Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 40 of 125
Found at i:12195808 original size:18 final size:18
Alignment explanation
Indices: 12195774--12195809 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12195764 TCCCCATTAT
*
12195774 TAAAAATAATAGAGAATA
1 TAAAAATAAAAGAGAATA
*
12195792 TAAAAATAAAAGTGAATA
1 TAAAAATAAAAGAGAATA
12195810 AATACTGTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (18 bp):
TAAAAATAAAAGAGAATA
Found at i:12196501 original size:21 final size:18
Alignment explanation
Indices: 12196488--12196522 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12196478 CTTCTTTGGA
**
12196488 ATCTTCTTCTTCTTCAAT
1 ATCTTCTTCTTCTTCTTT
12196506 ATCTTCTTCTTCTTCTT
1 ATCTTCTTCTTCTTCTT
12196523 CAGCTTGCTG
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:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (18 bp):
ATCTTCTTCTTCTTCTTT
Found at i:12198986 original size:24 final size:24
Alignment explanation
Indices: 12198953--12199040 Score: 115
Period size: 24 Copynumber: 3.7 Consensus size: 24
12198943 TTTGATTTTT
* ** *
12198953 GGCTCATAAGAGCTAACCACACTA
1 GGCTCGTAAGAGCTAACCATTCTG
12198977 GGCTCGTAAGAGCTAACCATTCTG
1 GGCTCGTAAGAGCTAACCATTCTG
* *
12199001 GGTTCGTAAGAGC-AAACATTCTG
1 GGCTCGTAAGAGCTAACCATTCTG
12199024 GGCTCGTAAGAGCTAAC
1 GGCTCGTAAGAGCTAAC
12199041 TTGTCTAGGT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.38
24 34 0.62
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (24 bp):
GGCTCGTAAGAGCTAACCATTCTG
Found at i:12202793 original size:24 final size:23
Alignment explanation
Indices: 12202759--12202894 Score: 166
Period size: 24 Copynumber: 5.8 Consensus size: 23
12202749 ATTTTGATTT
*
12202759 TGGGCTCGTAAGAACTAACCACTC
1 TGGGCTCGTAAGAGCTAACCA-TC
* *
12202783 TAGGCTCGTAAGAGCTAACCATTT
1 TGGGCTCGTAAGAGCTAACCA-TC
* *
12202807 TGAGCTTGTAAGAGCTAACCATTC
1 TGGGCTCGTAAGAGCTAACCA-TC
*
12202831 TGGGCTCATAAGAGCTAA-CATC
1 TGGGCTCGTAAGAGCTAACCATC
12202853 TGGGCTCGTAAGAGCTAACCTATC
1 TGGGCTCGTAAGAGCTAACC-ATC
*
12202877 TGGGCTCGTATGAGCTAA
1 TGGGCTCGTAAGAGCTAA
12202895 TTTTGTCTTA
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
22 19 0.20
23 3 0.03
24 75 0.77
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.26
Consensus pattern (23 bp):
TGGGCTCGTAAGAGCTAACCATC
Found at i:12205210 original size:14 final size:15
Alignment explanation
Indices: 12205174--12205211 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
12205164 AATAATTTTA
12205174 TATGGAATTTTGAAT
1 TATGGAATTTTGAAT
**
12205189 TAAAGAATTTT-AAT
1 TATGGAATTTTGAAT
12205203 TATGGAATT
1 TATGGAATT
12205212 AAAAGTTAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (15 bp):
TATGGAATTTTGAAT
Found at i:12206813 original size:24 final size:24
Alignment explanation
Indices: 12206780--12206896 Score: 157
Period size: 24 Copynumber: 4.9 Consensus size: 24
12206770 CGTTAATCTG
*
12206780 ATTCTCGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
*
12206804 ATTCTGGGCTCGTAAGAGCTAACT
1 ATTCTGGGCTCGTAAGAGCTAACC
* *
12206828 ATTTTGGACTCGTAAGAGCTAA-C
1 ATTCTGGGCTCGTAAGAGCTAACC
*
12206851 ATTCTGGGCTCGTAAGAACTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
*
12206875 TATT-TGGGCTCGTATGAGCTAA
1 -ATTCTGGGCTCGTAAGAGCTAA
12206897 TTTTTTCTGG
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
23 19 0.23
24 59 0.73
25 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.29
Consensus pattern (24 bp):
ATTCTGGGCTCGTAAGAGCTAACC
Found at i:12206864 original size:47 final size:48
Alignment explanation
Indices: 12206788--12206896 Score: 168
Period size: 47 Copynumber: 2.3 Consensus size: 48
12206778 TGATTCTCGG
*
12206788 CTCGTAAGAGCTAACCATTCTGGGCTCGTAAGAGCTAA-CTATTTTGGA
1 CTCGTAAGAGCTAACCATTCTGGGCTCGTAAGAACTAACCTA-TTTGGA
*
12206836 CTCGTAAGAGCTAA-CATTCTGGGCTCGTAAGAACTAACCTATTTGGG
1 CTCGTAAGAGCTAACCATTCTGGGCTCGTAAGAACTAACCTATTTGGA
*
12206883 CTCGTATGAGCTAA
1 CTCGTAAGAGCTAA
12206897 TTTTTTCTGG
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
47 40 0.70
48 17 0.30
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (48 bp):
CTCGTAAGAGCTAACCATTCTGGGCTCGTAAGAACTAACCTATTTGGA
Found at i:12206896 original size:71 final size:72
Alignment explanation
Indices: 12206780--12206921 Score: 198
Period size: 71 Copynumber: 2.0 Consensus size: 72
12206770 CGTTAATCTG
*
12206780 ATTCTCGGCTCGTAAGAGCTAACCATTCTGGGCTCGTAAGAGCTAACTATTT-TGGACTCGTAAG
1 ATTCTCGGCTCGTAAGAACTAACCATTCTGGGCTCGTAAGAGCTAACTATTTCTGGACTCGTAAG
12206844 AGCTAAC
66 AGCTAAC
* * * * **
12206851 ATTCTGGGCTCGTAAGAACTAACCTATT-TGGGCTCGTATGAGCTAATTTTTTCTGGACTCGTGT
1 ATTCTCGGCTCGTAAGAACTAACC-ATTCTGGGCTCGTAAGAGCTAACTATTTCTGGACTCGTAA
12206915 GAGCTAA
65 GAGCTAA
12206922 AGTTTTGAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
71 43 0.69
72 19 0.31
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (72 bp):
ATTCTCGGCTCGTAAGAACTAACCATTCTGGGCTCGTAAGAGCTAACTATTTCTGGACTCGTAAG
AGCTAAC
Found at i:12210827 original size:27 final size:28
Alignment explanation
Indices: 12210789--12210841 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
12210779 GCTTGATGAG
12210789 TAATCTGATTCT-GGCTCGAAAGAGCGT
1 TAATCTGATTCTGGGCTCGAAAGAGCGT
*
12210816 TAATCTGATTCTGGGCTCGTAAGAGC
1 TAATCTGATTCTGGGCTCGAAAGAGC
12210842 TAACCACTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (28 bp):
TAATCTGATTCTGGGCTCGAAAGAGCGT
Found at i:12210863 original size:24 final size:24
Alignment explanation
Indices: 12210828--12210939 Score: 124
Period size: 24 Copynumber: 4.7 Consensus size: 24
12210818 ATCTGATTCT
12210828 GGGCTCGTAAGAGCTAACCA-CTC
1 GGGCTCGTAAGAGCTAACCATCTC
12210851 GGGACTCGTAAGAGCTAACCATTCTC
1 GGG-CTCGTAAGAGCTAACCA-TCTC
* * *
12210877 -GGATCGTAAGAGCTAA-CATTTT
1 GGGCTCGTAAGAGCTAACCATCTC
*
12210899 GGGCTCGTAAGAGCTAACCTAT-TT
1 GGGCTCGTAAGAGCTAACC-ATCTC
*
12210923 GGGCTCGTATGAGCTAA
1 GGGCTCGTAAGAGCTAA
12210940 TTTTGTGTGG
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
22 2 0.03
23 20 0.26
24 49 0.63
25 4 0.05
26 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (24 bp):
GGGCTCGTAAGAGCTAACCATCTC
Found at i:12210931 original size:47 final size:48
Alignment explanation
Indices: 12210823--12210939 Score: 150
Period size: 47 Copynumber: 2.5 Consensus size: 48
12210813 CGTTAATCTG
12210823 ATTCTGGGCTCGTAAGAGCTAACCACTCGGGACTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACCACTCGGGACTCGTAAGAGCTAACC
* * * *
12210871 ATTCTCGGATCGTAAGAGCTAA-CATTTTGGG-CTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACCA-CTCGGGACTCGTAAGAGCTAACC
*
12210918 TATT-TGGGCTCGTATGAGCTAA
1 -ATTCTGGGCTCGTAAGAGCTAA
12210940 TTTTGTGTGG
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
47 33 0.55
48 27 0.45
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (48 bp):
ATTCTGGGCTCGTAAGAGCTAACCACTCGGGACTCGTAAGAGCTAACC
Found at i:12212349 original size:33 final size:33
Alignment explanation
Indices: 12212312--12212385 Score: 148
Period size: 33 Copynumber: 2.2 Consensus size: 33
12212302 GATGGCTCGG
12212312 CAGCAGCGACGTAGGGGCTTGGGGTGTGCAGCA
1 CAGCAGCGACGTAGGGGCTTGGGGTGTGCAGCA
12212345 CAGCAGCGACGTAGGGGCTTGGGGTGTGCAGCA
1 CAGCAGCGACGTAGGGGCTTGGGGTGTGCAGCA
12212378 CAGCAGCG
1 CAGCAGCG
12212386 CACAACAACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.19, C:0.23, G:0.45, T:0.14
Consensus pattern (33 bp):
CAGCAGCGACGTAGGGGCTTGGGGTGTGCAGCA
Found at i:12214274 original size:16 final size:16
Alignment explanation
Indices: 12214253--12214283 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12214243 ATAATGTGAA
12214253 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
12214269 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
12214284 AGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:12215278 original size:37 final size:37
Alignment explanation
Indices: 12215245--12215320 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
12215235 ATTGCGGTGG
* **
12215245 CAGTTTTGGGTGCAATCTGGAAGTGCTCATGCGGCGA
1 CAGTTTTGGGCGCAATCTAAAAGTGCTCATGCGGCGA
*
12215282 CAGTTTTGGGCGCAATCTAAAAGTGCTCATGCAGCGA
1 CAGTTTTGGGCGCAATCTAAAAGTGCTCATGCGGCGA
12215319 CA
1 CA
12215321 TTAGTAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (37 bp):
CAGTTTTGGGCGCAATCTAAAAGTGCTCATGCGGCGA
Found at i:12221648 original size:200 final size:200
Alignment explanation
Indices: 12221305--12221702 Score: 769
Period size: 200 Copynumber: 2.0 Consensus size: 200
12221295 GATTTGTCAT
12221305 AATATCAAGCACTTGTTGAAGAAAATCCTAATTGATATTGTTCATCATAAGGTAGTACTCATCTT
1 AATATCAAGCACTTGTTGAAGAAAATCCTAATTGATATTGTTCATCATAAGGTAGTACTCATCTT
12221370 CTTCAACATTAGGTAAGTTAAACAAATCATTGATGAACTTAGAAGTAAGAGGTACCTTTTTCTTT
66 CTTCAACATTAGGTAAGTTAAACAAATCATTGATGAACTTAGAAGTAAGAGGTACCTTTTTCTTT
*
12221435 CGAATGATGACCTTAGTAGCATATTGCATAGTCAAACTTGCATAGAACTCTTGAACTAGTTCATC
131 CGAATGATGACCTTAGTAGCATATTGCACAGTCAAACTTGCATAGAACTCTTGAACTAGTTCATC
12221500 ATCAC
196 ATCAC
12221505 AATATCAAGCACTTGTTGAAGAAAATCCTAATTGATATTGTTCATCATAAGGTAGTACTCATCTT
1 AATATCAAGCACTTGTTGAAGAAAATCCTAATTGATATTGTTCATCATAAGGTAGTACTCATCTT
* *
12221570 CTTCAACATTAGGTAAGTTAAACAAATCATTGATGGACTTAGAAGTAAGAGGTCCCTTTTTCTTT
66 CTTCAACATTAGGTAAGTTAAACAAATCATTGATGAACTTAGAAGTAAGAGGTACCTTTTTCTTT
12221635 CGAATGATGACCTTAGTAGCATATTGCACAGTCAAACTTGCATAGAACTCTTGAACTAGTTCATC
131 CGAATGATGACCTTAGTAGCATATTGCACAGTCAAACTTGCATAGAACTCTTGAACTAGTTCATC
12221700 ATC
196 ATC
12221703 GGGAAGTGAA
Statistics
Matches: 195, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
200 195 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (200 bp):
AATATCAAGCACTTGTTGAAGAAAATCCTAATTGATATTGTTCATCATAAGGTAGTACTCATCTT
CTTCAACATTAGGTAAGTTAAACAAATCATTGATGAACTTAGAAGTAAGAGGTACCTTTTTCTTT
CGAATGATGACCTTAGTAGCATATTGCACAGTCAAACTTGCATAGAACTCTTGAACTAGTTCATC
ATCAC
Found at i:12229845 original size:23 final size:22
Alignment explanation
Indices: 12229814--12229857 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
12229804 AAAGAAATAA
*
12229814 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
12229836 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
12229858 GAAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:12236708 original size:28 final size:26
Alignment explanation
Indices: 12236674--12236738 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
12236664 AATTCGATCC
12236674 AAATTATTTAATGAAATATTTTATATTT
1 AAATTATTTAAT-AAA-ATTTTATATTT
* *
12236702 AAATTATTAAATATAATTTTATATTT
1 AAATTATTTAATAAAATTTTATATTT
*
12236728 -TATTATTTAAT
1 AAATTATTTAAT
12236739 TTAGTCATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 9 0.27
26 11 0.33
27 2 0.06
28 11 0.33
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
AAATTATTTAATAAAATTTTATATTT
Found at i:12243525 original size:27 final size:26
Alignment explanation
Indices: 12243495--12243547 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
12243485 ATTAAAACCC
12243495 AAATTATTAATGAAAT-ATTTTATATTT
1 AAATTATTAA--AAATAATTTTATATTT
*
12243522 AAATTATTAAATATAATTTTATATTT
1 AAATTATTAAAAATAATTTTATATTT
12243548 TATTATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 3 0.12
26 11 0.46
27 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
AAATTATTAAAAATAATTTTATATTT
Found at i:12247787 original size:438 final size:438
Alignment explanation
Indices: 12246972--12250371 Score: 6503
Period size: 438 Copynumber: 7.8 Consensus size: 438
12246962 AAAATGACCT
12246972 AATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAATGTCTTGA
1 AATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAATGTCTTGA
12247037 CAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGACAAAGTAATATAAGAATATA
66 CAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGACAAAGTAATATAAGAATATA
*
12247102 AACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGATAAAATAGTTTATAGATCGAGTATGG
131 AACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGG
*
12247167 AAAAATAAATGATAAACTAAATGCAAAAAATAAATGGAATGTGATGAACGGCGGTGGAAGTGTTG
196 AAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTG
*
12247232 GCAAGATATCAAGGGCAAACAATGATGAATGATAATATTGAATGTATTCAGAGTATATTTATATA
261 GCAAGATATCAAGGGCAAACAATGATGAATGATAAGATTGAATGTATTCAGAGTATATTTATATA
* * *
12247297 TTCTAAAATGTCATTGGAATCCTTTAAAACTTGTACTGCTCTATCATGCAATTCTCATGGCAGTG
326 TTCTAAAATGTCATGGGAAACCTTTAAAACTTGTACTGCTCTATTATGCAATTCTCATGGCAGTG
12247362 ATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGA
391 ATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGA
*
12247410 AATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAAGGTCTTGA
1 AATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAATGTCTTGA
* *
12247475 CAAGAAATAACGTCAGGGTAAAGTTTCGTAGTTACTATGCTATGACAAAGTAATATAAGAATATA
66 CAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGACAAAGTAATATAAGAATATA
*
12247540 AACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGATAAAATAGTTTATAGATCGAGTATGG
131 AACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGG
12247605 AAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTG
196 AAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTG
* *
12247670 GCAAGATATCAAGGGCAAACAATGATGAATGATAAGATAGAATGTATTCAGGGTATATTTATATA
261 GCAAGATATCAAGGGCAAACAATGATGAATGATAAGATTGAATGTATTCAGAGTATATTTATATA
* *
12247735 TTCTAAAATGTCATGGGAAACCGTTAAAACTTGTACTGCTCTATTATGCAATTCTCATGGTAGTG
326 TTCTAAAATGTCATGGGAAACCTTTAAAACTTGTACTGCTCTATTATGCAATTCTCATGGCAGTG
12247800 ATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGA
391 ATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGA
12247848 AATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAATGTCTTGA
1 AATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAATGTCTTGA
12247913 CAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGACAAAGTAATATAAGAATATA
66 CAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGACAAAGTAATATAAGAATATA
* *
12247978 AACAAAGTACTAGAAATATAGGTGCTGGAAAATAAAAGATAAAATAGTTTATAGATCGAGTATGG
131 AACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGG
*
12248043 AAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGTCGGTGGAAGTGTTG
196 AAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTG
12248108 GCAAGATATCAAGGGCAAACAATGATGAATGATAAGATTGAATGTATTCAGAGTATATTTATATA
261 GCAAGATATCAAGGGCAAACAATGATGAATGATAAGATTGAATGTATTCAGAGTATATTTATATA
*
12248173 TTCTAAAATGTCATGGGAAACCTTTAAAACTTGTACTGCTCTATCATGCAATTCTCATGGCAGTG
326 TTCTAAAATGTCATGGGAAACCTTTAAAACTTGTACTGCTCTATTATGCAATTCTCATGGCAGTG
12248238 ATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGA
391 ATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGA
*
12248286 AATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAAGGTCTTGA
1 AATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAATGTCTTGA
*
12248351 CAAGAAATAATGTCAGGGTAAAGTTTCGTAGTTACTATGCTATGACAAAGTAATATAAGAATATA
66 CAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGACAAAGTAATATAAGAATATA
*
12248416 AACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGATAAAATAGTTTATAGATCGAGTATGG
131 AACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGG
12248481 AAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTG
196 AAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTG
*
12248546 GCAAGATATCAAGGGCAAACAATGATGAATGATAAGATTGAATGTATTCAGGGTATATTTATATA
261 GCAAGATATCAAGGGCAAACAATGATGAATGATAAGATTGAATGTATTCAGAGTATATTTATATA
12248611 TTCTAAAATGTCATGGGAAACCTTTAAAACTTGTACTGCTCTATTATGCAATTCTCATGGCAGTG
326 TTCTAAAATGTCATGGGAAACCTTTAAAACTTGTACTGCTCTATTATGCAATTCTCATGGCAGTG
12248676 ATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGA
391 ATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGA
12248724 AATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAATGTCTTGA
1 AATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAATGTCTTGA
12248789 CAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGACAAAGTAATATAAGAATATA
66 CAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGACAAAGTAATATAAGAATATA
*
12248854 AACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGAAAAAATAGTTTATATATCGAGTATGG
131 AACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGG
12248919 AAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTG
196 AAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTG
*
12248984 GCAAGATATCAAGGGCAAACAATGATGAATGATAAGATTGAATGTATTCAGGGTATATTTATATA
261 GCAAGATATCAAGGGCAAACAATGATGAATGATAAGATTGAATGTATTCAGAGTATATTTATATA
12249049 TTCTAAAATGTCATGGGAAACCTTTAAAACTTGTACTGCTCTATTATGCAATTCTCATGGCAGTG
326 TTCTAAAATGTCATGGGAAACCTTTAAAACTTGTACTGCTCTATTATGCAATTCTCATGGCAGTG
12249114 ATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGA
391 ATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGA
12249162 AATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAATGTCTTGA
1 AATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAATGTCTTGA
12249227 CAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGACAAAGTAATATAAGAATATA
66 CAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGACAAAGTAATATAAGAATATA
12249292 AACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGAAAAAAATAGTTTATAGATCGAGTATG
131 AACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAG-AAAAAATAGTTTATAGATCGAGTATG
12249357 GAAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTT
195 GAAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTT
*
12249422 GGCAAGATATCAAGGGCAAACAATGATGAATGATAAGATTGAATGTATTCAGGGTATATTTATAT
260 GGCAAGATATCAAGGGCAAACAATGATGAATGATAAGATTGAATGTATTCAGAGTATATTTATAT
12249487 ATTCTAAAATGTCATGGGAAACCTTTAAAACTTGTACTGCTCTATTATGCAATTCTCATGGCAGT
325 ATTCTAAAATGTCATGGGAAACCTTTAAAACTTGTACTGCTCTATTATGCAATTCTCATGGCAGT
12249552 GATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGA
390 GATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGA
12249601 AATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAATGTCTTGA
1 AATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAATGTCTTGA
12249666 CAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGACAAAGTAATATAAGAATATA
66 CAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGACAAAGTAATATAAGAATATA
12249731 AACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGG
131 AACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGG
12249796 AAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTG
196 AAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTG
12249861 GCAAGATATCAAGGGCAAACAATGATGAATGATAAGATTGAATGTATTCAGAGTATATTTATATA
261 GCAAGATATCAAGGGCAAACAATGATGAATGATAAGATTGAATGTATTCAGAGTATATTTATATA
* *
12249926 TTCTAAAATGTCATGGGAATCCTTTAAAACTTGTACTGCTCTATCATGCAATTCTCATGGCAGTG
326 TTCTAAAATGTCATGGGAAACCTTTAAAACTTGTACTGCTCTATTATGCAATTCTCATGGCAGTG
12249991 ATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGA
391 ATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGA
*
12250039 AATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAAGGTCTTGA
1 AATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAATGTCTTGA
* *
12250104 CAAGAAATAATGTCATGGTAAAGTTTCGTAGTTACTATGCTATGACAAAGTAATATAAGAATATA
66 CAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGACAAAGTAATATAAGAATATA
12250169 AACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGG
131 AACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGG
12250234 AAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTG
196 AAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTG
* *
12250299 GCAAGATATCAAGGGCAAACAACGATGAAAGATAAGATTGAATGTATTCAGAGTATATTTATATA
261 GCAAGATATCAAGGGCAAACAATGATGAATGATAAGATTGAATGTATTCAGAGTATATTTATATA
12250364 TTCTAAAA
326 TTCTAAAA
12250372 ATAAAAGATA
Statistics
Matches: 2920, Mismatches: 41, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
438 2483 0.85
439 437 0.15
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.30
Consensus pattern (438 bp):
AATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAATGTCTTGA
CAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGACAAAGTAATATAAGAATATA
AACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGG
AAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTG
GCAAGATATCAAGGGCAAACAATGATGAATGATAAGATTGAATGTATTCAGAGTATATTTATATA
TTCTAAAATGTCATGGGAAACCTTTAAAACTTGTACTGCTCTATTATGCAATTCTCATGGCAGTG
ATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGA
Found at i:12250490 original size:172 final size:172
Alignment explanation
Indices: 12250197--12250543 Score: 658
Period size: 172 Copynumber: 2.0 Consensus size: 172
12250187 TAGATGCTGG
12250197 AAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
1 AAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
12250262 AATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAACGATGA
66 AATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAACGATGA
12250327 AAGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTA
131 AAGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTA
*
12250369 AAAATAAAAGATAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
1 AAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
* *
12250434 AATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAATGGCAAACAATGATGA
66 AATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAACGATGA
*
12250499 ATGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTA
131 AAGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTA
12250541 AAA
1 AAA
12250544 TGTCATGGGA
Statistics
Matches: 171, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
172 171 1.00
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.27
Consensus pattern (172 bp):
AAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
AATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAACGATGA
AAGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTA
Found at i:12250918 original size:610 final size:610
Alignment explanation
Indices: 12249759--12250981 Score: 2347
Period size: 610 Copynumber: 2.0 Consensus size: 610
12249749 TAGATGCTGG
12249759 AAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
1 AAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
12249824 AATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAATGATGA
66 AATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAATGATGA
*
12249889 ATGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTAAAATGTCATGGGAATCCTTTAAA
131 ATGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTAAAATGTCATGGGAAACCTTTAAA
12249954 ACTTGTACTGCTCTATCATGCAATTCTCATGGCAGTGATCACAAACATTTAAACTCCCATTGCAT
196 ACTTGTACTGCTCTATCATGCAATTCTCATGGCAGTGATCACAAACATTTAAACTCCCATTGCAT
12250019 CAATGTGGAGCACATTGTGAAATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTC
261 CAATGTGGAGCACATTGTGAAATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTC
* *
12250084 AGTATATGTTAAGGTCTTGACAAGAAATAATGTCATGGTAAAGTTTCGTAGTTACTATGCTATGA
326 AGTATATGTTAAGGTCTTGACAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGA
12250149 CAAAGTAATATAAGAATATAAACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGAAAAAAT
391 CAAAGTAATATAAGAATATAAACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGAAAAAAT
12250214 AGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGAT
456 AGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGAT
12250279 GAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAACGATGAAAGATAAGATTGAATGT
521 GAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAACGATGAAAGATAAGATTGAATGT
12250344 ATTCAGAGTATATTTATATATTCTA
586 ATTCAGAGTATATTTATATATTCTA
*
12250369 AAAATAAAAGATAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
1 AAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
*
12250434 AATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAATGGCAAACAATGATGA
66 AATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAATGATGA
12250499 ATGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTAAAATGTCATGGGAAACCTTTAAA
131 ATGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTAAAATGTCATGGGAAACCTTTAAA
* *
12250564 ACTTGTACTGCTCTATTATGCAATTCTCATGGCAGTGATCACAAACATTTAAATTCCCATTGCAT
196 ACTTGTACTGCTCTATCATGCAATTCTCATGGCAGTGATCACAAACATTTAAACTCCCATTGCAT
12250629 CAATGTGGAGCACATTGTGAAATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTC
261 CAATGTGGAGCACATTGTGAAATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTC
*
12250694 AGTATATGTTAATGTCTTGACAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGA
326 AGTATATGTTAAGGTCTTGACAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGA
*
12250759 CAAAGTAATATAAGAATATAAACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGATAAAAT
391 CAAAGTAATATAAGAATATAAACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGAAAAAAT
12250824 AGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGAT
456 AGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGAT
* *
12250889 GAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAATGATGAATGATAAGATTGAATGT
521 GAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAACGATGAAAGATAAGATTGAATGT
12250954 ATTCAGAGTATATTTATATATTCTA
586 ATTCAGAGTATATTTATATATTCTA
12250979 AAA
1 AAA
12250982 TGTCATGGGA
Statistics
Matches: 602, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
610 602 1.00
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (610 bp):
AAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
AATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAATGATGA
ATGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTAAAATGTCATGGGAAACCTTTAAA
ACTTGTACTGCTCTATCATGCAATTCTCATGGCAGTGATCACAAACATTTAAACTCCCATTGCAT
CAATGTGGAGCACATTGTGAAATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTC
AGTATATGTTAAGGTCTTGACAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGA
CAAAGTAATATAAGAATATAAACAAAGTACTAGAAATATAGATGCTGGAAAATAAAAGAAAAAAT
AGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGAT
GAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAACGATGAAAGATAAGATTGAATGT
ATTCAGAGTATATTTATATATTCTA
Found at i:12250934 original size:438 final size:438
Alignment explanation
Indices: 12250369--12251418 Score: 2012
Period size: 438 Copynumber: 2.4 Consensus size: 438
12250359 ATATATTCTA
12250369 AAAATAAAAGATAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
1 AAAATAAAAGATAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
*
12250434 AATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAATGGCAAACAATGATGA
66 AATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAATGATGA
12250499 ATGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTAAAATGTCATGGGAAACCTTTAAA
131 ATGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTAAAATGTCATGGGAAACCTTTAAA
* *
12250564 ACTTGTACTGCTCTATTATGCAATTCTCATGGCAGTGATCACAAACATTTAAATTCCCATTGCAT
196 ACTTGTACTGCTCTATCATGCAATTCTCATGGCAGTGATCACAAACATTTAAACTCCCATTGCAT
12250629 CAATGTGGAGCACATTGTGAAATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTC
261 CAATGTGGAGCACATTGTGAAATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTC
*
12250694 AGTATATGTTAATGTCTTGACAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGA
326 AGTATATGTTAAGGTCTTGACAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGA
12250759 CAAAGTAATATAAGAATATAAACAAAGTACTAGAAATATAGATGCTGG
391 CAAAGTAATATAAGAATATAAACAAAGTACTAGAAATATAGATGCTGG
12250807 AAAATAAAAGATAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
1 AAAATAAAAGATAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
12250872 AATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAATGATGA
66 AATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAATGATGA
*
12250937 ATGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTAAAATGTCATGGGAATCCTTTAAA
131 ATGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTAAAATGTCATGGGAAACCTTTAAA
12251002 ACTTGTACTGCTCTATCATGCAATTCTCATGGCAGTGATCACAAACATTTAAACTCCCATTGCAT
196 ACTTGTACTGCTCTATCATGCAATTCTCATGGCAGTGATCACAAACATTTAAACTCCCATTGCAT
*
12251067 CAATGTGGAGCGCATTGTGAAATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTC
261 CAATGTGGAGCACATTGTGAAATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTC
*
12251132 AGTATATGTTAAGGTCTTGACAAGAAATAATGTCAGGGTAAAGTTTCGTAGTTACTATGCTATGA
326 AGTATATGTTAAGGTCTTGACAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGA
12251197 CAAAGTAATATAAGAATATAAACAAAGTACTAGAAATATAGATGCTGG
391 CAAAGTAATATAAGAATATAAACAAAGTACTAGAAATATAGATGCTGG
12251245 AAAATAAAAGA-AAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
1 AAAATAAAAGATAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
*
12251309 AATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAACGATGA
66 AATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAATGATGA
*
12251374 AAGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTAAAA
131 ATGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTAAAA
12251419 ATAAAAGATA
Statistics
Matches: 603, Mismatches: 9, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
437 161 0.27
438 442 0.73
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (438 bp):
AAAATAAAAGATAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
AATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAATGATGA
ATGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTAAAATGTCATGGGAAACCTTTAAA
ACTTGTACTGCTCTATCATGCAATTCTCATGGCAGTGATCACAAACATTTAAACTCCCATTGCAT
CAATGTGGAGCACATTGTGAAATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTC
AGTATATGTTAAGGTCTTGACAAGAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGA
CAAAGTAATATAAGAATATAAACAAAGTACTAGAAATATAGATGCTGG
Found at i:12251138 original size:610 final size:609
Alignment explanation
Indices: 12249912--12251747 Score: 1737
Period size: 610 Copynumber: 3.0 Consensus size: 609
12249902 ATGTATTCAG
* *
12249912 AGTATATTTATATATTCTAAAATGTCATGGGAATCCTTTAAAACTTGTACTGCTCTATCATGCAA
1 AGTATATTTATATATTCTAAAATGTCATGGGAAACCTTTAAAACTTGTACTGCTCTATTATGCAA
12249977 TTCTCATGGCAGTGATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGAAAT
66 TTCTCATGGCAGTGATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGAAAT
*
12250042 TAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAAGGTCTTGACAA
131 TAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAATGTCTTGACAA
*
12250107 GAAATAATGTCATGGTAAAGTTTCGTAGTTACTATGCTATGACAAAGTAATATAAGAATATAAAC
196 GAAATAATGTCA-GGTAAAGTTTAGTAGTTACTATGCTATGACAAAGTAATATAAGAATATAAAC
*
12250172 AAAGTACTAGAAATATAGATGCTGGAAAATAAAAGAAAAAATAGTTTATAGATCGAGTATGGAAA
260 AAAGTACTAGAAATATAGATGCTGGAAAATAAAAGATAAAATAGTTTATAGATCGAGTATGGAAA
12250237 AATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCA
325 AATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCA
*
12250302 AGATATCAAGGGCAAACAACGATGAAAGATAAGATTGAATGTATTCAGAGTATATTTATATATTC
390 AGATATCAAGGGCAAACAATGATGAAAGATAAGATTGAATGTATTCAGAGTATATTTATATATTC
*** * * * * * *** * **
12250367 TAAAA----AT---AAAAGATAAAATAGTT-TA-TAGATCGAGT-ATGGAAAAATAAATGATAAA
455 TAAAATGTCATGGGAAACCTTTAAA-ACTTGTACT-GCTCTA-TCATGCAATTCT-CATG--GCA
* * * *** * * * * * * **
12250422 CTAAATGCA-AAA-A-ATAAA-TGGTATGTG-ATGAACGGCGGTG-GAAGTGTTG---GCAAG--
514 GT-GAT-CACAAACATTTAAACTCCCAT-TGCATCAA-TGTGGAGCGCATTG-TGAAATTAAGTT
* * * ***
12250476 A-TATCAATGGCAAACAATG-ATGAATGATAAGATTGAATGTATTCAG
574 ATTGTC-TTGG-AAA-AA-GAAT-AATG-T--CA-TG---GTATTGTC
12250522 AGTATATTTATATATTCTAAAATGTCATGGGAAACCTTTAAAACTTGTACTGCTCTATTATGCAA
1 AGTATATTTATATATTCTAAAATGTCATGGGAAACCTTTAAAACTTGTACTGCTCTATTATGCAA
*
12250587 TTCTCATGGCAGTGATCACAAACATTTAAATTCCCATTGCATCAATGTGGAGCACATTGTGAAAT
66 TTCTCATGGCAGTGATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGAAAT
12250652 TAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAATGTCTTGACAA
131 TAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAATGTCTTGACAA
12250717 GAAATAATGTCAGGGTAAAGTTTAGTAGTTACTATGCTATGACAAAGTAATATAAGAATATAAAC
196 GAAATAATGTCA-GGTAAAGTTTAGTAGTTACTATGCTATGACAAAGTAATATAAGAATATAAAC
12250782 AAAGTACTAGAAATATAGATGCTGGAAAATAAAAGATAAAATAGTTTATAGATCGAGTATGGAAA
260 AAAGTACTAGAAATATAGATGCTGGAAAATAAAAGATAAAATAGTTTATAGATCGAGTATGGAAA
12250847 AATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCA
325 AATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCA
*
12250912 AGATATCAAGGGCAAACAATGATGAATGATAAGATTGAATGTATTCAGAGTATATTTATATATTC
390 AGATATCAAGGGCAAACAATGATGAAAGATAAGATTGAATGTATTCAGAGTATATTTATATATTC
*
12250977 TAAAATGTCATGGGAATCCTTTAAAACTTGTACTGCTCTATCATGCAATTCTCATGGCAGTGATC
455 TAAAATGTCATGGGAAACCTTTAAAACTTGTACTGCTCTATCATGCAATTCTCATGGCAGTGATC
12251042 ACAAACATTTAAACTCCCATTGCATCAATGTGGAGCGCATTGTGAAATTAAGTTATTGTCTTGGA
520 ACAAACATTTAAACTCCCATTGCATCAATGTGGAGCGCATTGTGAAATTAAGTTATTGTCTTGGA
12251107 AAAAGAATAATGTCATGGTATTGTC
585 AAAAGAATAATGTCATGGTATTGTC
* * * *** * *
12251132 AGTATATGTTA-AGGTCTTGACAAGAAATAATGTCA-GGGTAAA-GTTTCGTA-GT-TACT-ATG
1 AGTATAT-TTATA--TATT--C---TAA-AATGTCATGGG-AAACCTTTAAAACTTGTACTGCT-
* ** * *** * * *** *
12251191 CTATGA--CAA-AGTAATATAAG-AAT-ATAAACA---AAGTACTAGAAAT--AT-AGATGCTGG
55 CTATTATGCAATTCTCATGGCAGTGATCACAAACATTTAA--ACTCCCATTGCATCA-ATG-TGG
* *** * * * *** *
12251245 A--AAATAAAAGAAA-AATAGTTTATAGATCGAGTATGGAAAAA-TA-AATGAT-AAACTAAATG
116 AGCACAT-TGTGAAATTA-AG-TTATTG-TC---T-TGGAAAAAGAATAATG-TCATGGT-ATTG
* ** * * * * * * * *
12251304 -CA--AAAAATAAATGGT-ATG---TG--ATGAACGGC-GGTGGAAGTGTTGGCAAG--A-TAT-
171 TCAGTATATGTTAAT-GTCTTGACAAGAAAT-AATGTCAGGT-AAAGT-TTAG-TAGTTACTATG
* * * * * * * * * * * * *
12251355 CAAGGGCAAA-CAACGATGA-AAGATAAGATTGAATGTATTCAGAGTATATTTATATATTCT-AA
231 CTATGACAAAGTAA-TATAAGAATATAA-A--CAAAGTACT-AGA--A-A--TATAGATGCTGGA
12251417 AAATAAAAGATAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAAA
286 AAATAAAAGATAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAAA
*
12251482 ATAAATGGTATGTGATGAACGGCGGTTGAAGTGTTGGCAAGATATCAAGGGCAAACAATGATGAA
351 ATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAATGATGAA
12251547 AGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTAAAATGTCATGGGAAACCTTTAAAA
416 AGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTAAAATGTCATGGGAAACCTTTAAAA
12251612 CTTGTACTGCTCTATCATGCAATTCTCATGGCAGTGATCACAAACATTTAAACTCCCATTGCATC
481 CTTGTACTGCTCTATCATGCAATTCTCATGGCAGTGATCACAAACATTTAAACTCCCATTGCATC
*
12251677 AATGTGGAGCACATTGTGAAATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTC
546 AATGTGGAGCGCATTGTGAAATTAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTC
12251741 AGTATAT
1 AGTATAT
12251748 GTTAAGGTCT
Statistics
Matches: 1058, Mismatches: 105, Indels: 127
0.82 0.08 0.10
Matches are distributed among these distances:
601 8 0.01
602 11 0.01
603 6 0.01
604 13 0.01
605 10 0.01
606 8 0.01
607 14 0.01
608 10 0.01
609 342 0.32
610 480 0.45
611 13 0.01
612 16 0.02
613 18 0.02
614 8 0.01
615 21 0.02
616 20 0.02
617 32 0.03
618 18 0.02
619 3 0.00
620 4 0.00
621 3 0.00
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (609 bp):
AGTATATTTATATATTCTAAAATGTCATGGGAAACCTTTAAAACTTGTACTGCTCTATTATGCAA
TTCTCATGGCAGTGATCACAAACATTTAAACTCCCATTGCATCAATGTGGAGCACATTGTGAAAT
TAAGTTATTGTCTTGGAAAAAGAATAATGTCATGGTATTGTCAGTATATGTTAATGTCTTGACAA
GAAATAATGTCAGGTAAAGTTTAGTAGTTACTATGCTATGACAAAGTAATATAAGAATATAAACA
AAGTACTAGAAATATAGATGCTGGAAAATAAAAGATAAAATAGTTTATAGATCGAGTATGGAAAA
ATAAATGATAAACTAAATGCAAAAAATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAA
GATATCAAGGGCAAACAATGATGAAAGATAAGATTGAATGTATTCAGAGTATATTTATATATTCT
AAAATGTCATGGGAAACCTTTAAAACTTGTACTGCTCTATCATGCAATTCTCATGGCAGTGATCA
CAAACATTTAAACTCCCATTGCATCAATGTGGAGCGCATTGTGAAATTAAGTTATTGTCTTGGAA
AAAGAATAATGTCATGGTATTGTC
Found at i:12251547 original size:172 final size:171
Alignment explanation
Indices: 12251245--12251590 Score: 665
Period size: 172 Copynumber: 2.0 Consensus size: 171
12251235 TAGATGCTGG
12251245 AAAATAAAAGAAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAAA
1 AAAATAAAAGAAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAAA
12251310 ATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAACGATGAA
66 ATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAACGATGAA
12251375 AGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTA
131 AGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTA
12251416 AAAATAAAAGATAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
1 AAAATAAAAGA-AAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAA
* *
12251481 AATAAATGGTATGTGATGAACGGCGGTTGAAGTGTTGGCAAGATATCAAGGGCAAACAATGATGA
65 AATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAACGATGA
12251546 AAGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTA
130 AAGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTA
12251588 AAA
1 AAA
12251591 TGTCATGGGA
Statistics
Matches: 172, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
171 11 0.06
172 161 0.94
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (171 bp):
AAAATAAAAGAAAAATAGTTTATAGATCGAGTATGGAAAAATAAATGATAAACTAAATGCAAAAA
ATAAATGGTATGTGATGAACGGCGGTGGAAGTGTTGGCAAGATATCAAGGGCAAACAACGATGAA
AGATAAGATTGAATGTATTCAGAGTATATTTATATATTCTA
Found at i:12252551 original size:248 final size:248
Alignment explanation
Indices: 12252097--12252594 Score: 852
Period size: 248 Copynumber: 2.0 Consensus size: 248
12252087 TCACAAACAT
* *
12252097 TTAAATTCCCATTGCATTAATGTGGAGCACATTGTGAAAAGTCCACTTGAATAAACAATAAAGCA
1 TTAAACTCCCATTGCATCAATGTGGAGCACATTGTGAAAAGTCCACTTGAATAAACAATAAAGCA
* *
12252162 TTAGATTAACCATAAATCATTCATTAAAATATAACAAAATATTATCCAAAAAAATAACATTCATA
66 TTAGATTAACCATAAATCATTCATCAAAATATAACAAAATATTATCAAAAAAAATAACATTCATA
* * *
12252227 ACCGTTTCAACAAACTCAATTAAAAATAACTGAAAACCAAGGATGAACATAGGAGCTGTTGTCAC
131 ACCGTTTCAACAAACTCAATAAAAAATAACTAAAAACCAAGGATGAACATAGGAGCTGCTGTCAC
* *
12252292 CAGCTTCCTCCTTCTTCGGCACTTTGGGTAGATCTAGAGGGTAGGGCATCTTC
196 CAGCCTCCTCCTTCTCCGGCACTTTGGGTAGATCTAGAGGGTAGGGCATCTTC
*
12252345 TTAAACTCCCATTGCATCAATGTGGAGCACATTGTGAAAAGTCCACTTGAATAAACAGTAAAGCA
1 TTAAACTCCCATTGCATCAATGTGGAGCACATTGTGAAAAGTCCACTTGAATAAACAATAAAGCA
* *
12252410 TTAGATTAACCATAAATCATTCATCAAAATATAATAAAATATTTTCAAAAAAAATAACATTCATA
66 TTAGATTAACCATAAATCATTCATCAAAATATAACAAAATATTATCAAAAAAAATAACATTCATA
*
12252475 ACCGTTTCAACAAACTCAATAAAAAATAACTAAAAACCAAGGATGAACATAGGAGCTGCTGTCAG
131 ACCGTTTCAACAAACTCAATAAAAAATAACTAAAAACCAAGGATGAACATAGGAGCTGCTGTCAC
** *
12252540 CAGCCTCCTCCTTCTCCGGTTCTTTGGGTAGATCTAGAGGGTAGGGCGTCTTC
196 CAGCCTCCTCCTTCTCCGGCACTTTGGGTAGATCTAGAGGGTAGGGCATCTTC
12252593 TT
1 TT
12252595 CCTCATGTTC
Statistics
Matches: 234, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
248 234 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (248 bp):
TTAAACTCCCATTGCATCAATGTGGAGCACATTGTGAAAAGTCCACTTGAATAAACAATAAAGCA
TTAGATTAACCATAAATCATTCATCAAAATATAACAAAATATTATCAAAAAAAATAACATTCATA
ACCGTTTCAACAAACTCAATAAAAAATAACTAAAAACCAAGGATGAACATAGGAGCTGCTGTCAC
CAGCCTCCTCCTTCTCCGGCACTTTGGGTAGATCTAGAGGGTAGGGCATCTTC
Found at i:12253701 original size:2 final size:2
Alignment explanation
Indices: 12253694--12253734 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
12253684 GCCCTAAAGT
*
12253694 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12253735 CACTTATACT
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:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12260775 original size:84 final size:83
Alignment explanation
Indices: 12260652--12260818 Score: 264
Period size: 84 Copynumber: 2.0 Consensus size: 83
12260642 TTAAAACCAT
* *
12260652 TATTTTTGTCTTTTATATGTTGGGAAAAAATCAAGTTTTAGGAATACCTTGAATTAATTTGATTT
1 TATTTTTGTCTTTTATATATTGGGAAAAAATCAACTTTTAGGAATA-CTTGAATTAATTTGATTT
*
12260717 TCAAAG-AATTTTCGAAGTC
65 TAAAAGAAATTTT-GAAGTC
* *
12260736 TATTTTTTTCTTTTATATATTGGGCAAAAATCAACTTTTAGGAATACTTGAATTAATTTGATTTT
1 TATTTTTGTCTTTTATATATTGGGAAAAAATCAACTTTTAGGAATACTTGAATTAATTTGATTTT
12260801 AAAAGAAATTTTGAAGTC
66 AAAAGAAATTTTGAAGTC
12260819 GGAGGGACTT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
83 29 0.38
84 48 0.62
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.45
Consensus pattern (83 bp):
TATTTTTGTCTTTTATATATTGGGAAAAAATCAACTTTTAGGAATACTTGAATTAATTTGATTTT
AAAAGAAATTTTGAAGTC
Found at i:12277095 original size:17 final size:17
Alignment explanation
Indices: 12277075--12277107 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12277065 CAGCCATCAT
12277075 TTTGTTGTTTCCATTTC
1 TTTGTTGTTTCCATTTC
*
12277092 TTTGTTTTTTCCATTT
1 TTTGTTGTTTCCATTT
12277108 TTATTTTCTT
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:0.06, C:0.15, G:0.09, T:0.70
Consensus pattern (17 bp):
TTTGTTGTTTCCATTTC
Found at i:12287469 original size:77 final size:76
Alignment explanation
Indices: 12287306--12287484 Score: 207
Period size: 77 Copynumber: 2.3 Consensus size: 76
12287296 TAATTTGTGC
* * *
12287306 CCAGCGCTAGTCGGATATACCGACAATATCAAATGTGAGCCTAGCTCTAGTCGGATATACCAACA
1 CCAGCGCTAGTCGGATAAACCGACAATATCAAATGTGAGCCCAGCTCTAGTCGGATAAACCAACA
*
12287371 ATATTTTACTC
66 ATATTTTACTA
** * * * *
12287382 CCAGTTCTAGTCGAATAAACTGACAGATATCAAATGTGAGCCCAGCTCTAGTTGGATAAACCAAT
1 CCAGCGCTAGTCGGATAAACCGACA-ATATCAAATGTGAGCCCAGCTCTAGTCGGATAAACCAAC
* * *
12287447 GATGTTTT-GTAA
65 AATATTTTACT-A
*
12287459 CTAGCGCTAGTCGGATAAACCGACAA
1 CCAGCGCTAGTCGGATAAACCGACAA
12287485 AGATTTTCTC
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
76 22 0.27
77 61 0.73
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (76 bp):
CCAGCGCTAGTCGGATAAACCGACAATATCAAATGTGAGCCCAGCTCTAGTCGGATAAACCAACA
ATATTTTACTA
Found at i:12289520 original size:21 final size:22
Alignment explanation
Indices: 12289496--12289548 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
12289486 CTTTTATAAA
12289496 TTTTATTTATTCTT-ATGTC-AT
1 TTTTATTTATT-TTCATGTCTAT
12289517 TTTTATTTATTTTCATGTCTAT
1 TTTTATTTATTTTCATGTCTAT
*
12289539 TTATATTTAT
1 TTTTATTTAT
12289549 GTTTTTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 2 0.07
21 16 0.55
22 11 0.38
ACGTcount: A:0.21, C:0.08, G:0.04, T:0.68
Consensus pattern (22 bp):
TTTTATTTATTTTCATGTCTAT
Found at i:12291764 original size:42 final size:42
Alignment explanation
Indices: 12291717--12292113 Score: 514
Period size: 42 Copynumber: 9.5 Consensus size: 42
12291707 AAGGAAAGCA
* * * *
12291717 TTCATTGTATTTAGAAGCCAAGGTGTGGAAGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
* *
12291759 TTCATTGCATTTAGAGACTCAA-GAGTGGAGG-CCAATTTACTT
1 TTCATTGCATTTAGAGGC-CAAGGTGTGGAGGTCC-ATTTACTT
*
12291801 TTCATTGCATTTAGAGGCCTAA-GTGTGGAGGTCCGTTTACTT
1 TTCATTGCATTTAGAGGCC-AAGGTGTGGAGGTCCATTTACTT
* *
12291843 TTCATTTCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
* *
12291885 TTCATTTCATTTAGAGGCCCAA-GTGTGGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGG-CCAAGGTGTGGAGGTCCATTTACTT
* * *
12291927 TTCATTTCATTTAGAGGACTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
* * *
12291969 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCAATTTACTT
1 TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
* * * *
12292011 TTCATTGCATTTAAACGCCCAGGTGCGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
* *
12292053 TTCATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
*
12292095 TCCATTGCATTTAGAGGCC
1 TTCATTGCATTTAGAGGCC
12292114 CAGACGTAGA
Statistics
Matches: 316, Mismatches: 32, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
41 6 0.02
42 302 0.96
43 8 0.03
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
Found at i:12293121 original size:21 final size:21
Alignment explanation
Indices: 12293074--12293122 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
12293064 AAAGTAGTAT
* *
12293074 TTTTTTAACAAAGAAAGTTTA
1 TTTTTTAAAAAAGAAAATTTA
** *
12293095 GATTTTAAAAAATAAAATTTA
1 TTTTTTAAAAAAGAAAATTTA
12293116 TTTTTTA
1 TTTTTTA
12293123 GTCATTTTAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (21 bp):
TTTTTTAAAAAAGAAAATTTA
Found at i:12293802 original size:21 final size:21
Alignment explanation
Indices: 12293777--12293829 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
12293767 CTTGGATAAT
12293777 TTTTATTTATTCTT-ATTTC-A
1 TTTTATTTATT-TTCATTTCTA
12293797 TCTTTATTTATTTTCATTTCTA
1 T-TTTATTTATTTTCATTTCTA
12293819 TTTCTATTTAT
1 TTT-TATTTAT
12293830 GTTTTTTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.10
21 17 0.59
22 9 0.31
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTATTTATTTTCATTTCTA
Found at i:12294384 original size:3 final size:3
Alignment explanation
Indices: 12294376--12294415 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
12294366 AAATCTTTTA
12294376 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12294416 GATCGAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12302002 original size:18 final size:18
Alignment explanation
Indices: 12301981--12302019 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
12301971 ATGTCGACCT
* *
12301981 AACTGCCAATGTTGATGC
1 AACTGACAATGTCGATGC
12301999 AACTGACAATGTCGATGC
1 AACTGACAATGTCGATGC
12302017 AAC
1 AAC
12302020 CTGATGTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (18 bp):
AACTGACAATGTCGATGC
Found at i:12314351 original size:175 final size:175
Alignment explanation
Indices: 12314028--12314362 Score: 464
Period size: 175 Copynumber: 1.9 Consensus size: 175
12314018 CTTAATTTCA
* **
12314028 CTGACATCTTTACTCACATTTCATCTAATTTTAGTATTAATTGCTTCGACATATAGACATCAAGA
1 CTGACATCCTTACTCACATTTCATCTAATTTTAACATTAATTGCTTCGACATATAGACATCAAGA
* ** * *
12314093 ACCCATTCCTCATGGGATCGATATCCGATAGAATTATTCTATCAACTATACTTGCTTTGACGTGT
66 ACCCATTCCTCATGGGATCAATATCCGATAGAAGCAATCTATCAACTATACTTGCATTGACGTGT
*
12314158 GTCCGCTTGCACATTGCTGTGATGTTACAGATCGGATCAATTGCG
131 GTCCGCTTGCACATTGCTGTGACGTTACAGATCGGATCAATTGCG
* * *
12314203 CTGACATCCTTACT-AGCATTTTC-TCTAATTTTAACCTTAGTTGCTTCGACA-ATTGAACATCA
1 CTGACATCCTTACTCA-CA-TTTCATCTAATTTTAACATTAATTGCTTCGACATATAG-ACATCA
* *
12314265 AGAACTCC-TTCCTCGTGGGATCAATATCCGATAG-AGCAATCTATCAACTTTACTTGCATTGAC
63 AGAAC-CCATTCCTCATGGGATCAATATCCGATAGAAGCAATCTATCAACTATACTTGCATTGAC
12314328 GTGTGTCCGCTTGCACAATTGCTGTGACGTTACAG
127 GTGTGTCCGCTTGCAC-ATTGCTGTGACGTTACAG
12314363 GTCGACCATT
Statistics
Matches: 141, Mismatches: 14, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
174 44 0.31
175 91 0.65
176 6 0.04
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (175 bp):
CTGACATCCTTACTCACATTTCATCTAATTTTAACATTAATTGCTTCGACATATAGACATCAAGA
ACCCATTCCTCATGGGATCAATATCCGATAGAAGCAATCTATCAACTATACTTGCATTGACGTGT
GTCCGCTTGCACATTGCTGTGACGTTACAGATCGGATCAATTGCG
Found at i:12321833 original size:98 final size:99
Alignment explanation
Indices: 12321708--12321888 Score: 230
Period size: 99 Copynumber: 1.8 Consensus size: 99
12321698 AATAAAATGA
* * *
12321708 CATGAAAATAAATAACAACGAGATAAATTAAA-AAATTAAA-AA-AAATTAAATGCTAAAATAAA
1 CATGAAAATAAATAACAAAGAAATAAA-TAAACAAA--AAACAATAAATTAAATGCCAAAATAAA
12321770 CAAAC-AAATATAAA-AATAAAAATAATTTGGATTAGG
63 C-AACTAAATATAAATAATAAAAATAATTTGGATTAGG
*
12321806 CATGAAAATAAATGAA-AAATAAATAAATAAACAAAAAATCAATAAATTAAATGCCAAAATAAAC
1 CATGAAAATAAAT-AACAAAGAAATAAATAAACAAAAAA-CAATAAATTAAATGCCAAAATAAAC
12321870 AACTAAATATAAATAATAA
64 AACTAAATATAAATAATAA
12321889 TAAAAAAGAA
Statistics
Matches: 72, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
96 3 0.04
97 4 0.06
98 29 0.40
99 31 0.43
100 5 0.07
ACGTcount: A:0.65, C:0.07, G:0.06, T:0.22
Consensus pattern (99 bp):
CATGAAAATAAATAACAAAGAAATAAATAAACAAAAAACAATAAATTAAATGCCAAAATAAACAA
CTAAATATAAATAATAAAAATAATTTGGATTAGG
Found at i:12321835 original size:19 final size:19
Alignment explanation
Indices: 12321811--12321868 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
12321801 TTAGGCATGA
12321811 AAATAAATGAAAAATAAAT
1 AAATAAATGAAAAATAAAT
** *
12321830 AAATAAACAAAAAATCAAT
1 AAATAAATGAAAAATAAAT
*
12321849 AAATTAAATGCCAAAATAAA
1 AAA-TAAATG-AAAAATAAA
12321869 CAACTAAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 19 0.63
20 4 0.13
21 7 0.23
ACGTcount: A:0.71, C:0.07, G:0.03, T:0.19
Consensus pattern (19 bp):
AAATAAATGAAAAATAAAT
Found at i:12323461 original size:15 final size:15
Alignment explanation
Indices: 12323418--12323455 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
12323408 GGAAAATGAT
*
12323418 ATTAATCTAAAGT--
1 ATTAATCTAAACTAA
12323431 ATTAATCTAAACTAA
1 ATTAATCTAAACTAA
12323446 ATTAATCTAA
1 ATTAATCTAA
12323456 GTTAAAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
15 10 0.45
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.37
Consensus pattern (15 bp):
ATTAATCTAAACTAA
Found at i:12327000 original size:18 final size:18
Alignment explanation
Indices: 12326947--12327003 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
12326937 AGGATATTCC
*
12326947 TCAAGATCTTCTTCTTCC
1 TCAAGATCTTCTTCTTCT
*
12326965 TCAAGATCCTCTTCTTCT
1 TCAAGATCTTCTTCTTCT
12326983 TCAAGATCTTCTTCTTCT
1 TCAAGATCTTCTTCTTCT
12327001 TCA
1 TCA
12327004 GCTTGCTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.18, C:0.32, G:0.05, T:0.46
Consensus pattern (18 bp):
TCAAGATCTTCTTCTTCT
Found at i:12330099 original size:17 final size:17
Alignment explanation
Indices: 12330079--12330113 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12330069 TACAATGCAG
12330079 ATGTACTAACAAATGAA
1 ATGTACTAACAAATGAA
* *
12330096 ATGTAGTGACAAATGAA
1 ATGTACTAACAAATGAA
12330113 A
1 A
12330114 ATGCAATGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (17 bp):
ATGTACTAACAAATGAA
Found at i:12330123 original size:18 final size:17
Alignment explanation
Indices: 12330087--12330125 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
12330077 AGATGTACTA
* *
12330087 ACAAATGAAATGTAGTG
1 ACAAATGAAATGCAATG
12330104 ACAAATGAAAATGCAATG
1 ACAAATG-AAATGCAATG
12330122 ACAA
1 ACAA
12330126 CTAAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.54, C:0.10, G:0.18, T:0.18
Consensus pattern (17 bp):
ACAAATGAAATGCAATG
Found at i:12340750 original size:15 final size:15
Alignment explanation
Indices: 12340707--12340744 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
12340697 GGTGAATGAT
*
12340707 ATTAATCTAAAGT--
1 ATTAATCTAAACTAA
12340720 ATTAATCTAAACTAA
1 ATTAATCTAAACTAA
12340735 ATTAATCTAA
1 ATTAATCTAA
12340745 GTTAAAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
15 10 0.45
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.37
Consensus pattern (15 bp):
ATTAATCTAAACTAA
Found at i:12341462 original size:12 final size:12
Alignment explanation
Indices: 12341445--12341470 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12341435 AATTAAAAAA
12341445 ATAATAGCATTC
1 ATAATAGCATTC
12341457 ATAATAGCATTC
1 ATAATAGCATTC
12341469 AT
1 AT
12341471 CATAATAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATAATAGCATTC
Found at i:12348330 original size:24 final size:24
Alignment explanation
Indices: 12348301--12348351 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
12348291 AGAAATAATC
12348301 TTTCAATTAAACTCTATTTAATTG
1 TTTCAATTAAACTCTATTTAATTG
*
12348325 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTAATTG
12348349 TTT
1 TTT
12348352 AAGTCAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTAATTG
Found at i:12348360 original size:24 final size:24
Alignment explanation
Indices: 12348301--12348363 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
12348291 AGAAATAATC
*
12348301 TTTCAATTAAACTCTATTTAATTG
1 TTTCAATCAAACTCTATTTAATTG
* *
12348325 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATCAAACTCTATTTAATTG
12348349 TTT-AAGTCAAACTCT
1 TTTCAA-TCAAACTCT
12348364 TATTAGTCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 2 0.06
24 34 0.94
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (24 bp):
TTTCAATCAAACTCTATTTAATTG
Found at i:12350363 original size:48 final size:48
Alignment explanation
Indices: 12350256--12350365 Score: 168
Period size: 48 Copynumber: 2.3 Consensus size: 48
12350246 GAAATGATCC
*
12350256 TTCAATTAAACTCTGTTTAATTTTTTCAATTAAACTCTGTTTATTTGT
1 TTCAATCAAACTCTGTTTAATTTTTTCAATTAAACTCTGTTTATTTGT
*
12350304 TTCAATTAAACTCTGTTT-ATTTGTTTCAATTAAACTCTGTTTATTTGT
1 TTCAATCAAACTCTGTTTAATTT-TTTCAATTAAACTCTGTTTATTTGT
* *
12350352 TTGAGTCAAACTCT
1 TTCAATCAAACTCT
12350366 TATTAGTCTA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
47 4 0.07
48 54 0.93
ACGTcount: A:0.26, C:0.14, G:0.08, T:0.52
Consensus pattern (48 bp):
TTCAATCAAACTCTGTTTAATTTTTTCAATTAAACTCTGTTTATTTGT
Found at i:12350365 original size:24 final size:24
Alignment explanation
Indices: 12350256--12350353 Score: 180
Period size: 24 Copynumber: 4.1 Consensus size: 24
12350246 GAAATGATCC
12350256 TTCAATTAAACTCTGTTTAATTT-T
1 TTCAATTAAACTCTGTTT-ATTTGT
12350280 TTCAATTAAACTCTGTTTATTTGT
1 TTCAATTAAACTCTGTTTATTTGT
12350304 TTCAATTAAACTCTGTTTATTTGT
1 TTCAATTAAACTCTGTTTATTTGT
12350328 TTCAATTAAACTCTGTTTATTTGT
1 TTCAATTAAACTCTGTTTATTTGT
12350352 TT
1 TT
12350354 GAGTCAAACT
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.05
24 69 0.95
ACGTcount: A:0.26, C:0.12, G:0.07, T:0.55
Consensus pattern (24 bp):
TTCAATTAAACTCTGTTTATTTGT
Found at i:12352031 original size:17 final size:17
Alignment explanation
Indices: 12352009--12352062 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
12351999 TTAATTTAGT
12352009 TAGTTAGTTTAAAGAAA
1 TAGTTAGTTTAAAGAAA
* *
12352026 TAGTTAG-GT-AAG-TA
1 TAGTTAGTTTAAAGAAA
*
12352040 -AGTTAGTTTAAGGAAA
1 TAGTTAGTTTAAAGAAA
12352056 TAGTTAG
1 TAGTTAG
12352063 GTAGCAGTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
13 6 0.21
14 2 0.07
15 5 0.18
16 2 0.07
17 13 0.46
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (17 bp):
TAGTTAGTTTAAAGAAA
Found at i:12353685 original size:19 final size:19
Alignment explanation
Indices: 12353655--12353703 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
12353645 TTAATTGACA
12353655 TTTTTTAA-TTTTTCT-AGT
1 TTTTTTAACTTTTT-TAAGT
12353673 TTTTTTAACTTTTTTAAGT
1 TTTTTTAACTTTTTTAAGT
*
12353692 TTTTTAAACTTT
1 TTTTTTAACTTT
12353704 CTTTTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.69
Consensus pattern (19 bp):
TTTTTTAACTTTTTTAAGT
Found at i:12353849 original size:19 final size:18
Alignment explanation
Indices: 12353825--12353860 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12353815 GTATTTTTAA
12353825 AATTTACCTTATAATTTTC
1 AATTTA-CTTATAATTTTC
*
12353844 AATTTATTTATAATTTT
1 AATTTACTTATAATTTT
12353861 TCAAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (18 bp):
AATTTACTTATAATTTTC
Found at i:12360023 original size:2 final size:2
Alignment explanation
Indices: 12360011--12360058 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
12360001 CTTAGCATTC
12360011 AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12360052 AG AG AG A
1 AG AG AG A
12360059 CTCACGGGTG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12362309 original size:62 final size:62
Alignment explanation
Indices: 12362212--12362336 Score: 187
Period size: 62 Copynumber: 2.0 Consensus size: 62
12362202 CATCCAGACT
* * * * *
12362212 TCATTAAACCAAGGTTTGAGGAGCAAAATATGTTTAAACGTCTAGTCTTACTTACGGGATGG
1 TCATTAAACCAAGGCTTGAGGAACAAAAAATGTTTAAAAGTCTAGTCTAACTTACGGGATGG
* *
12362274 TCATTAAACCAAGGCTTGATGAACAAAAAATGTTTAAAATTCTAGTCTAACTTACGGGATGG
1 TCATTAAACCAAGGCTTGAGGAACAAAAAATGTTTAAAAGTCTAGTCTAACTTACGGGATGG
12362336 T
1 T
12362337 AGGGAGAGTC
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.30
Consensus pattern (62 bp):
TCATTAAACCAAGGCTTGAGGAACAAAAAATGTTTAAAAGTCTAGTCTAACTTACGGGATGG
Found at i:12363645 original size:12 final size:12
Alignment explanation
Indices: 12363613--12363645 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
12363603 CCTTGTCCTA
12363613 TTTTTTTTTCTT
1 TTTTTTTTTCTT
*
12363625 TTTCTTTTTCTT
1 TTTTTTTTTCTT
12363637 TTTTTTTTT
1 TTTTTTTTT
12363646 TAAATCTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:12363646 original size:6 final size:6
Alignment explanation
Indices: 12363613--12363644 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
12363603 CCTTGTCCTA
12363613 TTTT-T TTTTCT TTTTCT TTTTCT TTTT-T TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
12363645 TTAAATCTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 9 0.35
6 17 0.65
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (6 bp):
TTTTCT
Found at i:12364461 original size:24 final size:24
Alignment explanation
Indices: 12364428--12364483 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
12364418 ACATTAAACA
* *
12364428 AATATATTCATGAACATATAATTG
1 AATATGTTCATAAACATATAATTG
12364452 AATATGTTCATAAACATATAATTG
1 AATATGTTCATAAACATATAATTG
*
12364476 AACATGTT
1 AATATGTT
12364484 TACTAACAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (24 bp):
AATATGTTCATAAACATATAATTG
Found at i:12367231 original size:25 final size:23
Alignment explanation
Indices: 12367198--12367252 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
12367188 TCAAGTTTGT
12367198 TTAATTAACATAAACTTAATTCAA
1 TTAATTAACATAAACTTAA-TCAA
* *
12367222 TTAACTTAACTTAACCTTAATCAA
1 TTAA-TTAACATAAACTTAATCAA
12367246 -TAATTAA
1 TTAATTAA
12367253 TGGATATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 4 0.14
23 3 0.11
24 8 0.29
25 13 0.46
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (23 bp):
TTAATTAACATAAACTTAATCAA
Found at i:12380661 original size:24 final size:24
Alignment explanation
Indices: 12380628--12380730 Score: 127
Period size: 24 Copynumber: 4.3 Consensus size: 24
12380618 ACTCTATCTG
12380628 GGCTCGTAAGAGCTAATCATTCTA
1 GGCTCGTAAGAGCTAATCATTCTA
* * *
12380652 AGCTCGTAAGAGTTAATCATTCTT
1 GGCTCGTAAGAGCTAATCATTCTA
*
12380676 GGCTCTTAAGAGCTAATCATTC-A
1 GGCTCGTAAGAGCTAATCATTCTA
* * *
12380699 GGGTTCGTAAAAGCTAATAATTCTA
1 -GGCTCGTAAGAGCTAATCATTCTA
12380724 GGCTCGT
1 GGCTCGT
12380731 GTTGGCTAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
24 64 0.98
25 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (24 bp):
GGCTCGTAAGAGCTAATCATTCTA
Found at i:12385192 original size:23 final size:24
Alignment explanation
Indices: 12385123--12385200 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 24
12385113 AAACTCTGTT
* *
12385123 TGGGCTCGTATGAGCTAATCATTC
1 TGGGCTCTTAAGAGCTAATCATTC
*
12385147 TGGGCT-TGTAAGAGCTAATCATTA
1 TGGGCTCT-TAAGAGCTAATCATTC
12385171 TGGGCTCTTAAGAG-TAATCATTC
1 TGGGCTCTTAAGAGCTAATCATTC
12385194 TGGGCTC
1 TGGGCTC
12385201 GTGTTGGCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
23 15 0.31
24 32 0.67
25 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (24 bp):
TGGGCTCTTAAGAGCTAATCATTC
Found at i:12386388 original size:24 final size:24
Alignment explanation
Indices: 12386355--12386400 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
12386345 GGTTGGTTCA
* **
12386355 AAGGATAAGAAATGGAAGAAACGC
1 AAGGACAAGAAAAAGAAGAAACGC
12386379 AAGGACAAGAAAAAGAAGAAAC
1 AAGGACAAGAAAAAGAAGAAAC
12386401 CCCATGACGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.61, C:0.09, G:0.26, T:0.04
Consensus pattern (24 bp):
AAGGACAAGAAAAAGAAGAAACGC
Found at i:12395370 original size:25 final size:22
Alignment explanation
Indices: 12395332--12395395 Score: 56
Period size: 25 Copynumber: 2.6 Consensus size: 22
12395322 CCCTATTCTT
*
12395332 CCCCTTTGTGTCTCACTCCATCTCA
1 CCCCTTT-TTTCTC-CTCC-TCTCA
*
12395357 CCCCTTTATTTCTCCTTCTCTCA
1 CCCCTTT-TTTCTCCTCCTCTCA
12395380 CCATCCTTTTTTCTCC
1 CC--CCTTTTTTCTCC
12395396 ATTTTAGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 7 0.21
24 10 0.29
25 17 0.50
ACGTcount: A:0.09, C:0.44, G:0.03, T:0.44
Consensus pattern (22 bp):
CCCCTTTTTTCTCCTCCTCTCA
Found at i:12396920 original size:22 final size:22
Alignment explanation
Indices: 12396878--12396944 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 22
12396868 ATTCACATGT
**
12396878 TTTCTTACTCATGATTC-TTTTG
1 TTTC-TACTCATTTTTCTTTTTG
12396900 TTTCTACTCATTTTTCTTTTTTG
1 TTTCTACTCATTTTTC-TTTTTG
12396923 TTTCT-CT-ATTTCTCTCTTTTTG
1 TTTCTACTCATTT-T-TCTTTTTG
12396945 GCTAAACTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 14 0.36
22 13 0.33
23 12 0.31
ACGTcount: A:0.09, C:0.19, G:0.06, T:0.66
Consensus pattern (22 bp):
TTTCTACTCATTTTTCTTTTTG
Found at i:12396933 original size:21 final size:24
Alignment explanation
Indices: 12396895--12396944 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
12396885 CTCATGATTC
*
12396895 TTTTGTTTCTACTCATTTTTCT-T
1 TTTTGTTTCTACTCATTTCTCTCT
12396918 TTTTGTTTCT-CT-ATTTCTCTCT
1 TTTTGTTTCTACTCATTTCTCTCT
12396940 TTTTG
1 TTTTG
12396945 GCTAAACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 7 0.28
22 8 0.32
23 10 0.40
ACGTcount: A:0.06, C:0.18, G:0.06, T:0.70
Consensus pattern (24 bp):
TTTTGTTTCTACTCATTTCTCTCT
Found at i:12405552 original size:18 final size:18
Alignment explanation
Indices: 12405529--12405563 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12405519 TATTTACTTG
*
12405529 ATTGATGATTATATGTTT
1 ATTGATAATTATATGTTT
*
12405547 ATTGATAATTATTTGTT
1 ATTGATAATTATATGTT
12405564 AAAAGACTTA
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:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (18 bp):
ATTGATAATTATATGTTT
Found at i:12412589 original size:18 final size:18
Alignment explanation
Indices: 12412566--12412600 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12412556 TGTTTACTTG
*
12412566 ATTGATGATTATATGTTT
1 ATTGATAATTATATGTTT
*
12412584 ATTGATAATTATTTGTT
1 ATTGATAATTATATGTT
12412601 AAAAGACTCA
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:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (18 bp):
ATTGATAATTATATGTTT
Found at i:12416404 original size:5 final size:5
Alignment explanation
Indices: 12416394--12416423 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
12416384 GTTTATCTCT
12416394 AATTA AATTA AATTA AATTA AATT- AATTA A
1 AATTA AATTA AATTA AATTA AATTA AATTA A
12416424 TAAAGAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:12420142 original size:31 final size:31
Alignment explanation
Indices: 12420081--12420143 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
12420071 ACGGCAAGTA
*
12420081 ACTAAAATGATAAAAGCTTGTAACAGTAATG
1 ACTAAAATGATAAAAGCTTGTAACAATAATG
*
12420112 ACTAAAATGATAAAAG-TGTGTAGCAATAATG
1 ACTAAAATGATAAAAGCT-TGTAACAATAATG
12420143 A
1 A
12420144 TTATATTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.25
Consensus pattern (31 bp):
ACTAAAATGATAAAAGCTTGTAACAATAATG
Found at i:12421418 original size:15 final size:15
Alignment explanation
Indices: 12421398--12421426 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12421388 TGACCAATCT
12421398 TTTCAAATATATTAG
1 TTTCAAATATATTAG
12421413 TTTCAAATATATTA
1 TTTCAAATATATTA
12421427 ACTTATCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.48
Consensus pattern (15 bp):
TTTCAAATATATTAG
Found at i:12435015 original size:21 final size:21
Alignment explanation
Indices: 12434989--12435040 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
12434979 TGAGATAATA
12434989 CTACCGATACAAGT-ATGACTT
1 CTACCGATACAAGTCATG-CTT
* *
12435010 CTACCGAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
12435031 CTACCGATAC
1 CTACCGATAC
12435041 TAAAAACTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Found at i:12441919 original size:79 final size:79
Alignment explanation
Indices: 12441805--12442020 Score: 224
Period size: 79 Copynumber: 2.7 Consensus size: 79
12441795 GAAAAATGTG
* * * **
12441805 GCACCCAATGCCTGGCGGAATAACCGCGAAAGTGAG-TCCAACTTTAGTTGGATT-AACCAACAA
1 GCACCCAGTGCCTAGCGG-ATAACCGCGAAAGTGAGCT-CAACTCTAGTCAG-TTAAACCAACAA
12441868 ATATCCGTCAAATCCTA
63 ATATCCGTCAAATCCTA
* * *
12441885 GCACCTAGTGCTTAGCGGATAACCGC-AAATGTGAGCTCAACTCTAGTCAGTTAAACCGACAAAT
1 GCACCCAGTGCCTAGCGGATAACCGCGAAA-GTGAGCTCAACTCTAGTCAGTTAAACCAACAAAT
* *
12441949 ATCCGTCAAATCTTG
65 ATCCGTCAAATCCTA
* * * *
12441964 GCACCCAGTGCCTAGCGGATAAATCG-TAATTGTGAGCCCAACTCTAGTCAGTTAAAC
1 GCACCCAGTGCCTAGCGGAT-AACCGCGAA-AGTGAGCTCAACTCTAGTCAGTTAAAC
12442021 TGACAACATA
Statistics
Matches: 115, Mismatches: 15, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
78 5 0.04
79 64 0.56
80 46 0.40
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (79 bp):
GCACCCAGTGCCTAGCGGATAACCGCGAAAGTGAGCTCAACTCTAGTCAGTTAAACCAACAAATA
TCCGTCAAATCCTA
Found at i:12445941 original size:24 final size:23
Alignment explanation
Indices: 12445914--12445967 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
12445904 AAAACAAGTG
*
12445914 AAAAGAAC-AAAAAGAAAATGAGT
1 AAAAAAACAAAAAAGAAAA-GAGT
*
12445937 AAAAATACAAAAAAGAAAAGAGT
1 AAAAAAACAAAAAAGAAAAGAGT
12445960 AAGAAAAA
1 AA-AAAAA
12445968 GTGTGAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.74, C:0.04, G:0.15, T:0.07
Consensus pattern (23 bp):
AAAAAAACAAAAAAGAAAAGAGT
Found at i:12449527 original size:14 final size:14
Alignment explanation
Indices: 12449508--12449561 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
12449498 TTACCACAAG
12449508 ACAATATCATCCAA
1 ACAATATCATCCAA
*
12449522 ACAATATGATTACCACAA
1 ACAATATCA-T--C-CAA
12449540 GACAATATCATCCAA
1 -ACAATATCATCCAA
12449555 ACAATAT
1 ACAATAT
12449562 GATTATTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 15 0.45
15 4 0.12
16 1 0.03
17 1 0.03
18 4 0.12
19 8 0.24
ACGTcount: A:0.50, C:0.24, G:0.04, T:0.22
Consensus pattern (14 bp):
ACAATATCATCCAA
Found at i:12449540 original size:33 final size:33
Alignment explanation
Indices: 12449498--12449566 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
12449488 ACACTAACGT
12449498 TTACCACAAGACAATATCATCCAAACAATATGA
1 TTACCACAAGACAATATCATCCAAACAATATGA
12449531 TTACCACAAGACAATATCATCCAAACAATATGA
1 TTACCACAAGACAATATCATCCAAACAATATGA
12449564 TTA
1 TTA
12449567 TTTGGATCAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.23, G:0.06, T:0.23
Consensus pattern (33 bp):
TTACCACAAGACAATATCATCCAAACAATATGA
Found at i:12449544 original size:19 final size:19
Alignment explanation
Indices: 12449498--12449550 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
12449488 ACACTAACGT
12449498 TTACCACAAGACAATATCA
1 TTACCACAAGACAATATCA
*
12449517 -T--C-CAA-ACAATATGA
1 TTACCACAAGACAATATCA
12449531 TTACCACAAGACAATATCA
1 TTACCACAAGACAATATCA
12449550 T
1 T
12449551 CCAAACAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
14 8 0.30
15 4 0.15
16 1 0.04
17 1 0.04
18 4 0.15
19 9 0.33
ACGTcount: A:0.47, C:0.25, G:0.06, T:0.23
Consensus pattern (19 bp):
TTACCACAAGACAATATCA
Found at i:12449558 original size:19 final size:19
Alignment explanation
Indices: 12449503--12449558 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
12449493 AACGTTTACC
12449503 ACAAGACAATATCATCCAA
1 ACAAGACAATATCATCCAA
* **
12449522 ACAATATGAT-T-A-CC--
1 ACAAGACAATATCATCCAA
12449536 ACAAGACAATATCATCCAA
1 ACAAGACAATATCATCCAA
12449555 ACAA
1 ACAA
12449559 TATGATTATT
Statistics
Matches: 26, Mismatches: 6, Indels: 10
0.62 0.14 0.24
Matches are distributed among these distances:
14 7 0.27
15 1 0.04
16 3 0.12
17 3 0.12
18 1 0.04
19 11 0.42
ACGTcount: A:0.52, C:0.25, G:0.05, T:0.18
Consensus pattern (19 bp):
ACAAGACAATATCATCCAA
Found at i:12456690 original size:13 final size:14
Alignment explanation
Indices: 12456672--12456700 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12456662 TCAAACTTAC
12456672 TTTATTTTTAT-CT
1 TTTATTTTTATGCT
12456685 TTTATTTTTATGCT
1 TTTATTTTTATGCT
12456699 TT
1 TT
12456701 CAAACAACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTATTTTTATGCT
Found at i:12460580 original size:24 final size:24
Alignment explanation
Indices: 12460540--12460589 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
12460530 AATAATATTC
12460540 CAATTAAACTTTATTTATTTGTTT
1 CAATTAAACTTTATTTATTTGTTT
* *
12460564 CAATTAAATTTTGTTTATTTGTTT
1 CAATTAAACTTTATTTATTTGTTT
12460588 CA
1 CA
12460590 GTCGAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (24 bp):
CAATTAAACTTTATTTATTTGTTT
Found at i:12463932 original size:36 final size:35
Alignment explanation
Indices: 12463853--12463955 Score: 134
Period size: 36 Copynumber: 2.9 Consensus size: 35
12463843 AATATAATCA
* *
12463853 GTCACATGGCATAAAGAACATACTCACATATTTCT
1 GTCACATGGCATGAAGAACATACCCACATATTTCT
* * *
12463888 ATCTCATGGCATGAAGAACATACCCATATATTTTCT
1 GTCACATGGCATGAAGAACATACCCACATA-TTTCT
**
12463924 GTCACATGGCATGAAGAACATAAACACATATT
1 GTCACATGGCATGAAGAACATACCCACATATT
12463956 CACTTTCACA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 27 0.47
36 30 0.53
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (35 bp):
GTCACATGGCATGAAGAACATACCCACATATTTCT
Found at i:12464365 original size:23 final size:23
Alignment explanation
Indices: 12464035--12464363 Score: 498
Period size: 23 Copynumber: 14.3 Consensus size: 23
12464025 ATCTTAATTC
12464035 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
12464058 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
12464081 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
12464104 TTTAAGCATAAATCACATTAA-A
1 TTTAAGCACAAATCACATTAATA
*
12464126 TTTGAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
12464149 TATAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
12464172 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
12464195 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
12464218 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
** * *
12464241 TTTAAGCGTAAATCAAATTAATT
1 TTTAAGCACAAATCACATTAATA
12464264 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
12464287 TTTGAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
12464310 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
12464333 TTTAAGCATAAATTATATTAATA
1 TTTAAGCACAAATCACATTAATA
12464356 TTTAAGCA
1 TTTAAGCA
12464364 TACATATAAG
Statistics
Matches: 275, Mismatches: 30, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
22 20 0.07
23 255 0.93
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.33
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:12471884 original size:19 final size:20
Alignment explanation
Indices: 12471860--12471901 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
12471850 ACGAAATTAA
*
12471860 AAATTAAGCTTAATTAAA-T
1 AAATTAAGATTAATTAAACT
*
12471879 AAATTAAGATTGATTAAACT
1 AAATTAAGATTAATTAAACT
12471899 AAA
1 AAA
12471902 ACATGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (20 bp):
AAATTAAGATTAATTAAACT
Found at i:12474123 original size:19 final size:17
Alignment explanation
Indices: 12474086--12474125 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
12474076 AAAATTTAAA
*
12474086 TTAAAAAATTTACCGTT
1 TTAAAAAATTTACCCTT
12474103 TTAAAAAATTATAACCCTT
1 TTAAAAAATT-T-ACCCTT
12474122 TTAA
1 TTAA
12474126 TCTTTTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 1 0.05
19 9 0.45
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (17 bp):
TTAAAAAATTTACCCTT
Found at i:12474621 original size:2 final size:2
Alignment explanation
Indices: 12474616--12474644 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12474606 CCTTTTTTAT
12474616 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12474645 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12474955 original size:15 final size:16
Alignment explanation
Indices: 12474919--12474958 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
12474909 ATATTATAAA
12474919 TATAATTTTATCATTTT
1 TATAA-TTTATCATTTT
*
12474936 AATAATTTAT-ATTTT
1 TATAATTTATCATTTT
12474951 TATAATTT
1 TATAATTT
12474959 TTAAATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 12 0.57
16 5 0.24
17 4 0.19
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATTTATCATTTT
Found at i:12474987 original size:29 final size:31
Alignment explanation
Indices: 12474946--12475010 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 31
12474936 AATAATTTAT
*
12474946 ATTTTTATAATTTTT-AAATATTAAATTA-A
1 ATTTTTATAATTTTTAAAATATTAAAATATA
* *
12474975 ATTTTTATTATTTTTAAAATGTTAAAATATA
1 ATTTTTATAATTTTTAAAATATTAAAATATA
12475006 ATTTT
1 ATTTT
12475011 ATCATTACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 14 0.45
30 11 0.35
31 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (31 bp):
ATTTTTATAATTTTTAAAATATTAAAATATA
Found at i:12475011 original size:30 final size:29
Alignment explanation
Indices: 12474943--12475012 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
12474933 TTTAATAATT
* *
12474943 TATATTTTTATAATTTTTAAATATTAAAT
1 TATAATTTTATAATTTTTAAATATTAAAA
* *
12474972 TA-AATTTTTATTATTTTTAAAATGTTAAAA
1 TATAA-TTTTATAATTTTT-AAATATTAAAA
12475002 TATAATTTTAT
1 TATAATTTTAT
12475013 CATTACTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
28 1 0.03
29 14 0.41
30 17 0.50
31 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (29 bp):
TATAATTTTATAATTTTTAAATATTAAAA
Found at i:12475065 original size:83 final size:82
Alignment explanation
Indices: 12474916--12475071 Score: 188
Period size: 83 Copynumber: 1.9 Consensus size: 82
12474906 ATGATATTAT
* * * * * * **
12474916 AAATATAATTTTATCATTTTAATAATTTATATTTTTATAATTTTTAAATATTAAATTAAATTTTT
1 AAATATAATTTTATCA-TTTAATAATTTAAAATTTTATAATTATAAAAAATTAAATAAAAAATTT
*
12474981 ATTATTTTTAAAATGTTA
65 ATCATTTTTAAAATGTTA
*
12474999 AAATATAATTTTATCA-TTACTAATTTAAAATTTTATAAATTATAAAAAATCTAAATAAAAAATT
1 AAATATAATTTTATCATTTAATAATTTAAAATTTTAT-AATTATAAAAAAT-TAAATAAAAAATT
12475063 TATCATTTT
64 TATCATTTT
12475072 AAAGAGATTA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
81 17 0.28
82 10 0.16
83 34 0.56
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.51
Consensus pattern (82 bp):
AAATATAATTTTATCATTTAATAATTTAAAATTTTATAATTATAAAAAATTAAATAAAAAATTTA
TCATTTTTAAAATGTTA
Found at i:12475087 original size:83 final size:83
Alignment explanation
Indices: 12474911--12475088 Score: 184
Period size: 83 Copynumber: 2.1 Consensus size: 83
12474901 TTTATATGAT
* * * * * *
12474911 ATTATAAATATAATTTTATCATTTTAATAATTTATATTTTTATAATTTTTAAATATTAAATTAAA
1 ATTAT-AATATAATTTTATCA-TTTAATAATTTAAAATTTTATAATTATAAAAAATTAAATAAAA
** *
12474976 TTTTTATTATTTTTAAAATG
64 AATTTATCATTTTTAAAATG
* *
12474996 -TTAAAATATAATTTTATCA-TTACTAATTTAAAATTTTATAAATTATAAAAAATCTAAATAAAA
1 ATTATAATATAATTTTATCATTTAATAATTTAAAATTTTAT-AATTATAAAAAAT-TAAATAAAA
12475059 AATTTATCA-TTTTAAAGA-G
64 AATTTATCATTTTTAAA-ATG
12475078 ATTATAATATA
1 ATTATAATATA
12475089 TATACAAAGG
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
81 17 0.22
82 18 0.23
83 39 0.51
84 3 0.04
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.49
Consensus pattern (83 bp):
ATTATAATATAATTTTATCATTTAATAATTTAAAATTTTATAATTATAAAAAATTAAATAAAAAA
TTTATCATTTTTAAAATG
Found at i:12477084 original size:81 final size:84
Alignment explanation
Indices: 12476961--12477205 Score: 241
Period size: 93 Copynumber: 2.8 Consensus size: 84
12476951 AATTGCCTCT
* * * *
12476961 AGAATCCGTTGAACCTCCAAGTACTTCGA-AAACTCCGAAAGTTGTCAAAGAGAAAACCAAGAAG
1 AGAATCTGTTGAACCTCCAAGGACTTC-ACAAATTCCGGAAGTTGTCAAAGAGAAAACCAAGAAG
* *
12477025 AAGATC-AG-CA-AAGTTGA
65 AAGAACAAGACAGAAGCTGA
* * **
12477042 AGAATCTGTTGAACCTCCAAGGACTTCACTAATTTCGGAAGTTGTCCTAGAGAAAA-CAGAGAAG
1 AGAATCTGTTGAACCTCCAAGGACTTCACAAATTCCGGAAGTTGTCAAAGAGAAAACCA-AGAAG
12477106 AAGAACAAGGAAAAGATCAGTGAAGCTGA
65 AAGAAC------AAGA-CA--GAAGCTGA
*
12477135 AGAATCTGTTGAACCTCCAAGGGA-TTCACAAATTCCGGAAGTTGTCAAAGAGAAAACCGAGAAG
1 AGAATCTGTTGAACCTCCAA-GGACTTCACAAATTCCGGAAGTTGTCAAAGAGAAAACCAAGAAG
12477199 AAGAACA
65 AAGAACA
12477206 CGAAAAAGAT
Statistics
Matches: 133, Mismatches: 15, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
80 3 0.02
81 56 0.42
87 1 0.01
88 2 0.02
90 2 0.02
93 65 0.49
94 4 0.03
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (84 bp):
AGAATCTGTTGAACCTCCAAGGACTTCACAAATTCCGGAAGTTGTCAAAGAGAAAACCAAGAAGA
AGAACAAGACAGAAGCTGA
Found at i:12477187 original size:93 final size:93
Alignment explanation
Indices: 12477018--12477230 Score: 302
Period size: 93 Copynumber: 2.3 Consensus size: 93
12477008 AAGAGAAAAC
* * * * *
12477018 CAAGAAGAAGATCAGCAAAGTTGAAGAATCTGTTGAACCTCCAAGGACTTCACTAATTTCGGAAG
1 CAAGAAAAAGATCAGTAAAGCTGAAGAATCTGTTGAACCTCCAAGGACTTCACAAATTCCGGAAG
**
12477083 TTGTCCTAGAGAAAACAGAGAAGAAGAA
66 TTGTCAAAGAGAAAACAGAGAAGAAGAA
* *
12477111 CAAGGAAAAGATCAGTGAAGCTGAAGAATCTGTTGAACCTCCAAGGGA-TTCACAAATTCCGGAA
1 CAAGAAAAAGATCAGTAAAGCTGAAGAATCTGTTGAACCTCCAA-GGACTTCACAAATTCCGGAA
*
12477175 GTTGTCAAAGAGAAAACCGAGAAGAAGAA
65 GTTGTCAAAGAGAAAACAGAGAAGAAGAA
* *
12477204 CACGAAAAAGATCAGTAAAGCTAAAGA
1 CAAGAAAAAGATCAGTAAAGCTGAAGA
12477231 TAACAAGGCT
Statistics
Matches: 105, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
93 102 0.97
94 3 0.03
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (93 bp):
CAAGAAAAAGATCAGTAAAGCTGAAGAATCTGTTGAACCTCCAAGGACTTCACAAATTCCGGAAG
TTGTCAAAGAGAAAACAGAGAAGAAGAA
Found at i:12480116 original size:23 final size:24
Alignment explanation
Indices: 12480090--12480135 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
12480080 GTAAAATTTT
12480090 AATT-AATGATTAATTCG-ATTTAA
1 AATTGAATGATTAA-TCGAATTTAA
*
12480113 AATTGATTGATTAATCGAATTTA
1 AATTGAATGATTAATCGAATTTA
12480136 TTAAACTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.43
Consensus pattern (24 bp):
AATTGAATGATTAATCGAATTTAA
Found at i:12489381 original size:17 final size:19
Alignment explanation
Indices: 12489343--12489385 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
12489333 TCCTATTGAC
*
12489343 TAAAAA-AATTAATATTTA
1 TAAAAATAATTAATAGTTA
12489361 TAAAAATAATT-ATAGTT-
1 TAAAAATAATTAATAGTTA
12489378 TAAAAATA
1 TAAAAATA
12489386 TTTACTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 8 0.35
18 11 0.48
19 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
TAAAAATAATTAATAGTTA
Found at i:12490311 original size:3 final size:3
Alignment explanation
Indices: 12490299--12490343 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
12490289 TTTAGGGTTT
*
12490299 AAG AAG -AG AAG AAG AAG AAG AAG AAG AAG AAG AAG GAG AA- AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
12490344 AAAATGGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12490871 original size:21 final size:21
Alignment explanation
Indices: 12490845--12490887 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12490835 CTACGTGGCA
* *
12490845 AGTTAACTGGCCATATTAGCT
1 AGTTAACTGGCCACATAAGCT
*
12490866 AGTTAACTTGCCACATAAGCT
1 AGTTAACTGGCCACATAAGCT
12490887 A
1 A
12490888 TAACACCCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (21 bp):
AGTTAACTGGCCACATAAGCT
Found at i:12491717 original size:21 final size:21
Alignment explanation
Indices: 12491693--12491756 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
12491683 CCGACCCGAC
* *
12491693 CCATTGACCGTTGATAGTTGA
1 CCATTGACTGTTAATAGTTGA
12491714 CCATTGACTGTTAATAGTTGA
1 CCATTGACTGTTAATAGTTGA
12491735 CCATTGACTGTTAATAGTTGA
1 CCATTGACTGTTAATAGTTGA
12491756 C
1 C
12491757 TTTTGGGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (21 bp):
CCATTGACTGTTAATAGTTGA
Found at i:12492822 original size:5 final size:5
Alignment explanation
Indices: 12492812--12492845 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
12492802 AATTATAGGC
12492812 TTATT TTATT TTATCTT TTATT TTATT TTATT TT
1 TTATT TTATT TTA--TT TTATT TTATT TTATT TT
12492846 TGGGTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 22 0.81
7 5 0.19
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:12492834 original size:17 final size:16
Alignment explanation
Indices: 12492812--12492846 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
12492802 AATTATAGGC
12492812 TTATTTTATTTTATCTT
1 TTATTTTATTTTAT-TT
12492829 TTATTTTATTTTATTT
1 TTATTTTATTTTATTT
12492845 TT
1 TT
12492847 GGGTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (16 bp):
TTATTTTATTTTATTT
Found at i:12493862 original size:9 final size:9
Alignment explanation
Indices: 12493839--12493911 Score: 64
Period size: 8 Copynumber: 8.4 Consensus size: 9
12493829 GGTTTAAGAA
12493839 AAGAAAAAG
1 AAGAAAAAG
12493848 AA-AAAAAG
1 AAGAAAAAG
12493856 AAGAAAAAG
1 AAGAAAAAG
*
12493865 AAGAAGAAG
1 AAGAAAAAG
*
12493874 AAGGAGAAAG
1 AA-GAAAAAG
*
12493884 -AGAAGAAG
1 AAGAAAAAG
*
12493892 GAG-AAAAG
1 AAGAAAAAG
*
12493900 AA-AAAATG
1 AAGAAAAAG
12493908 AAGA
1 AAGA
12493912 TGCCTGAAGA
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
8 24 0.47
9 22 0.43
10 5 0.10
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.01
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:12493873 original size:15 final size:15
Alignment explanation
Indices: 12493837--12493898 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 15
12493827 AGGGTTTAAG
*
12493837 AAAAGAAAAAGAA-A
1 AAAAGAAGAAGAAGA
*
12493851 AAAAGAAGAAAAAGA
1 AAAAGAAGAAGAAGA
* *
12493866 AGAAGAAGAAGGAGA
1 AAAAGAAGAAGAAGA
* *
12493881 AAGAGAAGAAGGAGA
1 AAAAGAAGAAGAAGA
12493896 AAA
1 AAA
12493899 GAAAAAATGA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
14 11 0.28
15 28 0.72
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAAAGAAGAAGAAGA
Found at i:12494426 original size:21 final size:21
Alignment explanation
Indices: 12494402--12494442 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
12494392 CTACGTGGCA
12494402 AGTTAACTGGCCATATCAGCT
1 AGTTAACTGGCCATATCAGCT
*
12494423 AGTTAACTTGCCATATCAGC
1 AGTTAACTGGCCATATCAGC
12494443 GGTCCCGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (21 bp):
AGTTAACTGGCCATATCAGCT
Found at i:12494820 original size:23 final size:22
Alignment explanation
Indices: 12494737--12494820 Score: 77
Period size: 23 Copynumber: 3.9 Consensus size: 22
12494727 TCAACTTTTT
*
12494737 TTAAATATATATTGTTTTTTAAA
1 TTAAATATATATTATTTTTT-AA
*
12494760 TTAAATATATATTAATTTTTAA
1 TTAAATATATATTATTTTTTAA
** *
12494782 -TAGCT-T-TATT-TATTTTAA
1 TTAAATATATATTATTTTTTAA
12494800 GTTAAATATATATTATTTTTT
1 -TTAAATATATATTATTTTTT
12494821 TCGAATTCTA
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
18 6 0.13
19 4 0.09
20 4 0.09
21 4 0.09
22 6 0.13
23 23 0.49
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (22 bp):
TTAAATATATATTATTTTTTAA
Found at i:12494855 original size:18 final size:18
Alignment explanation
Indices: 12494832--12494878 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
12494822 CGAATTCTAC
12494832 TTTTAATTAATTTTTTTA
1 TTTTAATTAATTTTTTTA
* *
12494850 TTTTAAATTTATTTTTTTC
1 TTTT-AATTAATTTTTTTA
*
12494869 TTTAAATTAA
1 TTTTAATTAA
12494879 ATATATCTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTAATTAATTTTTTTA
Found at i:12494863 original size:19 final size:18
Alignment explanation
Indices: 12494832--12494878 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
12494822 CGAATTCTAC
12494832 TTTT-AATTAATTTTTTT
1 TTTTAAATTAATTTTTTT
*
12494849 ATTTTAAATTTATTTTTTT
1 -TTTTAAATTAATTTTTTT
*
12494868 CTTTAAATTAA
1 TTTTAAATTAA
12494879 ATATATCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTAAATTAATTTTTTT
Found at i:12508832 original size:29 final size:29
Alignment explanation
Indices: 12508790--12508847 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
12508780 TCGCATATAG
*
12508790 GACGCTCCTCGTTAGGAGCAAATCTGCCT
1 GACGCTCCTCGTTAGGAGCAAATCCGCCT
*
12508819 GACGTTCCTCGTTAGGAGCAAATCCGCCT
1 GACGCTCCTCGTTAGGAGCAAATCCGCCT
12508848 TCTCTTCTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.24
Consensus pattern (29 bp):
GACGCTCCTCGTTAGGAGCAAATCCGCCT
Found at i:12523153 original size:27 final size:27
Alignment explanation
Indices: 12523071--12523196 Score: 123
Period size: 27 Copynumber: 4.7 Consensus size: 27
12523061 CAGATTATGT
* * *
12523071 CACAAAGGCAGATCATTT-AGAGTTCGC
1 CACAAAAGCAGTTC-TTTCAGAGTACGC
* *
12523098 CACAAAGGCAGTTCTTTCAGAGTTCGC
1 CACAAAAGCAGTTCTTTCAGAGTACGC
*
12523125 CACAAAAGCAGTTCTTTCAGAGTAAGC
1 CACAAAAGCAGTTCTTTCAGAGTACGC
*
12523152 CACACAAATG--GTTCTTTCAAAGTACGC
1 CACA-AAA-GCAGTTCTTTCAGAGTACGC
* *
12523179 CATAAAGGCAGTTCTTTC
1 CACAAAAGCAGTTCTTTC
12523197 CTAATGTGTT
Statistics
Matches: 86, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
25 1 0.01
26 5 0.06
27 76 0.88
28 3 0.03
29 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (27 bp):
CACAAAAGCAGTTCTTTCAGAGTACGC
Found at i:12533567 original size:20 final size:20
Alignment explanation
Indices: 12533542--12533593 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
12533532 AGGGAAGTCG
12533542 AAGTTTGTAAGATCTCTTAC
1 AAGTTTGTAAGATCTCTTAC
12533562 AAGTTTGTAAGATCTCTTAC
1 AAGTTTGTAAGATCTCTTAC
12533582 AAGTTTGTAAGA
1 AAGTTTGTAAGA
12533594 CTGTTGACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (20 bp):
AAGTTTGTAAGATCTCTTAC
Found at i:12541896 original size:60 final size:59
Alignment explanation
Indices: 12541804--12541916 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 59
12541794 TTACAAATTG
* *
12541804 TATATTTTTATACATATATACTGTTATATATATATATACATATCAATGTTATATCCATA
1 TATATTTTTATACATATATACTCTTATATATATATATAAATATCAATGTTATATCCATA
* *
12541863 TATATTTTTTATACATATATACTAACTT-T-TATATATATAAATATCTATTTTATA
1 TATA-TTTTTATACATATATACT--CTTATATATATATATAAATATCAATGTTATA
12541917 AACACATACA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
59 4 0.09
60 40 0.85
61 1 0.02
62 2 0.04
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (59 bp):
TATATTTTTATACATATATACTCTTATATATATATATAAATATCAATGTTATATCCATA
Found at i:12544634 original size:15 final size:16
Alignment explanation
Indices: 12544609--12544640 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
12544599 AGTACATATG
12544609 CTCTCTTTTTCTTTTT
1 CTCTCTTTTTCTTTTT
12544625 CTCT-TTTTTCTTTTT
1 CTCTCTTTTTCTTTTT
12544640 C
1 C
12544641 ATTTCTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
CTCTCTTTTTCTTTTT
Found at i:12544645 original size:20 final size:21
Alignment explanation
Indices: 12544612--12544652 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
12544602 ACATATGCTC
*
12544612 TCTTTTTCTTTTTCTCTTTTT
1 TCTTTTTCTATTTCTCTTTTT
12544633 TCTTTTTC-ATTTCTCTTTTT
1 TCTTTTTCTATTTCTCTTTTT
12544653 ATGGGCATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (21 bp):
TCTTTTTCTATTTCTCTTTTT
Found at i:12547013 original size:16 final size:16
Alignment explanation
Indices: 12546994--12547032 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
12546984 GTGGCTTGGA
*
12546994 AGCAGCATGGCTCGGC
1 AGCAGCATAGCTCGGC
*
12547010 AGCAACATAGCTCGGC
1 AGCAGCATAGCTCGGC
*
12547026 CGCAGCA
1 AGCAGCA
12547033 GCACCAGACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.33, G:0.31, T:0.10
Consensus pattern (16 bp):
AGCAGCATAGCTCGGC
Found at i:12547463 original size:19 final size:20
Alignment explanation
Indices: 12547441--12547481 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
12547431 CAAACTTTGG
12547441 ATAATAATTAATATA-AATT
1 ATAATAATTAATATATAATT
* *
12547460 ATAATATTTAATTTATAATT
1 ATAATAATTAATATATAATT
12547480 AT
1 AT
12547482 TAAAGTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAATAATTAATATATAATT
Found at i:12548850 original size:30 final size:30
Alignment explanation
Indices: 12548723--12548878 Score: 133
Period size: 29 Copynumber: 5.3 Consensus size: 30
12548713 CATTTTCACT
* *
12548723 CTCAAACTTTTCAAAAATTCGAATTTGA-C
1 CTCAAACTTTCCAAAAATTTGAATTTGACC
** * * *
12548752 CTTGAACTTTCTAAAAA-TTAAGATTTAACC
1 CTCAAACTTTCCAAAAATTTGA-ATTTGACC
* * *
12548782 CTCGAAC-TTCCCAAAATTTGGATTTGACC
1 CTCAAACTTTCCAAAAATTTGAATTTGACC
*
12548811 C-CCAACTTTCCAAAAATTTGAATTTGACC
1 CTCAAACTTTCCAAAAATTTGAATTTGACC
* *
12548840 CTAAAACTTTCCAAAAATTT-AGATTTGAGC
1 CTCAAACTTTCCAAAAATTTGA-ATTTGACC
*
12548870 CTCGAACTT
1 CTCAAACTT
12548879 CTTAAAAATT
Statistics
Matches: 100, Mismatches: 21, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
28 6 0.06
29 55 0.55
30 39 0.39
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.33
Consensus pattern (30 bp):
CTCAAACTTTCCAAAAATTTGAATTTGACC
Found at i:12548864 original size:88 final size:89
Alignment explanation
Indices: 12548727--12548915 Score: 238
Period size: 88 Copynumber: 2.1 Consensus size: 89
12548717 TTCACTCTCA
* ** *
12548727 AACTTTTCAAAAATTCGAATTTGACCTTGAACTTTCTAAAAATTAAGATTTAACCCTCGAACTTC
1 AACTTTACAAAAATTCGAATTTGACCTAAAACTTTCCAAAAATTAAGATTTAACCCTCGAACTTC
* * *
12548792 -CCAAAATTTGGATTTGACCCCC-
66 TCAAAAATTTAGATTTAACCCCCG
* * * * *
12548814 AACTTTCCAAAAATTTGAATTTGACCCTAAAACTTTCCAAAAATTTAGATTTGAGCCTCGAACTT
1 AACTTTACAAAAATTCGAATTTGA-CCTAAAACTTTCCAAAAATTAAGATTTAACCCTCGAACTT
*
12548879 CTTAAAAATTTAGATTTAACCCCCG
65 CTCAAAAATTTAGATTTAACCCCCG
12548904 AACTTTACAAAA
1 AACTTTACAAAA
12548916 GTTACATTTT
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
87 22 0.26
88 35 0.41
89 18 0.21
90 11 0.13
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (89 bp):
AACTTTACAAAAATTCGAATTTGACCTAAAACTTTCCAAAAATTAAGATTTAACCCTCGAACTTC
TCAAAAATTTAGATTTAACCCCCG
Found at i:12548886 original size:30 final size:29
Alignment explanation
Indices: 12548727--12548915 Score: 143
Period size: 30 Copynumber: 6.4 Consensus size: 29
12548717 TTCACTCTCA
* * *
12548727 AACTTTTCAAAAA-TTCGAATTTGACCTTG
1 AACTTTCCAAAAATTTAG-ATTTGACCTCG
* * *
12548756 AACTTTCTAAAAATTAAGATTTAACCCTCG
1 AACTTTCCAAAAATTTAGATTTGA-CCTCG
* * * *
12548786 AAC-TTCCCAAAATTTGGATTTGACCCCC
1 AACTTTCCAAAAATTTAGATTTGACCTCG
**
12548814 AACTTTCCAAAAATTT-GAATTTGACCCTAA
1 AACTTTCCAAAAATTTAG-ATTTGA-CCTCG
12548844 AACTTTCCAAAAATTTAGATTTGAGCCTCG
1 AACTTTCCAAAAATTTAGATTTGA-CCTCG
* * *
12548874 AAC-TTCTTAAAAATTTAGATTTAACCCCCG
1 AACTTTC-CAAAAATTTAGATTTGA-CCTCG
*
12548904 AACTTTACAAAA
1 AACTTTCCAAAA
12548916 GTTACATTTT
Statistics
Matches: 126, Mismatches: 26, Indels: 15
0.75 0.16 0.09
Matches are distributed among these distances:
28 7 0.06
29 51 0.40
30 65 0.52
31 3 0.02
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (29 bp):
AACTTTCCAAAAATTTAGATTTGACCTCG
Found at i:12552265 original size:30 final size:30
Alignment explanation
Indices: 12552229--12552291 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
12552219 GCTGAGAGTA
*
12552229 AGGAGATGAGGGAAAGGGTGCAAGAACTTG
1 AGGAGATGAGGGAAAGGGTACAAGAACTTG
*
12552259 AGGAGATGAGGGAAAGGGTATAAGAACTTG
1 AGGAGATGAGGGAAAGGGTACAAGAACTTG
12552289 AGG
1 AGG
12552292 TCTCACTCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.05, G:0.43, T:0.14
Consensus pattern (30 bp):
AGGAGATGAGGGAAAGGGTACAAGAACTTG
Found at i:12554673 original size:6 final size:6
Alignment explanation
Indices: 12554661--12554695 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
12554651 GAAAGAGAAG
*
12554661 AAAAGA AAAAGA AAAAAA AAAAGA AAAA-A AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
12554696 GAGGTTAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:12554674 original size:11 final size:11
Alignment explanation
Indices: 12554658--12554695 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
12554648 AGAGAAAGAG
*
12554658 AAGAAAAGAAA
1 AAGAAAAAAAA
12554669 AAGAAAAAAAAA
1 AAG-AAAAAAAA
12554681 AAGAAAAAAAA
1 AAGAAAAAAAA
12554692 AAGA
1 AAGA
12554696 GAGGTTAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:12554681 original size:12 final size:12
Alignment explanation
Indices: 12554656--12554693 Score: 58
Period size: 12 Copynumber: 3.0 Consensus size: 12
12554646 AGAGAGAAAG
12554656 AGAAGAAAAGAAAA
1 AGAA-AAAA-AAAA
12554670 AGAAAAAAAAAA
1 AGAAAAAAAAAA
12554682 AGAAAAAAAAAA
1 AGAAAAAAAAAA
12554694 GAGAGGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 16 0.67
13 4 0.17
14 4 0.17
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAAA
Found at i:12555652 original size:49 final size:49
Alignment explanation
Indices: 12555532--12555724 Score: 167
Period size: 49 Copynumber: 3.9 Consensus size: 49
12555522 AAGACGAGAT
** * * * *
12555532 GGGAAAGATAAAAGCCACAACGATGAATCTTGTACCATAGGA-ATGT-AA
1 GGGAAAGATTGAAGCCACAATGGTGAATCTTATACCCT-GGAGATGTGAA
** * * * *
12555580 AAGAAGAGATTAAAGCTACAATGGCGAATCTTATACCTTGGAGATGTGATA
1 GGGAA-AGATTGAAGCCACAATGGTGAATCTTATACCCTGGAGATGTGA-A
* * *
12555631 -GGAAAGGTTGAAGCCACAATGGTGAACCTTATACCCTAGAGATGTGAA
1 GGGAAAGATTGAAGCCACAATGGTGAATCTTATACCCTGGAGATGTGAA
* * * *
12555679 GGGAAAGATTGAAACCGCAACGGTGAATCTTATACCCTGAAGATGT
1 GGGAAAGATTGAAGCCACAATGGTGAATCTTATACCCTGGAGATGT
12555725 AGAGATGTAT
Statistics
Matches: 116, Mismatches: 24, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
48 7 0.06
49 104 0.90
50 4 0.03
51 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (49 bp):
GGGAAAGATTGAAGCCACAATGGTGAATCTTATACCCTGGAGATGTGAA
Found at i:12556222 original size:44 final size:45
Alignment explanation
Indices: 12556000--12556543 Score: 537
Period size: 44 Copynumber: 12.3 Consensus size: 45
12555990 CCTCGACCAT
*
12556000 GGGGTAGATTGAAGCCATCATCCAATCTTTTA--CCTAGTCAAGA
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGA
* * * * *
12556043 GGGGCAGATTGAAGTCACCGTCCAATCTTTTACCCCTAATCTAGA
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGA
* * * *
12556088 GGGTCAGTTTGAAGCCAT--TCTAATCTTTTACCCCTAATCAAGA
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGA
* * *
12556131 GGGGTAGATTTAAGCC-T--TCCAATCTTTTACCCCTAGTCATGA
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGA
*
12556173 GGGGCAGATTGAAGCCATCTTCCAATCTTTTA-CCCTAGTCAAGA
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGA
* * * * * *
12556217 GGGGCAGATTGAAGTCACCGTCTAA-CATTTTACCCCTAATCTAGA
1 GGGGCAGATTGAAGCCATCATCCAATC-TTTTACCCCTAGTCAAGA
* * **
12556262 GGGGTA-AGTTGAAGCCAT--TCCAAACTTTTACTACTAGTCAAGA
1 GGGGCAGA-TTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGA
** * * *
12556305 GGGGCAGATTGAAGTTA-CTGTCCAATCTTTTA-CCCTAATCCAGA
1 GGGGCAGATTGAAGCCATC-ATCCAATCTTTTACCCCTAGTCAAGA
*
12556349 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCTCTAAGTCAAGA
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCCT-AGTCAAGA
* * *
12556395 GGGGCAGATTAAAGCTATCATCCAATCTTTTACCCCAATA-TCAAAA
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCC--TAGTCAAGA
* *
12556441 GGGGCA-ATTTTAAGCCATCATCCAATCTTTTACCCCTA-ACAAGA
1 GGGGCAGA-TTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGA
* ** *
12556485 GGGGTAGATTGAAGTAATCATCCAATCTTTTACCTCTAAGTCAAGA
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCCT-AGTCAAGA
*
12556531 GGGGTAGATTGAA
1 GGGGCAGATTGAA
12556544 ACTATTATCT
Statistics
Matches: 415, Mismatches: 64, Indels: 41
0.80 0.12 0.08
Matches are distributed among these distances:
42 37 0.09
43 95 0.23
44 111 0.27
45 76 0.18
46 94 0.23
47 1 0.00
48 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (45 bp):
GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCCTAGTCAAGA
Found at i:12556305 original size:174 final size:175
Alignment explanation
Indices: 12556000--12556543 Score: 638
Period size: 174 Copynumber: 3.1 Consensus size: 175
12555990 CCTCGACCAT
*
12556000 GGGGTAGATTGAAGCCATCATCCAATCTTTTA-CCTAGTCAAGAGGGGCAGATTGAAGTCACCGT
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCTAGTCAAGAGGGGCAGATTGAAGTCACCGT
* * * *
12556064 CCAATCTTTTACCCCTAATCTAGAGGGTCAGTTTGAAGCCATTCTAATCTTTTACCCCTAATCAA
66 CCAATCTTTTACCCCTAATCTAGAGGGTAAGTTTGAAGCCATTCCAAACTTTTACCACTAATCAA
* * * *
12556129 GAGGGGTAGATTTAAG-CCT-TCCAATCTTTTACCCCTAGT-CATGA
131 GAGGGGCAGATTGAAGTACTGTCCAATCTTTTA-CCCTAATCCA-GA
*
12556173 GGGGCAGATTGAAGCCATCTTCCAATCTTTTACCCTAGTCAAGAGGGGCAGATTGAAGTCACCGT
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCTAGTCAAGAGGGGCAGATTGAAGTCACCGT
* * *
12556238 CTAA-CATTTTACCCCTAATCTAGAGGGGTAAG-TTGAAGCCATTCCAAACTTTTACTACTAGTC
66 CCAATC-TTTTACCCCTAATCTAGA-GGGTAAGTTTGAAGCCATTCCAAACTTTTACCACTAATC
12556301 AAGAGGGGCAGATTGAAGTTACTGTCCAATCTTTTACCCTAATCCAGA
129 AAGAGGGGCAGATTGAAG-TACTGTCCAATCTTTTACCCTAATCCAGA
* *
12556349 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCTCTAAGTCAAGAGGGGCAGATTAAAG-CTAT
1 GGGGCAGATTGAAGCCATCATCCAATCTTTTACC-CT-AGTCAAGAGGGGCAGATTGAAGTC-AC
* * * * * * * *
12556413 CATCCAATCTTTTACCCCAATATCAAAAGGGGCAA-TTTTAAGCCATCATCCAATCTTTTACCCC
63 CGTCCAATCTTTTACCCCTA-ATCTAGA-GGGTAAGTTTGAAGCCAT--TCCAAACTTTTACCAC
* * * *
12556477 TAA-CAAGAGGGGTAGATTGAAGTAATCATCCAATCTTTTACCTCTAAGTCAAGA
124 TAATCAAGAGGGGCAGATTGAAGTACT-GTCCAATCTTTTACC-CTAA-TCCAGA
*
12556531 GGGGTAGATTGAA
1 GGGGCAGATTGAA
12556544 ACTATTATCT
Statistics
Matches: 321, Mismatches: 32, Indels: 27
0.84 0.08 0.07
Matches are distributed among these distances:
173 31 0.10
174 95 0.30
175 6 0.02
176 43 0.13
177 17 0.05
178 37 0.12
179 24 0.07
180 32 0.10
181 19 0.06
182 17 0.05
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (175 bp):
GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCTAGTCAAGAGGGGCAGATTGAAGTCACCGT
CCAATCTTTTACCCCTAATCTAGAGGGTAAGTTTGAAGCCATTCCAAACTTTTACCACTAATCAA
GAGGGGCAGATTGAAGTACTGTCCAATCTTTTACCCTAATCCAGA
Done.