Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 156 of 199
Found at i:46618613 original size:29 final size:30
Alignment explanation
Indices: 46618580--46618646 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 30
46618570 AAGTTAAGGT
46618580 TTAGGGTTTTTAATTAAATTAGGTTA-GGA
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGA
*
46618609 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGA
46618639 TTAGGGTT
1 TTAGGGTT
46618647 AAATTAGGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 26 0.72
30 10 0.28
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (30 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGA
Found at i:46618690 original size:25 final size:25
Alignment explanation
Indices: 46618662--46618729 Score: 118
Period size: 25 Copynumber: 2.7 Consensus size: 25
46618652 AGGTTAGGGT
*
46618662 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAAATTCTA
46618687 TTTTATTACATCAAATAAAATTCTA
1 TTTTATTACATCAAATAAAATTCTA
*
46618712 TTTTATTACATAAAATAA
1 TTTTATTACATCAAATAA
46618730 TATCAAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (25 bp):
TTTTATTACATCAAATAAAATTCTA
Found at i:46618765 original size:44 final size:45
Alignment explanation
Indices: 46618697--46618783 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 45
46618687 TTTTATTACA
46618697 TCAAATAAAATTCTATTTTATTACATAAAATAATATCAAAATAAC
1 TCAAATAAAATTCTATTTTATTACATAAAATAATATCAAAATAAC
* *
46618742 TCAAA-AAATTTCTATTTTTTTACATAAAATAATATCAAAATA
1 TCAAATAAAATTCTATTTTATTACATAAAATAATATCAAAATA
46618784 TTCAAAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 35 0.88
45 5 0.12
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (45 bp):
TCAAATAAAATTCTATTTTATTACATAAAATAATATCAAAATAAC
Found at i:46619229 original size:18 final size:18
Alignment explanation
Indices: 46619206--46619240 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
46619196 CGGAAAAGGA
*
46619206 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
46619224 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
46619241 AAACGCACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:46619891 original size:7 final size:7
Alignment explanation
Indices: 46619879--46619910 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
46619869 TTATACACAT
46619879 AATACTA
1 AATACTA
46619886 AATACTA
1 AATACTA
46619893 AATACTA
1 AATACTA
46619900 AATACTA
1 AATACTA
46619907 AATA
1 AATA
46619911 TCGATCCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:46620118 original size:20 final size:20
Alignment explanation
Indices: 46620081--46620118 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
46620071 TTTATTTTTA
*
46620081 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
46620101 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
46620119 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:46621076 original size:11 final size:11
Alignment explanation
Indices: 46621060--46621090 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
46621050 AAAAAAGGAG
46621060 TTAAGAGAAAC
1 TTAAGAGAAAC
*
46621071 TTAAGAGGAAC
1 TTAAGAGAAAC
46621082 TTAAGAGAA
1 TTAAGAGAA
46621091 TTTTTGAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (11 bp):
TTAAGAGAAAC
Found at i:46621722 original size:29 final size:28
Alignment explanation
Indices: 46621674--46621746 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
46621664 TTAAATTTAT
**
46621674 TAAAAAATATTAAAA-ATTATAAAAGTCA
1 TAAAAAATA-TAAAATATTATAAAAACCA
*
46621702 TAAAAGAATATAAAATTTTATAAAAACCA
1 TAAAA-AATATAAAATATTATAAAAACCA
46621731 TAAAAAATTATAAAAT
1 TAAAAAA-TATAAAAT
46621747 GCATCAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 12 0.31
29 27 0.69
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (28 bp):
TAAAAAATATAAAATATTATAAAAACCA
Found at i:46623319 original size:3 final size:3
Alignment explanation
Indices: 46623311--46623367 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
46623301 GTTGTGGTTT
46623311 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
46623359 ATA ATA ATA
1 ATA ATA ATA
46623368 GGGTTAAATG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:46625200 original size:9 final size:9
Alignment explanation
Indices: 46625186--46625210 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
46625176 GATATAGAAA
46625186 TAACATGTT
1 TAACATGTT
46625195 TAACATGTT
1 TAACATGTT
46625204 TAACATG
1 TAACATG
46625211 CTTGTATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (9 bp):
TAACATGTT
Found at i:46626153 original size:10 final size:11
Alignment explanation
Indices: 46626128--46626157 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
46626118 ACTTTGAAAA
46626128 AAAAATAAATT
1 AAAAATAAATT
46626139 AAAAATAAATT
1 AAAAATAAATT
46626150 AAAAATAA
1 AAAAATAA
46626158 TATAATCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAATAAATT
Found at i:46626159 original size:25 final size:25
Alignment explanation
Indices: 46626125--46626172 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
46626115 AGAACTTTGA
46626125 AAAAAAAATA-AATTAAAAATAAATT
1 AAAAAAAATATAA-TAAAAATAAATT
* *
46626150 AAAAATAATATAATCAAAATAAA
1 AAAAAAAATATAATAAAAATAAA
46626173 CCCCTCCCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (25 bp):
AAAAAAAATATAATAAAAATAAATT
Found at i:46631702 original size:20 final size:20
Alignment explanation
Indices: 46631664--46631702 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
46631654 TTAAAAGTTT
* *
46631664 ATAAAAGAAATTGTAAAAAG
1 ATAAAAAAAATTATAAAAAG
46631684 ATAAAAAAAATTATTAAAA
1 ATAAAAAAAATTA-TAAAA
46631703 TTTTACAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (20 bp):
ATAAAAAAAATTATAAAAAG
Found at i:46631918 original size:20 final size:20
Alignment explanation
Indices: 46631873--46631909 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46631863 AAATCTCTCC
46631873 AAAT-TACAAAATATAAAAT
1 AAATATACAAAATATAAAAT
*
46631892 AAATATACAAATTATAAA
1 AAATATACAAAATATAAA
46631910 TTTAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATATACAAAATATAAAAT
Found at i:46634570 original size:17 final size:17
Alignment explanation
Indices: 46634538--46634571 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
46634528 AATAGAAAAA
46634538 TAAGCATTTATTTTAAT
1 TAAGCATTTATTTTAAT
46634555 TAAG-ATTTATTATTAAT
1 TAAGCATTTATT-TTAAT
46634572 AAATAATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (17 bp):
TAAGCATTTATTTTAAT
Found at i:46660612 original size:2 final size:2
Alignment explanation
Indices: 46660605--46660648 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
46660595 TTGCAATGGA
46660605 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
46660647 TC
1 TC
46660649 AATGAATACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:46664479 original size:21 final size:21
Alignment explanation
Indices: 46664453--46664496 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
46664443 TATAAAGTGC
46664453 GCTGCTCATTCAACATTCATA
1 GCTGCTCATTCAACATTCATA
46664474 GCTGCTCATTCAACATTCATA
1 GCTGCTCATTCAACATTCATA
46664495 GC
1 GC
46664497 ATCTGTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (21 bp):
GCTGCTCATTCAACATTCATA
Found at i:46666631 original size:18 final size:18
Alignment explanation
Indices: 46666608--46666650 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
46666598 TTAATTTCAG
*
46666608 CATGCTGCCAGTCAAGAT
1 CATGCTGCCAATCAAGAT
**
46666626 CATGCTGTTAATCAAGAT
1 CATGCTGCCAATCAAGAT
46666644 CATGCTG
1 CATGCTG
46666651 GTCTTGCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (18 bp):
CATGCTGCCAATCAAGAT
Found at i:46674818 original size:27 final size:27
Alignment explanation
Indices: 46674788--46674839 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
46674778 TTTCCTTCCT
**
46674788 TAGATCGCCACAAAGGCTTCCATTTCA
1 TAGATCGCCACAAAAACTTCCATTTCA
*
46674815 TAGATTGCCACAAAAACTTCCATTT
1 TAGATCGCCACAAAAACTTCCATTT
46674840 TCTAACGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.29
Consensus pattern (27 bp):
TAGATCGCCACAAAAACTTCCATTTCA
Found at i:46675565 original size:25 final size:25
Alignment explanation
Indices: 46675532--46675588 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 25
46675522 AAATAAAGCC
*
46675532 TTACCTTTTCATACATTCAAACAAT
1 TTACTTTTTCATACATTCAAACAAT
*
46675557 TTACTTTTTCATACATTCAAGCAAT
1 TTACTTTTTCATACATTCAAACAAT
46675582 TCTACTT
1 T-TACTT
46675589 GTAAGGCCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 24 0.83
26 5 0.17
ACGTcount: A:0.32, C:0.23, G:0.02, T:0.44
Consensus pattern (25 bp):
TTACTTTTTCATACATTCAAACAAT
Found at i:46680212 original size:7 final size:7
Alignment explanation
Indices: 46680200--46680240 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
46680190 AGAGTATTGA
46680200 ATGAAAT
1 ATGAAAT
46680207 ATGAAAT
1 ATGAAAT
46680214 ATGAAAT
1 ATGAAAT
46680221 ATGAAAT
1 ATGAAAT
46680228 ATGAAAT
1 ATGAAAT
46680235 ATGAAA
1 ATGAAA
46680241 AAGATTCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.27
Consensus pattern (7 bp):
ATGAAAT
Found at i:46680912 original size:22 final size:20
Alignment explanation
Indices: 46680884--46680926 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
46680874 CCCCGAGCAA
46680884 CTTTAAAATGATTTTAAATTAT
1 CTTTAAAAT-ATTTT-AATTAT
*
46680906 CTTTAAAATCTTTTAATTAT
1 CTTTAAAATATTTTAATTAT
46680926 C
1 C
46680927 CAAAACTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 4 0.20
22 9 0.45
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.51
Consensus pattern (20 bp):
CTTTAAAATATTTTAATTAT
Found at i:46681354 original size:41 final size:41
Alignment explanation
Indices: 46681309--46681393 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
46681299 AATGAGATGT
*
46681309 TTATGTTTGTTTTGGCTTGAACCTGTGTCAAACAATCTGGG
1 TTATGTTTGTTTTGGCTTGAACCCGTGTCAAACAATCTGGG
46681350 TTATGTTTGTTTTGGCTTGAACCCGTGTCAAACAATCTGGG
1 TTATGTTTGTTTTGGCTTGAACCCGTGTCAAACAATCTGGG
46681391 TTA
1 TTA
46681394 GAGCCTAAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (41 bp):
TTATGTTTGTTTTGGCTTGAACCCGTGTCAAACAATCTGGG
Found at i:46682090 original size:63 final size:63
Alignment explanation
Indices: 46682013--46682141 Score: 231
Period size: 63 Copynumber: 2.0 Consensus size: 63
46682003 TCTTTTACTC
*
46682013 CATTGATTATAGATAAGATAATAATCATTGTTTTTTATATACTAAAAAAGTTAATATATATTA
1 CATTGATTATAGATAAGATAATAATCATTGTTTTTTATATACTAAAAAAGTTAATATATATCA
* *
46682076 CATTGATTATAGATAAGGTAATAATCATTGTTTTTTATATATTAAAAAAGTTAATATATATCA
1 CATTGATTATAGATAAGATAATAATCATTGTTTTTTATATACTAAAAAAGTTAATATATATCA
46682139 CAT
1 CAT
46682142 CATGTCATAC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (63 bp):
CATTGATTATAGATAAGATAATAATCATTGTTTTTTATATACTAAAAAAGTTAATATATATCA
Found at i:46685654 original size:19 final size:19
Alignment explanation
Indices: 46685627--46685669 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
46685617 TTTTATAATG
*
46685627 TTTTTTATTGCAAT-TTTAA
1 TTTTATATTGC-ATGTTTAA
*
46685646 TTTTATATTTCATGTTTAA
1 TTTTATATTGCATGTTTAA
46685665 TTTTA
1 TTTTA
46685670 GTTTTTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTATATTGCATGTTTAA
Found at i:46689010 original size:25 final size:25
Alignment explanation
Indices: 46688982--46689044 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
46688972 TCCACCGCTC
*
46688982 GTGAGAGCATACCAATTTATAGCTA
1 GTGAGAGCATACCAATCTATAGCTA
* *
46689007 GTGAGAGCATACCGATCTATAGCTC
1 GTGAGAGCATACCAATCTATAGCTA
* *
46689032 GAGTGAGCATACC
1 GTGAGAGCATACC
46689045 GATTCACAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (25 bp):
GTGAGAGCATACCAATCTATAGCTA
Found at i:46689045 original size:25 final size:24
Alignment explanation
Indices: 46688986--46689068 Score: 78
Period size: 25 Copynumber: 3.3 Consensus size: 24
46688976 CCGCTCGTGA
* * * *
46688986 GAGCATACCAATTTATAGCTAGTGA
1 GAGCATACCGA-TTATAGCTCGAGT
46689011 GAGCATACCGATCTATAGCTCGAGT
1 GAGCATACCGAT-TATAGCTCGAGT
*
46689036 GAGCATACCGATTCACAGCTCGTA-T
1 GAGCATACCGATT-ATAGCTCG-AGT
46689061 GAGCATAC
1 GAGCATAC
46689069 ATGTACATGA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
24 2 0.04
25 47 0.94
26 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (24 bp):
GAGCATACCGATTATAGCTCGAGT
Found at i:46689257 original size:31 final size:32
Alignment explanation
Indices: 46689222--46689283 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
46689212 TTTACATGAA
*
46689222 ATACATGGAAAT-GATTTTACATG-ATATATAG
1 ATACAT-GAAATGGATGTTACATGTATATATAG
*
46689253 ATACATGATATGGATGTTACATGTATATATA
1 ATACATGAAATGGATGTTACATGTATATATA
46689284 AACTTGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 4 0.15
31 16 0.59
32 7 0.26
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.37
Consensus pattern (32 bp):
ATACATGAAATGGATGTTACATGTATATATAG
Found at i:46693266 original size:19 final size:19
Alignment explanation
Indices: 46693226--46693270 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
46693216 ATTAGAAAAA
* *
46693226 TATAAAAATCGTAAAATTT
1 TATAAAAACCGTAAAATAT
46693245 TATAAAAACCGTAAGAA-AT
1 TATAAAAACCGTAA-AATAT
46693264 TATAAAA
1 TATAAAA
46693271 TATATAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.29
Consensus pattern (19 bp):
TATAAAAACCGTAAAATAT
Found at i:46693288 original size:18 final size:18
Alignment explanation
Indices: 46693258--46693299 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
46693248 AAAAACCGTA
*
46693258 AGAAATTATAAAATATAT
1 AGAAATTATAAAAAATAT
46693276 AGAAA-TATAAAAAAATAT
1 AGAAATTAT-AAAAAATAT
46693294 A-AAATT
1 AGAAATT
46693300 TTATAAAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (18 bp):
AGAAATTATAAAAAATAT
Found at i:46693297 original size:56 final size:55
Alignment explanation
Indices: 46693203--46693329 Score: 150
Period size: 56 Copynumber: 2.3 Consensus size: 55
46693193 TCAAATATTA
* *
46693203 AAAATTATTAAAAATTAGAAAAATATAAAAATCGTAAAATTTTATAAAAACCGTAAG
1 AAAATTA-TAAAAATTAGAAAAATAAAAAAATCATAAAATTTTAT-AAAACCGTAAG
* **
46693260 -AAATTATAAAATATATAGAAATATAAAAAAAT-ATAAAATTTTATAAAGTCGTAAG
1 AAAATTATAAAA-AT-TAGAAAAATAAAAAAATCATAAAATTTTATAAAACCGTAAG
46693315 AAAATTATACAAAAT
1 AAAATTATA-AAAAT
46693330 GTAAAGATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
55 14 0.23
56 29 0.48
57 18 0.30
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.29
Consensus pattern (55 bp):
AAAATTATAAAAATTAGAAAAATAAAAAAATCATAAAATTTTATAAAACCGTAAG
Found at i:46693318 original size:28 final size:28
Alignment explanation
Indices: 46693237--46693319 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 28
46693227 ATAAAAATCG
* *
46693237 TAAAATTTTATAAAAACCGTAAGAAATTA
1 TAAAATTTTAT-AAAATCGTAAGAAAATA
* * *
46693266 TAAAA-TATATAGAAAT-ATAAAAAAATA
1 TAAAATTTTATA-AAATCGTAAGAAAATA
*
46693293 TAAAATTTTATAAAGTCGTAAGAAAAT
1 TAAAATTTTATAAAATCGTAAGAAAAT
46693320 TATACAAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
27 17 0.40
28 20 0.48
29 5 0.12
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (28 bp):
TAAAATTTTATAAAATCGTAAGAAAATA
Found at i:46693764 original size:90 final size:92
Alignment explanation
Indices: 46693626--46693802 Score: 245
Period size: 90 Copynumber: 1.9 Consensus size: 92
46693616 GCTTAATTGC
* * *
46693626 TATTTTGAAAAATTTTGAGGCTCTTTTTGATGCACTTTGAAAGTTCAAGTACTCAATTGAGTG-A
1 TATTTTGAAAAAGTTTAAGGCTCTTTTTGATACACTTTGAAAGTTCAAGTACTCAATTGAGTGAA
*
46693690 -AAAAAAATAGGGGCTTAATTGCTTTT
66 GAAAAAAAAAGGGGCTTAATTGCTTTT
* *
46693716 TATTTTGAAGAAGTTTAAGGGC-CTTTTTGATACA-TGTTGAAAGTTCAAGTGCTCAATTGAGTG
1 TATTTTGAAAAAGTTTAA-GGCTCTTTTTGATACACT-TTGAAAGTTCAAGTACTCAATTGAGTG
46693779 CAAGAAAAAAAAAGGGGCTTAATT
64 -AAGAAAAAAAAAGGGGCTTAATT
46693803 ATTATTATTT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
89 1 0.01
90 52 0.68
91 3 0.04
92 1 0.01
93 19 0.25
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.36
Consensus pattern (92 bp):
TATTTTGAAAAAGTTTAAGGCTCTTTTTGATACACTTTGAAAGTTCAAGTACTCAATTGAGTGAA
GAAAAAAAAAGGGGCTTAATTGCTTTT
Found at i:46709848 original size:17 final size:17
Alignment explanation
Indices: 46709828--46709925 Score: 62
Period size: 17 Copynumber: 5.8 Consensus size: 17
46709818 TATTTTAATA
46709828 AATTTAATATTTAATTT
1 AATTTAATATTTAATTT
*
46709845 AATTTAATACTT-ATCTT
1 AATTTAATATTTAAT-TT
* *
46709862 GATTT--TATTTTA-TT
1 AATTTAATATTTAATTT
*
46709876 AATTTAATATTAAAATGATT
1 AATTTAATATT-TAAT--TT
* *
46709896 -ATCTTATTATTAAATTT
1 AAT-TTAATATTTAATTT
46709913 AATTTAATATTTA
1 AATTTAATATTTA
46709926 TCTTTTAGAT
Statistics
Matches: 62, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
14 6 0.10
15 4 0.06
16 7 0.11
17 28 0.45
18 2 0.03
19 6 0.10
20 9 0.15
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (17 bp):
AATTTAATATTTAATTT
Found at i:46709973 original size:61 final size:58
Alignment explanation
Indices: 46709903--46710015 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
46709893 ATTATCTTAT
* * *
46709903 TATTAAATTTAATTTAATATTTATCTTTTAGATAAATATTCTATTAATTTAATATATTTAA
1 TATTAAATTTAATCTAATACTTATC--TT-GATAAATATTATATTAATTTAATATATTTAA
* * *
46709964 TATTGAATTTAATCTAATACTTATCTTGATAAGTTTTATATTAATTTAATAT
1 TATTAAATTTAATCTAATACTTATCTTGATAAATATTATATTAATTTAATAT
46710016 TGAAGTGATT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 22 0.48
59 2 0.04
61 22 0.48
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (58 bp):
TATTAAATTTAATCTAATACTTATCTTGATAAATATTATATTAATTTAATATATTTAA
Found at i:46712781 original size:67 final size:69
Alignment explanation
Indices: 46712687--46712815 Score: 201
Period size: 68 Copynumber: 1.9 Consensus size: 69
46712677 TTTAATAAAT
*
46712687 TTAATATTAAATTTAATTTAATACTTATCTTGAT-AGTATT-TTATTAACTTAATATTAAAGTAA
1 TTAATATTAAATTTAATTTAATACTTATATTGATAAGTATTATT-TTAACTTAATATTAAAGTAA
46712750 GTATC
65 GTATC
* *
46712755 TTAATATT-AATTTAGTTTAATACTTATATTGATAAGTATTATTTTAATTTAATATTAAAGT
1 TTAATATTAAATTTAATTTAATACTTATATTGATAAGTATTATTTTAACTTAATATTAAAGT
46712816 TATTAAGTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
67 23 0.41
68 31 0.55
69 2 0.04
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (69 bp):
TTAATATTAAATTTAATTTAATACTTATATTGATAAGTATTATTTTAACTTAATATTAAAGTAAG
TATC
Found at i:46717398 original size:32 final size:32
Alignment explanation
Indices: 46717362--46717424 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
46717352 TTTGTTATTT
46717362 TTTATTAATTAAGTTTACTAATTACTTGTAGC
1 TTTATTAATTAAGTTTACTAATTACTTGTAGC
*
46717394 TTTATTAATTAAGTTTACTAATTTCTTGTAG
1 TTTATTAATTAAGTTTACTAATTACTTGTAG
46717425 ATTTCAATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52
Consensus pattern (32 bp):
TTTATTAATTAAGTTTACTAATTACTTGTAGC
Found at i:46718552 original size:5 final size:5
Alignment explanation
Indices: 46718542--46718567 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
46718532 CTACTTTAGA
46718542 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
46718568 ATTTTTTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:46721309 original size:34 final size:34
Alignment explanation
Indices: 46721266--46721332 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
46721256 GTTAGGAGTA
*
46721266 TTACATTTAGTGGTATCAGAGCTTCAATTTAGTG
1 TTACATTTAGTGGTATCAAAGCTTCAATTTAGTG
*
46721300 TTACATTTAGTGGTATCAAAGCTTCGATTTAGT
1 TTACATTTAGTGGTATCAAAGCTTCAATTTAGT
46721333 CGATTCTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (34 bp):
TTACATTTAGTGGTATCAAAGCTTCAATTTAGTG
Found at i:46727579 original size:107 final size:107
Alignment explanation
Indices: 46727383--46727584 Score: 264
Period size: 107 Copynumber: 1.9 Consensus size: 107
46727373 TAGTGTTTAA
* * * **
46727383 ATGTAAGACCATAGCTGGGCTATGGCATTTTAATTAAAAGACCATAACTGGGTTATGGCACCTTG
1 ATGTAAGACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGGGTTATGGCAACTCA
**
46727448 AACATAAGACCATGGTTGGACCATGGCAATATATATATATAT
66 AACATAAGACCATGGAAGGACCATGGCAATATATATATATAT
* * *
46727490 ATGTAAGACCATAGCTGGGCTGTGGCATTCTGATGATAAGACCATAACTGGGTTATGG-AACTAC
1 ATGTAAGACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGGGTTATGGCAACT-C
* *
46727554 AAACGTAAGACCATGGCAAGG-CCATGTCAAT
65 AAACATAAGACCATGG-AAGGACCATGGCAAT
46727585 GCATGTGTAA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
106 3 0.04
107 76 0.94
108 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (107 bp):
ATGTAAGACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGGGTTATGGCAACTCA
AACATAAGACCATGGAAGGACCATGGCAATATATATATATAT
Found at i:46736776 original size:26 final size:26
Alignment explanation
Indices: 46736744--46736817 Score: 105
Period size: 26 Copynumber: 2.8 Consensus size: 26
46736734 ACGCACCAAC
46736744 ATCGCAGTAAAGCTGCCAGTAATAGT
1 ATCGCAGTAAAGCTGCCAGTAATAGT
* * *
46736770 ATTGCAGCAAGGCTGCCAGTAATAGT
1 ATCGCAGTAAAGCTGCCAGTAATAGT
46736796 ATCGCAGT-AAGTCTGCCAGTAA
1 ATCGCAGTAAAG-CTGCCAGTAA
46736818 CAATATATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 2 0.05
26 39 0.95
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.23
Consensus pattern (26 bp):
ATCGCAGTAAAGCTGCCAGTAATAGT
Found at i:46737017 original size:27 final size:27
Alignment explanation
Indices: 46736987--46737045 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
46736977 AATCTTCTAG
*
46736987 GGGTACAACAGTCATTTTACCCTATGA
1 GGGTACAACAGTCATTTTACCCTACGA
*** *
46737014 GGGTATTTCGGTCATTTTACCCTACGA
1 GGGTACAACAGTCATTTTACCCTACGA
46737041 GGGTA
1 GGGTA
46737046 TTTCGGTTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (27 bp):
GGGTACAACAGTCATTTTACCCTACGA
Found at i:46737059 original size:27 final size:27
Alignment explanation
Indices: 46736997--46737052 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
46736987 GGGTACAACA
*
46736997 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTACGAGGGTATTTCG
46737024 GTCATTTTACCCTACGAGGGTATTTCG
1 GTCATTTTACCCTACGAGGGTATTTCG
46737051 GT
1 GT
46737053 TGTTTTATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (27 bp):
GTCATTTTACCCTACGAGGGTATTTCG
Found at i:46748241 original size:21 final size:21
Alignment explanation
Indices: 46748207--46748259 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
46748197 GTTGTAAGAC
*
46748207 ATTTCTAGATTTAGTTTAATGT
1 ATTTC-AGTTTTAGTTTAATGT
46748229 ATTTCAGTTTTAGTTTAATGT
1 ATTTCAGTTTTAGTTTAATGT
46748250 ATTTCAGTTT
1 ATTTCAGTTT
46748260 CTTTTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.25, C:0.06, G:0.13, T:0.57
Consensus pattern (21 bp):
ATTTCAGTTTTAGTTTAATGT
Found at i:46752865 original size:70 final size:70
Alignment explanation
Indices: 46752700--46752853 Score: 281
Period size: 70 Copynumber: 2.2 Consensus size: 70
46752690 GGTATATGGC
* **
46752700 ATGTATAGGCTAGTGTCAATAGGATACATTTTGAGATATGAAATTAGTTATGTGAGTTGGCTTGT
1 ATGTATAGGCTAGTGTCAATAGGATACGTTTTGAGATATGAAATTAGCCATGTGAGTTGGCTTGT
46752765 AAATG
66 AAATG
46752770 ATGTATAGGCTAGTGTCAATAGGATACGTTTTGAGATATGAAATTAGCCATGTGAGTTGGCTTGT
1 ATGTATAGGCTAGTGTCAATAGGATACGTTTTGAGATATGAAATTAGCCATGTGAGTTGGCTTGT
46752835 AAATG
66 AAATG
46752840 ATGTATAGGCTAGT
1 ATGTATAGGCTAGT
46752854 TTATTATGGA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 81 1.00
ACGTcount: A:0.31, C:0.07, G:0.27, T:0.36
Consensus pattern (70 bp):
ATGTATAGGCTAGTGTCAATAGGATACGTTTTGAGATATGAAATTAGCCATGTGAGTTGGCTTGT
AAATG
Found at i:46755017 original size:29 final size:29
Alignment explanation
Indices: 46754975--46755033 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
46754965 TTATTGATAG
46754975 TAAGGGTCGATTCTAGGTAATCCCGACCT
1 TAAGGGTCGATTCTAGGTAATCCCGACCT
*
46755004 TAAGGGTCGATTCTGGGTAATCCCGACCT
1 TAAGGGTCGATTCTAGGTAATCCCGACCT
46755033 T
1 T
46755034 CCGAATCAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (29 bp):
TAAGGGTCGATTCTAGGTAATCCCGACCT
Found at i:46759760 original size:20 final size:21
Alignment explanation
Indices: 46759720--46759765 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
46759710 GTATAAATAC
46759720 CCCCTTTTTATGTGTAATTTG
1 CCCCTTTTTATGTGTAATTTG
* *
46759741 CCCCTTTTTTTG-GTATTTTG
1 CCCCTTTTTATGTGTAATTTG
46759761 CCCCT
1 CCCCT
46759766 AATAATACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.09, C:0.26, G:0.13, T:0.52
Consensus pattern (21 bp):
CCCCTTTTTATGTGTAATTTG
Found at i:46768532 original size:26 final size:26
Alignment explanation
Indices: 46768502--46768554 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
46768492 TATGATAGTA
46768502 TGACTTTGGAAGATTATACACTTAAC
1 TGACTTTGGAAGATTATACACTTAAC
46768528 TGACTTTGGAAGATTATACACTTAAC
1 TGACTTTGGAAGATTATACACTTAAC
46768554 T
1 T
46768555 AATCTTTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (26 bp):
TGACTTTGGAAGATTATACACTTAAC
Found at i:46770528 original size:3 final size:3
Alignment explanation
Indices: 46770522--46770554 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
46770512 ATAAAATCTC
46770522 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
46770555 TTGGGAAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
CTG
Found at i:46782598 original size:3 final size:3
Alignment explanation
Indices: 46782590--46782627 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
46782580 TAATATAGGG
46782590 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
46782628 TAATAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:46782724 original size:17 final size:17
Alignment explanation
Indices: 46782698--46782735 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
46782688 GTAGTAAAAG
*
46782698 TAAAATAAAA-AATACAA
1 TAAAAGAAAATAATA-AA
46782715 TAAAAGAAAATAATAAA
1 TAAAAGAAAATAATAAA
46782732 TAAA
1 TAAA
46782736 TGTGAAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (17 bp):
TAAAAGAAAATAATAAA
Found at i:46783682 original size:16 final size:17
Alignment explanation
Indices: 46783663--46783695 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
46783653 TAAACAGAAT
*
46783663 AAACAGA-AAACGAAAA
1 AAACAGAGAAAAGAAAA
46783679 AAACAGAGAAAAGAAAA
1 AAACAGAGAAAAGAAAA
46783696 GAGAGCAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (17 bp):
AAACAGAGAAAAGAAAA
Found at i:46784475 original size:41 final size:41
Alignment explanation
Indices: 46784372--46784624 Score: 155
Period size: 41 Copynumber: 5.8 Consensus size: 41
46784362 AGTAGCTTTA
* * * * *
46784372 ATCTGCTCCACTGCAACTCCAGGGATATAAGATTGGTATATTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTG-ATA-T-G
* * *
46784416 ACCTGCTCCATTACAACTTCAGGGAGATAAGGTTTGATATG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGATATG
** * * *
46784457 ATCTGCTTTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAG----GT--TTGATA---T-G
* * * * * *
46784508 ATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTG--AT-ATG
*
46784552 AGTCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGATATG
1 A-TCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGATATG
* *
46784594 ATCTGCTCTACTGCAACTTCAGAGAGATAAG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAG
46784625 ATCTGCAATT
Statistics
Matches: 159, Mismatches: 36, Indels: 31
0.70 0.16 0.14
Matches are distributed among these distances:
41 52 0.33
42 3 0.02
43 5 0.03
44 30 0.19
45 34 0.21
47 8 0.05
50 1 0.01
51 26 0.16
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (41 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGATATG
Found at i:46784571 original size:45 final size:45
Alignment explanation
Indices: 46784371--46785218 Score: 311
Period size: 44 Copynumber: 18.8 Consensus size: 45
46784361 TAGTAGCTTT
* * * *
46784371 AATCTGCTCCACTGCAACTCCAGGGATATAAGATT-GGTATATTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* * * * * * *
46784415 AACCTGCTCCATTACAACTTCAGGGAGATAAGGTTTG--AT-AT-
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* ** * * *
46784456 GATCTGCTTTACTGCAACTTCAGAGAGATAAGA-TCTGTAATTTATAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTC-G----CTAT--CTTC
*
46784507 AATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* * * * * *
46784552 AGTCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTG--AT-AT-
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* * * *
46784593 GATCTGCTCTACTGCAACTTCAGAGAGATAAGA-TCTGCAATTTATAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTC-GC----TAT--CTTC
* * * * *
46784644 AATTTGTTTCACTGCAACTTCAGGGGAATAAGATTCACTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* * * *
46784689 AGTCTGTTCCACTGCAACTTCAGAGAAATAAGACTT-G-TAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGA-TTCGCTATCTTC
* * * * * * * *
46784733 AACCCGCTCCACTACAAATTCAGGGAGATAAGGTTTG--AT-AT-
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* * *
46784774 GATCTGCTCTACTGCAACTTCA-GAAAGATAAGA-TCTGCAATTTATAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAA-ATAAGATTC-GC----TAT--CTTC
* * * * *
46784825 AATTTGTTTCACTGCAATTTCAGGGAAATAAGATTCACTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* * * *
46784870 AGTCTCCTCCACTGCAACTTCAGGGAAATAAGACTT-G-TAACTAC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGA-TTCGCTATCTTC
* * * * * *
46784914 AA-CTGGCTCCACTACAACTTCAAGGAGATAAGGCTT-AC-AACTTC
1 AATCT-GCTCCACTGCAACTTCAGGGAAATAA-GATTCGCTATCTTC
* * * * *
46784958 AACCTGCTCCACTGTAACTTCAAGGAGATAACG-TTTGCTA---T-
1 AATCTGCTCCACTGCAACTTCAGGGAAATAA-GATTCGCTATCTTC
* ** * * *
46784999 GATCTGCTCCACTGCAACTTCAGATAGATAAGA-TCTGTTATTTAGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTC-GCTA--T--CTTC
* * * *
46785048 AATCCGTTCCACTACAACTTCAGGGAAATAATATTCGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* * ** * * *
46785093 AGTCTGCTCCACTGCAACTTCGGGGAGCTAAGAGTAG-TAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* * * * * * **
46785137 AACCTGTTCCACTGCAACTTCAGGGAGATACGACTAG-TGGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* * * *
46785181 AATCTACTCCACTACAACTTCAAGGAGATAAGATTCGC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGC
46785219 CATGATGACT
Statistics
Matches: 592, Mismatches: 152, Indels: 119
0.69 0.18 0.14
Matches are distributed among these distances:
40 7 0.01
41 104 0.18
42 4 0.01
43 11 0.02
44 193 0.33
45 133 0.22
46 4 0.01
47 16 0.03
48 1 0.00
49 28 0.05
50 5 0.01
51 77 0.13
52 9 0.02
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
Found at i:46784609 original size:137 final size:137
Alignment explanation
Indices: 46784364--46784720 Score: 527
Period size: 137 Copynumber: 2.6 Consensus size: 137
46784354 CTAGAATTAG
* * * * * * ** *
46784364 TAGCTTTAATCTGCTCCACTGCAACTCCAGGGATATAAGATT-GGTATATTCAACCTGCTCCATT
1 TAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACT
* *
46784428 ACAACTTCAGGGAGATAAGGTTTGATATGATCTGCTTTACTGCAACTTCAGAGAGATAAGATCTG
66 GCAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTG
*
46784493 TAATTTA
131 CAATTTA
46784500 TAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACT
1 TAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACT
*
46784565 GTAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTG
66 GCAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTG
46784630 CAATTTA
131 CAATTTA
* * * * *
46784637 TAGCTTCAATTTGTTTCACTGCAACTTCAGGGGAATAAGATTCACTATCTTCAGTCTGTTCCACT
1 TAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACT
* *
46784702 GCAACTTCAGAGAAATAAG
66 GCAACTTCAGGGAGATAAG
46784721 ACTTGTAACT
Statistics
Matches: 199, Mismatches: 21, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
136 38 0.19
137 161 0.81
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (137 bp):
TAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACT
GCAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTG
CAATTTA
Found at i:46784675 original size:92 final size:92
Alignment explanation
Indices: 46784561--46784856 Score: 313
Period size: 92 Copynumber: 3.2 Consensus size: 92
46784551 CAGTCTGCTC
*
46784561 CACTGTAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGA
1 CACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGA
46784626 TCTGCAATTTATAGCTTCAATTTGTTT
66 TCTGCAATTTATAGCTTCAATTTGTTT
* * * * * *
46784653 CACTGCAACTTCAGGG-GAATAAGATTCACT-ATCTTCAGTCTGTTCCACTGCAACTTCAGAGAA
1 CACTGCAACTTCAGGGAG-ATAAGGTT---TGAT-ATGA-TCTGCTCTACTGCAACTTCAGAGAG
* *** * *
46784716 ATAAGA-CT----TGTA-A-CTTCAACCCGCTC
60 ATAAGATCTGCAATTTATAGCTTCAATTTGTTT
* * *
46784742 CACTACAAATTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAAAGATAAGA
1 CACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGA
46784807 TCTGCAATTTATAGCTTCAATTTGTTT
66 TCTGCAATTTATAGCTTCAATTTGTTT
* *
46784834 CACTGCAATTTCAGGGAAATAAG
1 CACTGCAACTTCAGGGAGATAAG
46784857 ATTCACTATC
Statistics
Matches: 158, Mismatches: 31, Indels: 30
0.72 0.14 0.14
Matches are distributed among these distances:
85 27 0.17
86 5 0.03
87 2 0.01
89 29 0.18
90 5 0.03
91 5 0.03
92 50 0.32
94 2 0.01
95 5 0.03
96 28 0.18
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (92 bp):
CACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGA
TCTGCAATTTATAGCTTCAATTTGTTT
Found at i:46784772 original size:181 final size:181
Alignment explanation
Indices: 46784503--46784946 Score: 701
Period size: 181 Copynumber: 2.4 Consensus size: 181
46784493 TAATTTATAG
* * ** * **
46784503 CTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGA-TTCGCTATCTTCAGTCTGCTCCACTGT
1 CTTCAGTCTGTTCCACTGCAACTTCAGGGAAATAAGACTT-G-TAACTTCAACCCGCTCCACTAC
*
46784567 AACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCA
64 AACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAAAGATAAGATCTGCA
*
46784632 ATTTATAGCTTCAATTTGTTTCACTGCAACTTCAGGGGAATAAGATTCACTAT
129 ATTTATAGCTTCAATTTGTTTCACTGCAACTTCAGGGAAATAAGATTCACTAT
*
46784685 CTTCAGTCTGTTCCACTGCAACTTCAGAGAAATAAGACTTGTAACTTCAACCCGCTCCACTACAA
1 CTTCAGTCTGTTCCACTGCAACTTCAGGGAAATAAGACTTGTAACTTCAACCCGCTCCACTACAA
*
46784750 ATTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAAAGATAAGATCTGCAAT
66 CTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAAAGATAAGATCTGCAAT
*
46784815 TTATAGCTTCAATTTGTTTCACTGCAATTTCAGGGAAATAAGATTCACTAT
131 TTATAGCTTCAATTTGTTTCACTGCAACTTCAGGGAAATAAGATTCACTAT
** * **
46784866 CTTCAGTCTCCTCCACTGCAACTTCAGGGAAATAAGACTTGTAACTACAACTGGCTCCACTACAA
1 CTTCAGTCTGTTCCACTGCAACTTCAGGGAAATAAGACTTGTAACTTCAACCCGCTCCACTACAA
*
46784931 CTTCAAGGAGATAAGG
66 CTTCAGGGAGATAAGG
46784947 CTTACAACTT
Statistics
Matches: 241, Mismatches: 20, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
181 203 0.84
182 36 0.15
183 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (181 bp):
CTTCAGTCTGTTCCACTGCAACTTCAGGGAAATAAGACTTGTAACTTCAACCCGCTCCACTACAA
CTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAAAGATAAGATCTGCAAT
TTATAGCTTCAATTTGTTTCACTGCAACTTCAGGGAAATAAGATTCACTAT
Found at i:46784902 original size:96 final size:96
Alignment explanation
Indices: 46784595--46784902 Score: 327
Period size: 96 Copynumber: 3.3 Consensus size: 96
46784585 TTTGATATGA
* *
46784595 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTATAGCTTCAATTTGTTTCACTGCA
1 TCTGCTCCACTGCAACTTCAGAGAAATAAGATCTGCAATTTATAGCTTCAATTTGTTTCACTGCA
* *
46784660 ACTTCAGGGGAATAAGATTCACTATCTTCAG
66 AATTCAGGGAAATAAGATTCACTATCTTCAG
* * *** * * *
46784691 TCTGTTCCACTGCAACTTCAGAGAAATAAGA-CT----TGTA-A-CTTCAACCCGCTCCACTACA
1 TCTGCTCCACTGCAACTTCAGAGAAATAAGATCTGCAATTTATAGCTTCAATTTGTTTCACTGCA
* * * *
46784749 AATTCAGGGAGATAAGGTT---TGAT-ATGA-
66 AATTCAGGGAAATAAGATTCACT-ATCTTCAG
*
46784776 TCTGCTCTACTGCAACTTCAGA-AAGATAAGATCTGCAATTTATAGCTTCAATTTGTTTCACTGC
1 TCTGCTCCACTGCAACTTCAGAGAA-ATAAGATCTGCAATTTATAGCTTCAATTTGTTTCACTGC
*
46784840 AATTTCAGGGAAATAAGATTCACTATCTTCAG
65 AAATTCAGGGAAATAAGATTCACTATCTTCAG
* *
46784872 TCTCCTCCACTGCAACTTCAGGGAAATAAGA
1 TCTGCTCCACTGCAACTTCAGAGAAATAAGA
46784903 CTTGTAACTA
Statistics
Matches: 164, Mismatches: 33, Indels: 30
0.72 0.15 0.13
Matches are distributed among these distances:
84 2 0.01
85 26 0.16
86 5 0.03
87 2 0.01
89 29 0.18
90 4 0.02
91 4 0.02
92 30 0.18
94 2 0.01
95 5 0.03
96 53 0.32
97 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (96 bp):
TCTGCTCCACTGCAACTTCAGAGAAATAAGATCTGCAATTTATAGCTTCAATTTGTTTCACTGCA
AATTCAGGGAAATAAGATTCACTATCTTCAG
Found at i:46785193 original size:223 final size:224
Alignment explanation
Indices: 46784653--46785211 Score: 647
Period size: 223 Copynumber: 2.5 Consensus size: 224
46784643 CAATTTGTTT
* * * * * * * *
46784653 CACTGCAACTTCAGGGGAATAAGATTCACTATCTTCAGTCTGTTCCACTGCAACTTCAGAGAAAT
1 CACTGCAACTTCAGGGAAATAAGACT-AGTAACTACA-ACTGTTCCACTGCAACTTCAGGGAGAT
* * * * *
46784718 AAGACTTGTAACTTCAACCCGCTCCACTACAAATTCAGGGAGATAAGGTTTGATATGATCTGCTC
64 AAGACTAGTAACTTCAACCTGCTCCACTACAACTTCAAGGAGATAACGTTTGATATGATCTGCTC
* ** * * *
46784783 TACTGCAACTTCAGAAAGATAAGATCTGCAATTTATAGCTTCAATTTGTTTCACTGCAATTTCAG
129 CACTGCAACTTCAGAAAGATAAGATCTGCAATTTATAGCTTCAATCCGTTCCACTACAACTTCAG
46784848 GGAAATAAGATTCACTATCTTCAGTCTCCTC
194 GGAAATAAGATTCACTATCTTCAGTCTCCTC
* * * *
46784879 CACTGCAACTTCAGGGAAATAAGACTTGTAACTACAACTGGCTCCACTACAACTTCAAGGAGATA
1 CACTGCAACTTCAGGGAAATAAGACTAGTAACTACAACT-GTTCCACTGCAACTTCAGGGAGATA
* * ** *
46784944 AGGCTTA-CAACTTCAACCTGCTCCACTGTAACTTCAAGGAGATAACGTTTGCTATGATCTGCTC
65 AGAC-TAGTAACTTCAACCTGCTCCACTACAACTTCAAGGAGATAACGTTTGATATGATCTGCTC
* ** *
46785008 CACTGCAACTTCAGATAGATAAGATCTGTTA-TT-TAGCTTTAATCCGTTCCACTACAACTTCAG
129 CACTGCAACTTCAGAAAGATAAGATCTGCAATTTATAGCTTCAATCCGTTCCACTACAACTTCAG
* * *
46785071 GGAAATAATATTCGCTATCTTCAGTCTGCTC
194 GGAAATAAGATTCACTATCTTCAGTCTCCTC
* ** * *
46785102 CACTGCAACTTCGGGGAGCTAAGAGTAGTAACTTCAACCTGTTCCACTGCAACTTCAGGGAGATA
1 CACTGCAACTTCAGGGAAATAAGACTAGTAACTACAA-CTGTTCCACTGCAACTTCAGGGAGATA
* ** * *
46785167 CGACTAGTGGCTTCAATCTACTCCACTACAACTTCAAGGAGATAA
65 AGACTAGTAACTTCAACCTGCTCCACTACAACTTCAAGGAGATAA
46785212 GATTCGCCAT
Statistics
Matches: 276, Mismatches: 53, Indels: 11
0.81 0.16 0.03
Matches are distributed among these distances:
222 2 0.01
223 138 0.50
224 6 0.02
225 105 0.38
226 25 0.09
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (224 bp):
CACTGCAACTTCAGGGAAATAAGACTAGTAACTACAACTGTTCCACTGCAACTTCAGGGAGATAA
GACTAGTAACTTCAACCTGCTCCACTACAACTTCAAGGAGATAACGTTTGATATGATCTGCTCCA
CTGCAACTTCAGAAAGATAAGATCTGCAATTTATAGCTTCAATCCGTTCCACTACAACTTCAGGG
AAATAAGATTCACTATCTTCAGTCTCCTC
Found at i:46786105 original size:5 final size:5
Alignment explanation
Indices: 46786086--46786133 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
46786076 GGCCTCTCCT
* *
46786086 TTTTCC TTTCC TTTTC -TTT- TTTTC TTTTT TTTTC TTTTC TTTTC TTTT
1 TTTT-C TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
46786134 TTAAAAGTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
4 6 0.17
5 27 0.75
6 3 0.08
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:46786106 original size:18 final size:18
Alignment explanation
Indices: 46786085--46786123 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
46786075 TGGCCTCTCC
46786085 TTTTTCCTTTCCTTTTCT
1 TTTTTCCTTTCCTTTTCT
* **
46786103 TTTTTTCTTTTTTTTTCT
1 TTTTTCCTTTCCTTTTCT
46786121 TTT
1 TTT
46786124 CTTTTCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTCCTTTCCTTTTCT
Found at i:46789502 original size:3 final size:3
Alignment explanation
Indices: 46789496--46789564 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
46789486 GCAAATGATG
46789496 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
46789544 ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
46789565 TAAGTAACAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:46796593 original size:3 final size:3
Alignment explanation
Indices: 46796585--46796711 Score: 193
Period size: 3 Copynumber: 42.3 Consensus size: 3
46796575 TGGAAGATAT
46796585 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * * *
46796633 AAG GAG AAG AAG AAG GAG AAG AAG GAG AAG AAG AAG AAG AAG GAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
46796681 AATG -AG AAG AAG GAG AAG AAG AAG AAG AAG A
1 AA-G AAG AAG AAG AAG AAG AAG AAG AAG AAG A
46796712 GAAAATACCT
Statistics
Matches: 112, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
2 1 0.01
3 110 0.98
4 1 0.01
ACGTcount: A:0.62, C:0.00, G:0.37, T:0.01
Consensus pattern (3 bp):
AAG
Found at i:46805110 original size:25 final size:25
Alignment explanation
Indices: 46805082--46805132 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
46805072 TTAAACGATG
46805082 AACTTACTAAGCTTTACGAAAACTT
1 AACTTACTAAGCTTTACGAAAACTT
46805107 AACTTACTAAGCTTTACGAAAACTT
1 AACTTACTAAGCTTTACGAAAACTT
46805132 A
1 A
46805133 CTCGTGTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (25 bp):
AACTTACTAAGCTTTACGAAAACTT
Found at i:46815039 original size:17 final size:17
Alignment explanation
Indices: 46815014--46815046 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
46815004 ACAATTTCAC
46815014 TCAACTCCATGTTATAA
1 TCAACTCCATGTTATAA
*
46815031 TCAATTCCATGTTATA
1 TCAACTCCATGTTATA
46815047 GCATATACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.39
Consensus pattern (17 bp):
TCAACTCCATGTTATAA
Found at i:46821616 original size:125 final size:124
Alignment explanation
Indices: 46821394--46821649 Score: 379
Period size: 125 Copynumber: 2.1 Consensus size: 124
46821384 AAATAGTGGG
** * * * *
46821394 AAATCGCTTCTACCAGGATGCTATTTGAGAAAAAATTGTGAAATAGTGGCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATGAGAAAAAATTGTGAAATAGCGCCCTCGTGGACGCGATA
*
46821459 TCGCTACAGTGGTCATGTAAGAAATAATTTTTTTTTGACTTTTACTGAGCAAATAGTATA
66 TCGCTACAGTGGTCATGTAAGAAATAATTTTTTTTTGACGTTT-CTGAGCAAATAGTATA
* *
46821519 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATA
1 AAATCGCTGATACCAGGATGCTATATGAGAAAAAATTGTGAAATAGCGCCCTCGTGGACGCGATA
* * *
46821584 TCGCTACAGTTGGTCATGTAGGAAATAA-TTTTTTTTGACGTTTCTGAGCAAATAGTGTC
66 TCGCTACAG-TGGTCATGTAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATA
46821643 AAATCGC
1 AAATCGC
46821650 GCCCTCGTGG
Statistics
Matches: 118, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
124 21 0.18
125 80 0.68
126 17 0.14
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (124 bp):
AAATCGCTGATACCAGGATGCTATATGAGAAAAAATTGTGAAATAGCGCCCTCGTGGACGCGATA
TCGCTACAGTGGTCATGTAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATA
Found at i:46825006 original size:14 final size:15
Alignment explanation
Indices: 46824989--46825022 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
46824979 AATAAATATC
46824989 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
46825003 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
46825018 TAAAA
1 TAAAA
46825023 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:46825153 original size:28 final size:29
Alignment explanation
Indices: 46825121--46825176 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
46825111 TGAAAATATT
46825121 AAAAATTTTAAAATTAT-TTAAAAAAATA
1 AAAAATTTTAAAATTATCTTAAAAAAATA
*
46825149 AAAAATTTTAAAATTTTCTTAAAAAAAT
1 AAAAATTTTAAAATTATCTTAAAAAAAT
46825177 GAAATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
AAAAATTTTAAAATTATCTTAAAAAAATA
Found at i:46825247 original size:22 final size:22
Alignment explanation
Indices: 46825212--46825327 Score: 108
Period size: 22 Copynumber: 5.0 Consensus size: 22
46825202 TATGGATTTG
* *
46825212 GAGATTTTTTGAAGGAAATTGA
1 GAGAATTTTGGAAGGAAATTGA
*
46825234 GAGGATTTTGGAAGGAATTTGAGAGTTGA
1 GAGAATTTTGGAAGG-A----A-A-TTGA
*
46825263 GAGAATTTTGGAAGAAAATTGA
1 GAGAATTTTGGAAGGAAATTGA
*
46825285 GAGAATTTT-GAAGGGAATTGA
1 GAGAATTTTGGAAGGAAATTGA
*
46825306 GAGAATTTTTGAAGGAAATTGA
1 GAGAATTTTGGAAGGAAATTGA
46825328 TATTGAATTT
Statistics
Matches: 78, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
21 19 0.24
22 36 0.46
23 2 0.03
24 1 0.01
27 1 0.01
28 2 0.03
29 17 0.22
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (22 bp):
GAGAATTTTGGAAGGAAATTGA
Found at i:46825270 original size:29 final size:29
Alignment explanation
Indices: 46825230--46825287 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
46825220 TTGAAGGAAA
* * *
46825230 TTGAGAGGATTTTGGAAGGAATTTGAGAG
1 TTGAGAGAATTTTGGAAGAAAATTGAGAG
46825259 TTGAGAGAATTTTGGAAGAAAATTGAGAG
1 TTGAGAGAATTTTGGAAGAAAATTGAGAG
46825288 AATTTTGAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.34, T:0.29
Consensus pattern (29 bp):
TTGAGAGAATTTTGGAAGAAAATTGAGAG
Found at i:46825282 original size:51 final size:50
Alignment explanation
Indices: 46825212--46825308 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 50
46825202 TATGGATTTG
* * * *
46825212 GAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAA-GGAATTTGAGAGTTGA
1 GAGAATTTTGGAAGAAAATTGAGAGAATTTT-GAAGGGAA-TTGAGAGTTGA
46825263 GAGAATTTTGGAAGAAAATTGAGAGAATTTTGAAGGGAATTGAGAG
1 GAGAATTTTGGAAGAAAATTGAGAGAATTTTGAAGGGAATTGAGAG
46825309 AATTTTTGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
50 10 0.24
51 31 0.76
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (50 bp):
GAGAATTTTGGAAGAAAATTGAGAGAATTTTGAAGGGAATTGAGAGTTGA
Found at i:46836800 original size:44 final size:43
Alignment explanation
Indices: 46836704--46837171 Score: 199
Period size: 44 Copynumber: 10.8 Consensus size: 43
46836694 ATGATGGCAA
* *
46836704 ATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCA-ATA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAA---ATATAG
* **
46836748 ATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATCAAAATGATAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAAT-ATAG
* * * * ** *
46836792 ATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATC-GCAT-CAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAATATAG
* * *
46836833 GTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAATAA-ATCA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TCAA-AATAT-AG
** * * *
46836877 ATCTTATCTCCCTGAAGTTAAAGTAGAGCAGATTGAAGAA-ACCAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TCAA-AATA-TAG
* * ** *
46836922 -TCCTATCTCCCTGAAGTTGCAATGGAGGGGA-CTAAAATGATGG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATC-AAAAT-ATAG
** * ** * **
46836965 ATCTTATCTTTCTGAAGTTGTAGTAAAGTAGATC-GCATCA-A-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAAT-ATAG
* * ** * *
46837006 ACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTAACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAAT-ATAG
* * * * * * *
46837050 GTATTATCTCTCTGAAGCTGTAGTGGAGCAGACTGAATAA-ACCA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TCAA-AATA-TAG
* * * *
46837094 ATCATATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATGATGG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAAT-ATAG
* * *
46837138 ATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATC
46837172 GCATCAGATT
Statistics
Matches: 307, Mismatches: 93, Indels: 48
0.69 0.21 0.11
Matches are distributed among these distances:
41 54 0.18
42 7 0.02
43 15 0.05
44 224 0.73
45 6 0.02
46 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (43 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAATATAG
Found at i:46836997 original size:173 final size:171
Alignment explanation
Indices: 46836703--46837206 Score: 616
Period size: 173 Copynumber: 2.9 Consensus size: 171
46836693 GATGATGGCA
* * * * *
46836703 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCAA-TAATCCTATCTCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGAAGTGGAGCAGATTGAAG-AAACCAATCCTATCTCCCTGAAGTT
* *
46836767 GCAGTGGAGTGGATCAAAATGATAGATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATCGCATCA
65 GCAGTGGAGCGGAT-AAAATGATGGATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATCGCATCA
* *
46836832 GGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAA-TAAATC
129 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGT-AA-C
* * *
46836876 AATCTTATCTCCCTGAAGTTAAAGTAGAGCAGATTGAAGAAACCAGTCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGAAGTGGAGCAGATTGAAGAAACCAATCCTATCTCCCTGAAGTTG
* * * * *
46836941 CAATGGAGGGGACTAAAATGATGGATCTTATCTTTCTGAAGTTGTAGTAAAGTAGATCGCATCAA
66 CAGTGGAGCGGA-TAAAATGATGGATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATCGCATCAG
* **
46837006 ACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTAAC
130 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTAAC
* * * * * * * *
46837048 AGGTATTATCTCTCTGAAGCTGTAGTGGAGCAGACTGAATAAACCAATCATATCTCCCTGAAGTT
1 A-ATCTTATCTCCCTGAAGTTGAAGTGGAGCAGATTGAAGAAACCAATCCTATCTCCCTGAAGTT
* * *
46837113 GCAGTGGAGCGGATTAAAATGATGGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCGCATCA
65 GCAGTGGAGCGGA-TAAAATGATGGATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATCGCATCA
* ***
46837178 GATTTTATCTTTTTGAAGTTGCAGTGGAG
129 GATCTTATCTCCCTGAAGTTGCAGTGGAG
46837207 TAGGTAAAAT
Statistics
Matches: 283, Mismatches: 44, Indels: 8
0.84 0.13 0.02
Matches are distributed among these distances:
172 4 0.01
173 277 0.98
174 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (171 bp):
AATCTTATCTCCCTGAAGTTGAAGTGGAGCAGATTGAAGAAACCAATCCTATCTCCCTGAAGTTG
CAGTGGAGCGGATAAAATGATGGATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATCGCATCAGA
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTAAC
Found at i:46837939 original size:6 final size:6
Alignment explanation
Indices: 46837928--46837955 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
46837918 GGTTTCTTTC
46837928 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
46837956 TCTTCTTTCT
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:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:46839789 original size:13 final size:13
Alignment explanation
Indices: 46839759--46839792 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
46839749 TAATGGCATA
46839759 AAAATAATATAAAC
1 AAAATAA-ATAAAC
46839773 -AAATAAATAAAC
1 AAAATAAATAAAC
46839785 AAAATAAA
1 AAAATAAA
46839793 AAGCAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAATAAATAAAC
Found at i:46840202 original size:21 final size:20
Alignment explanation
Indices: 46840164--46840206 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
46840154 AAATAATAAT
* *
46840164 TATAAAAATATATATACATA
1 TATAAAAATAAAAATACATA
46840184 TATAAAAATAAAAATTACATA
1 TATAAAAATAAAAA-TACATA
46840205 TA
1 TA
46840207 AAAGTTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
TATAAAAATAAAAATACATA
Found at i:46840239 original size:21 final size:20
Alignment explanation
Indices: 46840181--46840239 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
46840171 ATATATATAC
* *
46840181 ATATATAAAAATAAAAATTAC
1 ATATA-AAAAATAAAAATAAA
**
46840202 ATATAAAAGTTACAAAATAAA
1 ATATAAAAAATA-AAAATAAA
46840223 ATATAAATAAATAAAAA
1 ATATAAA-AAATAAAAA
46840240 AATAGTAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 5 0.17
21 22 0.73
22 3 0.10
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.25
Consensus pattern (20 bp):
ATATAAAAAATAAAAATAAA
Found at i:46841790 original size:44 final size:44
Alignment explanation
Indices: 46841610--46842277 Score: 250
Period size: 44 Copynumber: 15.2 Consensus size: 44
46841600 TGTCTTGGAA
* * * *
46841610 AGATAAGATTCGCCGACTTCGATCTGCTCCGCTACTGCTTAGGG
1 AGATAAGATTCGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
** * * * *
46841654 AGATAAGA-TCTATAATCTTCAACCTTCTCCGCTACTGCTTAGGG
1 AGATAAGATTCGCT-GTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * *
46841698 AGACAAGGCTT-GGTGGCTTAAATCTGTTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCGCTGTCTTCAATCTG-CT-CCACTACTGCTTAGG-G
* *
46841742 AGATAAGATTCGCTGTCTTCGATCTGCTCCACTACTGCTTAGAG
1 AGATAAGATTCGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * *
46841786 AGATAAGATCTACAC--TCTTCAACCTTCTCCACTGCTGCTCAGGG
1 AGATAAGAT-T-CGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
46841830 AGACAAGGCTT-GGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCGCTGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* *
46841874 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
** * * * * * *
46841918 AGATAAGA-TCTATAATCTTCAACCTTCTCCGCTGCTGCTCAGGG
1 AGATAAGATTCGCT-GTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
46841962 AGACAAGGCTT-GGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCGCTGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* *
46842006 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * *
46842050 AGATAAGATCTACAC--TCTTCAACCTTCTCCACTACTGCTTAGGG
1 AGATAAGAT-T-CGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * * * * *
46842094 AGATAAGA-TCTACAATCTTCAACCTTCTACGCTACTGCTCAGGG
1 AGATAAGATTC-GCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
46842138 AGACAAGGCTT-GGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCGCTGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* * * *
46842182 AGATAAGATTC-ATCGTCTTCGATCTGCTCCACTATTCCTTAGGG
1 AGATAAGATTCGCT-GTCTTCAATCTGCTCCACTACTGCTTAGGG
** ** * * * *
46842226 AGATAAGATTTACAATCTTCAACCTTCTCCGCTGCTGCTTAGGG
1 AGATAAGATTCGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
*
46842270 AGACAAGA
1 AGATAAGA
46842278 CTTGGTTACC
Statistics
Matches: 450, Mismatches: 126, Indels: 96
0.67 0.19 0.14
Matches are distributed among these distances:
41 1 0.00
42 27 0.06
43 33 0.07
44 340 0.76
45 24 0.05
46 25 0.06
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.30
Consensus pattern (44 bp):
AGATAAGATTCGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:46841797 original size:132 final size:132
Alignment explanation
Indices: 46841560--46842096 Score: 894
Period size: 132 Copynumber: 4.1 Consensus size: 132
46841550 CACTGCAACT
* ** * *
46841560 TTAGGGAGATAAGATTTGGTGGCTTAAATCTACTTCCCACTGTCTTGGAAAGATAAGATTCGCCG
1 TTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCG
* * * *
46841625 ACTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGCTACT
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTACT
46841690 GC
131 GC
* *
46841692 TTAGGGAGACAAGGCTTGGTGGCTTAAATCTGTTTCCCACTATCTTGGAAAGATAAGATTCGCTG
1 TTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCG
* * *
46841757 TCTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTACACTCTTCAACCTTCTCCACTGCT
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTACT
46841822 GC
131 GC
*
46841824 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCG
1 TTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCG
* * *
46841889 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGCTGCT
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTACT
46841954 GC
131 GC
*
46841956 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCG
1 TTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCG
*
46842021 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACACTCTTCAACCTTCTCCACTACT
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTACT
46842086 GC
131 GC
46842088 TTAGGGAGA
1 TTAGGGAGA
46842097 TAAGATCTAC
Statistics
Matches: 379, Mismatches: 26, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 379 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (132 bp):
TTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCG
TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTACT
GC
Found at i:46842099 original size:176 final size:176
Alignment explanation
Indices: 46841900--46842277 Score: 648
Period size: 176 Copynumber: 2.1 Consensus size: 176
46841890 CTTCGATCTG
* * *
46841900 CTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTACGCTACTGCTCAGGGAGA
*
46841965 CAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATC
66 CAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCGATC
* *
46842030 TGCTCCACTACTGCTTAGGGAGATAAGATCTACACTCTTCAACCTT
131 TGCTCCACTACTCCTTAGGGAGATAAGATCTACAATCTTCAACCTT
46842076 CTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTACGCTACTGCTCAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTACGCTACTGCTCAGGGAGA
*
46842141 CAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCATCGTCTTCGATC
66 CAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCGATC
* *
46842206 TGCTCCACTATTCCTTAGGGAGATAAGATTTACAATCTTCAACCTT
131 TGCTCCACTACTCCTTAGGGAGATAAGATCTACAATCTTCAACCTT
* * *
46842252 CTCCGCTGCTGCTTAGGGAGACAAGA
1 CTCCACTACTGCTTAGGGAGATAAGA
46842278 CTTGGTTACC
Statistics
Matches: 190, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
176 190 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.29
Consensus pattern (176 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTACGCTACTGCTCAGGGAGA
CAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCGATC
TGCTCCACTACTCCTTAGGGAGATAAGATCTACAATCTTCAACCTT
Found at i:46854006 original size:13 final size:13
Alignment explanation
Indices: 46853988--46854020 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
46853978 AATGACATAA
46853988 AAATAATATAAAC-
1 AAATAA-ATAAACG
46854001 AAATAAATAAACG
1 AAATAAATAAACG
46854014 AAATAAA
1 AAATAAA
46854021 AATCAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (13 bp):
AAATAAATAAACG
Found at i:46854469 original size:21 final size:20
Alignment explanation
Indices: 46854412--46854469 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
46854402 TATATATGCG
* *
46854412 TATATAAAAATAAAAATTACA
1 TATA-AAAAATAAAAATAAAA
**
46854433 TATAAAAGTTACAAAATAAAA
1 TATAAAAAATA-AAAATAAAA
46854454 TATAAATAAATAAAAA
1 TATAAA-AAATAAAAA
46854470 AATAGTAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 5 0.17
21 21 0.72
22 3 0.10
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (20 bp):
TATAAAAAATAAAAATAAAA
Found at i:46875578 original size:21 final size:21
Alignment explanation
Indices: 46875552--46875592 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
46875542 CATTTTAGAG
46875552 TTAAAATAAAATTA-CTTTTTT
1 TTAAAA-AAAATTATCTTTTTT
*
46875573 TTAAAAAACATTATCTTTTT
1 TTAAAAAAAATTATCTTTTT
46875593 ACTTTGCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAAAAAAAATTATCTTTTTT
Found at i:46875916 original size:28 final size:29
Alignment explanation
Indices: 46875883--46875953 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
46875873 TTAGACGTTT
* *
46875883 AAAATTT-ATTTTTTTAATTTTATTTTCA
1 AAAATTTAATCTTTTTAATTTTAGTTTCA
* *
46875911 GAAATTTAATCTTTTTACTTTTAGTTTCA
1 AAAATTTAATCTTTTTAATTTTAGTTTCA
46875940 AAAA-TTAATTCTTT
1 AAAATTTAA-TCTTT
46875954 AATAATTGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 10 0.28
29 26 0.72
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.58
Consensus pattern (29 bp):
AAAATTTAATCTTTTTAATTTTAGTTTCA
Found at i:46876322 original size:10 final size:10
Alignment explanation
Indices: 46876299--46876333 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
46876289 GTTTTTTACT
*
46876299 AAAATATTATA
1 AAAAAATTA-A
46876310 AAAAAATTAA
1 AAAAAATTAA
46876320 AAAAAATTAA
1 AAAAAATTAA
46876330 AAAA
1 AAAA
46876334 TTATATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.65
11 8 0.35
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAAAATTAA
Found at i:46876812 original size:16 final size:17
Alignment explanation
Indices: 46876771--46876817 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
46876761 AGTAAAAAAC
*
46876771 TAGTATTATTATTATGGT
1 TAGTATTATT-TTATAGT
46876789 TAGTTATTATTTT-TAGT
1 TAG-TATTATTTTATAGT
46876806 TAGTATTATTTT
1 TAGTATTATTTT
46876818 GAGTATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 9 0.33
17 6 0.22
18 5 0.19
19 7 0.26
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.62
Consensus pattern (17 bp):
TAGTATTATTTTATAGT
Found at i:46885193 original size:284 final size:282
Alignment explanation
Indices: 46884576--46885239 Score: 1125
Period size: 284 Copynumber: 2.3 Consensus size: 282
46884566 GCATGTTGAA
46884576 AAAAAAGTTAGTAAAACACTCTTACTTCGGCTATTTCTTCGTATTTTTTTCTCCGCATTTTATTA
1 AAAAAAGTTAGTAAAACACTCTTACTTCGGC-ATTTCTTCGTATTTTTTTCTCCGCATTTTATTA
*
46884641 CTTTAAAAAATTTTATAATTTCTAATTTTATAAATTTATTAATTTAGTGTATTTTTTAAATTAAT
65 CTTTAAAAAATTTCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTATTTTTTAAATTAAT
* * *
46884706 TTAGTGTAAAAAAACGCTTATTCCTGGCCTTTGCTCGTATTATTTTCCTGAATTTTCTTACTTTC
130 TTAGTGTAAAAAAACCCTTATTCCTGGCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTTC
* *
46884771 AGTAAAAAAATATTTCCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTT
195 AATAAAAAAATATTTCCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTCAAATATTT
*
46884836 GTATTAATTATTTCTGAATTTTT
260 GTATTAATTACTTCTGAATTTTT
*
46884859 AAAAAAGTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGTATTTTATTA
1 AAAAAAGTTAGTAAAACACTCTTACTTCGG-CATTTCTTCGTATTTTTTTCTCCGCATTTTATTA
46884924 CTTTAAAAAATTTCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTATTTTTTAAATTAAT
65 CTTTAAAAAATTTCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTATTTTTTAAATTAAT
46884989 TTAGTGT-AAAAAACCCTTATTCCT-GCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTTT
130 TTAGTGTAAAAAAACCCTTATTCCTGGCC-TTTGCTCGTATTATTTTCCCGAATTTTATTACTTT
* *
46885052 CAATAAAAAAATTTATTTTCGTATTTTATTATTTTTTATTATTTCAGTACATTTTGTTTCAAATA
194 CAATAAAAAAA--TATTTCCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTCAAATA
46885117 TTTGTATTAATTACTTCTGAATTTTT
257 TTTGTATTAATTACTTCTGAATTTTT
* * * *
46885143 AAAAAATTTTGTAAAACACTCTTACCTCGGTCATTTCTTCATATTTTTTTCTCCGCATTTTATTA
1 AAAAAAGTTAGTAAAACACTCTTACTTCGG-CATTTCTTCGTATTTTTTTCTCCGCATTTTATTA
*
46885208 CTTTAAAAAAATTCATAATTTCTAATTTTATA
65 CTTTAAAAAATTTCATAATTTCTAATTTTATA
46885240 TTTTTACTTT
Statistics
Matches: 360, Mismatches: 17, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
281 3 0.01
282 59 0.16
283 133 0.37
284 165 0.46
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (282 bp):
AAAAAAGTTAGTAAAACACTCTTACTTCGGCATTTCTTCGTATTTTTTTCTCCGCATTTTATTAC
TTTAAAAAATTTCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTATTTTTTAAATTAATT
TAGTGTAAAAAAACCCTTATTCCTGGCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCA
ATAAAAAAATATTTCCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTCAAATATTTG
TATTAATTACTTCTGAATTTTT
Found at i:46885653 original size:14 final size:14
Alignment explanation
Indices: 46885636--46885765 Score: 55
Period size: 14 Copynumber: 9.5 Consensus size: 14
46885626 TCCTTCCTCC
46885636 TCTCTTCTTCTTCT
1 TCTCTTCTTCTTCT
46885650 TCTCTT-TT-TT-T
1 TCTCTTCTTCTTCT
*
46885661 TCTCTTCTCCTTTCCT
1 TCTCTTCTTC-TT-CT
* *
46885677 TTTCTT-TCCTTCT
1 TCTCTTCTTCTTCT
46885690 T-T-TTCTTTCTT-T
1 TCTCTTC-TTCTTCT
* *
46885702 TTTCTTCTTCTCCT
1 TCTCTTCTTCTTCT
*
46885716 T-TCCTTCTTTTTCT
1 TCT-CTTCTTCTTCT
46885730 T-TCTTTCTTTCTTCT
1 TCTC-TTC-TTCTTCT
* *
46885745 TCT-TTCCCTCTCCT
1 TCTCTT-CTTCTTCT
46885759 TCTCTTC
1 TCTCTTC
46885766 CCCCCACCCA
Statistics
Matches: 91, Mismatches: 9, Indels: 32
0.69 0.07 0.24
Matches are distributed among these distances:
11 9 0.10
12 6 0.07
13 16 0.18
14 40 0.44
15 13 0.14
16 7 0.08
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTCTTCTTCTTCT
Found at i:46885718 original size:34 final size:35
Alignment explanation
Indices: 46885680--46885747 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 35
46885670 CTTTCCTTTT
46885680 CTTTCCTTCTTTTTCTTTCTTT-TTTCTTCTTCTC
1 CTTTCCTTCTTTTTCTTTCTTTCTTTCTTCTTCTC
46885714 CTTTCCTTCTTTTTCTTTCTTTCTTTCTTCTTCT
1 CTTTCCTTCTTTTTCTTTCTTTCTTTCTTCTTCT
46885748 TTCCCTCTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 22 0.67
35 11 0.33
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (35 bp):
CTTTCCTTCTTTTTCTTTCTTTCTTTCTTCTTCTC
Found at i:46885759 original size:38 final size:34
Alignment explanation
Indices: 46885683--46885761 Score: 113
Period size: 34 Copynumber: 2.2 Consensus size: 34
46885673 TCCTTTTCTT
*
46885683 TCCTTCTTTTTCTTTCTTTTTTCTTCTTCTCCTT
1 TCCTTCTTTTTCTTTCTTTTTTCTTCTTCTCCTC
46885717 TCCTTCTTTTTCTTTCTTTCTTTCTTCTTCTTTCCCTC
1 TCCTTCTTTTTCTTTCTTT-TTTCTTCTTC--T-CCTC
46885755 TCCTTCT
1 TCCTTCT
46885762 CTTCCCCCCA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
34 19 0.47
35 10 0.25
37 1 0.03
38 10 0.25
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (34 bp):
TCCTTCTTTTTCTTTCTTTTTTCTTCTTCTCCTC
Found at i:46885905 original size:20 final size:21
Alignment explanation
Indices: 46885869--46885907 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
46885859 CACCTGCAAC
46885869 TTTTTTTTTCTGATTTTTGTT
1 TTTTTTTTTCTGATTTTTGTT
*
46885890 TTTTTTTTTTTG-TTTTTG
1 TTTTTTTTTCTGATTTTTG
46885908 GTATATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.85
Consensus pattern (21 bp):
TTTTTTTTTCTGATTTTTGTT
Found at i:46885916 original size:21 final size:22
Alignment explanation
Indices: 46885870--46885916 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
46885860 ACCTGCAACT
*
46885870 TTTTTTTTCTGATTTTTGT-TT
1 TTTTTTTTCTGATTTTTGTATA
*
46885891 TTTTTTTTTTG-TTTTTGGTATA
1 TTTTTTTTCTGATTTTT-GTATA
46885913 TTTT
1 TTTT
46885917 GGTAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 12 0.55
22 5 0.23
ACGTcount: A:0.06, C:0.02, G:0.11, T:0.81
Consensus pattern (22 bp):
TTTTTTTTCTGATTTTTGTATA
Found at i:46887029 original size:14 final size:13
Alignment explanation
Indices: 46886998--46887046 Score: 64
Period size: 13 Copynumber: 3.7 Consensus size: 13
46886988 ATCTCGTTAC
*
46886998 ATAAAAAAGTAAA
1 ATAAAAAATTAAA
46887011 ATAAAAAATTAAA
1 ATAAAAAATTAAA
46887024 ACT-AAAAATATAAA
1 A-TAAAAAAT-TAAA
46887038 ATAAAAAAT
1 ATAAAAAAT
46887047 AGTAAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
13 20 0.62
14 12 0.38
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (13 bp):
ATAAAAAATTAAA
Found at i:46887053 original size:14 final size:14
Alignment explanation
Indices: 46886998--46887052 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 14
46886988 ATCTCGTTAC
*
46886998 ATAAAAAA-GTAAA
1 ATAAAAAATATAAA
46887011 ATAAAAAAT-TAAA
1 ATAAAAAATATAAA
46887024 ACT-AAAAATATAAA
1 A-TAAAAAATATAAA
46887038 ATAAAAAATAGTAAA
1 ATAAAAAATA-TAAA
46887053 TTTTAAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
13 20 0.54
14 13 0.35
15 4 0.11
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (14 bp):
ATAAAAAATATAAA
Found at i:46888000 original size:21 final size:20
Alignment explanation
Indices: 46887951--46888000 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
46887941 TATAAGTATC
46887951 TTAATTA-TAAATTAATTAA
1 TTAATTATTAAATTAATTAA
46887970 -T-ATTAGATTAAATTAAATTAA
1 TTAATT--ATTAAATT-AATTAA
46887991 TTAATTATTA
1 TTAATTATTA
46888001 TTTTGAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
17 3 0.12
18 1 0.04
19 1 0.04
20 6 0.24
21 10 0.40
22 1 0.04
23 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAATTATTAAATTAATTAA
Found at i:46890234 original size:12 final size:13
Alignment explanation
Indices: 46890210--46890238 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
46890200 AATATAGTTA
46890210 TTATTTATTATTT
1 TTATTTATTATTT
46890223 TTATTT-TTATTT
1 TTATTTATTATTT
46890235 TTAT
1 TTAT
46890239 ATTCACGCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTATTTATTATTT
Found at i:46897488 original size:6 final size:6
Alignment explanation
Indices: 46897474--46897512 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
46897464 CCCATTATAG
*
46897474 TCCCAC TCCCCC TCCCCC TCCCCC TCCCCC TCCCCC TCC
1 TCCCCC TCCCCC TCCCCC TCCCCC TCCCCC TCCCCC TCC
46897513 TACTCTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.03, C:0.79, G:0.00, T:0.18
Consensus pattern (6 bp):
TCCCCC
Found at i:46897500 original size:18 final size:18
Alignment explanation
Indices: 46897474--46897517 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
46897464 CCCATTATAG
46897474 TCCCACTCCCCCTCCCCC
1 TCCCACTCCCCCTCCCCC
*
46897492 TCCCCCTCCCCCTCCCCC
1 TCCCACTCCCCCTCCCCC
*
46897510 TCCTACTC
1 TCCCACTC
46897518 TTTTAACCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.05, C:0.75, G:0.00, T:0.20
Consensus pattern (18 bp):
TCCCACTCCCCCTCCCCC
Found at i:46908365 original size:3 final size:3
Alignment explanation
Indices: 46908346--46908395 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
46908336 AATTTATTTC
* * *
46908346 ATA AT- ATA ATA AAA ATA ATA TTA ATA ATA ACA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
46908392 ATA A
1 ATA A
46908396 AATGTCATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:46918915 original size:36 final size:36
Alignment explanation
Indices: 46918841--46918945 Score: 120
Period size: 36 Copynumber: 2.9 Consensus size: 36
46918831 GGATGAGCGC
* * * * * * *
46918841 ATCAGTCAGAATAGATCCGAAAAGCTGCTGAACGAA
1 ATCAATCAAAATAGATTCGAAAGGCTACTAAACAAA
* *
46918877 ATCAATCAAAATAGATTTGAAAGGTTACTAAACAAA
1 ATCAATCAAAATAGATTCGAAAGGCTACTAAACAAA
*
46918913 ATCAGTCAAAATAGATTCGAAAGGCTACTAAAC
1 ATCAATCAAAATAGATTCGAAAGGCTACTAAAC
46918946 TGAATAGAGT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (36 bp):
ATCAATCAAAATAGATTCGAAAGGCTACTAAACAAA
Found at i:46926191 original size:26 final size:26
Alignment explanation
Indices: 46926159--46926241 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
46926149 AGTTTTACGG
46926159 TACACATAGTAGCCTTCACTTAGTAC
1 TACACATAGTAGCCTTCACTTAGTAC
* * *
46926185 TACACAT-GTAACCATCATTTA-T-C
1 TACACATAGTAGCCTTCACTTAGTAC
* * *
46926208 GATTCACGTAGTAGCCTTCACATAGTAC
1 --TACACATAGTAGCCTTCACTTAGTAC
46926236 TACACA
1 TACACA
46926242 GGTGACCAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 16 0.39
26 21 0.51
27 1 0.02
28 1 0.02
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.30
Consensus pattern (26 bp):
TACACATAGTAGCCTTCACTTAGTAC
Found at i:46926241 original size:51 final size:51
Alignment explanation
Indices: 46926009--46926347 Score: 326
Period size: 50 Copynumber: 6.7 Consensus size: 51
46925999 TATCACTCGA
* * * * *
46926009 TACACGTAGTAGCCTTCACATAGTACTACACACATAATCAGGTTTTAT-GG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGATTTATCGG
** * * * * *
46926059 TTTACATAGTAGCCTTCACATAGTACTATATACGTGATCAAGTTTTA-CGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGATTTATCGG
* * * *
46926109 TTCACGTAGTAGCCTTCACTTAGTACTACACACGTGATCAAGTTTTA-CGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGATTTATCGG
* * * * ** *
46926159 TACACATAGTAGCCTTCACTTAGTACTACACATGTAACCATCATTTATCGA
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGATTTATCGG
* * * *
46926210 TTCACGTAGTAGCCTTCACATAGTACTACACAGGTGACCAA-AGCTTCTCGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGA-TTTATCGG
* * * * * **
46926261 TACACATTGTAGCCTTCACTTAGTAGTACACATGTGACCATTATTTATCGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGATTTATCGG
*
46926312 TACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTG
46926348 TTCACCGATA
Statistics
Matches: 239, Mismatches: 46, Indels: 7
0.82 0.16 0.02
Matches are distributed among these distances:
50 126 0.53
51 112 0.47
52 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (51 bp):
TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGATTTATCGG
Found at i:46926291 original size:102 final size:101
Alignment explanation
Indices: 46926005--46926347 Score: 384
Period size: 102 Copynumber: 3.4 Consensus size: 101
46925995 CTTTTATCAC
* * * * * * * **
46926005 TCGATACACGTAGTAGCCTTCACATAGTACTACACACATAATCAGGTTTTATGGTTTACATAGTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTCTACGGTACACATAGTA
* * * * * * ***
46926070 GCCTTCACATAGTACTATATACGTGATCAAGTTTTA
66 GCCTTCACTTAGTACTACACATGTAACCATCATTTA
* * * *
46926106 -CGGTTCACGTAGTAGCCTTCACTTAGTACTACACACGTGATCAAGTTTTACGGTACACATAGTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTCTACGGTACACATAGTA
46926170 GCCTTCACTTAGTACTACACATGTAACCATCATTTA
66 GCCTTCACTTAGTACTACACATGTAACCATCATTTA
* *
46926206 TCGATTCACGTAGTAGCCTTCACATAGTACTACACAGGTGACCAAAGCTTCT-CGGTACACATTG
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTCTACGGTACACATAG
* * *
46926270 TAGCCTTCACTTAGTAGTACACATGTGACCATTATTTA
64 TAGCCTTCACTTAGTACTACACATGTAACCATCATTTA
* * *
46926308 TCGGTACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTG
46926348 TTCACCGATA
Statistics
Matches: 208, Mismatches: 31, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
100 82 0.39
101 38 0.18
102 85 0.41
103 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (101 bp):
TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTCTACGGTACACATAGTA
GCCTTCACTTAGTACTACACATGTAACCATCATTTA
Found at i:46926840 original size:16 final size:16
Alignment explanation
Indices: 46926819--46926872 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
46926809 CTTGACTCGA
46926819 ACTTTTGCACATTTAC
1 ACTTTTGCACATTTAC
** *
46926835 ACTTTTGC-C-CCTAA
1 ACTTTTGCACATTTAC
*
46926849 ACTTTTGCATATTTAC
1 ACTTTTGCACATTTAC
46926865 ACTTTTGC
1 ACTTTTGC
46926873 CCCAAACCTC
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 10 0.34
15 1 0.03
16 18 0.62
ACGTcount: A:0.22, C:0.26, G:0.07, T:0.44
Consensus pattern (16 bp):
ACTTTTGCACATTTAC
Found at i:46926854 original size:30 final size:29
Alignment explanation
Indices: 46926818--46926879 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 29
46926808 CCTTGACTCG
46926818 AACTTTTGCACATTTACACTTTTGCCCCTA
1 AACTTTTGCACATTTACACTTTTGCCCC-A
*
46926848 AACTTTTGCATATTTACACTTTTGCCCCA
1 AACTTTTGCACATTTACACTTTTGCCCCA
46926877 AAC
1 AAC
46926880 CTCGGAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.39
Consensus pattern (29 bp):
AACTTTTGCACATTTACACTTTTGCCCCA
Found at i:46930206 original size:14 final size:14
Alignment explanation
Indices: 46930169--46930199 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
46930159 AAATAGTTCG
46930169 AAAGAAAAAAATAA
1 AAAGAAAAAAATAA
*
46930183 AGAGAAAAAAATAA
1 AAAGAAAAAAATAA
46930197 AAA
1 AAA
46930200 TAGAAAAGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (14 bp):
AAAGAAAAAAATAA
Found at i:46930206 original size:16 final size:14
Alignment explanation
Indices: 46930171--46930197 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46930161 ATAGTTCGAA
46930171 AGAAAAAAATAAAG
1 AGAAAAAAATAAAG
46930185 AGAAAAAAATAAA
1 AGAAAAAAATAAA
46930198 AATAGAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.07
Consensus pattern (14 bp):
AGAAAAAAATAAAG
Found at i:46931581 original size:49 final size:48
Alignment explanation
Indices: 46931526--46931671 Score: 229
Period size: 49 Copynumber: 3.0 Consensus size: 48
46931516 TTTATTTTCT
*
46931526 CGATGCCATAGTCCAACTATGGTCTTACACATAATCACATATCACATAC
1 CGATGCCATAGCCCAACTATGGTCTTACAC-TAATCACATATCACATAC
*
46931575 CGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATAC
1 CGATGCCATAGCCCAACTATGGTCTTACAC-TAATCACATATCACATAC
*
46931624 CGATGCCATAGCCCAACTATGGTCTTATACTGAATCACATTATCACAT
1 CGATGCCATAGCCCAACTATGGTCTTACACT-AATCACA-TATCACAT
46931672 TTTCACATGT
Statistics
Matches: 90, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
48 1 0.01
49 81 0.90
50 8 0.09
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (48 bp):
CGATGCCATAGCCCAACTATGGTCTTACACTAATCACATATCACATAC
Found at i:46933796 original size:50 final size:50
Alignment explanation
Indices: 46933733--46934119 Score: 436
Period size: 50 Copynumber: 7.7 Consensus size: 50
46933723 TCACTCGATA
46933733 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
* *
46933783 CACGTAGTAGCCTTCACATAGTACTACACACATGATCAGGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
* * * * *
46933833 TACATAGTAGCCTTCAAATAGTACAATACACGTGATCAAGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
* *
46933883 CACGTAGTAGCCTTCACTTAGTACTACACACGTGATCAAGTTTTACGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
* * * * * *** *
46933933 CACATAGTAGCCTTCACTTAGTACTACACATGTAACCATCATTTATCGATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA-CGGTT
* * * *
46933984 CACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCT-CGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TTTTACGGTT
* * * * * * * *
46934035 CACATTGTAGCCTTCACTTAGTAGTACACATGTGA-CCATTATTTATCGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGT-TTTA-CGGTT
*
46934086 CACGTAGTAGCCTTCACACAGTACTACACACGTG
1 CACGTAGTAGCCTTCACATAGTACTACACACGTG
46934120 TTCACCGATA
Statistics
Matches: 280, Mismatches: 51, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
48 1 0.00
49 3 0.01
50 173 0.62
51 100 0.36
52 1 0.00
53 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
Found at i:46939880 original size:3 final size:3
Alignment explanation
Indices: 46939874--46939918 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
46939864 GATGATGATG
46939874 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
46939919 GTGACAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:46940112 original size:3 final size:3
Alignment explanation
Indices: 46940089--46940136 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
46940079 ATGGACAATG
*
46940089 ATA ATA ATG ATA GATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
46940134 ATA
1 ATA
46940137 GTGAGAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:46940181 original size:25 final size:24
Alignment explanation
Indices: 46940142--46940189 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
46940132 TAATAGTGAG
*
46940142 AAAAAAAGGAAAAATAGAAAAATT
1 AAAAAAAGAAAAAATAGAAAAATT
*
46940166 AAAAAAAGAAATAAATAGATAAAT
1 AAAAAAAGAAA-AAATAGAAAAAT
46940190 GTATAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (24 bp):
AAAAAAAGAAAAAATAGAAAAATT
Found at i:46940211 original size:16 final size:16
Alignment explanation
Indices: 46940174--46940214 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
46940164 TTAAAAAAAG
46940174 AAATAAATAGATAAAT
1 AAATAAATAGATAAAT
** *
46940190 GTATAAATATATAAAT
1 AAATAAATAGATAAAT
46940206 AAATAAATA
1 AAATAAATA
46940215 CAAAGGAAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (16 bp):
AAATAAATAGATAAAT
Found at i:46944437 original size:2 final size:2
Alignment explanation
Indices: 46944430--46944457 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
46944420 AAGTAATTGC
46944430 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
46944458 GATTTTAGTT
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):
AT
Found at i:46944929 original size:41 final size:41
Alignment explanation
Indices: 46944872--46944988 Score: 191
Period size: 41 Copynumber: 2.9 Consensus size: 41
46944862 ATATTTTTTG
46944872 GGCCTTCAGCGGCGTTTTTTATAAAGCGCCGCTAATGCACT
1 GGCCTTCAGCGGCGTTTTTTATAAAGCGCCGCTAATGCACT
* *
46944913 GGCCTTTAGCGGCGTTTTTTATAAAGCGCCGCTAATGCTCT
1 GGCCTTCAGCGGCGTTTTTTATAAAGCGCCGCTAATGCACT
*
46944954 GGCCTTCAGCGGCGTTTTTGA-AGAAGCGCCGCTAA
1 GGCCTTCAGCGGCGTTTTTTATA-AAGCGCCGCTAA
46944989 ACACCGCTAG
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 1 0.01
41 70 0.99
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (41 bp):
GGCCTTCAGCGGCGTTTTTTATAAAGCGCCGCTAATGCACT
Found at i:46946090 original size:2 final size:2
Alignment explanation
Indices: 46946083--46946116 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
46946073 AAAATAGAGC
46946083 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
46946117 TAAATTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46948334 original size:15 final size:15
Alignment explanation
Indices: 46948293--46948335 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
46948283 ACCACCAATT
46948293 TGTTTTCATTTCTAC
1 TGTTTTCATTTCTAC
*
46948308 TG-TTTCGGTTTCTAC
1 TGTTTTC-ATTTCTAC
*
46948323 TGTTTTCTTTTCT
1 TGTTTTCATTTCT
46948336 CTTATTTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.07, C:0.19, G:0.12, T:0.63
Consensus pattern (15 bp):
TGTTTTCATTTCTAC
Found at i:46948982 original size:22 final size:22
Alignment explanation
Indices: 46948954--46949259 Score: 69
Period size: 22 Copynumber: 13.6 Consensus size: 22
46948944 TAACTTATTA
46948954 ATATATATTTTAAAATATATATATAT
1 ATATATATTTT--AA-A-ATATATAT
*
46948980 ATATATATCTTTAAAATTTAATAT
1 ATATATAT-TTTAAAATAT-ATAT
* * *
46949004 GTATATATTTTAAAATTTAATTT
1 ATATATATTTTAAAATAT-ATAT
*
46949027 ATATATGTTTTGAAAATTTAATATAT
1 ATATATATTTT-AAAA--T-ATATAT
* *
46949053 ATGCATATACTTTCAAAATTTA-AT
1 AT--ATATA-TTTTAAAATATATAT
* * *
46949077 TTATATTTTTTTAAAATTTA-AT
1 ATATA-TATTTTAAAATATATAT
* * *
46949099 ATATAT-TTTTAATATAAATTTT
1 ATATATATTTTAAAATATA-TAT
* * * ** * *
46949121 AAATTTAATTTAACGTAAATTT
1 ATATATATTTTAAAATATATAT
* *
46949143 ATATAT-TTTTAACATATATTT
1 ATATATATTTTAAAATATATAT
* * *
46949164 CTACTGTATTTT-TAATATATAT
1 ATA-TATATTTTAAAATATATAT
* *
46949186 AT-TGAAAATTT--AATATATAT
1 ATAT-ATATTTTAAAATATATAT
* * *
46949206 GTATATACTTCTAAAATTTA-AT
1 ATATATA-TTTTAAAATATATAT
*
46949228 ATATAT-TTTTAAAATTTA-AT
1 ATATATATTTTAAAATATATAT
*
46949248 TTATAT-TTTTAA
1 ATATATATTTTAA
46949260 TATAATTTTT
Statistics
Matches: 215, Mismatches: 45, Indels: 46
0.70 0.15 0.15
Matches are distributed among these distances:
20 46 0.21
21 22 0.10
22 49 0.23
23 45 0.21
24 19 0.09
25 4 0.02
26 15 0.07
27 4 0.02
28 8 0.04
29 3 0.01
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (22 bp):
ATATATATTTTAAAATATATAT
Found at i:46949003 original size:28 final size:27
Alignment explanation
Indices: 46948954--46949104 Score: 130
Period size: 24 Copynumber: 6.0 Consensus size: 27
46948944 TAACTTATTA
*
46948954 ATATATATTTTAAAATAT-ATATATAT
1 ATATATATTTTAAAATTTAATATATAT
46948980 ATATATATCTTTAAAA-TT--TA-ATAT
1 ATATATAT-TTTAAAATTTAATATATAT
*
46949004 GTATATATTTTAAAATTTAAT-T-TAT
1 ATATATATTTTAAAATTTAATATATAT
* *
46949029 ATATGT-TTTGAAAATTTAATATATAT
1 ATATATATTTTAAAATTTAATATATAT
** *
46949055 GCATATACTTTCAAAATTTAAT-T-TAT
1 ATATATA-TTTTAAAATTTAATATATAT
46949081 AT-T-T-TTTTAAAATTTAATATATAT
1 ATATATATTTTAAAATTTAATATATAT
46949105 TTTTAATATA
Statistics
Matches: 102, Mismatches: 12, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
22 13 0.13
23 8 0.08
24 30 0.29
25 11 0.11
26 19 0.19
27 8 0.08
28 13 0.13
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.52
Consensus pattern (27 bp):
ATATATATTTTAAAATTTAATATATAT
Found at i:46949103 original size:52 final size:51
Alignment explanation
Indices: 46949000--46949104 Score: 160
Period size: 50 Copynumber: 2.1 Consensus size: 51
46948990 TTAAAATTTA
* *
46949000 ATATGTATATATTTTAAAATTTAATTTATATATGTTTTGAAAATTTAATAT
1 ATATGCATATATTTCAAAATTTAATTTATATATGTTTTGAAAATTTAATAT
*
46949051 ATATGCATATACTTTCAAAATTTAATTTATAT-T-TTTTTAAAATTTAATAT
1 ATATGCATATA-TTTCAAAATTTAATTTATATATGTTTTGAAAATTTAATAT
46949101 ATAT
1 ATAT
46949105 TTTTAATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
50 20 0.40
51 11 0.22
52 19 0.38
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (51 bp):
ATATGCATATATTTCAAAATTTAATTTATATATGTTTTGAAAATTTAATAT
Done.