Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 74 of 190
Found at i:21236589 original size:60 final size:59
Alignment explanation
Indices: 21236385--21236607 Score: 152
Period size: 60 Copynumber: 3.7 Consensus size: 59
21236375 ATCATCGATA
* * *
21236385 TATGAAAATGGATTGCTTCGAG-TATCAAATTATGAAAAGGGATGGTGACGACCATTGAAAAT
1 TATGAAAAGGGA-TGCTTC-AGCTATAAAATTATGAAAAGGGATGGTGACGACCA-T-CAAAT
* * * * * * * * *
21236447 T-GGAAAA-GGATG-GTGACGACCATAAAATTATGAAATGGGATGCCT-TCGGCTATC-AAT
1 TATGAAAAGGGATGCTTCA-G-CTATAAAATTATGAAAAGGGATG-GTGACGACCATCAAAT
*
21236504 CTATGAAAAGGGATGGCTTCGGCTATAAAATTATGAAAAGGGATGGTGACGACCATCAAAT
1 -TATGAAAAGGGAT-GCTTCAGCTATAAAATTATGAAAAGGGATGGTGACGACCATCAAAT
* ** **
21236565 TATGAAAAGGGATAGCCTCAGCTATCGAACCATGAAAAGGGAT
1 TATGAAAAGGGAT-GCTTCAGCTATAAAATTATGAAAAGGGAT
21236608 AACTTCAGTT
Statistics
Matches: 122, Mismatches: 28, Indels: 24
0.70 0.16 0.14
Matches are distributed among these distances:
57 4 0.03
58 3 0.02
59 9 0.07
60 93 0.76
61 11 0.09
62 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.24
Consensus pattern (59 bp):
TATGAAAAGGGATGCTTCAGCTATAAAATTATGAAAAGGGATGGTGACGACCATCAAAT
Found at i:21236600 original size:30 final size:30
Alignment explanation
Indices: 21236566--21236637 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
21236556 CCATCAAATT
*
21236566 ATGAAAAGGGATAGCCTCAGCTATCGAACC
1 ATGAAAAGGGATAACCTCAGCTATCGAACC
* * **
21236596 ATGAAAAGGGATAACTTCAGTTATCGAATT
1 ATGAAAAGGGATAACCTCAGCTATCGAACC
*
21236626 ACGAAAAGGGAT
1 ATGAAAAGGGAT
21236638 GTGTCAACCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (30 bp):
ATGAAAAGGGATAACCTCAGCTATCGAACC
Found at i:21236626 original size:90 final size:90
Alignment explanation
Indices: 21236449--21236638 Score: 242
Period size: 90 Copynumber: 2.1 Consensus size: 90
21236439 TTGAAAATTG
* * *
21236449 GAAAA-GGATGGTGACGACCATAAAATTATGAAATGGGATGCCTTCGGCTATCAATCTATGAAAA
1 GAAAAGGGATGGTGACGACCATAAAATTATGAAAAGGGATGCCTTCAGCTATCAATCCATGAAAA
** * *
21236513 GGGATGGCTTCGGCTATAAAATTAT
66 GGGATAACTTCAGCTATAAAATTAC
*
21236538 GAAAAGGGATGGTGACGACCATCAAATTATGAAAAGGGATAGCC-TCAGCTATCGAA-CCATGAA
1 GAAAAGGGATGGTGACGACCATAAAATTATGAAAAGGGAT-GCCTTCAGCTATC-AATCCATGAA
* **
21236601 AAGGGATAACTTCAGTTATCGAATTAC
64 AAGGGATAACTTCAGCTATAAAATTAC
21236628 GAAAAGGGATG
1 GAAAAGGGATG
21236639 TGTCAACCAT
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
89 5 0.06
90 77 0.89
91 5 0.06
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (90 bp):
GAAAAGGGATGGTGACGACCATAAAATTATGAAAAGGGATGCCTTCAGCTATCAATCCATGAAAA
GGGATAACTTCAGCTATAAAATTAC
Found at i:21237772 original size:42 final size:42
Alignment explanation
Indices: 21237725--21237813 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
21237715 AACATAAGCA
* *** * *
21237725 TGTGGGGTTATT-TCGAAGGATACATTTCCTGGGACATGGGCG
1 TGTGGGATTATTGT-GAAGGATACACGACCTGGCACACGGGCG
*
21237767 TGTGGGATTATTGTGAAGGGTACACGACCTGGCACACGGGCG
1 TGTGGGATTATTGTGAAGGATACACGACCTGGCACACGGGCG
21237809 TGTGG
1 TGTGG
21237814 CTTAGCTGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 38 0.97
43 1 0.03
ACGTcount: A:0.19, C:0.16, G:0.38, T:0.27
Consensus pattern (42 bp):
TGTGGGATTATTGTGAAGGATACACGACCTGGCACACGGGCG
Found at i:21238745 original size:25 final size:25
Alignment explanation
Indices: 21238711--21238769 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
21238701 TGCTACTTGC
*
21238711 ATAGCATCTATCAACCACCACAAAA
1 ATAGAATCTATCAACCACCACAAAA
21238736 ATAGAATCTATCAACCACCACAAAA
1 ATAGAATCTATCAACCACCACAAAA
21238761 ATAGAATCT
1 ATAGAATCT
21238770 CTACCATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.49, C:0.27, G:0.05, T:0.19
Consensus pattern (25 bp):
ATAGAATCTATCAACCACCACAAAA
Found at i:21242869 original size:17 final size:16
Alignment explanation
Indices: 21242835--21242866 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
21242825 GAATCTATTT
21242835 TTTTTTTCAACTTCAA
1 TTTTTTTCAACTTCAA
21242851 TTTTTTTCAACTTCAA
1 TTTTTTTCAACTTCAA
21242867 ATTGTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTTTTCAACTTCAA
Found at i:21243377 original size:19 final size:19
Alignment explanation
Indices: 21243350--21243393 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
21243340 GAACAAAGTA
21243350 TAAAATTCTCACACAAAAC
1 TAAAATTCTCACACAAAAC
*
21243369 TAAATTTCTCACACAAAAC
1 TAAAATTCTCACACAAAAC
21243388 TCAAAA
1 T-AAAA
21243394 ATATTCATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.52, C:0.25, G:0.00, T:0.23
Consensus pattern (19 bp):
TAAAATTCTCACACAAAAC
Found at i:21244085 original size:75 final size:75
Alignment explanation
Indices: 21243992--21244137 Score: 168
Period size: 75 Copynumber: 1.9 Consensus size: 75
21243982 TTATGAAAAC
** * * * * *
21243992 ACATAATGCAGGTCTTAAAGGATCCTA-ATGTATTAATGTAAAGCGTTAACTAAAGATGCATTCA
1 ACATAATGCACATCTTAAAAGAT-CTAGATGTATTAATGCAAAACATTAAATAAAGATGCATTCA
*
21244056 ATAAACAAGAA
65 ACAAACAAGAA
* * * *
21244067 ACATAATGCACATTTTAAAAGATGTAGTTGTATTAATGCAAAACATTAAATAAAGATGCATTTAA
1 ACATAATGCACATCTTAAAAGATCTAGATGTATTAATGCAAAACATTAAATAAAGATGCATTCAA
21244132 CAAACA
66 CAAACA
21244138 CTCATAAATT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
74 2 0.03
75 56 0.97
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (75 bp):
ACATAATGCACATCTTAAAAGATCTAGATGTATTAATGCAAAACATTAAATAAAGATGCATTCAA
CAAACAAGAA
Found at i:21244353 original size:75 final size:75
Alignment explanation
Indices: 21244255--21244416 Score: 184
Period size: 75 Copynumber: 2.2 Consensus size: 75
21244245 ATGACTTATG
* ** * * * * * *
21244255 AAAACACATAATACAGGTCTTAAAGGATCCTA-ATGTATTAATGTAAAGCGTTAACTAAAGATGC
1 AAAACACATAATGCACATTTTAAAAGAT-CTAGATGTATTAATGCAAAACATTAAATAAAGATGC
*
21244319 ATTCAATAAAC
65 ATTCAACAAAC
*
21244330 AAGAA-ACATAATGCACATTTTAAAAGATGTAGATGTATTAATGCAAAACATTAAATAAAGATGC
1 AA-AACACATAATGCACATTTTAAAAGATCTAGATGTATTAATGCAAAACATTAAATAAAGATGC
*
21244394 ATTTAACAAAC
65 ATTCAACAAAC
21244405 AAAACACATAAT
1 AAAACACATAAT
21244417 TAAAAATTGA
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
74 4 0.06
75 66 0.92
76 2 0.03
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.26
Consensus pattern (75 bp):
AAAACACATAATGCACATTTTAAAAGATCTAGATGTATTAATGCAAAACATTAAATAAAGATGCA
TTCAACAAAC
Found at i:21244369 original size:268 final size:268
Alignment explanation
Indices: 21243885--21244405 Score: 1006
Period size: 268 Copynumber: 1.9 Consensus size: 268
21243875 TCATAAAAAC
*
21243885 AACATATTTAATAACACTCATGCACATAAATTAAATGAACATGCAACTTAAACCATACTTGAAGT
1 AACATATTTAATAACACTCATACACATAAATTAAATGAACATGCAACTTAAACCATACTTGAAGT
*
21243950 AAATTAACAAATGAGATGATTTAATGCATGACTTATGAAAACACATAATGCAGGTCTTAAAGGAT
66 AAATTAACAAATGAGATGATTTAATGCATGACTTATGAAAACACATAATACAGGTCTTAAAGGAT
21244015 CCTAATGTATTAATGTAAAGCGTTAACTAAAGATGCATTCAATAAACAAGAAACATAATGCACAT
131 CCTAATGTATTAATGTAAAGCGTTAACTAAAGATGCATTCAATAAACAAGAAACATAATGCACAT
*
21244080 TTTAAAAGATGTAGTTGTATTAATGCAAAACATTAAATAAAGATGCATTTAACAAACACTCATAA
196 TTTAAAAGATGTAGATGTATTAATGCAAAACATTAAATAAAGATGCATTTAACAAACACTCATAA
21244145 ATTAAATG
261 ATTAAATG
21244153 AACATATTTAATAACACTCATACACATAAATTAAATGAACATGCAACTTAAACCATACTTGAAGT
1 AACATATTTAATAACACTCATACACATAAATTAAATGAACATGCAACTTAAACCATACTTGAAGT
*
21244218 AAATTAACGAATGAGATGATTTAATGCATGACTTATGAAAACACATAATACAGGTCTTAAAGGAT
66 AAATTAACAAATGAGATGATTTAATGCATGACTTATGAAAACACATAATACAGGTCTTAAAGGAT
21244283 CCTAATGTATTAATGTAAAGCGTTAACTAAAGATGCATTCAATAAACAAGAAACATAATGCACAT
131 CCTAATGTATTAATGTAAAGCGTTAACTAAAGATGCATTCAATAAACAAGAAACATAATGCACAT
21244348 TTTAAAAGATGTAGATGTATTAATGCAAAACATTAAATAAAGATGCATTTAACAAACA
196 TTTAAAAGATGTAGATGTATTAATGCAAAACATTAAATAAAGATGCATTTAACAAACA
21244406 AAACACATAA
Statistics
Matches: 249, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
268 249 1.00
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.28
Consensus pattern (268 bp):
AACATATTTAATAACACTCATACACATAAATTAAATGAACATGCAACTTAAACCATACTTGAAGT
AAATTAACAAATGAGATGATTTAATGCATGACTTATGAAAACACATAATACAGGTCTTAAAGGAT
CCTAATGTATTAATGTAAAGCGTTAACTAAAGATGCATTCAATAAACAAGAAACATAATGCACAT
TTTAAAAGATGTAGATGTATTAATGCAAAACATTAAATAAAGATGCATTTAACAAACACTCATAA
ATTAAATG
Found at i:21247633 original size:2 final size:2
Alignment explanation
Indices: 21247626--21247665 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
21247616 TTTCAAACCT
21247626 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21247666 AATTCTTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21250972 original size:163 final size:163
Alignment explanation
Indices: 21250781--21251105 Score: 650
Period size: 163 Copynumber: 2.0 Consensus size: 163
21250771 AAACAAGAGA
21250781 ACATTTGAATGAATAGAAACTGTATAAAGTGCTTCGGGTTTATAATGTTTTGTGTATATCATTTG
1 ACATTTGAATGAATAGAAACTGTATAAAGTGCTTCGGGTTTATAATGTTTTGTGTATATCATTTG
21250846 ATGTGGTGTTTCGAGATCTAAATTTGCATTTTTAACAAATTGAATGAGATTCGTAATAACTAACA
66 ATGTGGTGTTTCGAGATCTAAATTTGCATTTTTAACAAATTGAATGAGATTCGTAATAACTAACA
21250911 AAAATATTTGAGTTGGAAAAAATCTTAATCCTG
131 AAAATATTTGAGTTGGAAAAAATCTTAATCCTG
21250944 ACATTTGAATGAATAGAAACTGTATAAAGTGCTTCGGGTTTATAATGTTTTGTGTATATCATTTG
1 ACATTTGAATGAATAGAAACTGTATAAAGTGCTTCGGGTTTATAATGTTTTGTGTATATCATTTG
21251009 ATGTGGTGTTTCGAGATCTAAATTTGCATTTTTAACAAATTGAATGAGATTCGTAATAACTAACA
66 ATGTGGTGTTTCGAGATCTAAATTTGCATTTTTAACAAATTGAATGAGATTCGTAATAACTAACA
21251074 AAAATATTTGAGTTGGAAAAAATCTTAATCCT
131 AAAATATTTGAGTTGGAAAAAATCTTAATCCT
21251106 CTTGTGGCGC
Statistics
Matches: 162, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
163 162 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (163 bp):
ACATTTGAATGAATAGAAACTGTATAAAGTGCTTCGGGTTTATAATGTTTTGTGTATATCATTTG
ATGTGGTGTTTCGAGATCTAAATTTGCATTTTTAACAAATTGAATGAGATTCGTAATAACTAACA
AAAATATTTGAGTTGGAAAAAATCTTAATCCTG
Found at i:21256584 original size:12 final size:12
Alignment explanation
Indices: 21256556--21256600 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
21256546 TACAGGCCCT
*
21256556 CACCTCTGGATA
1 CACCTCTGGATG
21256568 CACCTCTGGATG
1 CACCTCTGGATG
* * *
21256580 TACCTCCGGTTG
1 CACCTCTGGATG
21256592 CACCTCTGG
1 CACCTCTGG
21256601 CTGTAGGCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.16, C:0.36, G:0.22, T:0.27
Consensus pattern (12 bp):
CACCTCTGGATG
Found at i:21259816 original size:33 final size:33
Alignment explanation
Indices: 21259774--21259838 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
21259764 ATCAGTATGG
21259774 TTATCACAGGGAGTCAACTTATGCAATTCAAAA
1 TTATCACAGGGAGTCAACTTATGCAATTCAAAA
21259807 TTATCACAGGGAGTCAACTTATGCAATTCAAA
1 TTATCACAGGGAGTCAACTTATGCAATTCAAA
21259839 TTAGGGTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (33 bp):
TTATCACAGGGAGTCAACTTATGCAATTCAAAA
Found at i:21260172 original size:2 final size:2
Alignment explanation
Indices: 21260165--21260195 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
21260155 TCCATTTTGA
*
21260165 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21260196 CCTACCATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:21264644 original size:21 final size:20
Alignment explanation
Indices: 21264610--21264665 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
21264600 TATTTTTTCC
*
21264610 AAAAATA-TAGAAATTTAT-T
1 AAAAATATTAAAAATTT-TGT
*
21264629 AAAATTATTCAAAAATTTTGT
1 AAAAATATT-AAAAATTTTGT
21264650 AAAAATATTAAAAATT
1 AAAAATATTAAAAATT
21264666 ATACTTTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 6 0.19
20 9 0.29
21 16 0.52
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (20 bp):
AAAAATATTAAAAATTTTGT
Found at i:21265262 original size:80 final size:80
Alignment explanation
Indices: 21265171--21265331 Score: 313
Period size: 80 Copynumber: 2.0 Consensus size: 80
21265161 TACCTTCTCA
*
21265171 TACTCTCTCACGTGGCTTTTCGGCCCTTTATAAATGCAACTTGTTCATGTTAGGAACACATCTCT
1 TACTCTCTCACGTGGCTTTTCGGCCCTTTATAAATGCAACTTGTTCATGATAGGAACACATCTCT
21265236 ACAAATCACTTTCAC
66 ACAAATCACTTTCAC
21265251 TACTCTCTCACGTGGCTTTTCGGCCCTTTATAAATGCAACTTGTTCATGATAGGAACACATCTCT
1 TACTCTCTCACGTGGCTTTTCGGCCCTTTATAAATGCAACTTGTTCATGATAGGAACACATCTCT
21265316 ACAAATCACTTTCAC
66 ACAAATCACTTTCAC
21265331 T
1 T
21265332 TATGAGCATA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.35
Consensus pattern (80 bp):
TACTCTCTCACGTGGCTTTTCGGCCCTTTATAAATGCAACTTGTTCATGATAGGAACACATCTCT
ACAAATCACTTTCAC
Found at i:21270628 original size:20 final size:19
Alignment explanation
Indices: 21270599--21270660 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
21270589 TAAATGCAAA
21270599 CTAAAATGAGCTGAATGAG
1 CTAAAATGAGCTGAATGAG
*
21270618 CTAAGAATGAGCTCG-TTGAG
1 CTAA-AATGAGCT-GAATGAG
*
21270638 CTAAAAATTGAGCTGAGTGAG
1 CT-AAAA-TGAGCTGAATGAG
21270659 CT
1 CT
21270661 TGAAGTAGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
19 4 0.11
20 17 0.47
21 15 0.42
ACGTcount: A:0.35, C:0.13, G:0.27, T:0.24
Consensus pattern (19 bp):
CTAAAATGAGCTGAATGAG
Found at i:21274939 original size:26 final size:27
Alignment explanation
Indices: 21274899--21274966 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
21274889 TTACCCAAAC
*
21274899 AAAATTTTGACGA-TTTTACCCTTGGT
1 AAAATTTTAACGATTTTTACCCTTGGT
* *
21274925 AAAATTTTAATGATTTTTTCCCTTGGT
1 AAAATTTTAACGATTTTTACCCTTGGT
21274952 AAAATTTTAAC-ATTT
1 AAAATTTTAACGATTT
21274967 ATATATATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 15 0.41
27 22 0.59
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (27 bp):
AAAATTTTAACGATTTTTACCCTTGGT
Found at i:21275127 original size:6 final size:6
Alignment explanation
Indices: 21275111--21275147 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
21275101 TGCAAATGGA
* *
21275111 TCATTT CCATTT TCATTT TCATTT CCATTT TCATTT T
1 TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT T
21275148 TGGAAACCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (6 bp):
TCATTT
Found at i:21275134 original size:18 final size:18
Alignment explanation
Indices: 21275111--21275147 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
21275101 TGCAAATGGA
21275111 TCATTTCCATTTTCATTT
1 TCATTTCCATTTTCATTT
21275129 TCATTTCCATTTTCATTT
1 TCATTTCCATTTTCATTT
21275147 T
1 T
21275148 TGGAAACCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (18 bp):
TCATTTCCATTTTCATTT
Found at i:21276208 original size:44 final size:43
Alignment explanation
Indices: 21276160--21276287 Score: 139
Period size: 44 Copynumber: 2.9 Consensus size: 43
21276150 AAAGAAAACG
*
21276160 AAATAAAATAATATATACAACAATTTAAAATAAATAATAGTTTA
1 AAAT-AAATAATATATAAAACAATTTAAAATAAATAATAGTTTA
* * * *
21276204 AAATAAATAATTTATAAAAACAATTCAAAATAAATAAAAAAGTTTC
1 AAATAAATAATATAT-AAAACAATTTAAAATAAAT--AATAGTTTA
* * * *
21276250 AAATAAACAATATATAAAAAAACTTAAAATAAACAATA
1 AAATAAATAATATATAAAACAATTTAAAATAAATAATA
21276288 ATAAAATAGT
Statistics
Matches: 69, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
43 13 0.19
44 21 0.30
45 15 0.22
46 20 0.29
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (43 bp):
AAATAAATAATATATAAAACAATTTAAAATAAATAATAGTTTA
Found at i:21276223 original size:17 final size:16
Alignment explanation
Indices: 21276182--21276214 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
21276172 ATATACAACA
21276182 ATTTAAAATAAATAAT
1 ATTTAAAATAAATAAT
21276198 AGTTTAAAATAAATAAT
1 A-TTTAAAATAAATAAT
21276215 TTATAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTTAAAATAAATAAT
Found at i:21276268 original size:26 final size:25
Alignment explanation
Indices: 21276236--21276321 Score: 109
Period size: 26 Copynumber: 3.4 Consensus size: 25
21276226 ATTCAAAATA
*
21276236 AATAAAAAAGTTTCAAATAAACAAT
1 AATAAAAAAGTTTAAAATAAACAAT
**
21276261 ATATAAAAAAACTTAAAATAAACAAT
1 A-ATAAAAAAGTTTAAAATAAACAAT
* *
21276287 AATAAAATAGTTTAAAATAAATAAT
1 AATAAAAAAGTTTAAAATAAACAAT
21276312 AATTAAAAAA
1 AA-TAAAAAA
21276322 TGACATATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
25 23 0.45
26 28 0.55
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (25 bp):
AATAAAAAAGTTTAAAATAAACAAT
Found at i:21276291 original size:25 final size:25
Alignment explanation
Indices: 21276236--21276322 Score: 102
Period size: 25 Copynumber: 3.4 Consensus size: 25
21276226 ATTCAAAATA
* *
21276236 AATAAAAAAGTTTCAAATAAACAAT
1 AATAAAAAAATTTAAAATAAACAAT
*
21276261 ATATAAAAAAACTTAAAATAAACAAT
1 A-ATAAAAAAATTTAAAATAAACAAT
* * *
21276287 AATAAAATAGTTTAAAATAAATAAT
1 AATAAAAAAATTTAAAATAAACAAT
*
21276312 AATTAAAAAAT
1 AATAAAAAAAT
21276323 GACATATAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
25 29 0.57
26 22 0.43
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (25 bp):
AATAAAAAAATTTAAAATAAACAAT
Found at i:21276305 original size:51 final size:46
Alignment explanation
Indices: 21276160--21276475 Score: 191
Period size: 46 Copynumber: 6.9 Consensus size: 46
21276150 AAAGAAAACG
* * *
21276160 AAATAAAATAATATATACAACAATTTAAAATAAAT---AATAGTTTA
1 AAAT-AAATAATATATAAAAAAATTCAAAATAAATAAAAATAGTTTA
* *
21276204 AAATAAATAATTTATAAAAACAATTCAAAATAAATAAAAA-AGTTTC
1 AAATAAATAATATATAAAAA-AATTCAAAATAAATAAAAATAGTTTA
*
21276250 AAATAAACAATATATAAAAAAACTT-AAAATAAACAATAATAAAATAGTTTA
1 AAATAAATAATATATAAAAAAA-TTCAAAAT--A-AAT-A-AAAATAGTTTA
* * *
21276301 AAATAAATAATA-ATTAAAAAA-T-GACAT--AT-AAAATAGTTTTTA
1 AAATAAATAATATATAAAAAAATTCAAAATAAATAAAAATAG--TTTA
* * *
21276343 GAA-AAATAATATAT-AAAAATTTAAAAGATAACATATATATAATAGTTTA
1 AAATAAATAATATATAAAAAAATTCAAA-ATAA-ATA-A-A-AATAGTTTA
* * * *
21276392 AAATAAATAATATATGAGAAAA---AAAATAATATGTAAAACAGTTTA
1 AAATAAATAATATATAAAAAAATTCAAAATAA-AT-AAAAATAGTTTA
* *
21276437 AAATAAATAATATA-AAAAAACTT-AAAATAAATAATAATA
1 AAATAAATAATATATAAAAAAATTCAAAATAAATAAAAATA
21276476 AAAGAGTTTT
Statistics
Matches: 215, Mismatches: 28, Indels: 58
0.71 0.09 0.19
Matches are distributed among these distances:
40 7 0.03
41 13 0.06
42 9 0.04
43 16 0.07
44 27 0.13
45 31 0.14
46 33 0.15
47 12 0.06
48 10 0.05
49 8 0.04
50 24 0.11
51 25 0.12
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (46 bp):
AAATAAATAATATATAAAAAAATTCAAAATAAATAAAAATAGTTTA
Found at i:21276404 original size:26 final size:24
Alignment explanation
Indices: 21276346--21276478 Score: 89
Period size: 26 Copynumber: 5.6 Consensus size: 24
21276336 GTTTTTAGAA
21276346 AAATAATATATAAAAATTTAAAAG
1 AAATAATATATAAAAATTTAAAAG
* * * *
21276370 ATAACATATATATAATAGTTTAAAAT
1 A-AATA-ATATATAAAAATTTAAAAG
* *
21276396 AAATAATATAT-GAGA---AAAA-
1 AAATAATATATAAAAATTTAAAAG
* *
21276415 AAATAATATGTAAAACAGTTTAAAAT
1 AAATAATATATAAAA-A-TTTAAAAG
* * *
21276441 AAATAATATAAAAAAACTTAAAAT
1 AAATAATATATAAAAATTTAAAAG
21276465 AAATAATA-ATAAAA
1 AAATAATATATAAAA
21276479 GAGTTTTTTT
Statistics
Matches: 84, Mismatches: 16, Indels: 19
0.71 0.13 0.16
Matches are distributed among these distances:
19 10 0.12
20 5 0.06
21 1 0.01
23 5 0.06
24 22 0.26
25 11 0.13
26 30 0.36
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (24 bp):
AAATAATATATAAAAATTTAAAAG
Found at i:21276429 original size:69 final size:69
Alignment explanation
Indices: 21276344--21276472 Score: 165
Period size: 69 Copynumber: 1.9 Consensus size: 69
21276334 TAGTTTTTAG
* * **
21276344 AAAAATAATATATAAAA-A-TTTAAAAGATAACAT-ATATATAATAGTTTAAAATAAATAATATA
1 AAAAATAATATATAAAACAGTTT-AAA-ATAA-ATAATATAAAAAAACTTAAAATAAATAATATA
21276406 TGAGAAA
63 TGAGAAA
*
21276413 AAAAATAATATGTAAAACAGTTTAAAATAAATAATATAAAAAAACTTAAAATAAATAATA
1 AAAAATAATATATAAAACAGTTTAAAATAAATAATATAAAAAAACTTAAAATAAATAATA
21276473 ATAAAAGAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
68 2 0.04
69 43 0.83
70 4 0.08
71 3 0.06
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (69 bp):
AAAAATAATATATAAAACAGTTTAAAATAAATAATATAAAAAAACTTAAAATAAATAATATATGA
GAAA
Found at i:21276452 original size:24 final size:24
Alignment explanation
Indices: 21276346--21276484 Score: 87
Period size: 24 Copynumber: 5.8 Consensus size: 24
21276336 GTTTTTAGAA
21276346 AAATAATATATAAAAA-TTTAAAAGAT
1 AAATAATATA-AAAAAGTTT-AAA-AT
* *
21276372 AACAT-ATATATAATAGTTTAAAAT
1 AA-ATAATATAAAAAAGTTTAAAAT
21276396 AAATAATATATGAGAAAA----AAAAT
1 AAATAATATA--A-AAAAGTTTAAAAT
* *
21276419 -AAT-ATGTAAAACAGTTTAAAAT
1 AAATAATATAAAAAAGTTTAAAAT
**
21276441 AAATAATATAAAAAAACTTAAAAT
1 AAATAATATAAAAAAGTTTAAAAT
*
21276465 AAATAATAATAAAAGAGTTT
1 AAATAAT-ATAAAAAAGTTT
21276485 TTTTAAATAA
Statistics
Matches: 87, Mismatches: 13, Indels: 27
0.69 0.10 0.21
Matches are distributed among these distances:
18 3 0.03
19 1 0.01
21 4 0.05
22 8 0.09
23 10 0.11
24 31 0.36
25 15 0.17
26 10 0.11
27 5 0.06
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (24 bp):
AAATAATATAAAAAAGTTTAAAAT
Found at i:21278159 original size:44 final size:44
Alignment explanation
Indices: 21278111--21278954 Score: 381
Period size: 44 Copynumber: 18.7 Consensus size: 44
21278101 GCTTTTCTCC
*
21278111 GCTCCACTGCAACTTCAAGGAGATAGGATTAGTAGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAATCT
* * * * *
21278155 GCTCCACTGCAACTTTAGGGAGATAAGATTGGTATCTTCAACCT
1 GCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAATCT
* * * * * * * *
21278199 GCCCCACTACAACTTTAGGAAGATAAGG-TTTGTGGCTTTAATAT
1 GCTCCACTGCAACTTCAGGGAGAT-AGGATTAGTAGCTTCAATCT
* * * * * *
21278243 GCTCCACTGCAACTTCAGGAAGAT-GAGATTTGTGGTTTTAATTT
1 GCTCCACTGCAACTTCAGGGAGATAG-GATTAGTAGCTTCAATCT
* *
21278287 GCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCCTGTCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAGGATTAGTA----G-CTTCAATCT
* * * * * ** * *
21278336 GCTCTACTGCAACTTTAGGGAGAAAAGATTTGTTTATTTTTAACCT
1 GCTCCACTGCAACTTCAGGGAGATAGGATTAG--TAGCTTCAATCT
* * * * * **
21278382 GTTCCACTACAACTTCAGGGAGATAAGGTTTGTGTA-TTTTTATCCT
1 GCTCCACTGCAACTTCAGGGAGAT-AGGATT-AGTAGCTTCAAT-CT
* *
21278428 GCTCCTCTGCAACTTCAGGGAGATAAGGATT-GT-GTCTTCGATCT
1 GCTCCACTGCAACTTCAGGGAGAT-AGGATTAGTAG-CTTCAATCT
* * * * * * *
21278472 ACTCCAATGTAATTTCAGGGAGA-AGAGGTTTGTAGCTTCGATCT
1 GCTCCACTGCAACTTCAGGGAGATAG-GATTAGTAGCTTCAATCT
* * * * * * *
21278516 ACTCCGA-TGGAACTTCAAGGAGATAAGAATTGGTAACTTCAACCT
1 GCTCC-ACTGCAACTTCAGGGAGAT-AGGATTAGTAGCTTCAATCT
*
21278561 GCTCCACTGCAACTTCAGGGAGATAAGGTTTGCAACTTGTAGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGAT-AGGATT---A---GTAGCTTCAATCT
* * * * * *
21278612 GTTCCACTGCAACTTCAGGGAAATAAGATTCGCT-GTCTTTAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAGGATTAG-TAG-CTTCAATCT
* * * * * * *
21278657 GCTCCGCTGCAATTTCAAGAAGATAAGACTT-GTAACTTCAACCT
1 GCTCCACTGCAACTTCAGGGAGATAGGA-TTAGTAGCTTCAATCT
*
21278701 GCTCCACTGCAACTTCAGGGAGATAAGG-TT--T-GCTAT-GATCT
1 GCTCCACTGCAACTTCAGGGAGAT-AGGATTAGTAGCT-TCAATCT
* * * *
21278742 GCTCTACTGCAACTTTAGAGAGATAAGATCTGCAATTTA-TAGCTTCAATCC
1 GCTCCACTGCAACTTCAGGGAGAT-AG----G--A-TTAGTAGCTTCAATCT
* * * * * * *
21278793 GTTCCACTACAACTTCAGGGAAATAAGATTCACTATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAGGATT-AGTAGCTTCAATCT
* * * * *
21278838 GCTCCACTGTAATTTCAGGGAGATAAGACTAGTAACTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAATCT
* * * * *
21278882 GGC-CCACTACAACTT-AGGGGGATAAGATTAGTGGCTTTAATCT
1 -GCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAATCT
* * *
21278925 GCTCCACTACAACTTCAAGGAGATAAGATT
1 GCTCCACTGCAACTTCAGGGAGATAGGATT
21278955 CACCATAATG
Statistics
Matches: 617, Mismatches: 132, Indels: 102
0.73 0.16 0.12
Matches are distributed among these distances:
41 29 0.05
42 7 0.01
43 43 0.07
44 249 0.40
45 118 0.19
46 61 0.10
47 4 0.01
48 3 0.00
49 37 0.06
50 7 0.01
51 59 0.10
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAATCT
Found at i:21278507 original size:185 final size:181
Alignment explanation
Indices: 21278146--21278592 Score: 444
Period size: 185 Copynumber: 2.5 Consensus size: 181
21278136 GGATTAGTAG
*
21278146 CTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGTATCTTCAACCTGCCCCACTACAA
1 CTTCAATCTGCTCCACTGCAACTTTAGGGAGAAAAGATTGGTATCTTCAACCTGCCCCACTACAA
* * *
21278211 CTTTAGGAAGATAAGGTTTGTGGCTTTAATATGCTCCACTGCAACTTCAGGAAGATGAGATTTGT
66 CTTCAGGAAGATAAGGTTTGTGACTTTAATATGCTCCACTGCAACTTCAGGAAGATAAGATTTGT
* * * *
21278276 GGTTTTAATTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCCTGT
131 GGTTTCAATCTACTCCAATGCAACTTCAGGGAGATAAGATTTGTAGCCTGT
* * * * **
21278327 CTTCAATCTGCTCTACTGCAACTTTAGGGAGAAAAGATTTGTTTATTTTTAACCTGTTCCACTAC
1 CTTCAATCTGCTCCACTGCAACTTTAGGGAGAAAAGA-TTG-GTATCTTCAACCTGCCCCACTAC
* * * * * *
21278392 AACTTCAGGGAGATAAGGTTTGTGTATTTTTATCCTGCTCCTCTGCAACTTCAGGGAGATAAGGA
64 AACTTCAGGAAGATAAGGTTTGTG-ACTTTAAT-ATGCTCCACTGCAACTTCAGGAAGATAA-GA
* * * *
21278457 -TTGT-GTCTTCGATCTACTCCAATGTAATTTCAGGGAGA-AGAGGTTTGTA----G-
126 TTTGTGGT-TTCAATCTACTCCAATGCAACTTCAGGGAGATA-AGATTTGTAGCCTGT
* * * * * * * * *
21278507 CTTCGATCTACTCCGA-TGGAACTTCAAGGAGATAAGAATTGGTAACTTCAACCTGCTCCACTGC
1 CTTCAATCTGCTCC-ACTGCAACTTTAGGGAGAAAAG-ATTGGTATCTTCAACCTGCCCCACTAC
*
21278571 AACTTCAGGGAGATAAGGTTTG
64 AACTTCAGGAAGATAAGGTTTG
21278593 CAACTTGTAG
Statistics
Matches: 220, Mismatches: 37, Indels: 20
0.79 0.13 0.07
Matches are distributed among these distances:
179 39 0.18
180 30 0.14
181 38 0.17
182 3 0.01
183 40 0.18
184 8 0.04
185 60 0.27
186 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (181 bp):
CTTCAATCTGCTCCACTGCAACTTTAGGGAGAAAAGATTGGTATCTTCAACCTGCCCCACTACAA
CTTCAGGAAGATAAGGTTTGTGACTTTAATATGCTCCACTGCAACTTCAGGAAGATAAGATTTGT
GGTTTCAATCTACTCCAATGCAACTTCAGGGAGATAAGATTTGTAGCCTGT
Found at i:21278787 original size:181 final size:180
Alignment explanation
Indices: 21278559--21278953 Score: 506
Period size: 181 Copynumber: 2.2 Consensus size: 180
21278549 TAACTTCAAC
* * * * * *
21278559 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCAACTTGTAGCTTCAATCTGTTCCACTGCAA
1 CTGCTCCACTGCAACTTCAGAGAGATAAGATCTGCAACTTATAGCTTCAATCCGTTCCACTACAA
* * * * *
21278624 CTTCAGGGAAATAAGATTCGCTGTCTTTAGTCTGCTCCGCTGCAATTTCAAGAAGATAAGACTTG
66 CTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTGCAATTTCAAGAAGATAAGACTAG
*
21278689 TAACTTCAACCT-GCTCCACTGCAACTTCAGGGAGATAAGGTTTGCTATGAT
131 TAACTTCAACCTGGC-CCACTACAACTT-AGGGAGATAAGGTTTGCTATGAT
* * *
21278740 CTGCTCTACTGCAACTTTAGAGAGATAAGATCTGCAATTTATAGCTTCAATCCGTTCCACTACAA
1 CTGCTCCACTGCAACTTCAGAGAGATAAGATCTGCAACTTATAGCTTCAATCCGTTCCACTACAA
* * *
21278805 CTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTGTAATTTCAGGGAGATAAGACTAG
66 CTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTGCAATTTCAAGAAGATAAGACTAG
* * * * *
21278870 TAACTTCAATCTGGCCCACTACAACTTAGGGGGATAAGATTAGTGGCTTTAAT
131 TAACTTCAACCTGGCCCACTACAACTTAGGGAGATAAGGTT--T-GCTATGAT
*
21278923 CTGCTCCACTACAACTTCA-AGGAGATAAGAT
1 CTGCTCCACTGCAACTTCAGA-GAGATAAGAT
21278954 TCACCATAAT
Statistics
Matches: 183, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
180 12 0.07
181 135 0.74
182 4 0.02
183 32 0.17
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (180 bp):
CTGCTCCACTGCAACTTCAGAGAGATAAGATCTGCAACTTATAGCTTCAATCCGTTCCACTACAA
CTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTGCAATTTCAAGAAGATAAGACTAG
TAACTTCAACCTGGCCCACTACAACTTAGGGAGATAAGGTTTGCTATGAT
Found at i:21278893 original size:89 final size:89
Alignment explanation
Indices: 21278603--21278952 Score: 266
Period size: 89 Copynumber: 3.9 Consensus size: 89
21278593 CAACTTGTAG
** * * * *
21278603 CTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTGTCTTTAGTCTGCTCCGCTGCA
1 CTTCAATCTGGCCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCA
* * *
21278668 ATTTCAAGAAGATAAGACTTGTAA
66 ATTTCAGGGAGATAAGACTAGTAA
* * * * * * *
21278692 CTTCAACCT-GCTCCACTGCAACTTCAGGGAGATAAGGTTTGCTA---TGA-TCTGCTCTACTGC
1 CTTCAATCTGGC-CCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGC
* *
21278752 AACTTT-AGAGAGATAAGATCTGCAATTTATA
65 AA-TTTCAGGGAGATAAGA-CT---A-GTA-A
* ** * *
21278783 GCTTCAATCCGTTCCACTACAACTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTGT
1 -CTTCAATCTGGCCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGC
21278848 AATTTCAGGGAGATAAGACTAGTAA
65 AATTTCAGGGAGATAAGACTAGTAA
** * ** * * *
21278873 CTTCAATCTGGCCCACTACAACTT-AGGGGGATAAGATTAG-TGGCTTTAATCTGCTCCACTACA
1 CTTCAATCTGGCCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCA
* *
21278936 ACTTCAAGGAGATAAGA
66 ATTTCAGGGAGATAAGA
21278953 TTCACCATAA
Statistics
Matches: 202, Mismatches: 44, Indels: 32
0.73 0.16 0.12
Matches are distributed among these distances:
85 22 0.11
86 7 0.03
87 32 0.16
88 12 0.06
89 57 0.28
90 3 0.01
91 3 0.01
92 35 0.17
95 7 0.03
96 24 0.12
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (89 bp):
CTTCAATCTGGCCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCA
ATTTCAGGGAGATAAGACTAGTAA
Found at i:21278907 original size:43 final size:43
Alignment explanation
Indices: 21278784--21278952 Score: 142
Period size: 43 Copynumber: 3.8 Consensus size: 43
21278774 CAATTTATAG
* * * * * *
21278784 CTTCAATCCGTTCCACTACAACTTCAGGGAAATAAGATTCACTAT
1 CTTCAATCTGCTCCACTACAACTT-AGGGAGATAAGACT-AGTAA
* ** *
21278829 CTTCAGTCTGCTCCACTGTAATTTCAGGGAGATAAGACTAGTAA
1 CTTCAATCTGCTCCACTACAACTT-AGGGAGATAAGACTAGTAA
* * **
21278873 CTTCAATCTGGC-CCACTACAACTTAGGGGGATAAGATTAGTGG
1 CTTCAATCT-GCTCCACTACAACTTAGGGAGATAAGACTAGTAA
* *
21278916 CTTTAATCTGCTCCACTACAACTTCAAGGAGATAAGA
1 CTTCAATCTGCTCCACTACAACTT-AGGGAGATAAGA
21278953 TTCACCATAA
Statistics
Matches: 100, Mismatches: 21, Indels: 7
0.78 0.16 0.05
Matches are distributed among these distances:
42 2 0.02
43 35 0.35
44 30 0.30
45 33 0.33
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (43 bp):
CTTCAATCTGCTCCACTACAACTTAGGGAGATAAGACTAGTAA
Found at i:21281904 original size:14 final size:14
Alignment explanation
Indices: 21281887--21281930 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
21281877 TATATACAAC
21281887 AATTTAAAATAAAT
1 AATTTAAAATAAAT
* *
21281901 AATTTATAA-AAAC
1 AATTTAAAATAAAT
*
21281914 AATTCAAAATAAAT
1 AATTTAAAATAAAT
21281928 AAT
1 AAT
21281931 AAAAAGTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (14 bp):
AATTTAAAATAAAT
Found at i:21281922 original size:27 final size:26
Alignment explanation
Indices: 21281871--21282129 Score: 165
Period size: 25 Copynumber: 10.3 Consensus size: 26
21281861 AAACGAAACA
* *
21281871 AAATAATATATACAACAATTTAAAAT
1 AAATAATATATAAAACAATTCAAAAT
*
21281897 AAATAATTTATAAAAACAATTCAAAAT
1 AAATAATATAT-AAAACAATTCAAAAT
**
21281924 AAAT-A-ATA-AAAA-GTTTC-AAAT
1 AAATAATATATAAAACAATTCAAAAT
*
21281945 AAACAATATATAAAA-AACTT-AAAAT
1 AAATAATATATAAAACAA-TTCAAAAT
* * *
21281970 AAGTAATA-ATAAAACAGTTTTAAAA-
1 AAATAATATATAAAACA-ATTCAAAAT
* *
21281995 AAATAATATATAAAA-ATTTAAAAGAT
1 AAATAATATATAAAACAATTCAAA-AT
* * *
21282021 AACAT-ATATAT--AATAGTTTAAAAT
1 AA-ATAATATATAAAACAATTCAAAAT
*
21282045 AAATAATATATGAGAAAAAATT-AAAAT
1 AAATAATATAT-A-AAACAATTCAAAAT
* * *
21282072 AAATAATATGTAAAACAGTTTAAAAT
1 AAATAATATATAAAACAATTCAAAAT
21282098 AAATAATATA-AAAA-AACTT-AAAAT
1 AAATAATATATAAAACAA-TTCAAAAT
21282122 AAATAATA
1 AAATAATA
21282130 AAAGAGTTTT
Statistics
Matches: 189, Mismatches: 23, Indels: 44
0.74 0.09 0.17
Matches are distributed among these distances:
21 7 0.04
22 4 0.02
23 9 0.05
24 42 0.22
25 44 0.23
26 44 0.23
27 34 0.18
28 5 0.03
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.29
Consensus pattern (26 bp):
AAATAATATATAAAACAATTCAAAAT
Found at i:21281952 original size:24 final size:25
Alignment explanation
Indices: 21281871--21282129 Score: 207
Period size: 26 Copynumber: 10.3 Consensus size: 25
21281861 AAACGAAACA
21281871 AAATAATATATACAACAA-TTTAAAAT
1 AAATAATATATA-AA-AAGTTTAAAAT
* * *
21281897 AAATAATTTATAAAAACAATTCAAAAT
1 AAATAATATAT-AAAA-AGTTTAAAAT
*
21281924 --A-AATA-ATAAAAAGTTTCAAAT
1 AAATAATATATAAAAAGTTTAAAAT
* **
21281945 AAACAATATATAAAAAACTTAAAAT
1 AAATAATATATAAAAAGTTTAAAAT
*
21281970 AAGTAATA-ATAAAACAGTTTTAAAA-
1 AAATAATATATAAAA-AG-TTTAAAAT
21281995 AAATAATATATAAAAA-TTTAAAAGAT
1 AAATAATATATAAAAAGTTT-AAA-AT
*
21282021 AACAT-ATATAT-AATAGTTTAAAAT
1 AA-ATAATATATAAAAAGTTTAAAAT
**
21282045 AAATAATATATGAGAAAAAATTAAAAT
1 AAATAATATAT-A-AAAAGTTTAAAAT
*
21282072 AAATAATATGTAAAACAGTTTAAAAT
1 AAATAATATATAAAA-AGTTTAAAAT
**
21282098 AAATAATATA-AAAAAACTTAAAAT
1 AAATAATATATAAAAAGTTTAAAAT
21282122 AAATAATA
1 AAATAATA
21282130 AAAGAGTTTT
Statistics
Matches: 189, Mismatches: 24, Indels: 42
0.74 0.09 0.16
Matches are distributed among these distances:
21 7 0.04
22 4 0.02
23 8 0.04
24 42 0.22
25 44 0.23
26 54 0.29
27 30 0.16
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.29
Consensus pattern (25 bp):
AAATAATATATAAAAAGTTTAAAAT
Found at i:21282009 original size:50 final size:49
Alignment explanation
Indices: 21281872--21282138 Score: 246
Period size: 50 Copynumber: 5.4 Consensus size: 49
21281862 AACGAAACAA
* * *
21281872 AATAATATATACAACAATTTAAAATAAATAATTTATAAAAACAATTCAAAAT
1 AATAATA-ATAAAACAGTTTAAAATAAATAATATATAAAAA-AATT-AAAAT
* * *
21281924 -A-AATAATAAAA-AGTTTCAAATAAACAATATATAAAAAACTTAAAAT
1 AATAATAATAAAACAGTTTAAAATAAATAATATATAAAAAAATTAAAAT
*
21281970 AAGTAATAATAAAACAGTTTTAAAA-AAATAATATAT-AAAAATTTAAAAGAT
1 AA-TAATAATAAAACAG-TTTAAAATAAATAATATATAAAAAAATT-AAA-AT
* * *
21282021 AA-CATATATATAATAGTTTAAAATAAATAATATATGAGAAAAAATTAAAAT
1 AATAATA-ATAAAACAGTTTAAAATAAATAATATAT-A-AAAAAATTAAAAT
* *
21282072 AAATAATATGTAAAACAGTTTAAAATAAATAATATA-AAAAAACTTAAAAT
1 -AATAATA-ATAAAACAGTTTAAAATAAATAATATATAAAAAAATTAAAAT
*
21282122 -A-AATAATAAAAGAGTTT
1 AATAATAATAAAACAGTTT
21282139 TTTTAAATAA
Statistics
Matches: 181, Mismatches: 20, Indels: 34
0.77 0.09 0.14
Matches are distributed among these distances:
46 15 0.08
47 8 0.04
48 23 0.13
49 32 0.18
50 49 0.27
51 14 0.08
52 5 0.03
53 35 0.19
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (49 bp):
AATAATAATAAAACAGTTTAAAATAAATAATATATAAAAAAATTAAAAT
Found at i:21282305 original size:22 final size:22
Alignment explanation
Indices: 21282280--21282322 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
21282270 CTCATGGCTA
21282280 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
21282302 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
21282323 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:21284616 original size:50 final size:50
Alignment explanation
Indices: 21284541--21284733 Score: 269
Period size: 50 Copynumber: 3.8 Consensus size: 50
21284531 ATTTGGGTAA
*
21284541 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTTGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*
21284591 AGAGGTCCCATGTAAAACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * *
21284641 AGAGGTCCCCCGTAAGACCATGTCTGGGACACGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * *
21284691 AGAACATTCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
21284734 TGTTATTATC
Statistics
Matches: 125, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 93 0.74
51 32 0.26
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:21288486 original size:25 final size:25
Alignment explanation
Indices: 21288440--21288506 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 25
21288430 ATTTAGCTAC
21288440 TTATTTGTTATCTTTTTACTTTATTTA
1 TTATTT-TTAT-TTTTTACTTTATTTA
* *
21288467 -TATTTTATATTTTTTCCTTTCTTTA
1 TTATTTT-TATTTTTTACTTTATTTA
21288492 TTATTTTTATTTTTT
1 TTATTTTTATTTTTT
21288507 TATAAAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
25 22 0.61
26 14 0.39
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.75
Consensus pattern (25 bp):
TTATTTTTATTTTTTACTTTATTTA
Found at i:21290768 original size:34 final size:34
Alignment explanation
Indices: 21290725--21290799 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
21290715 CAATAAAATA
21290725 TTATCAAAATAAACAAAAATAATATCATATGAAC
1 TTATCAAAATAAACAAAAATAATATCATATGAAC
*
21290759 TTATCAAAATACACAAAAATAATATCATATGAAC
1 TTATCAAAATAAACAAAAATAATATCATATGAAC
21290793 TTATCAA
1 TTATCAA
21290800 GGCTAAACAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.56, C:0.13, G:0.03, T:0.28
Consensus pattern (34 bp):
TTATCAAAATAAACAAAAATAATATCATATGAAC
Found at i:21291961 original size:69 final size:69
Alignment explanation
Indices: 21291817--21291972 Score: 190
Period size: 69 Copynumber: 2.3 Consensus size: 69
21291807 GGCTATTATA
* * *
21291817 GTAATCCCTGTGTTTACTGTCCCAACAGACTCCATTAGTTGCTATTGTCGAGTTATGGACTTACA
1 GTAATCCCTGTGTTTACTGTCCCAACAGACTCCATTAGTTGCCATAGTCGAGCTATGGACTTACA
21291882 CATC
66 CATC
** * *
21291886 ACAATCCCTGTGTTTACTGTCCCGAA-AGACTCCATTGGTTGCCATAGTTGAGCTAT-GATCTTA
1 GTAATCCCTGTGTTTACTGTCCC-AACAGACTCCATTAGTTGCCATAGTCGAGCTATGGA-CTTA
*
21291949 CACTTC
64 CACATC
* *
21291955 GTAATCCTTATGTTTACT
1 GTAATCCCTGTGTTTACT
21291973 ATCCAGACGG
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
68 2 0.03
69 69 0.95
70 2 0.03
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (69 bp):
GTAATCCCTGTGTTTACTGTCCCAACAGACTCCATTAGTTGCCATAGTCGAGCTATGGACTTACA
CATC
Found at i:21296424 original size:43 final size:43
Alignment explanation
Indices: 21296315--21296443 Score: 125
Period size: 43 Copynumber: 3.0 Consensus size: 43
21296305 AATTTGTACA
* * * * *
21296315 ATGCCAACGTCCCAGACGTGGTATTACATGTAATCACAGATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAAATCG
* * * * *
21296358 ATGTC-GCTGTCCTAAACAGGGTCTTACACGTAAACACAAATCG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAAACACAAATCG
* * *
21296401 ATGCCAACGTCCCAGATATGGTCTTACACATAAACACATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAAATCG
21296444 GAAATCCTAT
Statistics
Matches: 66, Mismatches: 18, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
42 1 0.02
43 64 0.97
44 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAAATCG
Found at i:21301062 original size:43 final size:43
Alignment explanation
Indices: 21301009--21301125 Score: 155
Period size: 43 Copynumber: 2.7 Consensus size: 43
21300999 CATAGGATTT
* *
21301009 TCGATATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCA
1 TCGATATGTGTTTACGTGTAAGACCACGTCTGGGACAGTGGCA
* *
21301052 TCGATTTGTGTTTACGTGTAAGACC-CTATCTGGGACAGTGGCA
1 TCGATATGTGTTTACGTGTAAGACCAC-GTCTGGGACAGTGGCA
* * *
21301095 TCGATATGTGATTACATGTAAGACTACGTCT
1 TCGATATGTGTTTACGTGTAAGACCACGTCT
21301126 AAGATGTTGG
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 1 0.02
43 61 0.97
44 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (43 bp):
TCGATATGTGTTTACGTGTAAGACCACGTCTGGGACAGTGGCA
Found at i:21301296 original size:15 final size:16
Alignment explanation
Indices: 21301271--21301303 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
21301261 GTAACGTATT
21301271 TGAATTATGAATTATG
1 TGAATTATGAATTATG
21301287 TGAA-TATGAATTATG
1 TGAATTATGAATTATG
21301302 TG
1 TG
21301304 TTAACATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (16 bp):
TGAATTATGAATTATG
Found at i:21302906 original size:41 final size:41
Alignment explanation
Indices: 21302845--21303002 Score: 239
Period size: 41 Copynumber: 3.9 Consensus size: 41
21302835 TTTAACATAT
* *
21302845 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCCA-A
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT-CAGA
* *
21302886 TCACCGACACTTAGCTTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
21302927 TTACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
21302968 TCACCGGCACTTAGCCTGCTAGGTTTGA-AACCTGA
1 TCACCGGCACTTAGCCTGCTAGGTTT-ATAACCTGA
21303003 AAATTTCAAT
Statistics
Matches: 107, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
40 2 0.02
41 104 0.97
42 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:21304716 original size:13 final size:13
Alignment explanation
Indices: 21304698--21304722 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21304688 CAATCAAATG
21304698 CACACAAAATAAA
1 CACACAAAATAAA
21304711 CACACAAAATAA
1 CACACAAAATAA
21304723 TATTAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:21306222 original size:11 final size:11
Alignment explanation
Indices: 21306206--21306275 Score: 70
Period size: 11 Copynumber: 6.0 Consensus size: 11
21306196 CTCTAAATCA
21306206 ACATTTAAGTC
1 ACATTTAAGTC
21306217 ACATTTAAGTC
1 ACATTTAAGTC
* *
21306228 ACA-CTCAGCATC
1 ACATTTAAG--TC
21306240 AACATTTAAGTC
1 -ACATTTAAGTC
21306252 ACATTTAAGTCAC
1 ACATTTAAGT--C
21306265 ACATTTAAGTC
1 ACATTTAAGTC
21306276 GACTTTCTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
10 3 0.06
11 25 0.51
12 4 0.08
13 14 0.29
14 3 0.06
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.31
Consensus pattern (11 bp):
ACATTTAAGTC
Found at i:21306268 original size:24 final size:24
Alignment explanation
Indices: 21306206--21306275 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
21306196 CTCTAAATCA
21306206 ACATTTAAGT--CACATTTAAGTC
1 ACATTTAAGTCACACATTTAAGTC
* *
21306228 ACA-CTCAG-CATCAACATTTAAGTC
1 ACATTTAAGTCA-C-ACATTTAAGTC
21306252 ACATTTAAGTCACACATTTAAGTC
1 ACATTTAAGTCACACATTTAAGTC
21306276 GACTTTCTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 3 0.08
22 3 0.08
23 1 0.03
24 25 0.66
25 4 0.11
26 2 0.05
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.31
Consensus pattern (24 bp):
ACATTTAAGTCACACATTTAAGTC
Found at i:21310536 original size:41 final size:41
Alignment explanation
Indices: 21310479--21310556 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
21310469 TTTAACATAT
*
21310479 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCCAA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCCAA
*
21310520 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
21310557 NNNNNNNNNN
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.29
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCCAA
Found at i:21311869 original size:13 final size:13
Alignment explanation
Indices: 21311851--21311875 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21311841 CAATCAAATG
21311851 CACACAAAATAAA
1 CACACAAAATAAA
21311864 CACACAAAATAA
1 CACACAAAATAA
21311876 TATTAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:21314858 original size:15 final size:15
Alignment explanation
Indices: 21314802--21314859 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
21314792 CAATACAAAT
*
21314802 AATTTCAAATTAAAAA
1 AATTT-AAATTAACAA
*
21314818 AATATTAAATTTAACAT
1 AAT-TTAAA-TTAACAA
* *
21314835 TATTGAAATTAACAA
1 AATTTAAATTAACAA
21314850 AATTTAAATT
1 AATTTAAATT
21314860 TTCGTCTTAC
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
15 14 0.42
16 10 0.30
17 9 0.27
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (15 bp):
AATTTAAATTAACAA
Found at i:21315895 original size:4 final size:4
Alignment explanation
Indices: 21315879--21315913 Score: 52
Period size: 4 Copynumber: 8.2 Consensus size: 4
21315869 ACTAATTAAA
21315879 TATT TAGTT TATT TATT TATT TATT TATT TGATT T
1 TATT TA-TT TATT TATT TATT TATT TATT T-ATT T
21315914 GATTAGTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 21 0.72
5 8 0.28
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:21320963 original size:16 final size:17
Alignment explanation
Indices: 21320942--21320978 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
21320932 AATTGATGAT
*
21320942 TTTAA-TAAAAATTTAA
1 TTTAATTAAAAAATTAA
21320958 TTTAATTAAAAAATTAA
1 TTTAATTAAAAAATTAA
21320975 TTTA
1 TTTA
21320979 TATACTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAATTAAAAAATTAA
Found at i:21329023 original size:3 final size:3
Alignment explanation
Indices: 21329015--21329044 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
21329005 ATATATATAG
*
21329015 TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21329045 CAAATAGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:21329036 original size:15 final size:15
Alignment explanation
Indices: 21329016--21329047 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
21329006 TATATATAGT
21329016 AATAATAATAATAAC
1 AATAATAATAATAAC
21329031 AATAATAATAATAAC
1 AATAATAATAATAAC
21329046 AA
1 AA
21329048 ATAGGGACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (15 bp):
AATAATAATAATAAC
Found at i:21329818 original size:45 final size:45
Alignment explanation
Indices: 21329789--21330706 Score: 1167
Period size: 45 Copynumber: 20.4 Consensus size: 45
21329779 CTGCCGATAC
* * *
21329789 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTACCAATAT
1 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
* * * * *
21329834 AGGAAAACAAGATCCGTTATCTTCGATCTACTTCGCCACTAGTGT
1 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
** ** *
21329879 -GGAAAGACAAGATCTACTATCTTTGATCTACTTCGCTGCCAGTAC
1 AGG-AAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
* *
21329924 AGGAATACAAGATCTGTTATCTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
* * * *
21329969 -GGAAAGACAAGATCTGCTATCTTTGATCTATTTCGCTACCAGTAC
1 AGG-AAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
21330014 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
* *
21330059 GGGAAGACAAGATCTGTTATCTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
* * *
21330104 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTACCAGTAC
1 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
* * *
21330149 AGGAAGACAAGATCCGTTATCTTCGATCTACTTCACCACCAGTAT
1 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
* ** ** *
21330194 GGGAAGACAAGATCTACTATCTTTGATCTACTTCGCTGCCAGTAC
1 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
* * * *
21330239 AGGAAGACAATATCCGTTATCTTCGATCTACTTTGCCACCAGTAT
1 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
* *
21330284 GGGAAGACAAGATCCGTTAT-TTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGTTATCTTT-GATCTACTTCGCCACCAGTAT
* * **
21330329 GGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAGTAT
1 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
* **
21330374 AGGAAGACAAGATCTGTTATCTTCGATCTACTTCGCCATTAGTAT
1 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
* * ** *
21330419 GGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAGTAC
1 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
* * *
21330464 AAGAAGACAAGATCCGTTATCTTTGATCTACTTCGCCACCAGCAT
1 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
* * *
21330509 GGGAAGACAAGATCCGTTATCTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
* * ** *
21330554 GGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAGTAC
1 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
* *
21330599 AGGAAGACAAGATCCGTTATCTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
* * * *
21330644 GGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAGTAC
1 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
*
21330689 GGGAAGACAAGATCTGTT
1 AGGAAGACAAGATCTGTT
21330707 GTTTTTCAAC
Statistics
Matches: 747, Mismatches: 120, Indels: 12
0.85 0.14 0.01
Matches are distributed among these distances:
44 6 0.01
45 734 0.98
46 7 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (45 bp):
AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
Found at i:21336649 original size:33 final size:33
Alignment explanation
Indices: 21336598--21336688 Score: 146
Period size: 33 Copynumber: 2.7 Consensus size: 33
21336588 TTGTCCGTTA
* * *
21336598 TCGGTGGATTCAGCACTTAGCAACCACCAGTGAT
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAG
21336632 TCGGGGAATCAGCACTTAGCAACCACCAATGAG
1 TCGGGGAATCAGCACTTAGCAACCACCAATGAG
21336665 TCGGGGAATCAGCACTTAGCAACC
1 TCGGGGAATCAGCACTTAGCAACC
21336689 CCTTGGGGGA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 50 0.93
34 4 0.07
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (33 bp):
TCGGGGAATCAGCACTTAGCAACCACCAATGAG
Found at i:21336701 original size:27 final size:27
Alignment explanation
Indices: 21336667--21336744 Score: 147
Period size: 27 Copynumber: 2.9 Consensus size: 27
21336657 CCAATGAGTC
*
21336667 GGGGAATCAGCACTTAGCAACCCCTTG
1 GGGGAATCAACACTTAGCAACCCCTTG
21336694 GGGGAATCAACACTTAGCAACCCCTTG
1 GGGGAATCAACACTTAGCAACCCCTTG
21336721 GGGGAATCAACACTTAGCAACCCC
1 GGGGAATCAACACTTAGCAACCCC
21336745 CTTCACATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (27 bp):
GGGGAATCAACACTTAGCAACCCCTTG
Found at i:21336840 original size:102 final size:102
Alignment explanation
Indices: 21336695--21336951 Score: 415
Period size: 102 Copynumber: 2.5 Consensus size: 102
21336685 AACCCCTTGG
* *
21336695 GGGAATCAACACTTAGCAACCCCTTGGGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAAT
1 GGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAAT
*
21336760 ACGGTAGAATCATCACTTAGCAACCACCAATGATTCA
66 ACGGTAGAATCAGCACTTAGCAACCACCAATGATTCA
* *
21336797 GGGAATCAGCATTTAGCAACCCCTTGGGGGAATCAGTACTTAGCAACCCCCTTCACATTTAAAAT
1 GGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAAT
* * *
21336862 ATGGTGGAATCAGCACTTAGCAACCACCAATGATTCG
66 ACGGTAGAATCAGCACTTAGCAACCACCAATGATTCA
* * *
21336899 GGGAATCAGCACGTAGCAACCCCTTGGAGGAATCAGCACTTAGCAATCCCCTT
1 GGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTT
21336952 TATATTCAAT
Statistics
Matches: 142, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 142 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (102 bp):
GGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAAT
ACGGTAGAATCAGCACTTAGCAACCACCAATGATTCA
Found at i:21344185 original size:33 final size:33
Alignment explanation
Indices: 21344116--21344377 Score: 143
Period size: 33 Copynumber: 7.7 Consensus size: 33
21344106 ATATAAAGGG
*
21344116 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
21344143 GGTTGCTAAGTGTTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * *
21344176 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--AT-CAT-T---GGT
* *
21344218 GGTTGCTAAGTGTTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
21344245 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* ** *
21344278 GGTTGCTAAGTGCTGATCCCACCGTGTCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGAATC----AT-TG---GT
* *
21344320 GGTTGCTAAGTGCTAATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
21344353 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
21344378 TAACGGACAA
Statistics
Matches: 181, Mismatches: 23, Indels: 55
0.70 0.09 0.21
Matches are distributed among these distances:
27 42 0.23
28 2 0.01
31 4 0.02
32 4 0.02
33 58 0.32
34 12 0.07
35 1 0.01
36 2 0.01
37 2 0.01
38 4 0.02
39 3 0.02
41 7 0.04
42 40 0.22
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:21344239 original size:102 final size:102
Alignment explanation
Indices: 21344111--21344341 Score: 399
Period size: 102 Copynumber: 2.3 Consensus size: 102
21344101 ATTGAATATA
*
21344111 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
21344176 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTG
66 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
*
21344213 AAGGGGGTTGCTAAGTGTTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
21344278 GGTTGCTAAGTGCTGATCCCACCGTGTCTTAAATGTG
66 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
* *
21344315 AAAGGGGTTGCTAAGTGCTAATTCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCC
21344342 GAATCACTGG
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 121 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.31
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
Found at i:21346961 original size:16 final size:16
Alignment explanation
Indices: 21346936--21346970 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
21346926 TTCTATGATG
*
21346936 AAATGCCATGCAGTCA
1 AAATGCCATGCAGCCA
*
21346952 AAATGTCATGCAGCCA
1 AAATGCCATGCAGCCA
21346968 AAA
1 AAA
21346971 CAAAACACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (16 bp):
AAATGCCATGCAGCCA
Found at i:21348874 original size:3 final size:3
Alignment explanation
Indices: 21348866--21348895 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
21348856 ATATATATAG
*
21348866 TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21348896 CAAATAGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:21350939 original size:24 final size:24
Alignment explanation
Indices: 21350911--21350959 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
21350901 CCACTAAAAA
21350911 ACAAGATTTTACCGTAATACTTTG
1 ACAAGATTTTACCGTAATACTTTG
21350935 ACAAGATTTTACCGTAATACTTTG
1 ACAAGATTTTACCGTAATACTTTG
21350959 A
1 A
21350960 TCTAATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (24 bp):
ACAAGATTTTACCGTAATACTTTG
Found at i:21361929 original size:16 final size:16
Alignment explanation
Indices: 21361908--21361941 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
21361898 CTTCAACCTC
*
21361908 TCATTTCCTTCTCATT
1 TCATTTCCTCCTCATT
21361924 TCATTTCCTCCTCATT
1 TCATTTCCTCCTCATT
21361940 TC
1 TC
21361942 CTCTCCGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.00, T:0.53
Consensus pattern (16 bp):
TCATTTCCTCCTCATT
Found at i:21362839 original size:13 final size:11
Alignment explanation
Indices: 21362811--21362844 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
21362801 ATTTTTTTCT
21362811 CATATATTGTA
1 CATATATTGTA
21362822 CATATATTGTA
1 CATATATTGTA
21362833 CATATATTGTA
1 CATATATTGTA
21362844 C
1 C
21362845 TAATTCCTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (11 bp):
CATATATTGTA
Found at i:21371019 original size:30 final size:30
Alignment explanation
Indices: 21370983--21371152 Score: 125
Period size: 30 Copynumber: 5.7 Consensus size: 30
21370973 AGCCGAAGCT
* * *
21370983 ATCCCTTTTCATTATTTGATGGTCATCACC
1 ATCCCTTTTCATAATTTGATGGCCATCACA
*
21371013 ATCCCTTTTCATAATTTGATAG-C-TCA-A
1 ATCCCTTTTCATAATTTGATGGCCATCACA
* * * *
21371040 GTTATCCCTTTTCACAATTCGATAGCCGA--AGCC
1 ---ATCCCTTTTCATAATTTGATGGCC-ATCA-CA
** * *
21371073 ATCCCTTTTCATTGTTCGATGGCCGTCACA
1 ATCCCTTTTCATAATTTGATGGCCATCACA
* * *
21371103 ATCCCTTTTCATTATTTGATGGTCGTCACA
1 ATCCCTTTTCATAATTTGATGGCCATCACA
21371133 ATCCCTTTTCATAATTTGAT
1 ATCCCTTTTCATAATTTGAT
21371153 AGCCGAGGCT
Statistics
Matches: 114, Mismatches: 16, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
28 3 0.03
29 1 0.01
30 107 0.94
31 3 0.03
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (30 bp):
ATCCCTTTTCATAATTTGATGGCCATCACA
Found at i:21371137 original size:90 final size:88
Alignment explanation
Indices: 21370971--21371183 Score: 239
Period size: 90 Copynumber: 2.4 Consensus size: 88
21370961 CCACGACTCA
* * * *
21370971 ATAGCCGAAGCTATCCCTTTTCATTATTTGATGGTCATCACCATCCCTTTTCATAATTTGATAGC
1 ATAGCCGAAGCCATCCCTTTTCATTATTCGATGGCCATCACAATCCCTTTTCATAATTTGATAGC
21371036 TCAAGTTATCCCTTTTCACAATTCG
66 TCAA--TATCCCTTTTCACAATTCG
* * * *
21371061 ATAGCCGAAGCCATCCCTTTTCATTGTTCGATGGCCGTCACAATCCCTTTTCATTATTTGATGGT
1 ATAGCCGAAGCCATCCCTTTTCATTATTCGATGGCCATCACAATCCCTTTTCATAATTTGATAG-
* *
21371126 CGTCACA-ATCCCTTTTCATAATTTG
65 C-TCA-ATATCCCTTTTCACAATTCG
* * * *
21371151 ATAGCCGAGGCTATCCTTTTTTATTATTTCGAT
1 ATAGCCGAAGCCATCCCTTTTCATTA-TTCGAT
21371184 AGCTGAAGTT
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
90 93 0.89
91 7 0.07
92 3 0.03
93 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (88 bp):
ATAGCCGAAGCCATCCCTTTTCATTATTCGATGGCCATCACAATCCCTTTTCATAATTTGATAGC
TCAATATCCCTTTTCACAATTCG
Found at i:21371177 original size:60 final size:60
Alignment explanation
Indices: 21370971--21371179 Score: 208
Period size: 60 Copynumber: 3.5 Consensus size: 60
21370961 CCACGACTCA
*
21370971 ATAGCCGAAGCTATCCCTTTTCATTATTTGATGGTCATCACCATCCCTTTTCATAATTTG
1 ATAGCCGAAGCTATCCCTTTTCATTATTTGATGGTCGTCACCATCCCTTTTCATAATTTG
* ** * * * * ** *
21371031 ATAGCTC-AAGTTATCCCTTTTCACAATTCGATAGCCG-AAGCCATCCCTTTTCATTGTTCG
1 ATAGC-CGAAGCTATCCCTTTTCATTATTTGATGGTCGTCA-CCATCCCTTTTCATAATTTG
* * * *
21371091 ATGGCCGTCA-CAATCCCTTTTCATTATTTGATGGTCGTCACAATCCCTTTTCATAATTTG
1 ATAGCCG-AAGCTATCCCTTTTCATTATTTGATGGTCGTCACCATCCCTTTTCATAATTTG
* * *
21371151 ATAGCCGAGGCTATCCTTTTTTATTATTT
1 ATAGCCGAAGCTATCCCTTTTCATTATTT
21371180 CGATAGCTGA
Statistics
Matches: 112, Mismatches: 31, Indels: 12
0.72 0.20 0.08
Matches are distributed among these distances:
59 2 0.02
60 107 0.96
61 3 0.03
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (60 bp):
ATAGCCGAAGCTATCCCTTTTCATTATTTGATGGTCGTCACCATCCCTTTTCATAATTTG
Found at i:21376894 original size:21 final size:21
Alignment explanation
Indices: 21376870--21376909 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
21376860 TGAGGTGAAA
21376870 AAATTTCTAGTTGACAAATCC
1 AAATTTCTAGTTGACAAATCC
* *
21376891 AAATTTGTAGTTGATAAAT
1 AAATTTCTAGTTGACAAAT
21376910 ATTATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (21 bp):
AAATTTCTAGTTGACAAATCC
Found at i:21378060 original size:20 final size:20
Alignment explanation
Indices: 21377979--21378068 Score: 94
Period size: 20 Copynumber: 4.5 Consensus size: 20
21377969 GAAGCAATTC
* *
21377979 TGACTTGTTTGAAAATCATTT
1 TGACTTGATT-AAAATTATTT
*
21378000 TGA-TATG-TTAAAATGATTT
1 TGACT-TGATTAAAATTATTT
* *
21378019 TAACTTGATTGAAATTATTT
1 TGACTTGATTAAAATTATTT
21378039 TGACTTGATTAAAATTATTT
1 TGACTTGATTAAAATTATTT
*
21378059 TGACCTGATT
1 TGACTTGATT
21378069 TTAAAATTGT
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
19 13 0.22
20 41 0.69
21 5 0.08
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.48
Consensus pattern (20 bp):
TGACTTGATTAAAATTATTT
Found at i:21378424 original size:18 final size:18
Alignment explanation
Indices: 21378398--21378434 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
21378388 TAAAAATATA
*
21378398 TATATATATTTGAAATTT
1 TATAAATATTTGAAATTT
*
21378416 TATAAATATTTTAAATTT
1 TATAAATATTTGAAATTT
21378434 T
1 T
21378435 TGAAAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TATAAATATTTGAAATTT
Found at i:21378447 original size:20 final size:21
Alignment explanation
Indices: 21378422--21378463 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
21378412 ATTTTATAAA
21378422 TATTTTAAA-TTTTTGAAAAT
1 TATTTTAAACTTTTTGAAAAT
*
21378442 TATTTTAAACTTTTTGATAAT
1 TATTTTAAACTTTTTGAAAAT
21378463 T
1 T
21378464 TTTATTTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (21 bp):
TATTTTAAACTTTTTGAAAAT
Found at i:21391113 original size:18 final size:18
Alignment explanation
Indices: 21391090--21391127 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
21391080 AGGGGATTAG
21391090 TGAAAAGTGAAATTAAAA
1 TGAAAAGTGAAATTAAAA
21391108 TGAAAAGTGAAATTAAAA
1 TGAAAAGTGAAATTAAAA
21391126 TG
1 TG
21391128 TAAGTTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (18 bp):
TGAAAAGTGAAATTAAAA
Found at i:21392933 original size:27 final size:27
Alignment explanation
Indices: 21392809--21392920 Score: 156
Period size: 27 Copynumber: 4.1 Consensus size: 27
21392799 TAAATGACCG
*
21392809 AAATTACTGAAATACCCTCGAAGGGT-
1 AAATTACTAAAATACCCTCGAAGGGTA
*
21392835 AAATTA-TCAAAATACCCTTGAAGGGTA
1 AAATTACT-AAAATACCCTCGAAGGGTA
* *
21392862 AAATTACCAAAATACCCTCCAAAGGGTA
1 AAATTACTAAAATACCCT-CGAAGGGTA
21392890 AAATTACTAAAATACCCTCGAAGGGTA
1 AAATTACTAAAATACCCTCGAAGGGTA
21392917 AAAT
1 AAAT
21392921 GACTGTTATA
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.01
26 22 0.29
27 28 0.37
28 24 0.32
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (27 bp):
AAATTACTAAAATACCCTCGAAGGGTA
Found at i:21392933 original size:55 final size:53
Alignment explanation
Indices: 21392818--21392923 Score: 151
Period size: 55 Copynumber: 2.0 Consensus size: 53
21392808 GAAATTACTG
* * *
21392818 AAATACCCTCGAAGGGTAAATTATCAAAATACCCTTGAAGGGTAAAATTACCA
1 AAATACCCTCAAAGGGTAAATTATCAAAATACCCTCGAAGGGTAAAATGACCA
21392871 AAATACCCTCCAAAGGGTAAAATTA-CTAAAATACCCTCGAAGGGTAAAATGAC
1 AAATACCCT-CAAAGGGT-AAATTATC-AAAATACCCTCGAAGGGTAAAATGAC
21392924 TGTTATACCC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
53 9 0.19
54 8 0.17
55 30 0.64
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (53 bp):
AAATACCCTCAAAGGGTAAATTATCAAAATACCCTCGAAGGGTAAAATGACCA
Found at i:21393180 original size:26 final size:26
Alignment explanation
Indices: 21393106--21393209 Score: 82
Period size: 26 Copynumber: 4.0 Consensus size: 26
21393096 ACAAATACTA
** *
21393106 TTACTGGCAGCTTTGCTGCATTACTG
1 TTACTGGCAGCTTTGCTGTGTTATTG
* * * * * *
21393132 ATACTAGCAACTCTACTGCGTTATTG
1 TTACTGGCAGCTTTGCTGTGTTATTG
* * *
21393158 TTACTGGCAGTTTTGCTGTGTTACTA
1 TTACTGGCAGCTTTGCTGTGTTATTG
* *
21393184 TTACTGGTAGCTTTGCTGTGATATTG
1 TTACTGGCAGCTTTGCTGTGTTATTG
21393210 GTGTGTTGGC
Statistics
Matches: 57, Mismatches: 21, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
26 57 1.00
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.41
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTGTGTTATTG
Found at i:21393376 original size:30 final size:29
Alignment explanation
Indices: 21393323--21393425 Score: 118
Period size: 30 Copynumber: 3.5 Consensus size: 29
21393313 GATTACTATT
*
21393323 TTGGGCTAAGGCCCACA-CTGTTACTGAA
1 TTGGGCTAAGGCCCACACCTGTTACTGTA
21393351 TTGGGCTAAGGCCCACACTCTGTTACTGTA
1 TTGGGCTAAGGCCCACAC-CTGTTACTGTA
* * * *
21393381 TTAGGTTATGGCCCACACACTGCTACTGTA
1 TTGGGCTAAGGCCCACAC-CTGTTACTGTA
* *
21393411 TAGGGCTCAGGCCCA
1 TTGGGCTAAGGCCCA
21393426 GACTGATTCT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
28 17 0.27
30 45 0.73
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.26
Consensus pattern (29 bp):
TTGGGCTAAGGCCCACACCTGTTACTGTA
Found at i:21403905 original size:18 final size:19
Alignment explanation
Indices: 21403870--21403908 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
21403860 GGGGTGTTAC
*
21403870 AATATTCTTTAGATTTTTT
1 AATATTCTTTAGAATTTTT
*
21403889 AATATT-TTTATAATTTTT
1 AATATTCTTTAGAATTTTT
21403907 AA
1 AA
21403909 AAATATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
AATATTCTTTAGAATTTTT
Found at i:21405823 original size:20 final size:23
Alignment explanation
Indices: 21405765--21405810 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
21405755 TCGATACCTG
21405765 GTAAAAGGTATCGATATAATTTT
1 GTAAAAGGTATCGATATAATTTT
21405788 GTAAAAGGTATCGATATAATTTT
1 GTAAAAGGTATCGATATAATTTT
21405811 ATGGGTATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.39
Consensus pattern (23 bp):
GTAAAAGGTATCGATATAATTTT
Found at i:21415183 original size:14 final size:14
Alignment explanation
Indices: 21415164--21415202 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
21415154 ATGCCTAATA
21415164 TTTGATTTTGCCTT
1 TTTGATTTTGCCTT
21415178 TTTGATTTTGCCTT
1 TTTGATTTTGCCTT
*
21415192 TTTTATTTTGC
1 TTTGATTTTGC
21415203 TCATCTCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.08, C:0.13, G:0.13, T:0.67
Consensus pattern (14 bp):
TTTGATTTTGCCTT
Found at i:21415814 original size:27 final size:27
Alignment explanation
Indices: 21415775--21415943 Score: 214
Period size: 27 Copynumber: 6.3 Consensus size: 27
21415765 ATTCATGGGC
* *
21415775 AAATGACCGAAATACCTTCGAAGGGTA
1 AAATGACCAAAATACCCTCGAAGGGTA
*
21415802 AAATGACTAAAATACCCTCGAAGGGTA
1 AAATGACCAAAATACCCTCGAAGGGTA
* *
21415829 AAATGACCGAAATACCCTCGAAAGGTA
1 AAATGACCAAAATACCCTCGAAGGGTA
* * *
21415856 AAATGACCAAAATACCCCCAAAAGGTA
1 AAATGACCAAAATACCCTCGAAGGGTA
**
21415883 AAATGACTGAAATACCCTCGAAGGGTA
1 AAATGACCAAAATACCCTCGAAGGGTA
**
21415910 AAATGACCAAAATA-CCTTTATAGGGTA
1 AAATGACCAAAATACCCTCGA-AGGGTA
21415937 AAATGAC
1 AAATGAC
21415944 TGTTATACCC
Statistics
Matches: 123, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
26 4 0.03
27 119 0.97
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATACCCTCGAAGGGTA
Found at i:21415857 original size:54 final size:54
Alignment explanation
Indices: 21415775--21415943 Score: 248
Period size: 54 Copynumber: 3.1 Consensus size: 54
21415765 ATTCATGGGC
* * *
21415775 AAATGACCGAAATACCTTCGAAGGGTAAAATGACTAAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTAAAATGACCAAAATACCCTCAAAGGGTA
* * *
21415829 AAATGACCGAAATACCCTCGAAAGGTAAAATGACCAAAATACCCCCAAAAGGTA
1 AAATGACCGAAATACCCTCGAAGGGTAAAATGACCAAAATACCCTCAAAGGGTA
* * * *
21415883 AAATGACTGAAATACCCTCGAAGGGTAAAATGACCAAAATACCTTTATAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTAAAATGACCAAAATACCCTCAAAGGGTA
21415937 AAATGAC
1 AAATGAC
21415944 TGTTATACCC
Statistics
Matches: 102, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 102 1.00
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.18
Consensus pattern (54 bp):
AAATGACCGAAATACCCTCGAAGGGTAAAATGACCAAAATACCCTCAAAGGGTA
Found at i:21415968 original size:81 final size:81
Alignment explanation
Indices: 21415775--21415925 Score: 239
Period size: 81 Copynumber: 1.9 Consensus size: 81
21415765 ATTCATGGGC
* ** * * *
21415775 AAATGACCGAAATACCTTCGAAGGGTAAAATGACTAAAATACCCTCGAAGGGTAAAATGACCGAA
1 AAATGACCAAAATACCCCCAAAAGGTAAAATGACTAAAATACCCTCGAAGGGTAAAATGACCAAA
21415840 ATACCCTCGAAAGGTA
66 ATACCCTCGAAAGGTA
*
21415856 AAATGACCAAAATACCCCCAAAAGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATGACCAAA
1 AAATGACCAAAATACCCCCAAAAGGTAAAATGACTAAAATACCCTCGAAGGGTAAAATGACCAAA
21415921 ATACC
66 ATACC
21415926 TTTATAGGGT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 63 1.00
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.16
Consensus pattern (81 bp):
AAATGACCAAAATACCCCCAAAAGGTAAAATGACTAAAATACCCTCGAAGGGTAAAATGACCAAA
ATACCCTCGAAAGGTA
Found at i:21416382 original size:28 final size:28
Alignment explanation
Indices: 21416341--21416407 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
21416331 CCCATATTAC
* *
21416341 ACTGTTACTACTTAGGGGTAAGGCCTAG
1 ACTGTTACTACTTAGGGCTAAGGCCCAG
* *
21416369 ACTGTTACTGCTTAGGGCTTAGGCCCAG
1 ACTGTTACTACTTAGGGCTAAGGCCCAG
*
21416397 ACTGTAACTAC
1 ACTGTTACTAC
21416408 ATGTCGTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.28
Consensus pattern (28 bp):
ACTGTTACTACTTAGGGCTAAGGCCCAG
Found at i:21418364 original size:18 final size:18
Alignment explanation
Indices: 21418341--21418385 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
21418331 TCTTGGTTCA
* *
21418341 TTTCAAGTACTTTAAAAT
1 TTTCAAGCACTTTAAAAC
21418359 TTTCAAGCACTTTAAAAC
1 TTTCAAGCACTTTAAAAC
*
21418377 TTTCCAGCA
1 TTTCAAGCA
21418386 TATCATAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.38
Consensus pattern (18 bp):
TTTCAAGCACTTTAAAAC
Found at i:21419492 original size:14 final size:14
Alignment explanation
Indices: 21419475--21419505 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
21419465 AACCATTTAT
21419475 TTTTAACTAAAAAG
1 TTTTAACTAAAAAG
*
21419489 TTTTAATTAAAAAG
1 TTTTAACTAAAAAG
21419503 TTT
1 TTT
21419506 GAGGAGCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (14 bp):
TTTTAACTAAAAAG
Found at i:21426350 original size:10 final size:10
Alignment explanation
Indices: 21426335--21426383 Score: 57
Period size: 10 Copynumber: 4.8 Consensus size: 10
21426325 ATGAACATGT
21426335 TTAATTTTGA
1 TTAATTTTGA
21426345 TTAATTTT-A
1 TTAATTTTGA
21426354 TATCAAATTTTGA
1 T-T--AATTTTGA
21426367 TTAATTTTGA
1 TTAATTTTGA
21426377 TT-ATTTT
1 TTAATTTT
21426384 CCACATATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
9 7 0.20
10 19 0.54
12 7 0.20
13 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (10 bp):
TTAATTTTGA
Found at i:21430462 original size:50 final size:50
Alignment explanation
Indices: 21430355--21430645 Score: 341
Period size: 50 Copynumber: 5.7 Consensus size: 50
21430345 GTAAAGAGAA
*
21430355 CCCAAGTAAGACCATGTCTGGGACATGGCATTGGCACCCTTGAGATCATGAGAGGT
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATGAGAGGT
** *
21430411 CCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGACGAGAGGT
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
* **
21430461 CCAATGTAAGACCATGTCTGGGACATGGCGCTGGCACCGAGATGAGAGGT
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
* * * **
21430511 CCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACT
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
* * * * * **
21430561 CCCATGTAAGACCATATCTGGGATATGGCATTGGCAGC-ACATGAAACAT
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
*
21430610 CCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
21430646 TGTTATTATA
Statistics
Matches: 207, Mismatches: 28, Indels: 7
0.86 0.12 0.03
Matches are distributed among these distances:
49 40 0.19
50 129 0.62
53 3 0.01
55 2 0.01
56 33 0.16
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (50 bp):
CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
Found at i:21436063 original size:5 final size:5
Alignment explanation
Indices: 21436053--21436096 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
21436043 ATGCTCGTGA
*
21436053 AAAAG AAAAG AAAAAG AAAAG AAAAG AGAAAG AACAAA AAAAG A
1 AAAAG AAAAG -AAAAG AAAAG AAAAG A-AAAG AA-AAG AAAAG A
21436097 GAGCATATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 20 0.59
6 14 0.41
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:21436067 original size:11 final size:11
Alignment explanation
Indices: 21436051--21436096 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
21436041 AAATGCTCGT
21436051 GAAAAAGAAAA
1 GAAAAAGAAAA
21436062 GAAAAAGAAAA
1 GAAAAAGAAAA
21436073 G-AAAAGAGAAA
1 GAAAAAGA-AAA
21436084 GAACAAA-AAAA
1 GAA-AAAGAAAA
21436095 GA
1 GA
21436097 GAGCATATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 6 0.19
11 21 0.66
12 2 0.06
13 3 0.09
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:21436074 original size:16 final size:16
Alignment explanation
Indices: 21436053--21436096 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
21436043 ATGCTCGTGA
21436053 AAAAGAAAAGAAAAAG
1 AAAAGAAAAGAAAAAG
*
21436069 AAAAGAAAAGAGAAAG
1 AAAAGAAAAGAAAAAG
*
21436085 AACAAAAAAAGA
1 AA-AAGAAAAGA
21436097 GAGCATATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAG
Found at i:21437419 original size:25 final size:23
Alignment explanation
Indices: 21437382--21437428 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
21437372 AACCATTCAT
21437382 TCTTCACTTTTCTCTCAGTTTTCTC
1 TCTTCACTTTTCT-TCA-TTTTCTC
21437407 TCTTCA-TTGTTCTTCATTTTCT
1 TCTTCACTT-TTCTTCATTTTCT
21437429 TCCCCATTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.29
24 5 0.24
25 10 0.48
ACGTcount: A:0.09, C:0.28, G:0.04, T:0.60
Consensus pattern (23 bp):
TCTTCACTTTTCTTCATTTTCTC
Found at i:21448778 original size:22 final size:19
Alignment explanation
Indices: 21448753--21448794 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
21448743 TTATAATCAT
21448753 TAATATATAATTATATCTATTA
1 TAATATAT-ATTA-AT-TATTA
21448775 TAATATATATTAATTATTA
1 TAATATATATTAATTATTA
21448794 T
1 T
21448795 CAACTTTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATATATTAATTATTA
Found at i:21449333 original size:21 final size:20
Alignment explanation
Indices: 21449309--21449350 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
21449299 TCACACCGCG
21449309 CCTTG-CTACTCGCACCAACAC
1 CCTTGTCTA-TCGCACC-ACAC
21449330 CCTTGTCTATCGCACCACAC
1 CCTTGTCTATCGCACCACAC
21449350 C
1 C
21449351 ATCAAGACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 12 0.60
22 3 0.15
ACGTcount: A:0.21, C:0.48, G:0.10, T:0.21
Consensus pattern (20 bp):
CCTTGTCTATCGCACCACAC
Found at i:21452410 original size:22 final size:22
Alignment explanation
Indices: 21452385--21452433 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
21452375 AATTATGAAC
*
21452385 ATATTGAATTTTAATTAATTTT
1 ATATTAAATTTTAATTAATTTT
* *
21452407 ATATCAAATTTTGATTAATTTT
1 ATATTAAATTTTAATTAATTTT
21452429 -TATTA
1 ATATTA
21452434 TTTTCGACAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (22 bp):
ATATTAAATTTTAATTAATTTT
Found at i:21453296 original size:18 final size:19
Alignment explanation
Indices: 21453273--21453311 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
21453263 ATTTGTGATG
*
21453273 TTAATATG-TTTAATTTAA
1 TTAATATGCTTAAATTTAA
21453291 TTAATATGCTTAAATTTAA
1 TTAATATGCTTAAATTTAA
21453310 TT
1 TT
21453312 CGTGTTACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (19 bp):
TTAATATGCTTAAATTTAA
Found at i:21461965 original size:34 final size:34
Alignment explanation
Indices: 21461894--21461965 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
21461884 AGCATATATT
* * *
21461894 TATACTTATAAACTACAAGTGCCGAATGCACATA
1 TATACTTATAAACCACAAGTGCCGAATACACAGA
* *
21461928 TATACTTATAATCCACATA-TGCCGAATACATAGA
1 TATACTTATAAACCACA-AGTGCCGAATACACAGA
21461962 TATA
1 TATA
21461966 TATATCCAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
34 31 0.97
35 1 0.03
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (34 bp):
TATACTTATAAACCACAAGTGCCGAATACACAGA
Found at i:21462212 original size:41 final size:41
Alignment explanation
Indices: 21462150--21462350 Score: 321
Period size: 41 Copynumber: 4.9 Consensus size: 41
21462140 TTTAAATAAA
*
21462150 TTCACTGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
* * *
21462191 TTCACCGTCACTTAGCTTGCTAGGCTTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
* * *
21462232 ATCACCGACACTTAGCCTGCTAGGCTTATAACCCGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
*
21462273 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCCGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
*
21462314 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGAT
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGAT
21462351 AATCTCAGAT
Statistics
Matches: 147, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 147 1.00
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.29
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
Found at i:21462585 original size:64 final size:63
Alignment explanation
Indices: 21462466--21462645 Score: 251
Period size: 64 Copynumber: 2.8 Consensus size: 63
21462456 GCAAACAAAC
* *
21462466 ATTCGAACCACATATGTA-T-AATTTACA-ACATTAAAATTCAGTTCAAAGAA-TTTGTAACCTA
1 ATTCGAACCACATATGTATTAAAATT-CATACATT-AAATTCAGCTCAAA-AACTTTGTAACCTA
21462527 T
63 T
21462528 ATTCGAACCACATATGTATGTAAAATTCATACATTAAATTCAGCTCAAAAACTTTGTAACCTAT
1 ATTCGAACCACATATGTAT-TAAAATTCATACATTAAATTCAGCTCAAAAACTTTGTAACCTAT
* *
21462592 ATTTGAACCACATATGTATATAAAATTCATACATTAAATTCAGCTCAAGAACTT
1 ATTCGAACCACATATGTAT-TAAAATTCATACATTAAATTCAGCTCAAAAACTT
21462646 GAAATATATA
Statistics
Matches: 108, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
62 18 0.17
63 2 0.02
64 79 0.73
65 9 0.08
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (63 bp):
ATTCGAACCACATATGTATTAAAATTCATACATTAAATTCAGCTCAAAAACTTTGTAACCTAT
Found at i:21466910 original size:15 final size:15
Alignment explanation
Indices: 21466890--21466923 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
21466880 AAAAAATGCC
21466890 ACATATACTTG-TCAT
1 ACATATA-TTGATCAT
21466905 ACATATATTGATCAT
1 ACATATATTGATCAT
21466920 ACAT
1 ACAT
21466924 GATTGAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (15 bp):
ACATATATTGATCAT
Found at i:21467510 original size:20 final size:20
Alignment explanation
Indices: 21467485--21467531 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
21467475 AGCTCGTTTC
*
21467485 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
21467505 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
21467525 CAGCTCA
1 CAGCTCA
21467532 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:21469136 original size:13 final size:13
Alignment explanation
Indices: 21469068--21469136 Score: 77
Period size: 13 Copynumber: 5.1 Consensus size: 13
21469058 AAAAAATTTC
*
21469068 GAAAAAAAAAAAA
1 GAAAAAAAAAGAA
*
21469081 GAAAAAAAGAAGTGA
1 GAAAAAAA-AAG-AA
21469096 GCAAAAAAAAAG-A
1 G-AAAAAAAAAGAA
21469109 GTAAAAAAAAAGAA
1 G-AAAAAAAAAGAA
21469123 GAAAAAAAAAGAA
1 GAAAAAAAAAGAA
21469136 G
1 G
21469137 TGAAAAGTCT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
13 33 0.67
14 4 0.08
15 5 0.10
16 7 0.14
ACGTcount: A:0.78, C:0.01, G:0.17, T:0.03
Consensus pattern (13 bp):
GAAAAAAAAAGAA
Found at i:21470184 original size:15 final size:15
Alignment explanation
Indices: 21470159--21470205 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
21470149 AGAAAATAAT
21470159 AAAGAAAATGAAAATG
1 AAAG-AAATGAAAATG
*
21470175 AAAGAAATGAAAAAG
1 AAAGAAATGAAAATG
21470190 AAA-AATATGAAAATG
1 AAAGAA-ATGAAAATG
21470205 A
1 A
21470206 GATTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 22 0.79
16 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (15 bp):
AAAGAAATGAAAATG
Found at i:21470252 original size:12 final size:12
Alignment explanation
Indices: 21470235--21470274 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
21470225 AGTGAAAAGC
21470235 AAAAAGAGATTG
1 AAAAAGAGATTG
*
21470247 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
21470259 AAAGAGAGCTTG
1 AAAAAGAGATTG
21470271 AAAA
1 AAAA
21470275 GAAATCGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.60, C:0.03, G:0.23, T:0.15
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:21472172 original size:20 final size:20
Alignment explanation
Indices: 21472147--21472193 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
21472137 AGCTCGTTTC
*
21472147 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
21472167 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
21472187 CAGCTCA
1 CAGCTCA
21472194 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:21475284 original size:6 final size:6
Alignment explanation
Indices: 21475273--21475300 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
21475263 AAAGAAAACA
21475273 AACCCT AACCCT AACCCT AACCCT AACC
1 AACCCT AACCCT AACCCT AACCCT AACC
21475301 TAAAACTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.50, G:0.00, T:0.14
Consensus pattern (6 bp):
AACCCT
Found at i:21485531 original size:10 final size:10
Alignment explanation
Indices: 21485516--21485542 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
21485506 ATTTATTAAC
21485516 AAACACATTT
1 AAACACATTT
21485526 AAACACATTT
1 AAACACATTT
21485536 AAACACA
1 AAACACA
21485543 CTAAACTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (10 bp):
AAACACATTT
Found at i:21485624 original size:20 final size:20
Alignment explanation
Indices: 21485590--21485631 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
21485580 ATTTATTAAC
*
21485590 AAACACATTAAAACACATTA
1 AAACACATTAAAACACACTA
**
21485610 AAACACATTTTAACACACTA
1 AAACACATTAAAACACACTA
21485630 AA
1 AA
21485632 CTTAATAAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (20 bp):
AAACACATTAAAACACACTA
Found at i:21485626 original size:10 final size:10
Alignment explanation
Indices: 21485590--21485618 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
21485580 ATTTATTAAC
21485590 AAACACATTA
1 AAACACATTA
21485600 AAACACATTA
1 AAACACATTA
21485610 AAACACATT
1 AAACACATT
21485619 TTAACACACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (10 bp):
AAACACATTA
Found at i:21485760 original size:34 final size:34
Alignment explanation
Indices: 21485718--21485791 Score: 114
Period size: 34 Copynumber: 2.2 Consensus size: 34
21485708 GTTGTTCTAG
*
21485718 CAATTAAATAAACT-AAGATAAGCATTTATTCCAA
1 CAATTAAATAAA-TAAAGATAAGAATTTATTCCAA
21485752 CAATTAAATAAATAAAGATAAGAATTTATTCCAA
1 CAATTAAATAAATAAAGATAAGAATTTATTCCAA
*
21485786 AAATTA
1 CAATTA
21485792 TTAACTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 1 0.03
34 36 0.97
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (34 bp):
CAATTAAATAAATAAAGATAAGAATTTATTCCAA
Found at i:21487240 original size:21 final size:22
Alignment explanation
Indices: 21487216--21487269 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
21487206 CCGTTGATTG
21487216 GTTTATCCACA-AATTTGAGCA
1 GTTTATCCACATAATTTGAGCA
** **
21487237 GTTTATCTGCATCGTTTGAGCA
1 GTTTATCCACATAATTTGAGCA
21487259 GTTTATCCACA
1 GTTTATCCACA
21487270 CTGTTGAGTG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (22 bp):
GTTTATCCACATAATTTGAGCA
Found at i:21487347 original size:62 final size:62
Alignment explanation
Indices: 21487275--21487419 Score: 173
Period size: 62 Copynumber: 2.3 Consensus size: 62
21487265 CCACACTGTT
* * *
21487275 GAGTGATTTATCCACACCATATTAACAAATTTTATCTGCAAACTCGTTGTGCATTCACAACC
1 GAGTGGTTTATCCACACCATATTAACAAATTTTATCTGCAAACCCGTTATGCATTCACAACC
* * *** * ** *
21487337 GAGTGGTTTATCTATATTGTATTAGCAGCTTTTATCTGCAAACCCGTTATGCATTCATAACC
1 GAGTGGTTTATCCACACCATATTAACAAATTTTATCTGCAAACCCGTTATGCATTCACAACC
*
21487399 TAGTGGTTTATCCACACCATA
1 GAGTGGTTTATCCACACCATA
21487420 CAAGTAGCTT
Statistics
Matches: 65, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (62 bp):
GAGTGGTTTATCCACACCATATTAACAAATTTTATCTGCAAACCCGTTATGCATTCACAACC
Found at i:21489343 original size:11 final size:11
Alignment explanation
Indices: 21489327--21489376 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
21489317 TCAATTATTT
21489327 TCTCAATTTCC
1 TCTCAATTTCC
*
21489338 TCTCAATTTGC
1 TCTCAATTTCC
21489349 TCTCAATTTCC
1 TCTCAATTTCC
*
21489360 TTCTAAATTT-C
1 -TCTCAATTTCC
21489371 TCTCAA
1 TCTCAA
21489377 ATCCATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 5 0.15
11 21 0.62
12 8 0.24
ACGTcount: A:0.22, C:0.30, G:0.02, T:0.46
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:21489355 original size:22 final size:22
Alignment explanation
Indices: 21489323--21489376 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
21489313 TCTCTCAATT
*
21489323 ATTT-TCTCAATTTCC-TCTCA
1 ATTTCTCTCAATTTCCTTCTAA
21489343 ATTTGCTCTCAATTTCCTTCTAA
1 ATTT-CTCTCAATTTCCTTCTAA
21489366 ATTTCTCTCAA
1 ATTTCTCTCAA
21489377 ATCCATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 4 0.13
22 18 0.60
23 8 0.27
ACGTcount: A:0.22, C:0.28, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTCTCTCAATTTCCTTCTAA
Found at i:21490595 original size:7 final size:7
Alignment explanation
Indices: 21490583--21490615 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
21490573 TAGTCGATTG
21490583 GTATTTA
1 GTATTTA
21490590 GTATTTA
1 GTATTTA
21490597 GTATTTA
1 GTATTTA
21490604 GTATTTA
1 GTATTTA
21490611 GTATT
1 GTATT
21490616 ATGTATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:21491821 original size:7 final size:7
Alignment explanation
Indices: 21491801--21491839 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
21491791 ATTTATTAAA
21491801 AATTTAT
1 AATTTAT
21491808 AAATTTAT
1 -AATTTAT
21491816 AATTTAT
1 AATTTAT
21491823 AA-TTA-
1 AATTTAT
21491828 AATTTAT
1 AATTTAT
21491835 AATTT
1 AATTT
21491840 GATTGACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
5 2 0.07
6 6 0.21
7 14 0.48
8 7 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AATTTAT
Found at i:21491892 original size:21 final size:21
Alignment explanation
Indices: 21491866--21492107 Score: 373
Period size: 21 Copynumber: 11.5 Consensus size: 21
21491856 CAAAAACTCT
*
21491866 AACCCTAACCTTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
21491887 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
*
21491909 AACCCTAACACTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
21491930 AACCCTAACCCTTAACTT-AA
1 AACCCTAACCCTTAACTTAAA
21491950 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
*
21491972 AAACCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
21491993 AACCCTAACCCCTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
21492014 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
*
21492036 AACCCTAA-CCTTAACTTTAA
1 AACCCTAACCCTTAACTTAAA
*
21492056 AA-CTTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
21492077 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
21492098 AACCCTAACC
1 AACCCTAACC
21492108 GTAACCCTTA
Statistics
Matches: 203, Mismatches: 11, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
19 2 0.01
20 23 0.11
21 129 0.64
22 49 0.24
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Done.