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 19 of 32
Found at i:10044216 original size:178 final size:181
Alignment explanation
Indices: 10043865--10044260 Score: 530
Period size: 180 Copynumber: 2.2 Consensus size: 181
10043855 TCCAATAATT
* * * *
10043865 AAATCTCAAAAATGCCAAAAGTGACTTCTTGAAAATTGCTAGGTGAGGAAATTATCCAAGATAAT
1 AAATCTCAAGAATGCCAAAAGTGACTTCTTGAAAATTGCTAGATGAGCAAATTATCCAAAATAAT
* *
10043930 GCCATGAACATTTGGAGGTTGTGAAAAATTTTCGATACTCGAGATGTACATAAATATTTAAATAA
66 GCCACGAACATTTGGAGGTTGTGAAAAATTTTCGATACTCAAGATGTACATAAATATTTAAATAA
* * * *
10043995 AATAAAAAAGATAAAAATTGTAAAATTAAATAAGTAAATTTTTCGATGGTG
131 AATAAAAAAGATAAAAATTATAAAATTAAATAAATAAATTTTTCAATGATG
* * * * * *
10044046 AAATATCAAGAATGCC-AAAGTGAATTCTTAAAAATTGCTATATGAGCAAATTGTCCAAAATTAT
1 AAATCTCAAGAATGCCAAAAGTGACTTCTTGAAAATTGCTAGATGAGCAAATTATCCAAAATAAT
* * * * * * *
10044110 GCCACGAGCGTTTGGAGGTTTTGGAAAA-TTTCGATA-TATAAGATTTATATAAATATTTAAATA
66 GCCACGAACATTTGGAGGTTGTGAAAAATTTTCGATACT-CAAGATGTACATAAATATTTAAATA
*
10044173 AAAT-AAAAAGATAAAAATTATAAAATTAAATAAATAGATTTTTCAATGATG
130 AAATAAAAAAGATAAAAATTATAAAATTAAATAAATAAATTTTTCAATGATG
*
10044224 AAATCTCAAGAATGCCAAAAGTGGCTTCTTGAAAATT
1 AAATCTCAAGAATGCCAAAAGTGACTTCTTGAAAATT
10044261 TCTTGCTAAG
Statistics
Matches: 185, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
178 58 0.31
179 50 0.27
180 63 0.34
181 14 0.08
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (181 bp):
AAATCTCAAGAATGCCAAAAGTGACTTCTTGAAAATTGCTAGATGAGCAAATTATCCAAAATAAT
GCCACGAACATTTGGAGGTTGTGAAAAATTTTCGATACTCAAGATGTACATAAATATTTAAATAA
AATAAAAAAGATAAAAATTATAAAATTAAATAAATAAATTTTTCAATGATG
Found at i:10044300 original size:179 final size:179
Alignment explanation
Indices: 10043865--10044319 Score: 524
Period size: 179 Copynumber: 2.5 Consensus size: 179
10043855 TCCAATAATT
* * * * * *
10043865 AAATCTCAAAAATGCCAAAAGTGACTTCTTGAAAATTGCTAGGTGAGGAAATTATCCAAGATAAT
1 AAATCTCAAGAATGCCAAAAGTGACTTCTTGAAAATTGCTTGAT-AAGAAATTATCCAAAATTAT
* * * * *
10043930 GCCATGAACATTTGGAGGTTGTGAAAAATTTTCGATACTCGAGATGTACATAAATATTTAAATAA
65 GCCATGAGCGTTTGGAGGTTTTGGAAAA-TTTCGATACTCAAGATGTACATAAATATTTAAATAA
* * * *
10043995 AATAAAAAAGATAAAAATTGTAAAATTAAATAAGTAAATTTTTCGATGGTG
129 AATAAAAAAGATAAAAATTATAAAATTAAATAAATAAATTTTTCAATGATG
* * * * *
10044046 AAATATCAAGAATGCC-AAAGTGAATTCTTAAAAATTGCTAT-ATGAGCAAATTGTCCAAAATTA
1 AAATCTCAAGAATGCCAAAAGTGACTTCTTGAAAATTGCT-TGATAAG-AAATTATCCAAAATTA
* * * *
10044109 TGCCACGAGCGTTTGGAGGTTTTGGAAAATTTCGATA-TATAAGATTTATATAAATATTTAAATA
64 TGCCATGAGCGTTTGGAGGTTTTGGAAAATTTCGATACT-CAAGATGTACATAAATATTTAAATA
*
10044173 AAAT-AAAAAGATAAAAATTATAAAATTAAATAAATAGATTTTTCAATGATG
128 AAATAAAAAAGATAAAAATTATAAAATTAAATAAATAAATTTTTCAATGATG
* * * * *
10044224 AAATCTCAAGAATGCCAAAAGTGGCTTCTTGAAAATTTCTTGCTAAGAAAGTTTTTCAAAATTAT
1 AAATCTCAAGAATGCCAAAAGTGACTTCTTGAAAATTGCTTGATAAGAAA-TTATCCAAAATTAT
* *
10044289 GTCC-TGAGCGTTTGAAGGTTTTAGAAAATTT
65 G-CCATGAGCGTTTGGAGGTTTTGGAAAATTT
10044320 TCAATATCAA
Statistics
Matches: 230, Mismatches: 37, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
178 62 0.27
179 93 0.40
180 61 0.27
181 14 0.06
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (179 bp):
AAATCTCAAGAATGCCAAAAGTGACTTCTTGAAAATTGCTTGATAAGAAATTATCCAAAATTATG
CCATGAGCGTTTGGAGGTTTTGGAAAATTTCGATACTCAAGATGTACATAAATATTTAAATAAAA
TAAAAAAGATAAAAATTATAAAATTAAATAAATAAATTTTTCAATGATG
Found at i:10047828 original size:32 final size:32
Alignment explanation
Indices: 10047790--10047853 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
10047780 AATAAGCATT
* *
10047790 CTAAAACATATCAACTTTTTAATAGAGTTATA
1 CTAAAACATACCAACTTTCTAATAGAGTTATA
*
10047822 CTAAAACATACCAAGTTTCTAATAGAGTTATA
1 CTAAAACATACCAACTTTCTAATAGAGTTATA
10047854 TGAAAATACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (32 bp):
CTAAAACATACCAACTTTCTAATAGAGTTATA
Found at i:10048151 original size:14 final size:15
Alignment explanation
Indices: 10048123--10048152 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10048113 TTCTATATTC
10048123 TTTTTATTTTGTTTA
1 TTTTTATTTTGTTTA
10048138 TTTTTATTTT-TTTA
1 TTTTTATTTTGTTTA
10048152 T
1 T
10048153 ATATATTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTTATTTTGTTTA
Found at i:10055905 original size:34 final size:34
Alignment explanation
Indices: 10055830--10055906 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 34
10055820 AAACTTTGCC
* * **
10055830 GTGTAACATTTGGTGTTGAAATTTTGATTTTGGA
1 GTGTAACATTTGATGTTAAAATTTTGACCTTGGA
* *
10055864 ATATAACATTTGATGTTAAAATTTTGACCTT-GA
1 GTGTAACATTTGATGTTAAAATTTTGACCTTGGA
10055897 TGTGTAACAT
1 -GTGTAACAT
10055907 CTTTTACTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
33 2 0.06
34 32 0.94
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.44
Consensus pattern (34 bp):
GTGTAACATTTGATGTTAAAATTTTGACCTTGGA
Found at i:10055919 original size:22 final size:20
Alignment explanation
Indices: 10055872--10055919 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
10055862 GAATATAACA
10055872 TTTGATGTTAAAATTTTGAC
1 TTTGATGTTAAAATTTTGAC
* * *
10055892 CTTGATGTGTAACATCTTTTAC
1 TTTGATGT-TAAAAT-TTTGAC
10055914 TTTGAT
1 TTTGAT
10055920 TTTAGTGCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 7 0.32
21 5 0.23
22 10 0.45
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (20 bp):
TTTGATGTTAAAATTTTGAC
Found at i:10056277 original size:20 final size:20
Alignment explanation
Indices: 10056234--10056278 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
10056224 TTAAAATGTG
* *
10056234 TAATAATTTTTTTTCAACTG
1 TAATAATTTTTTTTCAAATA
10056254 TAATAATATTTTTTT-AAATA
1 TAATAAT-TTTTTTTCAAATA
10056274 TAATA
1 TAATA
10056279 TGTAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (20 bp):
TAATAATTTTTTTTCAAATA
Found at i:10056309 original size:29 final size:30
Alignment explanation
Indices: 10056254--10056312 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
10056244 TTTTCAACTG
*
10056254 TAATAATATTTTTTTAAATATAATATGTAA
1 TAATAATATTTTTTTAAACATAATATGTAA
* *
10056284 TAATAATA-TTTTTTAAACGTAGTATGTAA
1 TAATAATATTTTTTTAAACATAATATGTAA
10056313 CTTGTTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (30 bp):
TAATAATATTTTTTTAAACATAATATGTAA
Found at i:10067611 original size:136 final size:136
Alignment explanation
Indices: 10067458--10067715 Score: 412
Period size: 136 Copynumber: 1.9 Consensus size: 136
10067448 TTTGAAAGAA
* *
10067458 AAAAAATCTTTAATTTAAATTTATATGCCAGTGTATTAATGTTGTTATTCTATAGTATATGTATT
1 AAAAAATCATTAATTTAAATTTATATGCCAGTGTATTAATGTTGTTATTCTATAGTATATGCATT
* * *
10067523 TCTATGACCGATTAATTCCCCG-TTTTGTTTTTAATTTCTTCTCATATAATATATAAATAAATAG
66 TCTACGACCAATT-ATTCCCAGTTTTTGTTTTTAATTTCTTCTCATATAATATATAAATAAATAG
10067587 TATGAAT
130 TATGAAT
* *
10067594 AAAAAAT-ATTAATTTTAAATTTATATGCCTGTGTATTAATGTTGTTATTCTATAGTTTATGCAT
1 AAAAAATCATTAA-TTTAAATTTATATGCCAGTGTATTAATGTTGTTATTCTATAGTATATGCAT
*
10067658 TTCTACGACCAATTATTTCCAGTTTTTGTTTTTAATTTCTTCTCATATAATATATAAA
65 TTCTACGACCAATTATTCCCAGTTTTTGTTTTTAATTTCTTCTCATATAATATATAAA
10067716 CAAAGAATAA
Statistics
Matches: 112, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
135 10 0.09
136 102 0.91
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.48
Consensus pattern (136 bp):
AAAAAATCATTAATTTAAATTTATATGCCAGTGTATTAATGTTGTTATTCTATAGTATATGCATT
TCTACGACCAATTATTCCCAGTTTTTGTTTTTAATTTCTTCTCATATAATATATAAATAAATAGT
ATGAAT
Found at i:10075024 original size:4 final size:4
Alignment explanation
Indices: 10075015--10075042 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
10075005 ACAAGAAAGT
10075015 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
10075043 TATATACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:10079364 original size:15 final size:16
Alignment explanation
Indices: 10079344--10079373 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
10079334 GTGATAAATG
10079344 ATTAAAAT-TTTATTT
1 ATTAAAATATTTATTT
10079359 ATTAAAATATTTATT
1 ATTAAAATATTTATT
10079374 ATTTTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTAAAATATTTATTT
Found at i:10079430 original size:23 final size:23
Alignment explanation
Indices: 10079387--10079449 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
10079377 TTAATAATTA
10079387 ATTTAAAATGTTAATAAATTA-TT
1 ATTT-AAATGTTAATAAATTATTT
*
10079410 ATTTAAATGTTAATATGATTATTT
1 ATTTAAATGTTAATA-AATTATTT
*
10079434 ATTTTAAT-TTAA-AAAT
1 ATTTAAATGTTAATAAAT
10079450 CTTAATAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 2 0.06
22 12 0.34
23 12 0.34
24 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (23 bp):
ATTTAAATGTTAATAAATTATTT
Found at i:10079432 original size:20 final size:21
Alignment explanation
Indices: 10079378--10079434 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 21
10079368 TTTATTATTT
*
10079378 TAATAATTAATTTAAAATGTTAA
1 TAATGATT-ATTT-AAATGTTAA
*
10079401 TAAATTATTATTTAAATGTTAA
1 T-AATGATTATTTAAATGTTAA
10079423 T-ATGATTATTTA
1 TAATGATTATTTA
10079435 TTTTAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 10 0.32
22 10 0.32
23 5 0.16
24 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
TAATGATTATTTAAATGTTAA
Found at i:10079471 original size:29 final size:26
Alignment explanation
Indices: 10079339--10079495 Score: 92
Period size: 27 Copynumber: 5.9 Consensus size: 26
10079329 AATAAGTGAT
10079339 AAATGATTAA-AATTT-TATTT-ATTA
1 AAAT-ATTAATAATTTATATTTAATTA
* * *
10079363 AAATATTTATTATTTTAATAATTAATTTA
1 AAATA-TTAATAATTT-ATATTTAA-TTA
* *
10079392 AAATGTTAATAAATTATTATTTAAATGT-
1 AAATATTAATAATTTA-TATTT-AAT-TA
* * *
10079420 TAATA-TGATTATTTAT-TTTAATTTAA
1 AAATATTAATAATTTATATTTAA-TT-A
*
10079446 AAATCTTAATAATTTATATTTCAATTA
1 AAATATTAATAATTTATATTT-AATTA
*
10079473 AAATATTAATAATTTATAATTAA
1 AAATATTAATAATTTATATTTAA
10079496 AACGTTAATT
Statistics
Matches: 99, Mismatches: 19, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
23 1 0.01
24 10 0.10
25 8 0.08
26 6 0.06
27 41 0.41
28 21 0.21
29 12 0.12
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (26 bp):
AAATATTAATAATTTATATTTAATTA
Found at i:10079503 original size:22 final size:22
Alignment explanation
Indices: 10079468--10079509 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
10079458 TTTATATTTC
*
10079468 AATTAAAATATTAATAATTTAT
1 AATTAAAACATTAATAATTTAT
* *
10079490 AATTAAAACGTTAATTATTT
1 AATTAAAACATTAATAATTT
10079510 TATTTTATTT
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:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
AATTAAAACATTAATAATTTAT
Found at i:10083567 original size:24 final size:24
Alignment explanation
Indices: 10083540--10083586 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
10083530 TTTTTATTTA
*
10083540 ATTAATT-AATTGTTAACATTTTTT
1 ATTAATTAAATT-TTAAAATTTTTT
*
10083564 ATTATTTAAATTTTAAAATTTTT
1 ATTAATTAAATTTTAAAATTTTT
10083587 AAATATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (24 bp):
ATTAATTAAATTTTAAAATTTTTT
Found at i:10091227 original size:31 final size:31
Alignment explanation
Indices: 10091189--10091248 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
10091179 ATCATTAATC
* *
10091189 ATAAAAACTTATTTGAATCA-AAATAAAAAAT
1 ATAAAAACTTAATTCAAT-ATAAATAAAAAAT
10091220 ATAAAAACTTAATTCAATATAAATAAAAA
1 ATAAAAACTTAATTCAATATAAATAAAAA
10091249 TCAAATATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (31 bp):
ATAAAAACTTAATTCAATATAAATAAAAAAT
Found at i:10099173 original size:3 final size:3
Alignment explanation
Indices: 10099165--10099205 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
10099155 CTGACATGTT
10099165 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
10099206 GTAATATGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:10103446 original size:6 final size:6
Alignment explanation
Indices: 10103435--10103462 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
10103425 TACGGCGCTG
10103435 TCTGTC TCTGTC TCTGTC TCTGTC TCTG
1 TCTGTC TCTGTC TCTGTC TCTGTC TCTG
10103463 GTCTTGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.18, T:0.50
Consensus pattern (6 bp):
TCTGTC
Found at i:10105890 original size:2 final size:2
Alignment explanation
Indices: 10105883--10105907 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10105873 TTCTCCTCAA
10105883 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
10105908 ATGATACTTG
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:10110054 original size:2 final size:2
Alignment explanation
Indices: 10110047--10110072 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10110037 TTGTCGTTGG
10110047 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
10110073 GTGTCTCTGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:10111139 original size:3 final size:3
Alignment explanation
Indices: 10111131--10111155 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
10111121 GATGTTTTCG
10111131 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
10111156 TTTTTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:10115381 original size:180 final size:181
Alignment explanation
Indices: 10115065--10115427 Score: 620
Period size: 180 Copynumber: 2.0 Consensus size: 181
10115055 CAAAAGGAGG
* *
10115065 TTACATGGTTAATCCATGGGATGATGCGGGTGATGAAACCATCAGCTGTGCAGGGATGTGATAAA
1 TTACATGATTAATCCATGGGATGATGCAGGTGATGAAACCATCAGCTGTGCAGGGATGTGATAAA
* *
10115130 GTTCCCCTTTCCTTTTCATGAACCATCTTTTGACATTATTTCCTGAACCAAAATACCAGATGGGG
66 GTTCCCCTTCCCTTTTCATGAACCATCTTTTGACATTATTTCCTGAACCAAAATACCAAATGGGG
10115195 TTTTTGTGAACTATGATGAACTT-AAGTAACTTTGTGGGTGATTGCTGTAA
131 TTTTTGTGAACTATGATGAACTTAAAGTAACTTTGTGGGTGATTGCTGTAA
*
10115245 TTACATGATTAATCCATTGGATGATGCAGGTGATGAAACCATCAGCTGTGCAGGGATGTGATAAA
1 TTACATGATTAATCCATGGGATGATGCAGGTGATGAAACCATCAGCTGTGCAGGGATGTGATAAA
* *
10115310 GTTCCCCTTCCCTTTTCATGAACCATCTTTTGACATTATTTCCTGAACCAAAATACTAAATGGGT
66 GTTCCCCTTCCCTTTTCATGAACCATCTTTTGACATTATTTCCTGAACCAAAATACCAAATGGGG
10115375 TTTTTGTGAACTATGATGAACTTAAGAGAAGTAACTTTGTGGGTGATTGCTGT
131 TTTTTGTGAACTATGATGAACTT---A-AAGTAACTTTGTGGGTGATTGCTGT
10115428 CCATTATTGC
Statistics
Matches: 171, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
180 146 0.85
185 25 0.15
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (181 bp):
TTACATGATTAATCCATGGGATGATGCAGGTGATGAAACCATCAGCTGTGCAGGGATGTGATAAA
GTTCCCCTTCCCTTTTCATGAACCATCTTTTGACATTATTTCCTGAACCAAAATACCAAATGGGG
TTTTTGTGAACTATGATGAACTTAAAGTAACTTTGTGGGTGATTGCTGTAA
Found at i:10122174 original size:8 final size:8
Alignment explanation
Indices: 10122161--10122199 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
10122151 GCTGACATGG
10122161 TTGAGGTT
1 TTGAGGTT
*
10122169 TTGAGGGT
1 TTGAGGTT
*
10122177 TTGAGGTG
1 TTGAGGTT
10122185 TTGAGGTT
1 TTGAGGTT
10122193 TT-AGGTT
1 TTGAGGTT
10122200 GTTTGGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
7 5 0.19
8 22 0.81
ACGTcount: A:0.13, C:0.00, G:0.41, T:0.46
Consensus pattern (8 bp):
TTGAGGTT
Found at i:10122522 original size:6 final size:6
Alignment explanation
Indices: 10122511--10122537 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
10122501 GGAAGAGACA
10122511 GTTTTG GTTTTG GTTTTG GTTTTG GTT
1 GTTTTG GTTTTG GTTTTG GTTTTG GTT
10122538 GTGTCCAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (6 bp):
GTTTTG
Found at i:10129307 original size:2 final size:2
Alignment explanation
Indices: 10129300--10129331 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
10129290 TAGAAAACAC
*
10129300 GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
10129332 AGATAGCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:10134863 original size:36 final size:36
Alignment explanation
Indices: 10134815--10134890 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
10134805 CACCATTGGA
* *
10134815 AAGAGCTCAAGTCAAGAAATGTTCAATTGCCAAATG
1 AAGAGCTAAAGTCAAGAAATGTTCAATTACCAAATG
*
10134851 AAGAGCTAAAGTCAAGAAATGTTGAATTACCAAATG
1 AAGAGCTAAAGTCAAGAAATGTTCAATTACCAAATG
10134887 AAGA
1 AAGA
10134891 ACACAAAGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.21
Consensus pattern (36 bp):
AAGAGCTAAAGTCAAGAAATGTTCAATTACCAAATG
Found at i:10136593 original size:13 final size:13
Alignment explanation
Indices: 10136544--10136594 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
10136534 AGATACTACT
10136544 TTTTTTTCTTTCG
1 TTTTTTTCTTTCG
* * * *
10136557 GTTTTATATTTCA
1 TTTTTTTCTTTCG
10136570 TTTTCTTTCTTTCG
1 TTTT-TTTCTTTCG
10136584 TTTTTTTCTTT
1 TTTTTTTCTTT
10136595 GGAGTCTCTC
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.75
Consensus pattern (13 bp):
TTTTTTTCTTTCG
Found at i:10138511 original size:21 final size:21
Alignment explanation
Indices: 10138463--10138509 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
10138453 ATTTGAAATA
**
10138463 ATATTTGTTTTTTTAGTTGAT
1 ATATTTGGATTTTTAGTTGAT
10138484 ATATTTGGATTTTTAGTT-AT
1 ATATTTGGATTTTTAGTTGAT
*
10138504 GTATTT
1 ATATTT
10138510 TGATATTGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.64
Consensus pattern (21 bp):
ATATTTGGATTTTTAGTTGAT
Found at i:10160652 original size:30 final size:28
Alignment explanation
Indices: 10160549--10160653 Score: 70
Period size: 30 Copynumber: 3.5 Consensus size: 28
10160539 TACATAACAC
* *
10160549 TTAAATAAAGT-TTTAAATTATTTATAAAAA
1 TTAAAT-AAGTCTTT-AATTTTTTAT-TAAA
* *
10160579 TTTAAATAAGTCATTAATTTTTTATTACA
1 -TTAAATAAGTCTTTAATTTTTTATTAAA
* *
10160608 TTCAATAAAATCTTTACA-TTTTTATTATGAA
1 TTAAAT-AAGTCTTTA-ATTTTTTATTA--AA
10160639 TTAAATAAGTCTTTA
1 TTAAATAAGTCTTTA
10160654 TAAGTAATAA
Statistics
Matches: 59, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
28 5 0.08
29 18 0.31
30 22 0.37
31 14 0.24
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.48
Consensus pattern (28 bp):
TTAAATAAGTCTTTAATTTTTTATTAAA
Found at i:10160816 original size:17 final size:17
Alignment explanation
Indices: 10160794--10160844 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
10160784 TAACATTTTA
*
10160794 ATTAATTATAATTAATT
1 ATTAATTATAAATAATT
*
10160811 ATTAATTATAAATATTT
1 ATTAATTATAAATAATT
10160828 ATTTAATT-TAAAATAAT
1 A-TTAATTAT-AAATAAT
10160845 AATATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 17 0.59
18 12 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTAATTATAAATAATT
Found at i:10169215 original size:346 final size:344
Alignment explanation
Indices: 10168497--10169531 Score: 1239
Period size: 342 Copynumber: 3.0 Consensus size: 344
10168487 TTCTCATTTA
*
10168497 GTAGGATAAATTATGTAAGTTTAAGTCAAATAAAAATTCCACCTCTGCACAAATACACGT-GGAC
1 GTAGGATAAATTATGTAA-TTTAAGTCAAAT-AAAATTCC-CCTCTGCACAAATACACTTAGGAC
* * * * *
10168561 GCATGCAGATGTAATTTAGGCTACTTTGCTACAAATTGCG-GGCATGTATCCTAGG-CATTGTTG
63 GCATGCAGATGCAATTTAGGCTACTTGGCTACACA-TCCGAGGCATGTATACTAGGCCA-TGTTG
** * * * *
10168624 AGAGAGGCACTAATGTGCACAGATGTCCCCACTAAGTTATGTGACACGTGTAACTCAGACCTTTT
126 AGAGACACACTAATGTGCACAGATGTCTCAACTAAGCTATGTGACACATGTAACTC-GACCTTTT
* * * * *
10168689 TACTTCAACTCTAGTTTGTCTCTTGAGGTTAAATATTGCAGACAATTAAATGAGTTTCTACTTAA
190 TACTTCAACTCTAGTTTGTCTCTTGAGGTTATATATGGCAGAGAATTGAATGAGTTTCTACTTTA
* ** * * *
10168754 ATTGCTTTTTGTTGTTTAGGAAATGGTAACAAGGGTTGAGATTGGGGTATGCTTTAAGTGTAGAA
255 ATTGCTTTTGGGCGTTTAGAAAATGGTAAC-TGGGTTGAGATTGGGGTATGCTTTAAGTGTAAAA
* ** *
10168819 GTTATGATCAATAAACAGTTTGTTGT
319 CTTACCATCAATAAACAGTTTGTTAT
* * * *
10168845 GTAGGATAAATTATGTAAATTTAAGTCAAATAAAAGTTTCCCTCCGCGCAAATATA-TTAGGACG
1 GTAGGATAAATTATGT-AATTTAAGTCAAATAAAA-TTCCCCTCTGCACAAATACACTTAGGACG
* * *
10168909 CGTGCAGATGCAATTTAGGCTACTTGGCTATACATCCGAGGCATGTATACTAGGCCATGCTGAGA
64 CATGCAGATGCAATTTAGGCTACTTGGCTACACATCCGAGGCATGTATACTAGGCCATGTTGAGA
* *
10168974 GACACACTAATGCGCACAGATATCTCAACTAAGCTATGTGACACATGTAACTCGACCTTTTTACT
129 GACACACTAATGTGCACAGATGTCTCAACTAAGCTATGTGACACATGTAACTCGACCTTTTTACT
* * * *
10169039 TCTACTCTAGTTTGTCTCTCGAGGTTATATATGGCAGAGAATTGAATGGGTTTCTACTTTTAACT
194 TCAACTCTAGTTTGTCTCTTGAGGTTATATATGGCAGAGAATTGAATGAGTTTCTAC-TTTAATT
* * * * *
10169104 GCTTTTGGGCATTTAGAAAATGGTAACTCGGTTGAGATT-GTGTAATGCTGTAGGTGTAAAACTT
258 GCTTTTGGGCGTTTAGAAAATGGTAACTGGGTTGAGATTGGGGT-ATGCTTTAAGTGTAAAACTT
*
10169168 ACCATCAATAAACAATTTGTTAT
322 ACCATCAATAAACAGTTTGTTAT
* * * *
10169191 GTAGGATAAATTATGTATATTTAAGTC--CT-AAATTGCGCTCTGCACAAATACACTTA-GATGC
1 GTAGGATAAATTATGTA-ATTTAAGTCAAATAAAATTCCCCTCTGCACAAATACACTTAGGACGC
* * *
10169252 ATGCAGATGCAATTTAAGCTACTTGGCTAGACATCCCAGGC-TCGTATACTAGGCCATGTTGAGA
65 ATGCAGATGCAATTTAGGCTACTTGGCTACACATCCGAGGCAT-GTATACTAGGCCATGTTGAGA
* ** * * * *
10169316 GACACACTAATTTGCATGGATGTCTCAACTAAGCTATGTGGCACATGTAACTCAACCATTTTACA
129 GACACACTAATGTGCACAGATGTCTCAACTAAGCTATGTGACACATGTAACTCGACCTTTTTACT
* * * * * *
10169381 TCAACACTAGTTTGTCCCTTGAGGTTATATATGGCACAGGATTGATTGAGTTTCTAGTTTAATTG
194 TCAACTCTAGTTTGTCTCTTGAGGTTATATATGGCAGAGAATTGAATGAGTTTCTACTTTAATTG
* * *
10169446 CTTCTGGGCGTTTAGAAAATGGTAAGTGGGTTGAGATTGGGGTATG-TTTAATGTGT-TAACTTA
259 CTTTTGGGCGTTTAGAAAATGGTAACTGGGTTGAGATTGGGGTATGCTTTAA-GTGTAAAACTTA
10169509 CCATCAATAAACAGTTTGTTAT
323 CCATCAATAAACAGTTTGTTAT
10169531 G
1 G
10169532 CATACCTGAT
Statistics
Matches: 589, Mismatches: 86, Indels: 32
0.83 0.12 0.05
Matches are distributed among these distances:
340 31 0.05
341 49 0.08
342 183 0.31
343 6 0.01
344 1 0.00
345 4 0.01
346 136 0.23
347 144 0.24
348 33 0.06
349 2 0.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (344 bp):
GTAGGATAAATTATGTAATTTAAGTCAAATAAAATTCCCCTCTGCACAAATACACTTAGGACGCA
TGCAGATGCAATTTAGGCTACTTGGCTACACATCCGAGGCATGTATACTAGGCCATGTTGAGAGA
CACACTAATGTGCACAGATGTCTCAACTAAGCTATGTGACACATGTAACTCGACCTTTTTACTTC
AACTCTAGTTTGTCTCTTGAGGTTATATATGGCAGAGAATTGAATGAGTTTCTACTTTAATTGCT
TTTGGGCGTTTAGAAAATGGTAACTGGGTTGAGATTGGGGTATGCTTTAAGTGTAAAACTTACCA
TCAATAAACAGTTTGTTAT
Found at i:10186470 original size:36 final size:37
Alignment explanation
Indices: 10186410--10186484 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 37
10186400 AACTTTTTAA
*
10186410 TTTTAATTCTTAAACTTAATATTTATTACAATCTTCT
1 TTTTAATTCTTAAACTTAACATTTATTACAATCTTCT
* *
10186447 TTTTAA-T-TTAAATCTTAACATTTATTTCACTCTTCT
1 TTTTAATTCTTAAA-CTTAACATTTATTACAATCTTCT
10186483 TT
1 TT
10186485 AACATTTAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 5 0.15
36 23 0.68
37 6 0.18
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (37 bp):
TTTTAATTCTTAAACTTAACATTTATTACAATCTTCT
Found at i:10186896 original size:17 final size:17
Alignment explanation
Indices: 10186871--10186904 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
10186861 TATAAAATAT
10186871 TAATATTTAAATCATAA
1 TAATATTTAAATCATAA
* *
10186888 TAATGTTTAAATTATAA
1 TAATATTTAAATCATAA
10186905 ATAAAATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
TAATATTTAAATCATAA
Found at i:10187314 original size:20 final size:20
Alignment explanation
Indices: 10187291--10187355 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
10187281 ATTAAATTAT
*
10187291 AAATAAAATATTAGTATTTA
1 AAATAAATTATTAGTATTTA
*
10187311 AAATATTAATTATTA-CA-TTA
1 AAATA--AATTATTAGTATTTA
* *
10187331 TAATAAATTACTAGTATTTA
1 AAATAAATTATTAGTATTTA
10187351 AAATA
1 AAATA
10187356 TTAATATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 7 0.20
19 1 0.03
20 19 0.54
21 1 0.03
22 7 0.20
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
AAATAAATTATTAGTATTTA
Found at i:10187347 original size:40 final size:41
Alignment explanation
Indices: 10187280--10187371 Score: 134
Period size: 40 Copynumber: 2.3 Consensus size: 41
10187270 ATCATAATAA
*
10187280 TATTAAATTATAAATAAAATATTAGTATTTAAAATATTAAT
1 TATTAAATTATAAATAAAATACTAGTATTTAAAATATTAAT
* *
10187321 TATTACATTAT-AATAAATTACTAGTATTTAAAATATTAA-
1 TATTAAATTATAAATAAAATACTAGTATTTAAAATATTAAT
10187360 TATTTAAATTAT
1 TA-TTAAATTAT
10187372 TAATTATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
39 2 0.04
40 34 0.74
41 10 0.22
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (41 bp):
TATTAAATTATAAATAAAATACTAGTATTTAAAATATTAAT
Found at i:10187374 original size:15 final size:15
Alignment explanation
Indices: 10187253--10187416 Score: 66
Period size: 15 Copynumber: 11.2 Consensus size: 15
10187243 AAATTAATTA
10187253 AAATTATTAATATTT
1 AAATTATTAATATTT
* *
10187268 TAATCA-TAATAATATT
1 AAATTATTAAT-AT-TT
10187284 AAATTA-TAA-A--T
1 AAATTATTAATATTT
* *
10187295 AAAATATTAGTATTT
1 AAATTATTAATATTT
*
10187310 AAAATATTAAT-TATT
1 AAATTATTAATAT-TT
*
10187325 ACATTA-T-A-A--T
1 AAATTATTAATATTT
* *
10187335 AAATTACTAGTATTT
1 AAATTATTAATATTT
*
10187350 AAAATATTAATATTT
1 AAATTATTAATATTT
10187365 AAATTATTAAT-TATT
1 AAATTATTAATAT-TT
*
10187380 -AATTGTTTAATTAAATTAT
1 AAATT-ATTAA-T--ATT-T
10187399 AAATTATTAATATTT
1 AAATTATTAATATTT
10187414 AAA
1 AAA
10187417 AATAAAATAA
Statistics
Matches: 111, Mismatches: 17, Indels: 42
0.65 0.10 0.25
Matches are distributed among these distances:
10 6 0.05
11 7 0.06
12 2 0.02
13 3 0.03
14 12 0.11
15 56 0.50
16 13 0.12
18 2 0.02
19 6 0.05
20 4 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AAATTATTAATATTT
Found at i:10187411 original size:55 final size:54
Alignment explanation
Indices: 10187281--10187412 Score: 139
Period size: 55 Copynumber: 2.4 Consensus size: 54
10187271 TCATAATAAT
*
10187281 ATTAAATTATAAA-TA-AAATATTAGTATTTAAAATATTAATTATTACATTATA
1 ATTAAATTATAAATTATAAATATTAATATTTAAAATATTAATTATTACATTATA
* * *
10187333 A-TAAATTACTAGTATT-TAAAATATTAATATTTAAATTATTAATTATTA-ATTGTTTA
1 ATTAAATTA-TA-AATTAT-AAATATTAATATTTAAAATATTAATTATTACA-T-TATA
*
10187389 ATTAAATTATAAATTATTAATATT
1 ATTAAATTATAAATTATAAATATT
10187413 TAAAAATAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
51 7 0.11
52 3 0.05
53 1 0.02
54 2 0.03
55 38 0.58
56 7 0.11
57 7 0.11
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (54 bp):
ATTAAATTATAAATTATAAATATTAATATTTAAAATATTAATTATTACATTATA
Found at i:10187749 original size:3 final size:3
Alignment explanation
Indices: 10187741--10187766 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10187731 ATTAGGGTTG
10187741 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
10187767 CCCTAATCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:10199944 original size:19 final size:21
Alignment explanation
Indices: 10199907--10199947 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
10199897 TATATAGTGT
*
10199907 GTTAATATATTACTGTATATA
1 GTTAATATAGTACTGTATATA
10199928 GTTAATAT-GTACT-TATATA
1 GTTAATATAGTACTGTATATA
10199947 G
1 G
10199948 CATATAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (21 bp):
GTTAATATAGTACTGTATATA
Found at i:10207682 original size:106 final size:107
Alignment explanation
Indices: 10207478--10207693 Score: 416
Period size: 106 Copynumber: 2.0 Consensus size: 107
10207468 CCCCACCAAA
10207478 GAATGTAAAGCTTATGGTATGAAAGAGGTTCTTTACAACGAAAAACTTAAAAGTGTAAAAATAGA
1 GAATGTAAAGCTTATGGTATGAAAGAGGTTCTTTACAACGAAAAACTTAAAAGTGTAAAAATAGA
10207543 TTATCAATAGCAGAGTTTTGAGCTTCTTGTGTCCAAAAGTGG
66 TTATCAATAGCAGAGTTTTGAGCTTCTTGTGTCCAAAAGTGG
*
10207585 GAATGTAAAGCTTATGGTATGAAAGAGGTTCTTTACAAGGAAAAACTT-AAAGTGTAAAAATAGA
1 GAATGTAAAGCTTATGGTATGAAAGAGGTTCTTTACAACGAAAAACTTAAAAGTGTAAAAATAGA
10207649 TTATCAATAGCAGAGTTTTGAGCTTCTTGTGTCCAAAAGTGG
66 TTATCAATAGCAGAGTTTTGAGCTTCTTGTGTCCAAAAGTGG
10207691 GAA
1 GAA
10207694 AACTGTAATT
Statistics
Matches: 108, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
106 61 0.56
107 47 0.44
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (107 bp):
GAATGTAAAGCTTATGGTATGAAAGAGGTTCTTTACAACGAAAAACTTAAAAGTGTAAAAATAGA
TTATCAATAGCAGAGTTTTGAGCTTCTTGTGTCCAAAAGTGG
Found at i:10222402 original size:29 final size:29
Alignment explanation
Indices: 10222333--10222410 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
10222323 GAGTTAATAA
* * *
10222333 AGAAA-AGTTGTACGTGAATAGGTACAAG
1 AGAAAGAGTTGTACATGAACAGGAACAAG
* *
10222361 AGAGAGAGCTGTACATGAACAGGAACAAG
1 AGAAAGAGTTGTACATGAACAGGAACAAG
10222390 AGCAAAG-GTTGTACATGAACA
1 AG-AAAGAGTTGTACATGAACA
10222411 AGTATAAGAG
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 4 0.10
29 34 0.83
30 3 0.07
ACGTcount: A:0.44, C:0.12, G:0.28, T:0.17
Consensus pattern (29 bp):
AGAAAGAGTTGTACATGAACAGGAACAAG
Found at i:10231256 original size:2 final size:2
Alignment explanation
Indices: 10231251--10231282 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10231241 GCGAGCGACT
10231251 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
10231283 TTACCTCCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:10242472 original size:11 final size:11
Alignment explanation
Indices: 10242456--10242480 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10242446 TTATAATTAA
10242456 TAATATTTTTT
1 TAATATTTTTT
10242467 TAATATTTTTT
1 TAATATTTTTT
10242478 TAA
1 TAA
10242481 AATTAGACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATATTTTTT
Found at i:10243086 original size:19 final size:21
Alignment explanation
Indices: 10243064--10243109 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 21
10243054 TGAAGAAAAC
* *
10243064 TTTTGAGCGTTTT-GAGT-AT
1 TTTTGAGCATTTTAGAATGAT
*
10243083 TTTTAAGCATTTTAGAATGAT
1 TTTTGAGCATTTTAGAATGAT
10243104 TTTTGA
1 TTTTGA
10243110 TATACGAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
19 11 0.52
20 3 0.14
21 7 0.33
ACGTcount: A:0.24, C:0.04, G:0.20, T:0.52
Consensus pattern (21 bp):
TTTTGAGCATTTTAGAATGAT
Found at i:10243376 original size:22 final size:22
Alignment explanation
Indices: 10243348--10243452 Score: 102
Period size: 22 Copynumber: 4.7 Consensus size: 22
10243338 AGGTATTACT
* *
10243348 TGACTAGTTGGTAAGTGTTGCG
1 TGACTAGTTAGTAAGTATTGCG
* *
10243370 TGACTAGTTAGTAAGCATTGCA
1 TGACTAGTTAGTAAGTATTGCG
* * *
10243392 TGATTTGTTAGTAAGTCATTACG
1 TGACTAGTTAGTAAGT-ATTGCG
* *
10243415 TGACTAGTTAGTAAGGTAATGTG
1 TGACTAGTTAGTAA-GTATTGCG
*
10243438 TGATTAGTTAGTAAG
1 TGACTAGTTAGTAAG
10243453 GCATTGTGTG
Statistics
Matches: 66, Mismatches: 15, Indels: 4
0.78 0.18 0.05
Matches are distributed among these distances:
22 32 0.48
23 32 0.48
24 2 0.03
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.37
Consensus pattern (22 bp):
TGACTAGTTAGTAAGTATTGCG
Found at i:10243440 original size:23 final size:23
Alignment explanation
Indices: 10243369--10243465 Score: 79
Period size: 23 Copynumber: 4.3 Consensus size: 23
10243359 TAAGTGTTGC
* *
10243369 GTGACTAGTTAGTAA-GCATTGC
1 GTGACTAGTTAGTAAGGCAATGT
* * * * * **
10243391 ATGATTTGTTAGTAAGTCATTAC
1 GTGACTAGTTAGTAAGGCAATGT
*
10243414 GTGACTAGTTAGTAAGGTAATGT
1 GTGACTAGTTAGTAAGGCAATGT
* *
10243437 GTGATTAGTTAGTAAGGCATTGT
1 GTGACTAGTTAGTAAGGCAATGT
10243460 GTGACT
1 GTGACT
10243466 TAGACATTGT
Statistics
Matches: 57, Mismatches: 17, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
22 12 0.21
23 45 0.79
ACGTcount: A:0.28, C:0.08, G:0.27, T:0.37
Consensus pattern (23 bp):
GTGACTAGTTAGTAAGGCAATGT
Found at i:10243465 original size:46 final size:45
Alignment explanation
Indices: 10243368--10243457 Score: 117
Period size: 46 Copynumber: 2.0 Consensus size: 45
10243358 GTAAGTGTTG
* * *
10243368 CGTGACTAGTTAGTAAGCATTGCATGATTTGTTAGTAAGTCATTA
1 CGTGACTAGTTAGTAAGCAATGCATGATTAGTTAGTAAGGCATTA
* **
10243413 CGTGACTAGTTAGTAAGGTAATGTGTGATTAGTTAGTAAGGCATT
1 CGTGACTAGTTAGTAA-GCAATGCATGATTAGTTAGTAAGGCATT
10243458 GTGTGACTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
45 16 0.42
46 22 0.58
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.37
Consensus pattern (45 bp):
CGTGACTAGTTAGTAAGCAATGCATGATTAGTTAGTAAGGCATTA
Found at i:10253183 original size:2 final size:2
Alignment explanation
Indices: 10253178--10253207 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10253168 ATATTCTAAG
10253178 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
10253208 TTGAAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10270955 original size:49 final size:48
Alignment explanation
Indices: 10270876--10271024 Score: 131
Period size: 49 Copynumber: 3.0 Consensus size: 48
10270866 TATGACCAGC
* * *
10270876 TAAAATTTTTTAAATTTTT-TACTATATATATATATTTTAAAGGTCTCTT
1 TAAAATTTTTAAAATTTTTAT-TTAT-TATATATATTTTAAAGATCTCTT
* *
10270925 TAAAATTTTTAAAAGCTTTTATTTATTATATATATTTTTTAATGATCTCTT
1 TAAAATTTTTAAAA-TTTTTATTTATTATATATA--TTTTAAAGATCTCTT
* * * *
10270976 TCAAAATTTATGAAATTATTTATTTATAATATAT-TTTTAATGATTCTCT
1 T-AAAATTTTTAAAATT-TTTATTTATTATATATATTTTAAAGA-TCTCT
10271025 CAAAATAATA
Statistics
Matches: 84, Mismatches: 9, Indels: 13
0.79 0.08 0.12
Matches are distributed among these distances:
49 30 0.36
50 12 0.14
51 16 0.19
52 26 0.31
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (48 bp):
TAAAATTTTTAAAATTTTTATTTATTATATATATTTTAAAGATCTCTT
Found at i:10271008 original size:52 final size:51
Alignment explanation
Indices: 10270898--10271030 Score: 150
Period size: 51 Copynumber: 2.7 Consensus size: 51
10270888 AATTTTTTAC
* * * *
10270898 TATATATATATATTTTAAAGGTCTCTTT-AAAATTTTTAAAAGCTTTTATT
1 TATATATATATTTTTTAATGATCTCTTTCAAAATTTATAAAAGCTTTTATT
* *
10270948 TATTATATATATTTTTTAATGATCTCTTTCAAAATTTATGAAA-TTATTTATT
1 TA-TATATATATTTTTTAATGATCTCTTTCAAAATTTATAAAAGCT-TTTATT
*
10271000 TATA-ATATA-TTTTTAATGAT-TCTCTCAAAAT
1 TATATATATATTTTTTAATGATCTCTTTCAAAAT
10271031 AATATTTTAT
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
48 10 0.14
49 11 0.15
50 7 0.10
51 26 0.36
52 19 0.26
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.53
Consensus pattern (51 bp):
TATATATATATTTTTTAATGATCTCTTTCAAAATTTATAAAAGCTTTTATT
Found at i:10271338 original size:17 final size:16
Alignment explanation
Indices: 10271316--10271348 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
10271306 TTTTTTCTTT
10271316 CTATTTATATTATTTAA
1 CTATTTATA-TATTTAA
10271333 CTATTTATATATTTAA
1 CTATTTATATATTTAA
10271349 TCATTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
CTATTTATATATTTAA
Found at i:10271394 original size:7 final size:7
Alignment explanation
Indices: 10271384--10271428 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
10271374 TATTTAACTA
10271384 TTTATAT
1 TTTATAT
10271391 TTTATAT
1 TTTATAT
*
10271398 ATTATTAT
1 TTTA-TAT
10271406 TTTATAT
1 TTTATAT
*
10271413 TTAATAT
1 TTTATAT
*
10271420 TTTAAAT
1 TTTATAT
10271427 TT
1 TT
10271429 AAATAGAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
7 26 0.81
8 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTATAT
Found at i:10271400 original size:15 final size:15
Alignment explanation
Indices: 10271382--10271423 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
10271372 TGTATTTAAC
10271382 TATTTATATTTTATA
1 TATTTATATTTTATA
10271397 TA-TTATTATTTTATA
1 TATTTA-TATTTTATA
*
10271412 T-TTAATATTTTA
1 TATTTATATTTTA
10271424 AATTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTATATTTTATA
Found at i:10271430 original size:14 final size:14
Alignment explanation
Indices: 10271382--10271430 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
10271372 TGTATTTAAC
10271382 TATTT-ATATTTTA
1 TATTTAATATTTTA
*
10271395 TATATTATTATTTTA
1 TAT-TTAATATTTTA
10271410 TATTTAATATTTTA
1 TATTTAATATTTTA
*
10271424 AATTTAA
1 TATTTAA
10271431 ATAGAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 3 0.10
14 18 0.58
15 10 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTTAATATTTTA
Found at i:10271799 original size:21 final size:20
Alignment explanation
Indices: 10271771--10271809 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
10271761 AATCTTGAAG
* *
10271771 AAATTGATATTTTTAAAATA
1 AAATTGATACTTATAAAATA
10271791 AAATCTGATACTTATAAAA
1 AAAT-TGATACTTATAAAA
10271810 CTATTATAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (20 bp):
AAATTGATACTTATAAAATA
Found at i:10280126 original size:2 final size:2
Alignment explanation
Indices: 10280108--10280148 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
10280098 ATAGCTGCAA
*
10280108 AT AT A- AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10280149 TGCGGAGATG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:10284908 original size:24 final size:23
Alignment explanation
Indices: 10284871--10284915 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
10284861 TTTTTTTAAT
10284871 TAATAAAAAATTAATAAAATTATA
1 TAATAAAAAATTAA-AAAATTATA
* *
10284895 TAATAATAATTTAAAAAATTA
1 TAATAAAAAATTAAAAAATTA
10284916 ATCAAGAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
TAATAAAAAATTAAAAAATTATA
Found at i:10284925 original size:23 final size:24
Alignment explanation
Indices: 10284881--10284926 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
10284871 TAATAAAAAA
*
10284881 TTAATAAAATTATATAATAATAAT
1 TTAATAAAATTATATAAGAATAAT
10284905 TTAA-AAAATTA-ATCAAGAATAA
1 TTAATAAAATTATAT-AAGAATAA
10284927 AATTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 14 0.70
24 4 0.20
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
TTAATAAAATTATATAAGAATAAT
Found at i:10292973 original size:49 final size:49
Alignment explanation
Indices: 10292917--10293011 Score: 154
Period size: 49 Copynumber: 1.9 Consensus size: 49
10292907 TTGTTATTTT
* *
10292917 CTTTACTTGCATATCAAGTAGGTTTAAGTGTAATTGGCTATTATAATTA
1 CTTTACTTGCACATCAAGTAAGTTTAAGTGTAATTGGCTATTATAATTA
* *
10292966 CTTTACTTGCACATCAAGTAAGTTTAAGTTTAATTGGTTATTATAA
1 CTTTACTTGCACATCAAGTAAGTTTAAGTGTAATTGGCTATTATAA
10293012 ATAGCCCTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.43
Consensus pattern (49 bp):
CTTTACTTGCACATCAAGTAAGTTTAAGTGTAATTGGCTATTATAATTA
Found at i:10301035 original size:6 final size:6
Alignment explanation
Indices: 10301024--10301055 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
10301014 TTATGTAAAC
10301024 AATTAA AATTAA AATTAA AATTAA AATTAA AA
1 AATTAA AATTAA AATTAA AATTAA AATTAA AA
10301056 CTAATAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATTAA
Found at i:10301932 original size:15 final size:16
Alignment explanation
Indices: 10301906--10301938 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
10301896 TATTTTTTTG
10301906 TATGTATATATTTATT
1 TATGTATATATTTATT
*
10301922 TATGT-TATATTTGTT
1 TATGTATATATTTATT
10301937 TA
1 TA
10301939 ATAAATCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (16 bp):
TATGTATATATTTATT
Found at i:10302167 original size:14 final size:14
Alignment explanation
Indices: 10302148--10302175 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10302138 TTAATTTTAA
10302148 TAACCGAACTATCC
1 TAACCGAACTATCC
10302162 TAACCGAACTATCC
1 TAACCGAACTATCC
10302176 AAAGAACCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.36, G:0.07, T:0.21
Consensus pattern (14 bp):
TAACCGAACTATCC
Found at i:10304424 original size:22 final size:20
Alignment explanation
Indices: 10304374--10304425 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
10304364 CATATCAACA
*
10304374 TAATGCCATGTCAACATGAT
1 TAATGCCATGTCAACATAAT
*
10304394 T-GTGCCATGTCAGCACATAAT
1 TAATGCCATGTCA--ACATAAT
10304415 TAATGCCATGT
1 TAATGCCATGT
10304426 TACCAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 1 0.04
21 7 0.27
22 8 0.31
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (20 bp):
TAATGCCATGTCAACATAAT
Found at i:10318997 original size:5 final size:5
Alignment explanation
Indices: 10318987--10319014 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
10318977 ACCTCTGTCG
10318987 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
10319015 TTTGATTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:10319458 original size:3 final size:3
Alignment explanation
Indices: 10319450--10319487 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
10319440 GTGAACATGT
*
10319450 AGA AGA AGA AGA AAA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
10319488 CAGAGGATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:10320321 original size:31 final size:31
Alignment explanation
Indices: 10320286--10320367 Score: 130
Period size: 31 Copynumber: 2.6 Consensus size: 31
10320276 TAATAGTTTG
* *
10320286 CAATTCAGTGTCTTCTATGTTATTGATATCT
1 CAATTCAGTGTCTTCTATGTTATTGAGATAT
10320317 CAATTCAGTGTCTTCTATGTTATTGAGATAT
1 CAATTCAGTGTCTTCTATGTTATTGAGATAT
10320348 CAATTCAGTGTAC-TCTATGT
1 CAATTCAGTGT-CTTCTATGT
10320368 CGCCTTCTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 47 0.98
32 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (31 bp):
CAATTCAGTGTCTTCTATGTTATTGAGATAT
Found at i:10331591 original size:24 final size:25
Alignment explanation
Indices: 10331559--10331605 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
10331549 AATTATAAAC
10331559 AAAATATTA-ATATCTAAAATAAATT
1 AAAATATTATATAT-TAAAATAAATT
*
10331584 AAAA-ATTATATATTATAATAAA
1 AAAATATTATATATTAAAATAAA
10331606 GAGTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
AAAATATTATATATTAAAATAAATT
Found at i:10337524 original size:21 final size:21
Alignment explanation
Indices: 10337486--10337526 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
10337476 AAGTAGTGTT
* **
10337486 TTTTTTTTTTAATTTTATTTG
1 TTTTTTTTTCAACATTATTTG
10337507 TTTTTTTTTCAACATTATTT
1 TTTTTTTTTCAACATTATTT
10337527 TTGCAAGGTT
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:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTTTTTTCAACATTATTTG
Found at i:10339694 original size:20 final size:20
Alignment explanation
Indices: 10339656--10339692 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
10339646 TCCCAAGTAG
10339656 TTTTATTTAGTTTCTTTTAA
1 TTTTATTTAGTTTCTTTTAA
*
10339676 TTTTATTT-GTTTGTTTT
1 TTTTATTTAGTTTCTTTT
10339693 TATTCAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.14, C:0.03, G:0.08, T:0.76
Consensus pattern (20 bp):
TTTTATTTAGTTTCTTTTAA
Found at i:10348536 original size:27 final size:27
Alignment explanation
Indices: 10348506--10348574 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
10348496 AAGCCCCATC
10348506 AGTGAAAGAACTACAAGATTTAAAAAT
1 AGTGAAAGAACTACAAGATTTAAAAAT
*
10348533 AGTGAAAGAACTGCAAGATTTAAAAAT
1 AGTGAAAGAACTACAAGATTTAAAAAT
10348560 AGTGAAAGAACTACA
1 AGTGAAAGAACTACA
10348575 TGCAGTGGCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (27 bp):
AGTGAAAGAACTACAAGATTTAAAAAT
Found at i:10367932 original size:4 final size:4
Alignment explanation
Indices: 10367923--10367953 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
10367913 TCTTCTCTCC
10367923 CCTT CCTT CCTT CCTT CCTT CCTT CCTT CCT
1 CCTT CCTT CCTT CCTT CCTT CCTT CCTT CCT
10367954 CCATTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (4 bp):
CCTT
Found at i:10368224 original size:20 final size:21
Alignment explanation
Indices: 10368192--10368230 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
10368182 AGGAAGGTAC
10368192 TTTCTTTGC-TTTTGTTTTTT
1 TTTCTTTGCTTTTTGTTTTTT
10368212 TTTCTTT-CTTTTTTGTTTT
1 TTTCTTTGC-TTTTTGTTTT
10368231 AAATGTGCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.06
20 7 0.41
21 9 0.53
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.82
Consensus pattern (21 bp):
TTTCTTTGCTTTTTGTTTTTT
Found at i:10368621 original size:152 final size:151
Alignment explanation
Indices: 10368344--10368648 Score: 443
Period size: 152 Copynumber: 2.0 Consensus size: 151
10368334 TTAAAGAAAA
* * * *
10368344 GAATTTGTTGAATACTGGGGTGGTTTTCTTCTGGGTTTAACTTGTTATGGAAAATCTAGCTTTGA
1 GAATTTGTTGAATACTGCGGTGGTGTTCTTCTCGGCTTAACTTGTTATGGAAAATCTAGCTTTGA
** *
10368409 TTTTGGCTAATTGTGTAAAGAACTAATCTAAGTTGCGTGGTTTTTGTAGTGTTAGACATGCTTAC
66 TTTTGGCTAATTACGTAAAGAACTAATCTAAGTTGCGTAGTTTTTGTAGTGTTAGACATGCTTAC
10368474 TGCCTCATTAATGTTCAATTTT
131 TGCCTCATTAATGTTC-ATTTT
* * *
10368496 GAATTTGTTGAATAGTTCGGTGGTGTTCTTCTCGGCTTAA-TTGGTTATGTAAAATCTAGCTTTG
1 GAATTTGTTGAATACTGCGGTGGTGTTCTTCTCGGCTTAACTT-GTTATGGAAAATCTAGCTTTG
* *
10368560 ATTTTGGCTAATTACGTAAAGAACTGATCTAATTTGCGTAGTTTTTGTAGTGTTATG-CATGCTT
65 ATTTTGGCTAATTACGTAAAGAACTAATCTAAGTTGCGTAGTTTTTGTAGTGTTA-GACATGCTT
* *
10368624 ACTTCCTCCTTAATGTTCATTTT
129 ACTGCCTCATTAATGTTCATTTT
10368647 GA
1 GA
10368649 TGTATAAATG
Statistics
Matches: 137, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
151 9 0.07
152 127 0.93
153 1 0.01
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (151 bp):
GAATTTGTTGAATACTGCGGTGGTGTTCTTCTCGGCTTAACTTGTTATGGAAAATCTAGCTTTGA
TTTTGGCTAATTACGTAAAGAACTAATCTAAGTTGCGTAGTTTTTGTAGTGTTAGACATGCTTAC
TGCCTCATTAATGTTCATTTT
Found at i:10384250 original size:16 final size:17
Alignment explanation
Indices: 10384208--10384255 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
10384198 CAACTTAAAA
*
10384208 TTAATTATATTTATATG
1 TTAATAATATTTATATG
10384225 TTAATAATATTTA-AT-
1 TTAATAATATTTATATG
10384240 TTAAGTAATATGTTAT
1 TTAA-TAATAT-TTAT
10384256 TTCTTTTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 4 0.15
16 8 0.30
17 15 0.56
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
TTAATAATATTTATATG
Found at i:10391410 original size:15 final size:15
Alignment explanation
Indices: 10391392--10391467 Score: 88
Period size: 15 Copynumber: 5.2 Consensus size: 15
10391382 TATTTTAAAT
10391392 ATTTGTATTCATTTA
1 ATTTGTATTCATTTA
*
10391407 ATTT-TAAAT-ATTTA
1 ATTTGT-ATTCATTTA
10391421 ATTTGTATTCATTTA
1 ATTTGTATTCATTTA
*
10391436 ATTT-TAAAT-ATTTA
1 ATTTGT-ATTCATTTA
10391450 ATTTGTATTCATTTA
1 ATTTGTATTCATTTA
10391465 ATT
1 ATT
10391468 GATTTCTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
14 24 0.47
15 27 0.53
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (15 bp):
ATTTGTATTCATTTA
Found at i:10391410 original size:24 final size:24
Alignment explanation
Indices: 10391383--10391448 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 24
10391373 GCCTTACATT
10391383 ATTTTAAATATTTGTATTCATTTA
1 ATTTTAAATATTTGTATTCATTTA
10391407 ATTTTAAATATTTAATTTGTATTCATTTA
1 ATTTT-AA-A--T-ATTTGTATTCATTTA
10391436 ATTTTAAATATTT
1 ATTTTAAATATTT
10391449 AATTTGTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
24 9 0.24
25 3 0.08
26 1 0.03
27 1 0.03
28 3 0.08
29 20 0.54
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (24 bp):
ATTTTAAATATTTGTATTCATTTA
Found at i:10391421 original size:14 final size:14
Alignment explanation
Indices: 10391402--10391453 Score: 70
Period size: 14 Copynumber: 3.6 Consensus size: 14
10391392 ATTTGTATTC
10391402 ATTTAATTTTAAAT
1 ATTTAATTTTAAAT
*
10391416 ATTTAATTTGT-ATT
1 ATTTAATTT-TAAAT
10391430 CATTTAATTTTAAAT
1 -ATTTAATTTTAAAT
10391445 ATTTAATTT
1 ATTTAATTT
10391454 GTATTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 21 0.64
15 12 0.36
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTTAATTTTAAAT
Found at i:10391430 original size:29 final size:29
Alignment explanation
Indices: 10391392--10391467 Score: 152
Period size: 29 Copynumber: 2.6 Consensus size: 29
10391382 TATTTTAAAT
10391392 ATTTGTATTCATTTAATTTTAAATATTTA
1 ATTTGTATTCATTTAATTTTAAATATTTA
10391421 ATTTGTATTCATTTAATTTTAAATATTTA
1 ATTTGTATTCATTTAATTTTAAATATTTA
10391450 ATTTGTATTCATTTAATT
1 ATTTGTATTCATTTAATT
10391468 GATTTCTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (29 bp):
ATTTGTATTCATTTAATTTTAAATATTTA
Found at i:10391601 original size:2 final size:2
Alignment explanation
Indices: 10391596--10391634 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
10391586 ATATATATAT
* * *
10391596 AG AG AG AG AA AA AG AG AG AG AG AC AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
10391635 ATTCATTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.56, C:0.03, G:0.41, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10424820 original size:18 final size:19
Alignment explanation
Indices: 10424786--10424822 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
10424776 ACTGATGCTG
10424786 TAGCAAATGAAACCAAAGA
1 TAGCAAATGAAACCAAAGA
*
10424805 TAGCAAA-GAAAGCAAAGA
1 TAGCAAATGAAACCAAAGA
10424823 GGGCAAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.59, C:0.14, G:0.19, T:0.08
Consensus pattern (19 bp):
TAGCAAATGAAACCAAAGA
Found at i:10424828 original size:18 final size:18
Alignment explanation
Indices: 10424787--10424831 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
10424777 CTGATGCTGT
*
10424787 AGCAAATGAAACCAAAGAT
1 AGCAAA-GAAACCAAAGAG
*
10424806 AGCAAAGAAAGCAAAGAG
1 AGCAAAGAAACCAAAGAG
*
10424824 GGCAAAGA
1 AGCAAAGA
10424832 TAAAGGTTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.58, C:0.13, G:0.24, T:0.04
Consensus pattern (18 bp):
AGCAAAGAAACCAAAGAG
Found at i:10429447 original size:2 final size:2
Alignment explanation
Indices: 10429440--10429467 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10429430 TCTATTTATT
10429440 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
10429468 ACTTCATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10434631 original size:57 final size:56
Alignment explanation
Indices: 10434540--10434653 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 56
10434530 AAAGTGGAAA
*
10434540 GGTGGAGAAAAACTCCAATAACATGAAACAGAAAACTA-CACTAACAATAAAATAG
1 GGTGGAGAAAAACTCCAACAACATGAAACAGAAAACTACCACTAACAATAAAATAG
* **
10434595 GGTGGAGACACAACCTCCAACAACATGAAATGGAAAACTACCACTAACAATAAAATAG
1 GGTGGAGA-A-AAACTCCAACAACATGAAACAGAAAACTACCACTAACAATAAAATAG
10434653 G
1 G
10434654 AACCACAATG
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
55 8 0.15
56 1 0.02
57 25 0.48
58 18 0.35
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (56 bp):
GGTGGAGAAAAACTCCAACAACATGAAACAGAAAACTACCACTAACAATAAAATAG
Found at i:10446607 original size:30 final size:29
Alignment explanation
Indices: 10446521--10446607 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 29
10446511 CCTTGTATTG
* * *
10446521 TTATTTTGAATCAAATAAACCCTTGTACTT
1 TTATTTTGAGTCAAA-AAAACCTTATACTT
* * *
10446551 TTATTTTGAGCCAAAAGAGCCTTTATACTT
1 TTATTTTGAGTCAAAAAAACC-TTATACTT
10446581 TTATTTTGAGTCAAAAAAACTCTTATA
1 TTATTTTGAGTCAAAAAAAC-CTTATA
10446608 ACGAATGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
29 4 0.09
30 42 0.89
31 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.41
Consensus pattern (29 bp):
TTATTTTGAGTCAAAAAAACCTTATACTT
Found at i:10461402 original size:29 final size:30
Alignment explanation
Indices: 10461370--10461470 Score: 88
Period size: 29 Copynumber: 3.5 Consensus size: 30
10461360 GTGCAAATGA
10461370 TGTTACACGTCAT-TTTAAAAAAATGTTAT
1 TGTTACACGTCATATTTAAAAAAATGTTAT
* *
10461399 TGTTACACATCATGA-TT-AAAAAAGGTTAT
1 TGTTACACGTCAT-ATTTAAAAAAATGTTAT
* * *
10461428 T-ATACA--TCATATTGGAAAAAAAATATTAT
1 TGTTACACGTCATATT--TAAAAAAATGTTAT
10461457 TGTTACACGTCATA
1 TGTTACACGTCATA
10461471 CACACCATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
25 1 0.02
26 5 0.09
28 4 0.07
29 35 0.62
30 6 0.11
32 5 0.09
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (30 bp):
TGTTACACGTCATATTTAAAAAAATGTTAT
Found at i:10461516 original size:30 final size:30
Alignment explanation
Indices: 10461476--10461554 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 30
10461466 TCATACACAC
10461476 CATATTGAAAAAAATATTGTTATTACATGT
1 CATATTGAAAAAAATATTGTTATTACATGT
* * *
10461506 CCTGTTG-AAAAAATATTTTTATTACATGT
1 CATATTGAAAAAAATATTGTTATTACATGT
* *
10461535 CATATTTAAAAAAATTTTGT
1 CATATTGAAAAAAATATTGT
10461555 CACATTTTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 25 0.62
30 15 0.38
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.43
Consensus pattern (30 bp):
CATATTGAAAAAAATATTGTTATTACATGT
Found at i:10467717 original size:12 final size:12
Alignment explanation
Indices: 10467679--10467734 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
10467669 CACCACCATC
*
10467679 CCTTCCCCCACT
1 CCTTCCACCACT
* *
10467691 CCATCCCCCACT
1 CCTTCCACCACT
10467703 CCTTCCACCACT
1 CCTTCCACCACT
*
10467715 CCTGCCACCAC-
1 CCTTCCACCACT
10467726 CTCTTCCAC
1 C-CTTCCAC
10467735 TGCCTGGACC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
11 1 0.03
12 37 0.97
ACGTcount: A:0.14, C:0.62, G:0.02, T:0.21
Consensus pattern (12 bp):
CCTTCCACCACT
Found at i:10467725 original size:24 final size:24
Alignment explanation
Indices: 10467671--10467734 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
10467661 ACCACGGCCA
*
10467671 CCACCA-TCCCTTCCCCCACTCCAT
1 CCACCACT-CCTTCCACCACTCCAT
*
10467695 CCCCCACTCCTTCCACCACTCC-T
1 CCACCACTCCTTCCACCACTCCAT
10467718 GCCACCAC-CTCTTCCAC
1 -CCACCACTC-CTTCCAC
10467735 TGCCTGGACC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 2 0.06
24 31 0.91
25 1 0.03
ACGTcount: A:0.16, C:0.62, G:0.02, T:0.20
Consensus pattern (24 bp):
CCACCACTCCTTCCACCACTCCAT
Found at i:10470826 original size:26 final size:26
Alignment explanation
Indices: 10470782--10470842 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
10470772 ACAGGAAAAG
** *
10470782 CCTCATCCTTAGAGGAATTGTTCAGT
1 CCTCATCCTTAGACAAATTGCTCAGT
* *
10470808 CCTCATCCTTGGACAAATTGCTCATT
1 CCTCATCCTTAGACAAATTGCTCAGT
10470834 CCTCATCCT
1 CCTCATCCT
10470843 CAGGATCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.34
Consensus pattern (26 bp):
CCTCATCCTTAGACAAATTGCTCAGT
Found at i:10474566 original size:3 final size:3
Alignment explanation
Indices: 10474558--10474594 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
10474548 ACATACTTTA
10474558 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
10474595 GGAATAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:10482664 original size:31 final size:30
Alignment explanation
Indices: 10482628--10482685 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
10482618 TAAATTTAAT
10482628 ATTTTAAAAAATTTAAAAATGAA-TATTTCTA
1 ATTTTAAAAAA-TTAAAAAT-AATTATTTCTA
10482659 ATTTTAAAAAATTAAAAATAATTATTT
1 ATTTTAAAAAATTAAAAATAATTATTT
10482686 TTTATCTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 2 0.08
30 13 0.50
31 11 0.42
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (30 bp):
ATTTTAAAAAATTAAAAATAATTATTTCTA
Found at i:10483975 original size:29 final size:27
Alignment explanation
Indices: 10483912--10483975 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
10483902 ATTTATTGAT
* *
10483912 ATTAAAT-TTTATTATATTTAATATAT
1 ATTAAATATTTATAATATTTAATATAA
*
10483938 ATTATAATATTTATAATTATTTACTATAA
1 ATTA-AATATTTATAA-TATTTAATATAA
10483967 ATTTAAATA
1 A-TTAAATA
10483976 ATATAATCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 4 0.13
27 3 0.10
28 6 0.19
29 15 0.48
30 3 0.10
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTAAATATTTATAATATTTAATATAA
Found at i:10485698 original size:9 final size:9
Alignment explanation
Indices: 10485684--10485709 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
10485674 AAAATAAATA
10485684 TTATTATTG
1 TTATTATTG
10485693 TTATTATTG
1 TTATTATTG
10485702 TTATTATT
1 TTATTATT
10485710 AGATGGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (9 bp):
TTATTATTG
Found at i:10488869 original size:19 final size:20
Alignment explanation
Indices: 10488845--10488885 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
10488835 GATACAGTTC
10488845 TTTCTTTCT-ATTTATTTTT
1 TTTCTTTCTGATTTATTTTT
*
10488864 TTTCTTTCTGATTTGTTTTT
1 TTTCTTTCTGATTTATTTTT
10488884 TT
1 TT
10488886 ATATTGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.07, C:0.10, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTCTTTCTGATTTATTTTT
Found at i:10496853 original size:1 final size:1
Alignment explanation
Indices: 10496847--10496874 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
10496837 CAGGTATATT
10496847 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
10496875 TGCATGAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:10498465 original size:16 final size:18
Alignment explanation
Indices: 10498444--10498477 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
10498434 TTTGCCTGGT
10498444 AGGATGG-A-GAAGTGGG
1 AGGATGGCAGGAAGTGGG
10498460 AGGATGGCAGGAAGTGGG
1 AGGATGGCAGGAAGTGGG
10498478 TAGAAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.29, C:0.03, G:0.56, T:0.12
Consensus pattern (18 bp):
AGGATGGCAGGAAGTGGG
Found at i:10499919 original size:88 final size:87
Alignment explanation
Indices: 10499823--10500001 Score: 331
Period size: 88 Copynumber: 2.0 Consensus size: 87
10499813 GTACTAATAT
*
10499823 CTTAATGTGATCAGCATTATGTGTGAATCCTTATTTCAAATTATCCAGAACCATTTGGATACAAT
1 CTTAATGTGATCAGCATTATGTGTGAATCCTTATGTCAAATTATCCAGAACCATTTGGATAC-AT
10499888 CCTGTATAAGTATCTGAATGTGA
65 CCTGTATAAGTATCTGAATGTGA
10499911 CTTAATGTGATCAGCATTATGTGTGAATCCTTATGTCAAATTATCCAGAACCATTTGGATACATC
1 CTTAATGTGATCAGCATTATGTGTGAATCCTTATGTCAAATTATCCAGAACCATTTGGATACATC
*
10499976 CTGTATTAGTATCTGAATGTGA
66 CTGTATAAGTATCTGAATGTGA
10499998 CTTA
1 CTTA
10500002 CATCTTATTC
Statistics
Matches: 89, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
87 28 0.31
88 61 0.69
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (87 bp):
CTTAATGTGATCAGCATTATGTGTGAATCCTTATGTCAAATTATCCAGAACCATTTGGATACATC
CTGTATAAGTATCTGAATGTGA
Found at i:10509510 original size:12 final size:13
Alignment explanation
Indices: 10509493--10509522 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
10509483 AATCCTCCAT
10509493 AAAAACCAAA-AA
1 AAAAACCAAATAA
10509505 AAAAACCAAATAA
1 AAAAACCAAATAA
10509518 AAAAA
1 AAAAA
10509523 ATATAGATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.83, C:0.13, G:0.00, T:0.03
Consensus pattern (13 bp):
AAAAACCAAATAA
Found at i:10510171 original size:3 final size:3
Alignment explanation
Indices: 10510163--10510223 Score: 99
Period size: 3 Copynumber: 21.0 Consensus size: 3
10510153 CATAGGAGAG
10510163 GAA GAA GAA GAA GAA GAA -AA GAA -AA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
10510209 GAA GAA GAA GCA GAA
1 GAA GAA GAA GAA GAA
10510224 TACAAACACT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:10523525 original size:32 final size:32
Alignment explanation
Indices: 10523489--10523557 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
10523479 TGATTGATGC
*
10523489 TTTTTGCTATTT-GTCTTTGATTTTCTATTCAT
1 TTTTTG-TATTTGGCCTTTGATTTTCTATTCAT
* **
10523521 TTTTTGTTTTTGGCCTTTTCTTTTCTATTCAT
1 TTTTTGTATTTGGCCTTTGATTTTCTATTCAT
10523553 TTTTT
1 TTTTT
10523558 TCAAAAGAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 4 0.12
32 28 0.88
ACGTcount: A:0.09, C:0.13, G:0.09, T:0.70
Consensus pattern (32 bp):
TTTTTGTATTTGGCCTTTGATTTTCTATTCAT
Found at i:10537345 original size:9 final size:9
Alignment explanation
Indices: 10537333--10537378 Score: 60
Period size: 9 Copynumber: 5.2 Consensus size: 9
10537323 GGAGAGAAAG
10537333 AAAGAAAAA
1 AAAGAAAAA
10537342 AAAG-AAAA
1 AAAGAAAAA
*
10537350 AACGAAAAA
1 AAAGAAAAA
10537359 AGAA-AAAAA
1 A-AAGAAAAA
10537368 AAAGAAAAA
1 AAAGAAAAA
10537377 AA
1 AA
10537379 TACAAAAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 9 0.28
9 22 0.69
10 1 0.03
ACGTcount: A:0.87, C:0.02, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:10537349 original size:8 final size:8
Alignment explanation
Indices: 10537327--10537378 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
10537317 GTGAAAGGAG
*
10537327 AGAAAGAA
1 AGAAAAAA
10537335 AGAAAAAAA
1 AG-AAAAAA
10537344 AGAAAAAA
1 AGAAAAAA
*
10537352 CGAAAAAAGA
1 AG-AAAAA-A
*
10537362 AAAAAAAA
1 AGAAAAAA
10537370 AGAAAAAA
1 AGAAAAAA
10537378 A
1 A
10537379 TACAAAAGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
8 18 0.50
9 17 0.47
10 1 0.03
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:10541671 original size:2 final size:2
Alignment explanation
Indices: 10541629--10541655 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10541619 GCCAAGCTTT
10541629 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
10541656 GAAAACTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10551364 original size:2 final size:2
Alignment explanation
Indices: 10551352--10551406 Score: 74
Period size: 2 Copynumber: 27.5 Consensus size: 2
10551342 TTTTACAAAT
* * *
10551352 TA TA AA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
10551394 TA CA TA TA TA TA T
1 TA TA TA TA TA TA T
10551407 TTGCCGTCGC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:10562216 original size:28 final size:26
Alignment explanation
Indices: 10562163--10562218 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
10562153 GTTTGAATGC
* *
10562163 ATAAAAAATCTATTTACAAATTAAAA
1 ATAAAAAATATATTTACAAAATAAAA
*
10562189 ATAAAAAATATCATTTATTAAAATAAAA
1 ATAAAAAATAT-ATTTA-CAAAATAAAA
10562217 AT
1 AT
10562219 GCTTGTGCGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 10 0.40
27 5 0.20
28 10 0.40
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (26 bp):
ATAAAAAATATATTTACAAAATAAAA
Found at i:10563465 original size:21 final size:20
Alignment explanation
Indices: 10563439--10563477 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10563429 TGGTATAATG
*
10563439 TTTAAAAAGATTTTTAAATTA
1 TTTAAAAA-AATTTTAAATTA
10563460 TTTAAAAAAATTTTAAAT
1 TTTAAAAAAATTTTAAAT
10563478 AAATGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TTTAAAAAAATTTTAAATTA
Found at i:10563499 original size:13 final size:13
Alignment explanation
Indices: 10563455--10563501 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
10563445 AAGATTTTTA
10563455 AATTATTTAAAAA-
1 AATT-TTTAAAAAT
*
10563468 AATTTTAAATAAAT
1 AATTTTTAA-AAAT
*
10563482 GATTTTTAAAAAT
1 AATTTTTAAAAAT
10563495 AATTTTT
1 AATTTTT
10563502 TATTATTCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 4 0.14
13 17 0.61
14 7 0.25
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
AATTTTTAAAAAT
Found at i:10585523 original size:18 final size:18
Alignment explanation
Indices: 10585500--10585563 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
10585490 AGTTTTCCGA
10585500 ACACAAGACTATAATACC
1 ACACAAGACTATAATACC
* * **
10585518 ACACAAAACTTGATACTTAGGA
1 ACACAAGAC-T-ATA-ATA-CC
10585540 ACACAAGACTATAATACC
1 ACACAAGACTATAATACC
10585558 ACACAA
1 ACACAA
10585564 AACTTGATAC
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
18 14 0.41
19 3 0.09
20 6 0.18
21 3 0.09
22 8 0.24
ACGTcount: A:0.50, C:0.25, G:0.08, T:0.17
Consensus pattern (18 bp):
ACACAAGACTATAATACC
Found at i:10585553 original size:40 final size:40
Alignment explanation
Indices: 10585498--10585578 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
10585488 TTAGTTTTCC
10585498 GAACACAAGACTATAATACCACACAAAACTTGATACTTAG
1 GAACACAAGACTATAATACCACACAAAACTTGATACTTAG
10585538 GAACACAAGACTATAATACCACACAAAACTTGATACTTAG
1 GAACACAAGACTATAATACCACACAAAACTTGATACTTAG
10585578 G
1 G
10585579 TCCAATATTA
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:0.47, C:0.22, G:0.11, T:0.20
Consensus pattern (40 bp):
GAACACAAGACTATAATACCACACAAAACTTGATACTTAG
Found at i:10586829 original size:43 final size:43
Alignment explanation
Indices: 10586760--10586841 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
10586750 TTTCTTACCT
* *
10586760 TTTGTTTCTTTTCACCTATTTATCCTCTTCCACCTACATAATA
1 TTTGCTTCTTTTCACCTATTTATCCTCTTCCACCCACATAATA
*
10586803 TTTGCTTCTTTTCACCTATTTTTCCTCTTCCACCCACAT
1 TTTGCTTCTTTTCACCTATTTATCCTCTTCCACCCACAT
10586842 GGTGGTATGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.17, C:0.32, G:0.02, T:0.49
Consensus pattern (43 bp):
TTTGCTTCTTTTCACCTATTTATCCTCTTCCACCCACATAATA
Found at i:10589828 original size:18 final size:18
Alignment explanation
Indices: 10589807--10589841 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10589797 AAACTTAACC
*
10589807 AATAATTAAAAAATTTAT
1 AATAAATAAAAAATTTAT
*
10589825 AATAAATAATAAATTTA
1 AATAAATAAAAAATTTA
10589842 CATAACATGT
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAAATAAAAAATTTAT
Found at i:10590728 original size:2 final size:2
Alignment explanation
Indices: 10590704--10590743 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
10590694 AAAAGACAAA
* *
10590704 AG AG A- AG AG AA AG AG AA AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
10590744 AAAAGGCATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10591093 original size:16 final size:16
Alignment explanation
Indices: 10591072--10591121 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
10591062 NNNNNNNNAA
10591072 TAAAATATTAATATTT
1 TAAAATATTAATATTT
10591088 TAAAATATTAATGA--T
1 TAAAATATTAAT-ATTT
*
10591103 TAAATTATTAATATTT
1 TAAAATATTAATATTT
10591119 TAA
1 TAA
10591122 TCAAATAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 1 0.03
15 12 0.40
16 16 0.53
17 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
TAAAATATTAATATTT
Found at i:10591104 original size:23 final size:23
Alignment explanation
Indices: 10591078--10591122 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
10591068 NNAATAAAAT
10591078 ATTAATATT-TTAAAATATTAATG
1 ATTAA-ATTATTAAAATATTAATG
* *
10591101 ATTAAATTATTAATATTTTAAT
1 ATTAAATTATTAAAATATTAAT
10591123 CAAATAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATTAAATTATTAAAATATTAATG
Found at i:10591217 original size:33 final size:34
Alignment explanation
Indices: 10591112--10591218 Score: 82
Period size: 34 Copynumber: 3.2 Consensus size: 34
10591102 TTAAATTATT
* *
10591112 AATATTTTAATCAAATAATCAATTATTAATA-TTT-A
1 AATATTTAAATAAAATAA--AA-TATTAATATTTTAA
* **
10591147 AATA-TAAAATAAAATAAAATAATT--TATCATAA
1 AATATTTAAATAAAATAAAAT-ATTAATATTTTAA
10591179 TAATATTTAAAT-AAATAAAATATTAATATTTTAA
1 -AATATTTAAATAAAATAAAATATTAATATTTTAA
10591213 AATATT
1 AATATT
10591219 AATGACTAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
30 2 0.04
31 2 0.04
32 9 0.16
33 19 0.33
34 21 0.37
35 4 0.07
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (34 bp):
AATATTTAAATAAAATAAAATATTAATATTTTAA
Found at i:10591750 original size:16 final size:16
Alignment explanation
Indices: 10591729--10591759 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
10591719 TAATAACTAT
10591729 TTTATTCTATTCTCAC
1 TTTATTCTATTCTCAC
10591745 TTTATTCTATTCTCA
1 TTTATTCTATTCTCA
10591760 TAAAATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTATTCTATTCTCAC
Found at i:10592440 original size:11 final size:11
Alignment explanation
Indices: 10592424--10592460 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
10592414 GAGCTCCGGG
10592424 TTCTTTTTCTT
1 TTCTTTTTCTT
10592435 TTC-TTTTCTT
1 TTCTTTTTCTT
*
10592445 TTTTTTTTC-T
1 TTCTTTTTCTT
10592455 TTCTTT
1 TTCTTT
10592461 CCTCCTTGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 15 0.65
11 8 0.35
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:10592445 original size:16 final size:15
Alignment explanation
Indices: 10592424--10592460 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
10592414 GAGCTCCGGG
10592424 TTCTTTTTCTTTTCTT
1 TTCTTTTTCTTTTC-T
*
10592440 TTCTTTTTTTTTTCT
1 TTCTTTTTCTTTTCT
10592455 TTCTTT
1 TTCTTT
10592461 CCTCCTTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTCTTTTTCTTTTCT
Found at i:10598784 original size:10 final size:10
Alignment explanation
Indices: 10598769--10598796 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
10598759 CCCTAATTTG
10598769 CTCGTTTCCC
1 CTCGTTTCCC
10598779 CTCGTTTCCC
1 CTCGTTTCCC
10598789 CTCGTTTC
1 CTCGTTTC
10598797 AGTTATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.46, G:0.11, T:0.43
Consensus pattern (10 bp):
CTCGTTTCCC
Done.