pattern (26 bp):
TTTCTTTCTCTTTTCTTTCCTGCCCA
Found at i:12657674 original size:24 final size:24
Alignment explanation
Indices: 12657626--12657681 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
12657616 TTTTTTTCTT
* *
12657626 TTTCTTTTCTTTCTTGCCCATTTC
1 TTTCTTTTCTTTCCTGCCCACTTC
12657650 TTTCTCTTTCTTTCCTGCCC-CTTC
1 TTTCT-TTTCTTTCCTGCCCACTTC
*
12657674 TTTTTTTT
1 TTTCTTTT
12657682 TCTCTCACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 3 0.11
24 12 0.43
25 13 0.46
ACGTcount: A:0.02, C:0.30, G:0.04, T:0.64
Consensus pattern (24 bp):
TTTCTTTTCTTTCCTGCCCACTTC
Found at i:12658791 original size:59 final size:59
Alignment explanation
Indices: 12658653--12659062 Score: 427
Period size: 59 Copynumber: 7.0 Consensus size: 59
12658643 TAATTTAAAA
* * * * * *
12658653 AAAAATTAAAATTCTTAAACTTGATCTAGGCTCAACCTATATCAGGACAGGTTCG----
1 AAAAATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATATCAGAATAGGTTCGATTT
** * * * * * *
12658708 AAAAATTAAAATTTTTA-AGTTTAATTTAGGCACGACCTATCTCAAAATAGGTTAGATTT
1 AAAAATTAAAATTCCTAGA-CTTAATCTAGGCTCGACCTATATCAGAATAGGTTCGATTT
* * * *
12658767 AAAAATTAAAATTCCTAGACTTAATTTAGGCTCGACTTATCTCAAAATAGGTTCGATTT
1 AAAAATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATATCAGAATAGGTTCGATTT
* * * * *
12658826 AAAGATTAAAATTCCCAGAGTTAATCTAGGTTTGACCTATATCAGAATAGGTTCGATTT
1 AAAAATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATATCAGAATAGGTTCGATTT
* * * *
12658885 AAAAATTGAAATTCCTAGACTTGATCTAGGCTTGACCTATATCAGAATAGGTTTGATTT
1 AAAAATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATATCAGAATAGGTTCGATTT
* * * * * * * *
12658944 AAAAGTTAAAATTTCTAAACTTGATCTAAGCTCGACCTATATCAGAACAGGTTTGACTT
1 AAAAATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATATCAGAATAGGTTCGATTT
* * *
12659003 AAAAA-TGAAATTCCTAGACTTAATCTAGGCTCGATCTATATCAGAACAGGTTCGATTT
1 AAAAATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATATCAGAATAGGTTCGATTT
12659061 AA
1 AA
12659063 TTCTCTAATA
Statistics
Matches: 299, Mismatches: 50, Indels: 9
0.84 0.14 0.03
Matches are distributed among these distances:
54 1 0.00
55 42 0.14
58 47 0.16
59 208 0.70
60 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (59 bp):
AAAAATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATATCAGAATAGGTTCGATTT
Found at i:12670454 original size:11 final size:11
Alignment explanation
Indices: 12670431--12670464 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
12670421 TACCGAACAA
*
12670431 TTTCTTCTCTT
1 TTTCTTTTCTT
*
12670442 TTTTTTTTCTT
1 TTTCTTTTCTT
12670453 TTTCTTTTCTT
1 TTTCTTTTCTT
12670464 T
1 T
12670465 CTTGCCCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:12677777 original size:10 final size:10
Alignment explanation
Indices: 12677749--12677777 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
12677739 TAAATCCATT
12677749 TTTCATAAAA
1 TTTCATAAAA
12677759 TTT-ATAAAA
1 TTTCATAAAA
12677768 TTTCATAAAA
1 TTTCATAAAA
12677778 ACTACCTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (10 bp):
TTTCATAAAA
Found at i:12680372 original size:15 final size:15
Alignment explanation
Indices: 12680333--12680372 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
12680323 CTTTATAATG
* *
12680333 TAATGTGATCACAGA
1 TAATGTGATTACAAA
*
12680348 TAATATGATTACAAA
1 TAATGTGATTACAAA
12680363 TAATGTGATT
1 TAATGTGATT
12680373 GTAAAGAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.35
Consensus pattern (15 bp):
TAATGTGATTACAAA
Found at i:12681201 original size:22 final size:24
Alignment explanation
Indices: 12681158--12681203 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
12681148 TAATCATAAT
12681158 ATAGAACTAATGATAATAAAAAAA
1 ATAGAACTAATGATAATAAAAAAA
12681182 ATAGAACTAA-GAT-ATAAAAAAA
1 ATAGAACTAATGATAATAAAAAAA
12681204 TGTAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 9 0.41
23 3 0.14
24 10 0.45
ACGTcount: A:0.67, C:0.04, G:0.09, T:0.20
Consensus pattern (24 bp):
ATAGAACTAATGATAATAAAAAAA
Found at i:12685770 original size:15 final size:16
Alignment explanation
Indices: 12685750--12685790 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
12685740 TATTGGATCT
12685750 GAATCATTTTGAG-TC
1 GAATCATTTTGAGTTC
*
12685765 GAATCATGTTGAGTTC
1 GAATCATTTTGAGTTC
*
12685781 AAATCATTTT
1 GAATCATTTT
12685791 AGATTCAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.41
Consensus pattern (16 bp):
GAATCATTTTGAGTTC
Found at i:12690317 original size:26 final size:26
Alignment explanation
Indices: 12690278--12690328 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
12690268 ACATTATTCG
*
12690278 GTATCATCTTCATATTATTCTTTGTT
1 GTATCATCTTCATATTACTCTTTGTT
12690304 GTATCAT-TTACATATTACTCTTTGT
1 GTATCATCTT-CATATTACTCTTTGT
12690329 ATTCATTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.22, C:0.16, G:0.08, T:0.55
Consensus pattern (26 bp):
GTATCATCTTCATATTACTCTTTGTT
Found at i:12690701 original size:24 final size:24
Alignment explanation
Indices: 12690674--12690727 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
12690664 CTATTCATGG
* * *
12690674 TGCTTCTCCTACTGCTCCTCTTCC
1 TGCTTCTACTACTGCCCCTCCTCC
*
12690698 TGCTTCTACTACTGCCCCTCCTCT
1 TGCTTCTACTACTGCCCCTCCTCC
12690722 TGCTTC
1 TGCTTC
12690728 AGGTACTGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.06, C:0.44, G:0.09, T:0.41
Consensus pattern (24 bp):
TGCTTCTACTACTGCCCCTCCTCC
Found at i:12690892 original size:24 final size:24
Alignment explanation
Indices: 12690863--12690912 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
12690853 ATATGCAGAT
* * *
12690863 GCAGTCAATGTAGTTGGAGATTCA
1 GCAGTCAATGCAGTTAGAGATCCA
12690887 GCAGTCAATGCAGTTAGAGATCCA
1 GCAGTCAATGCAGTTAGAGATCCA
12690911 GC
1 GC
12690913 GAGCGATGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (24 bp):
GCAGTCAATGCAGTTAGAGATCCA
Done.