Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 123 of 145
Found at i:41023791 original size:87 final size:87
Alignment explanation
Indices: 41023626--41023792 Score: 253
Period size: 87 Copynumber: 1.9 Consensus size: 87
41023616 CCTATCTCCT
* * *
41023626 TGAGTAGTAGTGGAGTAGGCTGAGAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
1 TGAGTAGCAGCGGAGTAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
* *
41023691 GAAGTCCCCAGCCTTATTTCCC
66 GAAGACACCAGCCTTATTTCCC
* * *
41023713 TGAGTAGCAGCGGAGTAGGTTGAAAATTACAGATGTTATCTCCCTAAGCAGTAGTGGAGTAGATC
1 TGAGTAGCAGCGGAGTAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
*
41023778 GAAGACACTAGCCTT
66 GAAGACACCAGCCTT
41023793 GCCTCTCTCG
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (87 bp):
TGAGTAGCAGCGGAGTAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
GAAGACACCAGCCTTATTTCCC
Found at i:41023820 original size:87 final size:87
Alignment explanation
Indices: 41023621--41023924 Score: 233
Period size: 87 Copynumber: 3.5 Consensus size: 87
41023611 TGAATCCTAT
* * * * * *
41023621 CTCCTTGAGTAGTAGTGGAGTAGGCTGAGAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGC
1 CTCCCTGAGTAGCAGCGGAGCAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGC
* * *
41023686 AGATCGAAGTCCCCAGCCTTAT
66 AGATCGAAGACACCAGCCTTAC
* * * *
41023708 TTCCCTGAGTAGCAGCGGAGTAGGTTGAAAATTACAGATGTTATCTCCCTAAGCAGTAGTGGAGT
1 CTCCCTGAGTAGCAGCGGAGCAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGC
* *
41023773 AGATCGAAGACACTAGCCTTGC
66 AGATCGAAGACACCAGCCTTAC
* * * * * * * *
41023795 CTCTCTCG-GTTGCAGCAGGA-CAGGTT-AAAGA-TAGTAGATCTTACCTTCCTGTA-CTGACAG
1 CTCCCT-GAGTAGCAGC-GGAGCAGGTTGAAA-ATTA-CAGATCTTATCTCCCT-AAGCAG-TAG
* * * *
41023855 TGAAGCAGATTGAAGACACTAGCCTTGC
60 TGGAGCAGATCGAAGACACCAGCCTTAC
* * *
41023883 CTCCCTGAGTTGCAGCGAAGCAGGTT-AAAAATAGCAGATCTT
1 CTCCCTGAGTAGCAGCGGAGCAGGTTGAAAATTA-CAGATCTT
41023925 GCCTTCTTGC
Statistics
Matches: 178, Mismatches: 30, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
86 5 0.03
87 109 0.61
88 64 0.36
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (87 bp):
CTCCCTGAGTAGCAGCGGAGCAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGC
AGATCGAAGACACCAGCCTTAC
Found at i:41023883 original size:88 final size:88
Alignment explanation
Indices: 41023773--41023993 Score: 275
Period size: 88 Copynumber: 2.5 Consensus size: 88
41023763 GTAGTGGAGT
* * * *
41023773 AGATCGAAGACACTAGCCTTGCCTCTCTCG-GTTGCAGC-AGGACAGGTTAAAGATAGTAGATCT
1 AGATCGAAGACACTAGCCTTGCCTCCCT-GAGTTGCAGCGAAG-CAGGTTAAAAATAGCAGATCT
* * *
41023836 TACCTTCCTGTACTGACAGTGAAGC
64 TACCTTCCTGCACCGACAGCGAAGC
* *
41023861 AGATTGAAGACACTAGCCTTGCCTCCCTGAGTTGCAGCGAAGCAGGTTAAAAATAGCAGATCTTG
1 AGATCGAAGACACTAGCCTTGCCTCCCTGAGTTGCAGCGAAGCAGGTTAAAAATAGCAGATCTTA
*
41023926 CCTTCTTGCACCGACAGCGAAGC
66 CCTTCCTGCACCGACAGCGAAGC
* * * * *
41023949 AGATCGAAGACACCAACCTTGCCCCCCTGGGTTGTAGCGAAGCAG
1 AGATCGAAGACACTAGCCTTGCCTCCCTGAGTTGCAGCGAAGCAG
41023994 TTGAACTAGA
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
87 1 0.01
88 112 0.97
89 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (88 bp):
AGATCGAAGACACTAGCCTTGCCTCCCTGAGTTGCAGCGAAGCAGGTTAAAAATAGCAGATCTTA
CCTTCCTGCACCGACAGCGAAGC
Found at i:41024381 original size:45 final size:45
Alignment explanation
Indices: 41024326--41024602 Score: 261
Period size: 45 Copynumber: 6.0 Consensus size: 45
41024316 CAGGTTGAAA
* *
41024326 ATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCAAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAG
* * * * * *
41024371 ATAGTAGATCTTGTCTTCATATATTGGTAGTGTAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAG
** ** *
41024416 ATAATAGATCTAATCTTCCTGTATTGGCAGCGAAGTAGATCAAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAG
41024461 ATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAATG
1 ATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAA-G
* * * *
41024507 -TGGCAG-TCTTATCTCCCTGAGTAGCAGTGGAGCAGCGAAGTAGATCAAAG
1 ATAGCAGATCTTGTCTTCCT-A-T---A-TTG-GCAGCGAAGTAGATCAAAG
* * * ** *
41024557 ATAGCAAATCTTGTCTTCTTGTGCTGGCAGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAG
41024602 A
1 A
41024603 CACCAGTCCT
Statistics
Matches: 188, Mismatches: 34, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
44 10 0.05
45 139 0.74
46 3 0.02
49 1 0.01
50 4 0.02
51 22 0.12
52 9 0.05
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (45 bp):
ATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAG
Found at i:41024568 original size:96 final size:96
Alignment explanation
Indices: 41024442--41024634 Score: 271
Period size: 96 Copynumber: 2.0 Consensus size: 96
41024432 TCCTGTATTG
* *
41024442 GCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAATG
1 GCAGCGAAGTAGATCAAAGATAGCAAATCTTGTCTTCCTATACTGGCAGCGAAGTAGATCAAA-G
*** * *
41024507 -TGGCAGTCTTATCTCCCTGAGTAGCAGTGGA
65 ACACCAGTCCTATCTCCCTGAGCAGCAGTGGA
* * * *
41024538 GCAGCGAAGTAGATCAAAGATAGCAAATCTTGTCTTCTTGTGCTGGCAGCGAAGTAGATCGAAGA
1 GCAGCGAAGTAGATCAAAGATAGCAAATCTTGTCTTCCTATACTGGCAGCGAAGTAGATCAAAGA
41024603 CACCAGTCCTATCTCCCTGAGCAGCAGTGGA
66 CACCAGTCCTATCTCCCTGAGCAGCAGTGGA
41024634 G
1 G
41024635 TAGGTCAAAG
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
95 1 0.01
96 84 0.99
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (96 bp):
GCAGCGAAGTAGATCAAAGATAGCAAATCTTGTCTTCCTATACTGGCAGCGAAGTAGATCAAAGA
CACCAGTCCTATCTCCCTGAGCAGCAGTGGA
Found at i:41024772 original size:122 final size:119
Alignment explanation
Indices: 41024603--41024891 Score: 370
Period size: 116 Copynumber: 2.4 Consensus size: 119
41024593 AGATCGAAGA
* * ** * * *
41024603 CACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTCAAAGTTTGTAGATTCTGCAGTAGTGGG
1 CACCAATCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATTGTAGA---TGCAATAGTGGA
* * *
41024668 GCAGATCGAAGACGACGAATCTTATCTTCCCAAGGTATTAGGGAAGCAAATTTAAGC
63 GCAGATCGAAGACGACAAATCCTATCTTCCCAAGGTAGTAGGGAAGCAAATTTAAGC
*
41024725 CACCAATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGT--A-GCAATAGTGGAGCA
1 CACCAATCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATGCAATAGTGGAGCA
* * *
41024787 GATCGAAGATGGCAAATCCTATCTTCCCAAGGTAGTAGGGAAGCATATTTAAGC
66 GATCGAAGACGACAAATCCTATCTTCCCAAGGTAGTAGGGAAGCAAATTTAAGC
* *
41024841 CATCAATCCCT-TCTCCCTGAGCAGTAGTGAAGTAGGTTGAAGATTGTAGAT
1 CACCAAT-CCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATTGTAGAT
41024892 CCTGTCTCCT
Statistics
Matches: 146, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
116 100 0.68
117 3 0.02
118 1 0.01
120 1 0.01
122 41 0.28
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (119 bp):
CACCAATCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATGCAATAGTGGAGCA
GATCGAAGACGACAAATCCTATCTTCCCAAGGTAGTAGGGAAGCAAATTTAAGC
Found at i:41028157 original size:16 final size:17
Alignment explanation
Indices: 41028136--41028168 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
41028126 CTCTAAAAAC
41028136 TTTAAAAAAT-ATTTTT
1 TTTAAAAAATCATTTTT
41028152 TTTAAAAAATCATTTTT
1 TTTAAAAAATCATTTTT
41028169 AGCCATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAAAAAATCATTTTT
Found at i:41035189 original size:49 final size:50
Alignment explanation
Indices: 41035061--41035201 Score: 176
Period size: 49 Copynumber: 2.8 Consensus size: 50
41035051 TCATTTTACG
* * * * *
41035061 CCACAAAGGCTATTCTTTTATATTTCACTACAAAGGCTTTCTTTCAAATTA
1 CCACAAAGGCT-TTCTTTCATATTACGCCACAAAGGCTTTCTTTCAAACTA
* *
41035112 TGCCACAAGGGCTTTCTTTCATATTACGCCACAAAGGCTTTCTTTCATACTA
1 --CCACAAAGGCTTTCTTTCATATTACGCCACAAAGGCTTTCTTTCAAACTA
*
41035164 -CACAAAGGCTTTCTTTCATACTACGCCACAAAGGCTTT
1 CCACAAAGGCTTTCTTTCATATTACGCCACAAAGGCTTT
41035202 TCCTTATCTG
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
49 36 0.46
52 33 0.42
53 10 0.13
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (50 bp):
CCACAAAGGCTTTCTTTCATATTACGCCACAAAGGCTTTCTTTCAAACTA
Found at i:41035200 original size:75 final size:80
Alignment explanation
Indices: 41035033--41035201 Score: 231
Period size: 75 Copynumber: 2.2 Consensus size: 80
41035023 TTCATGGTTT
* * *
41035033 GCCACAAAGGCTTTCAATTCATTTTACGCCACAAAGGCTATTCTTTTATATTTCACTACAAAGGC
1 GCCACAAAGGCTTTCAATTCATATTACGCCACAAAGGCTATTCTTTCATATCTCACTACAAAGGC
* *
41035098 TTTCTTTCAAATTAT
66 TTTCTTTCAAACTAC
* *
41035113 GCCACAAGGGCTTTC-TTTCATATTACGCCACAAAGGCT-TTCTTTCATA-CT-AC-ACAAAGGC
1 GCCACAAAGGCTTTCAATTCATATTACGCCACAAAGGCTATTCTTTCATATCTCACTACAAAGGC
*
41035173 TTTCTTTCATACTAC
66 TTTCTTTCAAACTAC
41035188 GCCACAAAGGCTTT
1 GCCACAAAGGCTTT
41035202 TCCTTATCTG
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
75 33 0.41
76 2 0.03
77 1 0.01
78 9 0.11
79 21 0.26
80 14 0.17
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.34
Consensus pattern (80 bp):
GCCACAAAGGCTTTCAATTCATATTACGCCACAAAGGCTATTCTTTCATATCTCACTACAAAGGC
TTTCTTTCAAACTAC
Found at i:41035203 original size:27 final size:26
Alignment explanation
Indices: 41035007--41035201 Score: 200
Period size: 26 Copynumber: 7.5 Consensus size: 26
41034997 TCGTGATTTA
* * *
41035007 CCACAGAGGCTTTCTTTTCATGGTT-TG
1 CCACAAAGGCTTTC-TTTCAT-ATTACG
* *
41035034 CCACAAAGGCTTTCAATTCATTTTACG
1 CCACAAAGGCTTTC-TTTCATATTACG
* * *
41035061 CCACAAAGGCTATTCTTTTATATTTCA
1 CCACAAAGGCT-TTCTTTCATATTACG
* * *
41035088 CTACAAAGGCTTTCTTTCAAATTATG
1 CCACAAAGGCTTTCTTTCATATTACG
*
41035114 CCACAAGGGCTTTCTTTCATATTACG
1 CCACAAAGGCTTTCTTTCATATTACG
*
41035140 CCACAAAGGCTTTCTTTCATACTA--
1 CCACAAAGGCTTTCTTTCATATTACG
*
41035164 -CACAAAGGCTTTCTTTCATACTACG
1 CCACAAAGGCTTTCTTTCATATTACG
41035189 CCACAAAGGCTTT
1 CCACAAAGGCTTT
41035202 TCCTTATCTG
Statistics
Matches: 141, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
23 23 0.16
26 68 0.48
27 47 0.33
28 3 0.02
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (26 bp):
CCACAAAGGCTTTCTTTCATATTACG
Found at i:41037060 original size:18 final size:19
Alignment explanation
Indices: 41037034--41037081 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
41037024 TATGATTAGG
*
41037034 TTGGCTTGGGTAATTGGGT
1 TTGGATTGGGTAATTGGGT
* *
41037053 TTGG-TTGGATACTTGGGT
1 TTGGATTGGGTAATTGGGT
41037071 TTGGATTGGGT
1 TTGGATTGGGT
41037082 TTAGGTGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.10, C:0.04, G:0.42, T:0.44
Consensus pattern (19 bp):
TTGGATTGGGTAATTGGGT
Found at i:41038199 original size:8 final size:8
Alignment explanation
Indices: 41038188--41038218 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
41038178 AGTTTAAAGA
41038188 TTAAATTG
1 TTAAATTG
41038196 TTAAATTG
1 TTAAATTG
*
41038204 TTAAGTTG
1 TTAAATTG
41038212 TTAAATT
1 TTAAATT
41038219 TGGCATGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (8 bp):
TTAAATTG
Found at i:41048029 original size:59 final size:56
Alignment explanation
Indices: 41047936--41048044 Score: 130
Period size: 59 Copynumber: 1.9 Consensus size: 56
41047926 AGCCTTCAAT
* * * *
41047936 ATTTACAAAATTTCATTTTAGTTCTAATTTTAAAAAATAAATAAATTTTTTGTTAAC
1 ATTTACAAAATTTCAATTTAGTTCTAACTCTAAAAAATAAA-AAATATTTTGTTAAC
*
41047993 ATTTACAAAATTTATCAATTTAG-TCTGAACTCTAAAAATTAAAAAATATTTT
1 ATTTACAAAA-TT-TCAATTTAGTTCT-AACTCTAAAAAATAAAAAATATTTT
41048045 AAAAAAAGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
57 10 0.23
58 13 0.30
59 21 0.48
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (56 bp):
ATTTACAAAATTTCAATTTAGTTCTAACTCTAAAAAATAAAAAATATTTTGTTAAC
Found at i:41049500 original size:31 final size:29
Alignment explanation
Indices: 41049465--41049540 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
41049455 TAATGGCTCG
*
41049465 GTGACTAAAATGTTACAATACAATAACATAA
1 GTGACTAAAATGTAAC-ATACAA-AACATAA
* * * *
41049496 GTGACTAAAACGTAACATTCCAAATATAA
1 GTGACTAAAATGTAACATACAAAACATAA
41049525 GTGACTAAAATGTAAC
1 GTGACTAAAATGTAAC
41049541 TTGAGGTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 21 0.54
30 4 0.10
31 14 0.36
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (29 bp):
GTGACTAAAATGTAACATACAAAACATAA
Found at i:41058194 original size:4 final size:4
Alignment explanation
Indices: 41058185--41058211 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
41058175 GCTATAATGT
41058185 TAAC TAAC TAAC TAAC TAAC TAAC TAA
1 TAAC TAAC TAAC TAAC TAAC TAAC TAA
41058212 AGAAAACCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAC
Found at i:41059835 original size:27 final size:27
Alignment explanation
Indices: 41059795--41059853 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
41059785 TTTACCAAAG
**
41059795 AGGCTTTCTTTTCATGGTT-TGCCACAA
1 AGGCTTTCAATTCAT-GTTATGCCACAA
*
41059822 AGGCTTTCAATTCATTTTATGCCACAA
1 AGGCTTTCAATTCATGTTATGCCACAA
41059849 AGGCT
1 AGGCT
41059854 ACTCTTTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (27 bp):
AGGCTTTCAATTCATGTTATGCCACAA
Found at i:41059862 original size:27 final size:26
Alignment explanation
Indices: 41059815--41059982 Score: 201
Period size: 26 Copynumber: 6.4 Consensus size: 26
41059805 TTCATGGTTT
* * *
41059815 GCCACAAAGGCTTTCAATTCATTTTAT
1 GCCACAAAGGCTTTC-TTTCATATTAC
* *
41059842 GCCACAAAGGCTACTCTTTCATATTGC
1 GCCACAAAGGCT-TTCTTTCATATTAC
* * *
41059869 ACCTCAAAGGCATTCTTTCATATTAC
1 GCCACAAAGGCTTTCTTTCATATTAC
41059895 GCCACAAAGGCTTTCTTTCATATTAC
1 GCCACAAAGGCTTTCTTTCATATTAC
* *
41059921 ACCACAAAGGCTTTCTTTCATACTAC
1 GCCACAAAGGCTTTCTTTCATATTAC
* *
41059947 GCCATAAAGGCTTTCTTTCATACTAC
1 GCCACAAAGGCTTTCTTTCATATTAC
*
41059973 ACCACAAAGG
1 GCCACAAAGG
41059983 TTTTTCCTTA
Statistics
Matches: 121, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
26 91 0.75
27 28 0.23
28 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (26 bp):
GCCACAAAGGCTTTCTTTCATATTAC
Found at i:41059930 original size:52 final size:52
Alignment explanation
Indices: 41059816--41059982 Score: 226
Period size: 52 Copynumber: 3.2 Consensus size: 52
41059806 TCATGGTTTG
* * * * *
41059816 CCACAAAGGCTTTCAATTCATTTTATGCCACAAAGGCTACTCTTTCATATTGCA
1 CCACAAAGGCTTTC-TTTCATATTACGCCACAAAGGCT-TTCTTTCATATTACA
* *
41059870 CCTCAAAGGCATTCTTTCATATTACGCCACAAAGGCTTTCTTTCATATTACA
1 CCACAAAGGCTTTCTTTCATATTACGCCACAAAGGCTTTCTTTCATATTACA
* * *
41059922 CCACAAAGGCTTTCTTTCATACTACGCCATAAAGGCTTTCTTTCATACTACA
1 CCACAAAGGCTTTCTTTCATATTACGCCACAAAGGCTTTCTTTCATATTACA
41059974 CCACAAAGG
1 CCACAAAGG
41059983 TTTTTCCTTA
Statistics
Matches: 101, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
52 69 0.68
53 20 0.20
54 12 0.12
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.32
Consensus pattern (52 bp):
CCACAAAGGCTTTCTTTCATATTACGCCACAAAGGCTTTCTTTCATATTACA
Found at i:41067343 original size:57 final size:57
Alignment explanation
Indices: 41067262--41067394 Score: 162
Period size: 57 Copynumber: 2.4 Consensus size: 57
41067252 CAGAGTCTCG
* * * * *
41067262 CCACAAAAGC-ATCATTTAAGAGGTTTGCCACGAAGGCTTAGCC-TTCTAGAGTTTTA
1 CCACAAAGGCTATCATTTAACAGGTTCGCCACAAAGGCTT-GCCTTTCTAGAGTTCTA
*
41067318 CCACAAAGGCTATCATTTAACAGGTTCGCCACAAAGGCTTGCCTTTCTAGAGTTCTG
1 CCACAAAGGCTATCATTTAACAGGTTCGCCACAAAGGCTTGCCTTTCTAGAGTTCTA
* * *
41067375 GCACAAAGACTGTCATTTAA
1 CCACAAAGGCTATCATTTAA
41067395 TAGTTGTTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
56 12 0.18
57 54 0.82
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (57 bp):
CCACAAAGGCTATCATTTAACAGGTTCGCCACAAAGGCTTGCCTTTCTAGAGTTCTA
Found at i:41080456 original size:57 final size:56
Alignment explanation
Indices: 41080339--41080470 Score: 140
Period size: 57 Copynumber: 2.3 Consensus size: 56
41080329 CTTTACTTTA
* * * * **
41080339 AGAGTCTTGCCACAAAGGCATCCTTGAAGAGGTTTGCCATGAAGGCTTACCCTTCT
1 AGAGTTTTGCCACAAAGGCATCCTTGAACAAGTTCGCCACAAAGGCTTACCCTTCT
* * *
41080395 AGAGTTTTGCCGCAAAGGCCATCCTTTAACAAGTTCGCCACAAAGGCTT-CCCTTTT
1 AGAGTTTTGCCACAAAGG-CATCCTTGAACAAGTTCGCCACAAAGGCTTACCCTTCT
* *
41080451 CAGAGTTTTTCCATAAAGGC
1 -AGAGTTTTGCCACAAAGGC
41080471 TGCCCTTTAG
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
56 23 0.37
57 39 0.63
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (56 bp):
AGAGTTTTGCCACAAAGGCATCCTTGAACAAGTTCGCCACAAAGGCTTACCCTTCT
Found at i:41085809 original size:26 final size:26
Alignment explanation
Indices: 41085763--41085946 Score: 194
Period size: 26 Copynumber: 7.1 Consensus size: 26
41085753 ACAAACATTG
** *
41085763 TTCTTTCATATTGCGCGACAAAGGCT
1 TTCTTTCATATCACGCCACAAAGGCT
**
41085789 TTCATTT-ATATCACGCCACAAAGTTT
1 TTC-TTTCATATCACGCCACAAAGGCT
41085815 TTCTTTCATA-CTACGCCACAAAGGCT
1 TTCTTTCATATC-ACGCCACAAAGGCT
* * *
41085841 TTCTTCCATATTACACCACAAAGGCT
1 TTCTTTCATATCACGCCACAAAGGCT
* * *
41085867 TTTTTTCATA-CTACGGCACAAAGGTT
1 TTCTTTCATATC-ACGCCACAAAGGCT
*
41085893 TTCTTTCATATTACGCCACAAAGGCT
1 TTCTTTCATATCACGCCACAAAGGCT
* *
41085919 TCCTTTCATATTACGCCACAAAGGCT
1 TTCTTTCATATCACGCCACAAAGGCT
41085945 TT
1 TT
41085947 TCATTATTTT
Statistics
Matches: 130, Mismatches: 22, Indels: 12
0.79 0.13 0.07
Matches are distributed among these distances:
25 4 0.03
26 123 0.95
27 3 0.02
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.35
Consensus pattern (26 bp):
TTCTTTCATATCACGCCACAAAGGCT
Found at i:41085836 original size:52 final size:53
Alignment explanation
Indices: 41085724--41085951 Score: 230
Period size: 52 Copynumber: 4.3 Consensus size: 53
41085714 TCATGGTTTT
* * * * * *
41085724 CCACAAAGCCTTTCAATTCATTTTACGCCACAAACATTGTTCTTTCATATTGCG
1 CCACAAAGGCTTTC-ATTCATATTACGCCACAAACGTTTTTCTTTCATACTACG
* * *
41085778 CGACAAAGGCTTTCATTTATATCACGCCACAAA-GTTTTTCTTTCATACTACG
1 CCACAAAGGCTTTCATTCATATTACGCCACAAACGTTTTTCTTTCATACTACG
* * *
41085830 CCACAAAGGCTTTC-TTCCATATTACACCACAAAGGCTTTT-TTTCATACTACG
1 CCACAAAGGCTTTCATT-CATATTACGCCACAAACGTTTTTCTTTCATACTACG
* * * ** * *
41085882 GCACAAAGGTTTTCTTTCATATTACGCCACAAA-GGCTTCCTTTCATATTACG
1 CCACAAAGGCTTTCATTCATATTACGCCACAAACGTTTTTCTTTCATACTACG
41085934 CCACAAAGGCTTTTCATT
1 CCACAAAGGC-TTTCATT
41085952 ATTTTTCGTG
Statistics
Matches: 145, Mismatches: 24, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
51 5 0.03
52 99 0.68
53 29 0.20
54 12 0.08
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (53 bp):
CCACAAAGGCTTTCATTCATATTACGCCACAAACGTTTTTCTTTCATACTACG
Found at i:41085862 original size:78 final size:79
Alignment explanation
Indices: 41085780--41085951 Score: 242
Period size: 78 Copynumber: 2.2 Consensus size: 79
41085770 ATATTGCGCG
* *
41085780 ACAAAGGCTTTCATTT-ATA-TCACGCCACAAAGTTTTTCTTTCATACTACGCCACAAAGGCTTT
1 ACAAAGGCTTTCATTTCATACT-ACGCCACAAAGGTTTTCTTTCATACTACGCCACAAAGGCTTC
41085843 CTTCCATATTACACC
65 CTTCCATATTACACC
* * *
41085858 ACAAAGGCTTT-TTTTCATACTACGGCACAAAGGTTTTCTTTCATATTACGCCACAAAGGCTTCC
1 ACAAAGGCTTTCATTTCATACTACGCCACAAAGGTTTTCTTTCATACTACGCCACAAAGGCTTCC
* *
41085922 TTTCATATTACGCC
66 TTCCATATTACACC
41085936 ACAAAGGCTTTTCATT
1 ACAAAGGC-TTTCATT
41085952 ATTTTTCGTG
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
77 3 0.04
78 73 0.89
79 4 0.05
80 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.34
Consensus pattern (79 bp):
ACAAAGGCTTTCATTTCATACTACGCCACAAAGGTTTTCTTTCATACTACGCCACAAAGGCTTCC
TTCCATATTACACC
Found at i:41086359 original size:26 final size:25
Alignment explanation
Indices: 41086301--41086574 Score: 251
Period size: 26 Copynumber: 10.5 Consensus size: 25
41086291 TCATGGTTTT
*
41086301 CCACAAAGGCTTTCAATTCATTTTACG
1 CCACAAAGGCTTTC--TTCATATTACG
* *
41086328 CCACAAAGGCTTTAGTTTATATTACG
1 CCACAAAGGCTTT-CTTCATATTACG
* *
41086354 CCACAAAGGCTTTCTTTCATACTATG
1 CCACAAAGGCTTTC-TTCATATTACG
* *
41086380 CCATAAAAGCTTTCTTCCATATTACG
1 CCACAAAGGCTTTCTT-CATATTACG
* * *
41086406 CCACAATGGCTTTCTTCCATACTACA
1 CCACAAAGGCTTTCTT-CATATTACG
* * * *
41086432 CCACAAATGCTTTTGTTCATACTATG
1 CCACAAAGGC-TTTCTTCATATTACG
*
41086458 CCACAAATGCTTTCTTCCATATTACG
1 CCACAAAGGCTTTCTT-CATATTACG
*
41086484 CCACAAAGGCTTTCTTCCATACTACG
1 CCACAAAGGCTTTCTT-CATATTACG
*
41086510 CCACAAAGGCTTCCTTTCATATTACG
1 CCACAAAGGCTTTC-TTCATATTACG
** * * *
41086536 TTATAAAGGTTTTCTTTCATATTATG
1 CCACAAAGGCTTTC-TTCATATTACG
41086562 CCACAAAGGCTTT
1 CCACAAAGGCTTT
41086575 TCATTATTTC
Statistics
Matches: 203, Mismatches: 38, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
25 7 0.03
26 176 0.87
27 20 0.10
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (25 bp):
CCACAAAGGCTTTCTTCATATTACG
Found at i:41086417 original size:78 final size:78
Alignment explanation
Indices: 41086323--41086574 Score: 319
Period size: 78 Copynumber: 3.2 Consensus size: 78
41086313 TCAATTCATT
* * *
41086323 TTACGCCACAAAGGCTTTAGTT-TATATTACGCCACAAAGGCTTTCTTTCATACTATGCCATAAA
1 TTACGCCACAAAGGCTTT-CTTCCATACTACGCCACAAAGGCTTTCTTTCATACTATGCCATAAA
41086387 AGCTTTCTTCCATA
65 AGCTTTCTTCCATA
* * * *
41086401 TTACGCCACAATGGCTTTCTTCCATACTACACCACAAATGCTTT-TGTTCATACTATGCCACAAA
1 TTACGCCACAAAGGCTTTCTTCCATACTACGCCACAAAGGCTTTCT-TTCATACTATGCCATAAA
*
41086465 TGCTTTCTTCCATA
65 AGCTTTCTTCCATA
* * * ** *
41086479 TTACGCCACAAAGGCTTTCTTCCATACTACGCCACAAAGGCTTCCTTTCATATTACGTTATAAAG
1 TTACGCCACAAAGGCTTTCTTCCATACTACGCCACAAAGGCTTTCTTTCATACTATGCCATAAAA
* *
41086544 GTTTTCTTTCATA
66 GCTTTCTTCCATA
*
41086557 TTATGCCACAAAGGCTTT
1 TTACGCCACAAAGGCTTT
41086575 TCATTATTTC
Statistics
Matches: 150, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
77 3 0.02
78 146 0.97
79 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (78 bp):
TTACGCCACAAAGGCTTTCTTCCATACTACGCCACAAAGGCTTTCTTTCATACTATGCCATAAAA
GCTTTCTTCCATA
Found at i:41092972 original size:20 final size:22
Alignment explanation
Indices: 41092935--41092974 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
41092925 AAATTAAGTA
41092935 TTTTCATTAAGATTTTGTTATG
1 TTTTCATTAAGATTTTGTTATG
41092957 TTTT-ATTAAG-TTTTGTTA
1 TTTTCATTAAGATTTTGTTA
41092975 AATCCAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 6 0.33
22 4 0.22
ACGTcount: A:0.23, C:0.03, G:0.12, T:0.62
Consensus pattern (22 bp):
TTTTCATTAAGATTTTGTTATG
Found at i:41093863 original size:119 final size:119
Alignment explanation
Indices: 41093652--41093874 Score: 446
Period size: 119 Copynumber: 1.9 Consensus size: 119
41093642 ATGTGCTAGG
41093652 CCGTGTAACTCTCGAAATGCAACCTTTAAAAACCAACAGGAGACACACACCCGTGTCTTAGACCG
1 CCGTGTAACTCTCGAAATGCAACCTTTAAAAACCAACAGGAGACACACACCCGTGTCTTAGACCG
41093717 TGTGGACAAGAAATAAGGCAATTTCAAGTCATTCCTTTCGGGCATGTGGCTTGA
66 TGTGGACAAGAAATAAGGCAATTTCAAGTCATTCCTTTCGGGCATGTGGCTTGA
41093771 CCGTGTAACTCTCGAAATGCAACCTTTAAAAACCAACAGGAGACACACACCCGTGTCTTAGACCG
1 CCGTGTAACTCTCGAAATGCAACCTTTAAAAACCAACAGGAGACACACACCCGTGTCTTAGACCG
41093836 TGTGGACAAGAAATAAGGCAATTTCAAGTCATTCCTTTC
66 TGTGGACAAGAAATAAGGCAATTTCAAGTCATTCCTTTC
41093875 ACCTATTTCA
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 104 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (119 bp):
CCGTGTAACTCTCGAAATGCAACCTTTAAAAACCAACAGGAGACACACACCCGTGTCTTAGACCG
TGTGGACAAGAAATAAGGCAATTTCAAGTCATTCCTTTCGGGCATGTGGCTTGA
Found at i:41100128 original size:29 final size:30
Alignment explanation
Indices: 41100086--41100146 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 30
41100076 GCCTCTTCAA
41100086 CAAGATTGGCTCTAATTTG-TAGTCTCCAT
1 CAAGATTGGCTCTAATTTGATAGTCTCCAT
41100115 CAAGATTGGCTCTAATTTGAATAGTCTCCAT
1 CAAGATTGGCTCTAATTTG-ATAGTCTCCAT
41100146 C
1 C
41100147 TCTTTGTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 19 0.63
31 11 0.37
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (30 bp):
CAAGATTGGCTCTAATTTGATAGTCTCCAT
Found at i:41101345 original size:3 final size:3
Alignment explanation
Indices: 41101331--41101370 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
41101321 TTTTGGGAGA
* *
41101331 AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
41101371 GGAAAAGAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:41102616 original size:26 final size:26
Alignment explanation
Indices: 41102564--41102621 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
41102554 ACATATATGG
* *
41102564 TCACACGAGCTGTGAAATTAGTATGC
1 TCACACGAGCTGTGAAATGAGCATGC
* *
41102590 TCACATGAGCTGTGAAATGAGCCTGC
1 TCACACGAGCTGTGAAATGAGCATGC
*
41102616 TTACAC
1 TCACAC
41102622 AAGCAGTAGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (26 bp):
TCACACGAGCTGTGAAATGAGCATGC
Found at i:41108340 original size:565 final size:565
Alignment explanation
Indices: 41107266--41108377 Score: 1992
Period size: 565 Copynumber: 2.0 Consensus size: 565
41107256 CCAAAGTTGC
41107266 GTTAAAGCTTTTGAGGTAATAAAATAAAAATTGATATCCGCTCCAATTATCATCACCCCTAACTA
1 GTTAAAGCTTTTGAGGTAATAAAATAAAAATTGATATCCGCTCCAATTATCATCACCCCTAACTA
* *
41107331 GTCAGAACCTTTTATTATTATGTGTGATGCTAGTGATTATGTAACAGGTGCAGTCTTGGGACAAA
66 GTCAGAACCTTTTATTATTATGTGTGATGCTAGTGATTATGTAACAAGTGCAGTCTTGAGACAAA
41107396 AGCAGAATAACATCTTTGGGGCTATTCATTATGCTAGTAAAATGTTAAATTCGGCACTGCAACTA
131 AGCAGAATAACATCTTTGGGGCTATTCATTATGCTAGTAAAATGTTAAATTCGGCACTGCAACTA
41107461 CGCTACAACTGAAAAAGAGATGCTAGTTGTAGTGTTCACTTGTGAAAAACTTTAACCCTACTTAA
196 CGCTACAACTGAAAAAGAGATGCTAGTTGTAGTGTTCACTTGTGAAAAACTTTAACCCTACTTAA
41107526 TTATAAATAGAGTATATGTGTATATTGACCATTCTGCATTAAAATATGTTATGAAGAATAAAGAA
261 TTATAAATAGAGTATATGTGTATATTGACCATTCTGCATTAAAATATGTTATGAAGAATAAAGAA
* *
41107591 ACCAAAGCTAGACTAATGAGATGGGTTTTACTGCTTCAGGAATTCAATTTATGGATAATGGATAG
326 ACAAAAGCTAGACTAATGAGATGGGTTTTACTACTTCAGGAATTCAATTTATGGATAATGGATAG
*
41107656 GAAGAGGACTGAGAACCAAATTGCAGATCATTTATCCAAAATTGAGAATGATTTAAAAGTAGAGA
391 GAAGAGGACTGAGAACCAAATTGCAGATAATTTATCCAAAATTGAGAATGATTTAAAAGTAGAGA
*
41107721 ATATTGGAGAAATTAAAGAAACTTTCGCAGATGAGCAACTATTTAGATTAGATATCCATCAGATC
456 ATATTGGAGAAATTAAAGAAACTTTCGCAGATGAGCAACTATTTAGAGTAGATATCCATCAGATC
41107786 ATGCTGAGTGAGCATACAACACCGTAGAATAACATATTATTATGT
521 ATGCTGAGTGAGCATACAACACCGTAGAATAACATATTATTATGT
* *
41107831 GTTAAAGCTTTTGAGGTAATAAAATAAAAATTGATA-CCTGCTTCAGTTATCATCACCCCTAACT
1 GTTAAAGCTTTTGAGGTAATAAAATAAAAATTGATATCC-GCTCCAATTATCATCACCCCTAACT
* *
41107895 AGTCAGAACTTTTTATTATTATGTGTGATGCTAGTGATTATGTAGCAAGTGCAGTCTTGAGACAA
65 AGTCAGAACCTTTTATTATTATGTGTGATGCTAGTGATTATGTAACAAGTGCAGTCTTGAGACAA
* * * *
41107960 AAGTATAATAACTTCTTTGGGGCTATTCATTATGGTAGTAAAATGTTAAATTCGGCACTGCAACT
130 AAGCAGAATAACATCTTTGGGGCTATTCATTATGCTAGTAAAATGTTAAATTCGGCACTGCAACT
* *
41108025 ACGCTACAACTGAAAAAGAGATGCTAGTTGTAGTGTTCACTTGTGAAAAATTTTAACCTTACTTA
195 ACGCTACAACTGAAAAAGAGATGCTAGTTGTAGTGTTCACTTGTGAAAAACTTTAACCCTACTTA
*
41108090 ATTATAAATAGAGTATATGTGTATATTGACCATTCTGCCTTAAAATATGTTATGAAGAATAAAGA
260 ATTATAAATAGAGTATATGTGTATATTGACCATTCTGCATTAAAATATGTTATGAAGAATAAAGA
*
41108155 AACAAAAGCTAGACTAATGAGATGGGTTTTACTACTTCAGGAATTCGATTTATGGATAATGGATA
325 AACAAAAGCTAGACTAATGAGATGGGTTTTACTACTTCAGGAATTCAATTTATGGATAATGGATA
* * *
41108220 GGAAGGGGACTGAGAACCAAATTGCAGATAATTTATCTAAACTTGAGAATGATTTAAAAGTAGAG
390 GGAAGAGGACTGAGAACCAAATTGCAGATAATTTATCCAAAATTGAGAATGATTTAAAAGTAGAG
* * *
41108285 AATATTGGAGAAATTAAAGAAACTTTCGTAGATGAGCAATTATTTAGGGTAGATATCCATCAGAT
455 AATATTGGAGAAATTAAAGAAACTTTCGCAGATGAGCAACTATTTAGAGTAGATATCCATCAGAT
41108350 CATGCTGAGTGAGCATACAACACCGTAG
520 CATGCTGAGTGAGCATACAACACCGTAG
41108378 TATGCAGATT
Statistics
Matches: 522, Mismatches: 24, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
564 2 0.00
565 520 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (565 bp):
GTTAAAGCTTTTGAGGTAATAAAATAAAAATTGATATCCGCTCCAATTATCATCACCCCTAACTA
GTCAGAACCTTTTATTATTATGTGTGATGCTAGTGATTATGTAACAAGTGCAGTCTTGAGACAAA
AGCAGAATAACATCTTTGGGGCTATTCATTATGCTAGTAAAATGTTAAATTCGGCACTGCAACTA
CGCTACAACTGAAAAAGAGATGCTAGTTGTAGTGTTCACTTGTGAAAAACTTTAACCCTACTTAA
TTATAAATAGAGTATATGTGTATATTGACCATTCTGCATTAAAATATGTTATGAAGAATAAAGAA
ACAAAAGCTAGACTAATGAGATGGGTTTTACTACTTCAGGAATTCAATTTATGGATAATGGATAG
GAAGAGGACTGAGAACCAAATTGCAGATAATTTATCCAAAATTGAGAATGATTTAAAAGTAGAGA
ATATTGGAGAAATTAAAGAAACTTTCGCAGATGAGCAACTATTTAGAGTAGATATCCATCAGATC
ATGCTGAGTGAGCATACAACACCGTAGAATAACATATTATTATGT
Found at i:41112886 original size:30 final size:30
Alignment explanation
Indices: 41112852--41112909 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
41112842 CAGCGGACAG
41112852 TTCCGACATATTAAATTAACTAACACACAC
1 TTCCGACATATTAAATTAACTAACACACAC
41112882 TTCCGACATATTAAATTAACTAACACAC
1 TTCCGACATATTAAATTAACTAACACAC
41112910 TCTAACCCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.43, C:0.26, G:0.03, T:0.28
Consensus pattern (30 bp):
TTCCGACATATTAAATTAACTAACACACAC
Found at i:41119735 original size:5 final size:5
Alignment explanation
Indices: 41119725--41119751 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
41119715 GAGTCTGTAA
41119725 TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TT
41119752 ATATGGACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:41121188 original size:20 final size:20
Alignment explanation
Indices: 41121163--41121220 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
41121153 TACGAGATTG
41121163 CACTTCGATGCCTCTGTTTA
1 CACTTCGATGCCTCTGTTTA
* *
41121183 CACTTC-AGTGCCTTTGTTTG
1 CACTTCGA-TGCCTCTGTTTA
* *
41121203 CACTTCGTTGTCTCTGTT
1 CACTTCGATGCCTCTGTT
41121221 AGCATCCCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.10, C:0.28, G:0.17, T:0.45
Consensus pattern (20 bp):
CACTTCGATGCCTCTGTTTA
Found at i:41127319 original size:1 final size:1
Alignment explanation
Indices: 41127272--41127299 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
41127262 CCTCATATAA
41127272 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
41127300 CTAAAAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:41127826 original size:24 final size:24
Alignment explanation
Indices: 41127777--41127826 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
41127767 AAAAAATCTA
* *
41127777 TTTTTTTACTGTTTTATTGCTGTT
1 TTTTTTTACTATTTTATTGCTATT
* *
41127801 TTTTTTTACTATTTTTTTGTTATT
1 TTTTTTTACTATTTTATTGCTATT
41127825 TT
1 TT
41127827 CTTGTTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.10, C:0.06, G:0.08, T:0.76
Consensus pattern (24 bp):
TTTTTTTACTATTTTATTGCTATT
Found at i:41128046 original size:16 final size:16
Alignment explanation
Indices: 41128022--41128057 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41128012 GAAATATTTA
*
41128022 TTTTAATTTTTTATAT
1 TTTTAATTTATTATAT
*
41128038 TTTTGATTTATTATAT
1 TTTTAATTTATTATAT
41128054 TTTT
1 TTTT
41128058 TAAAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTTAATTTATTATAT
Found at i:41128607 original size:16 final size:17
Alignment explanation
Indices: 41128588--41128620 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
41128578 GAAAAAAAGT
*
41128588 AAATTAATTAAA-ATAA
1 AAATTAAATAAACATAA
41128604 AAATTAAATAAACATAA
1 AAATTAAATAAACATAA
41128621 TTATTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATTAAATAAACATAA
Found at i:41142662 original size:16 final size:16
Alignment explanation
Indices: 41142641--41142671 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41142631 ATTGTGTTGA
*
41142641 GAAAATTATTTAATTG
1 GAAAATTAATTAATTG
41142657 GAAAATTAATTAATT
1 GAAAATTAATTAATT
41142672 TAAACTAATT
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:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
GAAAATTAATTAATTG
Found at i:41152298 original size:19 final size:19
Alignment explanation
Indices: 41152265--41152304 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
41152255 AAAATATCAT
*
41152265 ATTAATTTTAATTTATTTG
1 ATTAATTTTAATTTACTTG
41152284 ATTAA-TTTAATTTTACTTG
1 ATTAATTTTAA-TTTACTTG
41152303 AT
1 AT
41152305 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTAATTTTAATTTACTTG
Found at i:41156618 original size:24 final size:23
Alignment explanation
Indices: 41156591--41156648 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
41156581 CGATAACAAT
41156591 ATGCAAAAAATTATACCAATAAAA
1 ATGCAAAAAATT-TACCAATAAAA
* * * *
41156615 ATGCAAACAAGTTGCCAGTAAAA
1 ATGCAAAAAATTTACCAATAAAA
*
41156638 ATGCAATAAAT
1 ATGCAAAAAAT
41156649 CTCCATTCCC
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (23 bp):
ATGCAAAAAATTTACCAATAAAA
Found at i:41160429 original size:26 final size:26
Alignment explanation
Indices: 41160383--41160458 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
41160373 ATGAATTTTC
* **
41160383 TCAAAATTTTACTAGAAGTAAAATCA
1 TCAAAATTTTACTGGGGGTAAAATCA
* * * *
41160409 TTAAAATTTTATTGGGGGTAAAGTCG
1 TCAAAATTTTACTGGGGGTAAAATCA
*
41160435 TCAAACTTTTACTGGGGGTAAAAT
1 TCAAAATTTTACTGGGGGTAAAAT
41160459 TGAGATAAGA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.34
Consensus pattern (26 bp):
TCAAAATTTTACTGGGGGTAAAATCA
Found at i:41163056 original size:20 final size:19
Alignment explanation
Indices: 41163031--41163105 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
41163021 GAAATGTAAT
41163031 CAAAGACACCAATGTGCAAA
1 CAAAGACACCAA-GTGCAAA
*
41163051 CAAAGACACCGAAGTGCATA
1 CAAAGACACC-AAGTGCAAA
* ** *
41163071 TAGCGGCACCAAAGTGCAAA
1 CAAAGACACC-AAGTGCAAA
*
41163091 CAAAGGCACCGAAGT
1 CAAAGACACC-AAGT
41163106 ACATAACTAG
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.44, C:0.25, G:0.21, T:0.09
Consensus pattern (19 bp):
CAAAGACACCAAGTGCAAA
Found at i:41163187 original size:20 final size:20
Alignment explanation
Indices: 41163164--41163251 Score: 81
Period size: 20 Copynumber: 4.4 Consensus size: 20
41163154 AACATGAATA
41163164 TGCTATCAAGAGCACCGTAG
1 TGCTATCAAGAGCACCGTAG
* **
41163184 TGCTAACAAGAGCA-CAAATG
1 TGCTATCAAGAGCACCGTA-G
* * *
41163204 TACTATCAGGAGCACGGATA-
1 TGCTATCAAGAGCACCG-TAG
*
41163224 TGCAATCAAGAGCACCGTAG
1 TGCTATCAAGAGCACCGTAG
41163244 TGCTATCA
1 TGCTATCA
41163252 GGAGGACTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 8
0.69 0.19 0.11
Matches are distributed among these distances:
19 4 0.08
20 45 0.90
22 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (20 bp):
TGCTATCAAGAGCACCGTAG
Found at i:41165295 original size:2 final size:2
Alignment explanation
Indices: 41165290--41165314 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41165280 GTTAATGCTT
41165290 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
41165315 TCTGTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:41173219 original size:237 final size:238
Alignment explanation
Indices: 41172804--41173279 Score: 945
Period size: 237 Copynumber: 2.0 Consensus size: 238
41172794 AAAGGATCGA
41172804 AAAGAGGATGTTGAATTCATCCAAATATGATATTTTGATAAGGAAAGGCCACTGAATGACAACGG
1 AAAGAGGATGTTGAATTCATCCAAATATGATATTTTGATAAGGAAAGGCCACTGAATGACAACGG
41172869 CCCATGGTGGTTGGTGTGGCAATAAGTGGTGGTGAACAATGGTTTTATGGAAAAATGGTGAACGG
66 CCCATGGTGGTTGGTGTGGCAATAAGTGGTGGTGAACAATGGTTTTATGGAAAAATGGTGAACGG
41172934 TGGTTTGCTAATATGATATTTTTACTAGCAACTATTTACTTTAATTTAAAATATATTTATTTAAA
131 TGGTTTGCTAATATGATATTTTTACTAGCAACTATTTACTTTAATTTAAAATATATTTATTTAAA
41172999 TACTTTTACTATATATTAATATATAAATAAAA-ATTTTTTATT
196 TACTTTTACTATATATTAATATATAAATAAAATATTTTTTATT
41173041 AAAGAGGATGTTGAATTCATCCAAATATGATATTTTGATAAGGAAAGGCCACTGAATGACAACGG
1 AAAGAGGATGTTGAATTCATCCAAATATGATATTTTGATAAGGAAAGGCCACTGAATGACAACGG
41173106 CCCATGGTGGTTGGTGTGGCAATAAGTGGTGGTGAACAATGGTTTTATGGAAAAATGGTGAACGG
66 CCCATGGTGGTTGGTGTGGCAATAAGTGGTGGTGAACAATGGTTTTATGGAAAAATGGTGAACGG
41173171 TGGTTTGCTAATATGATATTTTTACTAGCAACTATTTACTTTAATTTAAAATATATTTATTTAAA
131 TGGTTTGCTAATATGATATTTTTACTAGCAACTATTTACTTTAATTTAAAATATATTTATTTAAA
41173236 TACTTTTACTATATATTAATATATAAATAAAATATTTTTTATT
196 TACTTTTACTATATATTAATATATAAATAAAATATTTTTTATT
41173279 A
1 A
41173280 TTAAGGGTAA
Statistics
Matches: 238, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
237 227 0.95
238 11 0.05
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (238 bp):
AAAGAGGATGTTGAATTCATCCAAATATGATATTTTGATAAGGAAAGGCCACTGAATGACAACGG
CCCATGGTGGTTGGTGTGGCAATAAGTGGTGGTGAACAATGGTTTTATGGAAAAATGGTGAACGG
TGGTTTGCTAATATGATATTTTTACTAGCAACTATTTACTTTAATTTAAAATATATTTATTTAAA
TACTTTTACTATATATTAATATATAAATAAAATATTTTTTATT
Found at i:41173434 original size:27 final size:27
Alignment explanation
Indices: 41173363--41173427 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
41173353 GTCTTATTCC
*
41173363 ATTCCATTACAGTCCTATTACACTCTT
1 ATTCCATTACAGTCCTATTACAATCTT
**
41173390 ATTTGATTACAGTCCTATTACAATCTT
1 ATTCCATTACAGTCCTATTACAATCTT
41173417 ATTCCATTACA
1 ATTCCATTACA
41173428 ACCCTATCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.29, C:0.25, G:0.05, T:0.42
Consensus pattern (27 bp):
ATTCCATTACAGTCCTATTACAATCTT
Found at i:41175912 original size:46 final size:46
Alignment explanation
Indices: 41175732--41175939 Score: 213
Period size: 46 Copynumber: 4.5 Consensus size: 46
41175722 AGTTTTTGCC
* * * *
41175732 CAGGTTCTCAGCTCTTGCATATGTTGCGGACTGGAGAATACATA-TT
1 CAGGTTCCCAACTCCTGCATATGTTGCGAACTGGAGAATACA-AGTT
* ** ** *
41175778 CAAGTTCCCAGTTCCTATATATGTTGCGGACTGGAGAATAC-AGATT
1 CAGGTTCCCAACTCCTGCATATGTTGCGAACTGGAGAATACAAG-TT
*
41175824 CAGGTTCCCAACTCCTGCATATGTTGCAAACTGGAGAATACAAGTT
1 CAGGTTCCCAACTCCTGCATATGTTGCGAACTGGAGAATACAAGTT
* * * *
41175870 TAGGTTCCCAACTCTTGCATATGTTGCGAACTAGAGAATACAATTT
1 CAGGTTCCCAACTCCTGCATATGTTGCGAACTGGAGAATACAAGTT
* * * *
41175916 TAGGTTCCTAGCTCCTGCAGATGT
1 CAGGTTCCCAACTCCTGCATATGT
41175940 GGAAACGCAT
Statistics
Matches: 137, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
44 1 0.01
46 134 0.98
47 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (46 bp):
CAGGTTCCCAACTCCTGCATATGTTGCGAACTGGAGAATACAAGTT
Found at i:41180056 original size:26 final size:27
Alignment explanation
Indices: 41180024--41180093 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
41180014 AACAGAGATC
41180024 GCCACAAAGGCTTCCTTT-CAAAAATA
1 GCCACAAAGGCTTCCTTTACAAAAATA
** *
41180050 GCCACAAAGG-TTTTTTTAACAAAGATA
1 GCCACAAAGGCTTCCTTT-ACAAAAATA
*
41180077 GTCACAAAGGCTTCCTT
1 GCCACAAAGGCTTCCTT
41180094 ATAGAAACTG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
25 5 0.14
26 10 0.29
27 16 0.46
28 4 0.11
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (27 bp):
GCCACAAAGGCTTCCTTTACAAAAATA
Found at i:41183221 original size:44 final size:45
Alignment explanation
Indices: 41183103--41183224 Score: 133
Period size: 45 Copynumber: 2.7 Consensus size: 45
41183093 ATCGGCTTCA
** *
41183103 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTCTG
1 ATCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGCCATCTCAG
* * * *
41183148 ATCT-ATCCCACTGCAACTTCAGGGGGATAAGACCTG-CTTACTCAG
1 ATCTGCT-CCACTGCAACCTCAGGGAGATAAGACCTGCCAT-CTCAG
*
41183193 -TCTGCTCCACTACAACCTCAGGGAGATAAGAC
1 ATCTGCTCCACTGCAACCTCAGGGAGATAAGAC
41183225 ATGATGTGAT
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
44 29 0.46
45 34 0.54
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.24
Consensus pattern (45 bp):
ATCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGCCATCTCAG
Found at i:41183323 original size:218 final size:218
Alignment explanation
Indices: 41182945--41183402 Score: 756
Period size: 218 Copynumber: 2.1 Consensus size: 218
41182935 ATAATTGGGT
* * * *
41182945 ACTTCAGGGGAATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACCTCAAGGAGATAAGACCTA
1 ACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCACTACAACCTCAAGGAGATAAGACATA
* *
41183010 ATGCGATTCACTCTACTGCAACTTCAGAAAGATAAGATCCATTACTTTAATCCGCTCCACTACAA
66 ATGCGATCCACTCTACTGCAACTTCAGAAAGATAAGATCCATTACTTTAATCCGCTCAACTACAA
* *
41183075 TTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGC
131 TTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCCACTGCAACCTCAGGAAGATAAGATTTGC
*
41183140 CATC-TCTGATCTATCCCACTGCA
196 CATCTTC-AATCTATCCCACTGCA
* *
41183163 ACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCACTACAACCTCAGGGAGATAAGACATG
1 ACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCACTACAACCTCAAGGAGATAAGACATA
* * *
41183228 ATGTGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCATTACTTTAATCCGCTCAACTACAA
66 ATGCGATCCACTCTACTGCAACTTCAGAAAGATAAGATCCATTACTTTAATCCGCTCAACTACAA
41183293 TTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCCACTGCAACCTCAGGAAGATAAGATTTGC
131 TTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCCACTGCAACCTCAGGAAGATAAGATTTGC
* *
41183358 CATCTTCAATCTGTCCCATTGCA
196 CATCTTCAATCTATCCCACTGCA
41183381 ACTTCAGGGGGATAAGACCTGC
1 ACTTCAGGGGGATAAGACCTGC
41183403 GATTTCCCAA
Statistics
Matches: 223, Mismatches: 16, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
218 221 0.99
219 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (218 bp):
ACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCACTACAACCTCAAGGAGATAAGACATA
ATGCGATCCACTCTACTGCAACTTCAGAAAGATAAGATCCATTACTTTAATCCGCTCAACTACAA
TTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCCACTGCAACCTCAGGAAGATAAGATTTGC
CATCTTCAATCTATCCCACTGCA
Found at i:41183370 original size:45 final size:44
Alignment explanation
Indices: 41183024--41183397 Score: 180
Period size: 44 Copynumber: 8.5 Consensus size: 44
41183014 GATTCACTCT
** * * *
41183024 ACTGCAACTTCAGAAAGATAAGA--TCCATTACTTTAATCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTTGCA-T-CTTCAATCTGCTCC
* * * **
41183068 ACTACAATTTCAGGGAGATAGGATTAT-CGGCTTCAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATT-TGCATCTTCAATCTGCTCC
* * *
41183112 ACTGCAACCTCAGGGAGATAAGATTTGCCATC-TCTGATCT-ATCCC
1 ACTGCAACTTCAGGGAGATAAGATTTG-CATCTTC-AATCTGCT-CC
* ** * *
41183157 ACTGCAACTTCAGGGGGATAAGACCTGCTTAC-TCAGTCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTTGCAT-CTTCAATCTGCTCC
* * ** * * ** *
41183201 ACTACAACCTCAGGGAGATAAGACATG-AT-GT-GATCCACTCT
1 ACTGCAACTTCAGGGAGATAAGATTTGCATCTTCAATCTGCTCC
* * * * * *
41183242 ACTGTAACTTCAGAGAGATAAGA--TCCATTACTTTAATCCGCTCA
1 ACTGCAACTTCAGGGAGATAAGATTTGCA-T-CTTCAATCTGCTCC
* * * *
41183286 ACTACAATTTCAGGGAGATAGGATTAT-CAGCTTCAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATT-TGCATCTTCAATCTGCTCC
* *
41183330 ACTGCAACCTCAGGAAGATAAGATTTGCCATCTTCAATCTG-TCCC
1 ACTGCAACTTCAGGGAGATAAGATTTG-CATCTTCAATCTGCT-CC
* *
41183375 ATTGCAACTTCAGGGGGATAAGA
1 ACTGCAACTTCAGGGAGATAAGA
41183398 CCTGCGATTT
Statistics
Matches: 246, Mismatches: 63, Indels: 41
0.70 0.18 0.12
Matches are distributed among these distances:
39 1 0.00
40 1 0.00
41 25 0.10
42 1 0.00
43 4 0.02
44 141 0.57
45 68 0.28
46 3 0.01
47 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (44 bp):
ACTGCAACTTCAGGGAGATAAGATTTGCATCTTCAATCTGCTCC
Found at i:41191298 original size:22 final size:22
Alignment explanation
Indices: 41191256--41191299 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
41191246 TAAACTGGAC
**
41191256 ATTTATTTGGTTTATTTTATTT
1 ATTTATTTGGTTTATAATATTT
41191278 ATTTATTTGAGTTT-TAATATTT
1 ATTTATTTG-GTTTATAATATTT
41191300 GGGCTCGGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (22 bp):
ATTTATTTGGTTTATAATATTT
Found at i:41191640 original size:15 final size:15
Alignment explanation
Indices: 41191601--41191642 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
41191591 TTCATGCAGT
*
41191601 GACTTGCTCACAACA
1 GACTTGTTCACAACA
*
41191616 GACACT-TTCACAACA
1 GAC-TTGTTCACAACA
41191631 GACTTGTTCACA
1 GACTTGTTCACA
41191643 TCCTCCAGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.33, C:0.31, G:0.12, T:0.24
Consensus pattern (15 bp):
GACTTGTTCACAACA
Found at i:41193285 original size:62 final size:63
Alignment explanation
Indices: 41193159--41193288 Score: 156
Period size: 62 Copynumber: 2.1 Consensus size: 63
41193149 CTTTAACCTA
* * * * * *
41193159 ATAATTTTAGATATTTCAATTGTATTACACAAATTGTTTCACTCACGTTGTTTGTATATTTTG
1 ATAATTTTACACATTTCAATTGTATTACACAAATTGTTTCACTCACATTATTTGCATATATTG
* * *
41193222 ATAATTTTACACATTTCAATT-TATTATACAAATTGTTTC-TTCCATATTATTTGCATATATTG
1 ATAATTTTACACATTTCAATTGTATTACACAAATTGTTTCACT-CACATTATTTGCATATATTG
41193284 ATAAT
1 ATAAT
41193289 GTCGTTGATT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
61 1 0.02
62 37 0.65
63 19 0.33
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.49
Consensus pattern (63 bp):
ATAATTTTACACATTTCAATTGTATTACACAAATTGTTTCACTCACATTATTTGCATATATTG
Found at i:41203657 original size:140 final size:141
Alignment explanation
Indices: 41203491--41203771 Score: 537
Period size: 140 Copynumber: 2.0 Consensus size: 141
41203481 AATATTTTTA
41203491 AATATATATATATATATATGGCTCTTTCAGCGCAAAACTAGTGATTGGTTTTTGTTTTCTCGCTA
1 AATATATATATATATATATGGCTCTTTCAGCGCAAAACTAGTGATTGGTTTTTGTTTTCTCGCTA
41203556 TAATACTCTCTTGAGTAATTGGGAAATGGATTTAGAAAAAATGAATAAAATATATTTTAAATATT
66 TAATACTCTCTTGAGTAATTGGGAAATGGATTTAGAAAAAATGAATAAAATATATTTTAAATATT
41203621 -ATTTTTGATT
131 GATTTTTGATT
**
41203631 AATATATATATATATATATGGCTCTTTCATTGCAAAACTAGTGATTGGTTTTTGTTTTCTCGCTA
1 AATATATATATATATATATGGCTCTTTCAGCGCAAAACTAGTGATTGGTTTTTGTTTTCTCGCTA
41203696 TAATACTCTCTTGAGTAATTGGGAAATGGATTTAGAAAAAATGAATAAAATATATTTTAAATATT
66 TAATACTCTCTTGAGTAATTGGGAAATGGATTTAGAAAAAATGAATAAAATATATTTTAAATATT
41203761 GATTTTTGATT
131 GATTTTTGATT
41203772 CAAATCTTAT
Statistics
Matches: 138, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
140 128 0.93
141 10 0.07
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (141 bp):
AATATATATATATATATATGGCTCTTTCAGCGCAAAACTAGTGATTGGTTTTTGTTTTCTCGCTA
TAATACTCTCTTGAGTAATTGGGAAATGGATTTAGAAAAAATGAATAAAATATATTTTAAATATT
GATTTTTGATT
Found at i:41211241 original size:28 final size:29
Alignment explanation
Indices: 41211210--41211269 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
41211200 TTGCAATGAA
* * *
41211210 TTAGGACATATTA-AAACTCACAATTAAT
1 TTAGAACAAATTAGAAACACACAATTAAT
**
41211238 TTAGAACAAATTAGAAACACTTAATTAAT
1 TTAGAACAAATTAGAAACACACAATTAAT
41211267 TTA
1 TTA
41211270 TGTTCAGATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (29 bp):
TTAGAACAAATTAGAAACACACAATTAAT
Found at i:41212309 original size:15 final size:16
Alignment explanation
Indices: 41212280--41212314 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
41212270 AACAATTGCA
41212280 TTTAATGTTGAAAAAT
1 TTTAATGTTGAAAAAT
41212296 TTTAATGTTGAAAAAT
1 TTTAATGTTGAAAAAT
41212312 TTT
1 TTT
41212315 GGTTTAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (16 bp):
TTTAATGTTGAAAAAT
Found at i:41222660 original size:43 final size:43
Alignment explanation
Indices: 41222599--41222688 Score: 171
Period size: 43 Copynumber: 2.1 Consensus size: 43
41222589 TAAAAAGTCC
*
41222599 ATGGTTAGCCATGGCATGATCTAGTGGTGAACAGGTAAGCTTT
1 ATGGTTAGCCATGGCATGATCTAGTGGTGAACAAGTAAGCTTT
41222642 ATGGTTAGCCATGGCATGATCTAGTGGTGAACAAGTAAGCTTT
1 ATGGTTAGCCATGGCATGATCTAGTGGTGAACAAGTAAGCTTT
41222685 ATGG
1 ATGG
41222689 CATAAAAGGG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (43 bp):
ATGGTTAGCCATGGCATGATCTAGTGGTGAACAAGTAAGCTTT
Found at i:41225930 original size:333 final size:333
Alignment explanation
Indices: 41225324--41225989 Score: 1316
Period size: 333 Copynumber: 2.0 Consensus size: 333
41225314 CATCACAAGT
41225324 GAATTAATTCACAAATGGATTTAGAATTAATTCATCTTAGGTATAGTCCAATGTATCATTCTACC
1 GAATTAATTCACAAATGGATTTAGAATTAATTCATCTTAGGTATAGTCCAATGTATCATTCTACC
41225389 AATGAATCCATCTATATCTCTACTCGTGGAGTCAATTGCATTAATAGCTAAGACTAGCCATCTCC
66 AATGAATCCATCTATATCTCTACTCGTGGAGTCAATTGCATTAATAGCTAAGACTAGCCATCTCC
41225454 CCAGTTGGAATTATAGACAACATAATAATCCTTCTCAGTATTTGAATCAAATGCTCACTTTGATT
131 CCAGTTGGAATTATAGACAACATAATAATCCTTCTCAGTATTTGAATCAAATGCTCACTTTGATT
41225519 TTTTATGGGATTACGGGCTCATTTAGATTATCTACTGAAGTAAGTTGCCTTTCTTGCAATGTAAA
196 TTTTATGGGATTACGGGCTCATTTAGATTATCTACTGAAGTAAGTTGCCTTTCTTGCAATGTAAA
41225584 CGTTTTTTACAATACCACTTATCTTCAATTTGAACTTTAGACAATCAATAAGCTAATATTTACTT
261 CGTTTTTTACAATACCACTTATCTTCAATTTGAACTTTAGACAATCAATAAGCTAATATTTACTT
41225649 GTCACAAA
326 GTCACAAA
41225657 GAATTAATTCACAAATGGATTTAGAATTAATTCATCTTAGGTATAGTCCAATGTATCATTCTACC
1 GAATTAATTCACAAATGGATTTAGAATTAATTCATCTTAGGTATAGTCCAATGTATCATTCTACC
41225722 AATGAATCCATCTATATCTCTACTCGTGGAGTCAATTGCATTAATAGCTAAGACTAGCCATCTCC
66 AATGAATCCATCTATATCTCTACTCGTGGAGTCAATTGCATTAATAGCTAAGACTAGCCATCTCC
41225787 CCAGTTGGAATTATAGACAA-ATAATAATCCCTTCTCAGTATTTGAATCAAATGCTCACTTTGAT
131 CCAGTTGGAATTATAGACAACATAATAAT-CCTTCTCAGTATTTGAATCAAATGCTCACTTTGAT
41225851 TTTTTATGGGATTACGGGCTCATTTAGATTATCTACTGAAGTAAGTTGCCTTTCTTGCAATGTAA
195 TTTTTATGGGATTACGGGCTCATTTAGATTATCTACTGAAGTAAGTTGCCTTTCTTGCAATGTAA
41225916 ACGTTTTTTACAATACCACTTATCTTCAATTTGAACTTTAGACAATCAATAAGCTAATATTTACT
260 ACGTTTTTTACAATACCACTTATCTTCAATTTGAACTTTAGACAATCAATAAGCTAATATTTACT
41225981 TGTCACAAA
325 TGTCACAAA
41225990 TTTGCTATGC
Statistics
Matches: 332, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
332 8 0.02
333 324 0.98
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.36
Consensus pattern (333 bp):
GAATTAATTCACAAATGGATTTAGAATTAATTCATCTTAGGTATAGTCCAATGTATCATTCTACC
AATGAATCCATCTATATCTCTACTCGTGGAGTCAATTGCATTAATAGCTAAGACTAGCCATCTCC
CCAGTTGGAATTATAGACAACATAATAATCCTTCTCAGTATTTGAATCAAATGCTCACTTTGATT
TTTTATGGGATTACGGGCTCATTTAGATTATCTACTGAAGTAAGTTGCCTTTCTTGCAATGTAAA
CGTTTTTTACAATACCACTTATCTTCAATTTGAACTTTAGACAATCAATAAGCTAATATTTACTT
GTCACAAA
Found at i:41226029 original size:15 final size:15
Alignment explanation
Indices: 41226005--41226036 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41225995 TATGCATGCA
*
41226005 AAATATAAAAGACAT
1 AAATACAAAAGACAT
41226020 AAATACAAAAGACAT
1 AAATACAAAAGACAT
41226035 AA
1 AA
41226037 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:41227935 original size:27 final size:27
Alignment explanation
Indices: 41227901--41228015 Score: 158
Period size: 27 Copynumber: 4.3 Consensus size: 27
41227891 CGAAAAGGTT
*
41227901 GTAAAATTATCGAAATACCTCCGAAGG
1 GTAAAATTATCGAAATACCCCCGAAGG
* *
41227928 GTAAAATTATCGAAATACCCTCGAAAG
1 GTAAAATTATCGAAATACCCCCGAAGG
* * *
41227955 ATAAAACTATCGAAATACCCCCAAAGG
1 GTAAAATTATCGAAATACCCCCGAAGG
* *
41227982 GTAAAATTATCAAAATACCCCCGTAGG
1 GTAAAATTATCGAAATACCCCCGAAGG
41228009 GTAAAAT
1 GTAAAAT
41228016 GACTGTTATA
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 75 1.00
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (27 bp):
GTAAAATTATCGAAATACCCCCGAAGG
Found at i:41230995 original size:22 final size:22
Alignment explanation
Indices: 41230967--41231009 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
41230957 TATGAGGAAT
* *
41230967 GGGAAATTAAAGGGAATCAACA
1 GGGAAATTAAAGAGAAACAACA
41230989 GGGAAATTAAAGAGAAACAAC
1 GGGAAATTAAAGAGAAACAAC
41231010 GCTACAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.09, G:0.26, T:0.12
Consensus pattern (22 bp):
GGGAAATTAAAGAGAAACAACA
Found at i:41242933 original size:23 final size:23
Alignment explanation
Indices: 41242866--41242972 Score: 107
Period size: 23 Copynumber: 4.9 Consensus size: 23
41242856 CCTAATCCGT
*
41242866 ATACGACACAT-AAGTGTCTGAA
1 ATACGACACATGAAGTGCCTGAA
*
41242888 AT--GACACATGAGGTGCCTG--
1 ATACGACACATGAAGTGCCTGAA
* *
41242907 ATACGACACACGAGGTGCCTGAA
1 ATACGACACATGAAGTGCCTGAA
* *
41242930 ATACGACACATAAAGTGCCTGAT
1 ATACGACACATGAAGTGCCTGAA
* *
41242953 ATATGACACATAAAGTGCCT
1 ATACGACACATGAAGTGCCT
41242973 TTATGGTGAA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
19 2 0.03
20 7 0.10
21 23 0.32
22 2 0.03
23 38 0.53
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (23 bp):
ATACGACACATGAAGTGCCTGAA
Found at i:41242948 original size:44 final size:41
Alignment explanation
Indices: 41242866--41242953 Score: 104
Period size: 44 Copynumber: 2.1 Consensus size: 41
41242856 CCTAATCCGT
* * * *
41242866 ATACGACACATAAGTGTCTGAAATGACACATGAGGTGCCTG
1 ATACGACACAGAAGTGCCTGAAATGACACATAAAGTGCCTG
*
41242907 ATACGACACACGAGGTGCCTGAAATACGACACATAAAGTGCCTG
1 ATACGACACA-GAAGTGCCTGAAAT--GACACATAAAGTGCCTG
41242951 ATA
1 ATA
41242954 TATGACACAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 10 0.26
42 11 0.28
44 18 0.46
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (41 bp):
ATACGACACAGAAGTGCCTGAAATGACACATAAAGTGCCTG
Found at i:41245208 original size:33 final size:32
Alignment explanation
Indices: 41245169--41245265 Score: 97
Period size: 32 Copynumber: 2.9 Consensus size: 32
41245159 AAGAAAAATT
*
41245169 CAGGAAAAAGAATCTTGAAGAAATTGAATCTGA
1 CAGGAAAAA-AAACTTGAAGAAATTGAATCTGA
* * * *
41245202 CGGGAAAAAAAACTAGGAGAAATTGAAAT-GGA
1 CAGGAAAAAAAACTTGAAGAAATTG-AATCTGA
*
41245234 CATGAAAATAAAACCTTGAAGAAATTGAATCT
1 CAGGAAAA-AAAA-CTTGAAGAAATTGAATCT
41245266 TACTTGGAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
32 21 0.42
33 18 0.36
34 11 0.22
ACGTcount: A:0.51, C:0.09, G:0.21, T:0.20
Consensus pattern (32 bp):
CAGGAAAAAAAACTTGAAGAAATTGAATCTGA
Found at i:41245688 original size:21 final size:21
Alignment explanation
Indices: 41245647--41245688 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
41245637 ATAGATAATG
*
41245647 AAAAAATATATAAATTATTTT
1 AAAAAATATATAAAATATTTT
*
41245668 AAAAATTATAGTAAAAT-TTTT
1 AAAAAATATA-TAAAATATTTT
41245689 CTCTTGACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
AAAAAATATATAAAATATTTT
Found at i:41247407 original size:2 final size:2
Alignment explanation
Indices: 41247400--41247424 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41247390 GTCATTGCTT
41247400 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
41247425 GTTTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:41247471 original size:25 final size:24
Alignment explanation
Indices: 41247424--41247473 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
41247414 TCTCTCTCTC
*
41247424 TGTTTTTTATTTTACTTTATTTCT
1 TGTTTTTTATTTTACATTATTTCT
41247448 TGTTTTTTAGTTTTTACATT-TTTCT
1 TGTTTTTTA--TTTTACATTATTTCT
41247473 T
1 T
41247474 ATCAGGTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 9 0.39
25 6 0.26
26 8 0.35
ACGTcount: A:0.12, C:0.08, G:0.06, T:0.74
Consensus pattern (24 bp):
TGTTTTTTATTTTACATTATTTCT
Found at i:41252754 original size:4 final size:4
Alignment explanation
Indices: 41252745--41252783 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
41252735 ACTCGCTTCT
* **
41252745 TTAC TTAC TTAC TCAC TTGT TTAC TTAC TTAC TTAC TTA
1 TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTA
41252784 AATAACTCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.51
Consensus pattern (4 bp):
TTAC
Found at i:41252758 original size:20 final size:20
Alignment explanation
Indices: 41252733--41252782 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
41252723 ATTAGAATCT
*
41252733 TTACTCGCTTCTTTACTTAC
1 TTACTCACTTCTTTACTTAC
*
41252753 TTACTCACTTGTTTACTTAC
1 TTACTCACTTCTTTACTTAC
*
41252773 TTACTTACTT
1 TTACTCACTT
41252783 AAATAACTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.26, G:0.04, T:0.52
Consensus pattern (20 bp):
TTACTCACTTCTTTACTTAC
Found at i:41253100 original size:50 final size:50
Alignment explanation
Indices: 41253032--41253222 Score: 195
Period size: 50 Copynumber: 3.8 Consensus size: 50
41253022 TTTTCTGTAT
* * **
41253032 TGCCAATGCCATATCCCAGATATGGTCTTACATAGGAGTTCCCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATAGGACCTCCCATATCGG
* *** * *
41253082 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATAGGACCTCCCATATCGG
* * ** *
41253132 TGCCTACGCCATGTCCCAGACATGGTCTTACAT-GAGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATAG-GACCTCCCATATCGG
* * * *
41253182 TGCCAACGCCATGTCCCAGGCATGATCTTACATGGGACCTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATAGGACCTC
41253223 ATTCCCTTAA
Statistics
Matches: 121, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
49 1 0.01
50 119 0.98
51 1 0.01
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATAGGACCTCCCATATCGG
Found at i:41255213 original size:22 final size:22
Alignment explanation
Indices: 41255188--41255230 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
41255178 TAACAATTTA
*
41255188 GGTTCAACTTTAGGGCTCAATG
1 GGTTCAACTTTAAGGCTCAATG
41255210 GGTTCAACTTTAAGGCTCAAT
1 GGTTCAACTTTAAGGCTCAAT
41255231 TATCCATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.33
Consensus pattern (22 bp):
GGTTCAACTTTAAGGCTCAATG
Found at i:41260980 original size:12 final size:12
Alignment explanation
Indices: 41260959--41260988 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
41260949 TAAGTGAGTT
*
41260959 ACACGACCTAGC
1 ACACGGCCTAGC
41260971 ACACGGCCTAGC
1 ACACGGCCTAGC
41260983 ACACGG
1 ACACGG
41260989 GCGTGTGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.40, G:0.23, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:41263685 original size:37 final size:37
Alignment explanation
Indices: 41263644--41263719 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
41263634 AACATAAAAG
*
41263644 AAATTAAACAAATGAAAGGTAAGAAATAAAATAAGGA
1 AAATTAAACAAATGAAAAGTAAGAAATAAAATAAGGA
* *
41263681 AAATTAAATAAATGAAAAGTAAGAAATCAAATAAGGA
1 AAATTAAACAAATGAAAAGTAAGAAATAAAATAAGGA
41263718 AA
1 AA
41263720 TATGTATCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.66, C:0.03, G:0.14, T:0.17
Consensus pattern (37 bp):
AAATTAAACAAATGAAAAGTAAGAAATAAAATAAGGA
Found at i:41266063 original size:25 final size:25
Alignment explanation
Indices: 41266024--41266118 Score: 111
Period size: 25 Copynumber: 3.8 Consensus size: 25
41266014 TCCTTTACAT
*
41266024 GTATGCTCATACGAGCTGTGAATCG
1 GTATGCTCACACGAGCTGTGAATCG
* *
41266049 GTATGCTCACTCGAGCTGT-AGATTG
1 GTATGCTCACACGAGCTGTGA-ATCG
* * *
41266074 GTATGCTCTCACGAGCTATAAATCG
1 GTATGCTCACACGAGCTGTGAATCG
*
41266099 GTATGCTGACACGAGCTGTG
1 GTATGCTCACACGAGCTGTG
41266119 GGTCGAAACG
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
24 1 0.02
25 55 0.96
26 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTGAATCG
Found at i:41267460 original size:25 final size:25
Alignment explanation
Indices: 41267421--41267515 Score: 111
Period size: 25 Copynumber: 3.8 Consensus size: 25
41267411 TCCTTTACAT
*
41267421 GTATGCTCATACGAGCTGTGAATCG
1 GTATGCTCACACGAGCTGTGAATCG
* *
41267446 GTATGCTCACTCGAGCTGT-AGATTG
1 GTATGCTCACACGAGCTGTGA-ATCG
* * *
41267471 GTATGCTCTCACGAGCTATAAATCG
1 GTATGCTCACACGAGCTGTGAATCG
*
41267496 GTATGCTGACACGAGCTGTG
1 GTATGCTCACACGAGCTGTG
41267516 GGTCGAAACG
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
24 1 0.02
25 55 0.96
26 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTGAATCG
Found at i:41270371 original size:12 final size:11
Alignment explanation
Indices: 41270346--41270383 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
41270336 TGAACAAGTG
41270346 AATTTTA-ATT
1 AATTTTATATT
41270356 AATTTTATAGTT
1 AATTTTATA-TT
41270368 AATTTT-TATT
1 AATTTTATATT
41270378 AATTTT
1 AATTTT
41270384 GACTATTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 3 0.12
12 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
AATTTTATATT
Found at i:41271792 original size:46 final size:46
Alignment explanation
Indices: 41271725--41271819 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
41271715 CCAGAGAAGG
41271725 ACCAAAGAGATAAACTTTGAGAATATGAATCAAGGAAACGGAGCAA
1 ACCAAAGAGATAAACTTTGAGAATATGAATCAAGGAAACGGAGCAA
41271771 ACCAAAGAGATAAACTTTGAGAATATGAATCAAGGAAACGGAGCAA
1 ACCAAAGAGATAAACTTTGAGAATATGAATCAAGGAAACGGAGCAA
41271817 ACC
1 ACC
41271820 TTGCTCAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.49, C:0.15, G:0.21, T:0.15
Consensus pattern (46 bp):
ACCAAAGAGATAAACTTTGAGAATATGAATCAAGGAAACGGAGCAA
Found at i:41278348 original size:26 final size:26
Alignment explanation
Indices: 41278311--41278596 Score: 403
Period size: 26 Copynumber: 11.0 Consensus size: 26
41278301 CACGGTGTTG
41278311 ACCAAAATACCCTCGATGGGTAAATT
1 ACCAAAATACCCTCGATGGGTAAATT
*
41278337 ACCAAAAGACCCTCGATGGGTAAATT
1 ACCAAAATACCCTCGATGGGTAAATT
* **
41278363 ACCGAAATACCCTTAATGGGTAAATT
1 ACCAAAATACCCTCGATGGGTAAATT
41278389 ACCAAAATACCCTCGATGGGTAAATT
1 ACCAAAATACCCTCGATGGGTAAATT
*
41278415 AACAAAATACCCTCGATGGGTAAATT
1 ACCAAAATACCCTCGATGGGTAAATT
***
41278441 ATTTAAATACCCTCGATGGGTAAATT
1 ACCAAAATACCCTCGATGGGTAAATT
*
41278467 ACCAAATTACCCTCGATGGGTAAATT
1 ACCAAAATACCCTCGATGGGTAAATT
* *
41278493 ACTAAAATACCCTTGATGGGTAAATT
1 ACCAAAATACCCTCGATGGGTAAATT
** *
41278519 ACTGAAATACCCTCGATGGATAAATT
1 ACCAAAATACCCTCGATGGGTAAATT
* * *
41278545 ATCGAAATACCCTTGATGGGTAAATT
1 ACCAAAATACCCTCGATGGGTAAATT
*
41278571 ACCGAAATACCCT-GATGGGTAAATT
1 ACCAAAATACCCTCGATGGGTAAATT
41278596 A
1 A
41278597 TTGAAATATC
Statistics
Matches: 233, Mismatches: 27, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
25 13 0.06
26 220 0.94
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (26 bp):
ACCAAAATACCCTCGATGGGTAAATT
Found at i:41278802 original size:27 final size:27
Alignment explanation
Indices: 41278764--41278828 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
41278754 ATGGAGGAAG
* *
41278764 TACTGTTTCTGGTGGCTCTACCACA-A
1 TACTGTTACTGGTGGCTATACCACATA
*
41278790 TTACTGTTACTGGTGGCTATGCCACATA
1 -TACTGTTACTGGTGGCTATACCACATA
41278818 TACTG-TACTGG
1 TACTGTTACTGG
41278829 CAGCTCGACT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.18
27 27 0.79
28 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTATACCACATA
Found at i:41280162 original size:107 final size:107
Alignment explanation
Indices: 41279974--41280182 Score: 382
Period size: 107 Copynumber: 2.0 Consensus size: 107
41279964 AGCAGGACCA
*
41279974 TTTGTGACCCCTCCAATCTTTCTTGGGAATTTATTTTGACATAATTTTCCAAGAAATTATCCCCT
1 TTTGTGACCCCTCCAATCTTTCTTGAGAATTTATTTTGACATAATTTTCCAAGAAATTATCCCCT
* *
41280039 AAATGGGAAAAGAAATTTTTAGTTTCAAATAAAAGGGTCTCG
66 AAATGGAAAAAGAAATTTTTAATTTCAAATAAAAGGGTCTCG
41280081 TTTGTGACCCCTCCAATCTTTCTTGAGAATTTATTTTGACATAATTTTCCAAGAAATTATCCCCT
1 TTTGTGACCCCTCCAATCTTTCTTGAGAATTTATTTTGACATAATTTTCCAAGAAATTATCCCCT
*
41280146 AAATGGAAAAATAAATTTTTAATTTCAAATAAAAGGG
66 AAATGGAAAAAGAAATTTTTAATTTCAAATAAAAGGG
41280183 CCAATTTTGA
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 98 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (107 bp):
TTTGTGACCCCTCCAATCTTTCTTGAGAATTTATTTTGACATAATTTTCCAAGAAATTATCCCCT
AAATGGAAAAAGAAATTTTTAATTTCAAATAAAAGGGTCTCG
Found at i:41282122 original size:16 final size:16
Alignment explanation
Indices: 41282101--41282132 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41282091 ATTTTGTTGC
*
41282101 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
41282117 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
41282133 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:41282422 original size:51 final size:51
Alignment explanation
Indices: 41282360--41282537 Score: 202
Period size: 51 Copynumber: 3.5 Consensus size: 51
41282350 CCGGTTCACA
*
41282360 TAGTAGCCTGCACATAGTACTACACATGTGACCAGCACTATCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAGCACTATCTGGTACACG
* * * * * *
41282411 TA-TCAGCCTGCACATAGTACTACACATGTTATC-GAAGCTATCCGGTACGCA
1 TAGT-AGCCTGCACATAGTACTACACATGTGACCAGCA-CTATCTGGTACACG
* * * *
41282462 TAGTAGCCTGCACATAGTACTACACATGCGCCCTATCA-T-TTTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACC-AGCACTATCTGGTACACG
41282512 TAGTAGCCTGCACATAGTACTACACA
1 TAGTAGCCTGCACATAGTACTACACA
41282538 NNNNNNNNNN
Statistics
Matches: 105, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
50 36 0.34
51 67 0.64
52 1 0.01
53 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCAGCACTATCTGGTACACG
Found at i:41322115 original size:483 final size:483
Alignment explanation
Indices: 41321196--41322165 Score: 1733
Period size: 483 Copynumber: 2.0 Consensus size: 483
41321186 AATAGGTGTG
41321196 ATTTCAAAGAATACAAATTGAGAGATGGATCATGCTTTAAATGTGGTTCTTATGACCATTTTCTT
1 ATTTCAAAGAATACAAATTGAGAGATGGATCATGCTTTAAATGTGGTTCTTATGACCATTTTCTT
* *
41321261 CGAGACTGCCTTGAAAGATCTGATAGGGAGAAAGCTCAGAACAGTCGTTCGAGTAACACGGCTGC
66 CGAGACTACCTTGAAAGATCTGATAGGGAGAAAGCTCAGAACACTCGTTCGAGTAACACGGCTGC
41321326 GAGAGGGAGACCATCCAGAAATAGTGGAAATACGGGTAATAGTCGATGTGGAACGAAATATTCTA
131 GAGAGGGAGACCATCCAGAAATAGTGGAAATACGGGTAATAGTCGATGTGGAACGAAATATTCTA
41321391 CGGTTAGATCTGAGGCTCGGGCATATGCAATTCGAGCTCGTGAGAAAGCTTCAGCACCTAATGTG
196 CGGTTAGATCTGAGGCTCGGGCATATGCAATTCGAGCTCGTGAGAAAGCTTCAGCACCTAATGTG
** * * * *
41321456 GTTATTGGTACATTTTCTATCTTTGATACTAATGTTAATGCTTTGATTGACTCGAGGTCAACACC
261 AATACTGGTACATTTTCTATCTTTGATACTAATGTTAATGATCTGATTGACCCGAGGTCAACACC
41321521 CTCATATATATGCACAACCTTAGTGTCAGATAAGAAAATACCTTATGAGTCAACTGAATTTGTGA
326 CTCATATATATGCACAACCTTAGTGTCAGATAAGAAAATACCTTATGAGTCAACTGAATTTGTGA
* *
41321586 TTAAAGTAACGAATCCTTTAGACCAGTATGTGTTAGTTGATAAAGTTTATAGAAACTGTCTTTTG
391 TTAAAGTAACGAATCCTTTAGACCAATATGTGTTAGTTGATAAAGTTTATAGAAACTATCTTTTG
41321651 ATGATTCAGGATTGCAACTTTCTTGCTA
456 ATGATTCAGGATTGCAACTTTCTTGCTA
* * *
41321679 ATTTCGAAGAATGCAAATTGAGAGATGGATCGTGCTTTAAATGTGGTTCTTATGACCATTTTCTT
1 ATTTCAAAGAATACAAATTGAGAGATGGATCATGCTTTAAATGTGGTTCTTATGACCATTTTCTT
*
41321744 CGAGACTACCTTGAAAGATCTGATAGGGAGAAAGCTCAGAACACTCGTTCGAGTAACACGGCTGG
66 CGAGACTACCTTGAAAGATCTGATAGGGAGAAAGCTCAGAACACTCGTTCGAGTAACACGGCTGC
41321809 GAGAGGGAGACCATCCAGAAATAGTGGAAATACGGGTAATAGTCGATGTGGAACGAAATATTCTA
131 GAGAGGGAGACCATCCAGAAATAGTGGAAATACGGGTAATAGTCGATGTGGAACGAAATATTCTA
* *
41321874 CGGTTAGATCTGAGGCTCGGGCATATGCAATTCGAGCTCGTGAGGAAGCTTCAGCACCTGATGTG
196 CGGTTAGATCTGAGGCTCGGGCATATGCAATTCGAGCTCGTGAGAAAGCTTCAGCACCTAATGTG
41321939 AATACTGGTACATTTTCTATCTTTGATACTAATGTTAATGATCTGATTGACCCGAGGTCAACACC
261 AATACTGGTACATTTTCTATCTTTGATACTAATGTTAATGATCTGATTGACCCGAGGTCAACACC
* *
41322004 GTCATATATATGCACGACCTTAGTGTCAGATAAGAAAATACCTTATGAGTCAACTGAATTTGTGA
326 CTCATATATATGCACAACCTTAGTGTCAGATAAGAAAATACCTTATGAGTCAACTGAATTTGTGA
* * * *
41322069 TTAAAGTAACGAATCCTTTGGGCCAATATGTGTTAGTTGGTAAAGTTTGTAGAAACTATCTTTTG
391 TTAAAGTAACGAATCCTTTAGACCAATATGTGTTAGTTGATAAAGTTTATAGAAACTATCTTTTG
*
41322134 ATGATTCAGGATTGCAACTTTCTTGCTG
456 ATGATTCAGGATTGCAACTTTCTTGCTA
41322162 ATTT
1 ATTT
41322166 GATGCTATTA
Statistics
Matches: 464, Mismatches: 23, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
483 464 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Consensus pattern (483 bp):
ATTTCAAAGAATACAAATTGAGAGATGGATCATGCTTTAAATGTGGTTCTTATGACCATTTTCTT
CGAGACTACCTTGAAAGATCTGATAGGGAGAAAGCTCAGAACACTCGTTCGAGTAACACGGCTGC
GAGAGGGAGACCATCCAGAAATAGTGGAAATACGGGTAATAGTCGATGTGGAACGAAATATTCTA
CGGTTAGATCTGAGGCTCGGGCATATGCAATTCGAGCTCGTGAGAAAGCTTCAGCACCTAATGTG
AATACTGGTACATTTTCTATCTTTGATACTAATGTTAATGATCTGATTGACCCGAGGTCAACACC
CTCATATATATGCACAACCTTAGTGTCAGATAAGAAAATACCTTATGAGTCAACTGAATTTGTGA
TTAAAGTAACGAATCCTTTAGACCAATATGTGTTAGTTGATAAAGTTTATAGAAACTATCTTTTG
ATGATTCAGGATTGCAACTTTCTTGCTA
Found at i:41330196 original size:14 final size:14
Alignment explanation
Indices: 41330179--41330211 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
41330169 TAAATATTGC
*
41330179 CCATTAAAAATCAT
1 CCATGAAAAATCAT
41330193 CCATGAAAAATCAT
1 CCATGAAAAATCAT
41330207 CCATG
1 CCATG
41330212 CATCGTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.24
Consensus pattern (14 bp):
CCATGAAAAATCAT
Found at i:41348553 original size:17 final size:17
Alignment explanation
Indices: 41348531--41348563 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41348521 ATGAATGAAA
41348531 AAATGCTAGGGAAATTG
1 AAATGCTAGGGAAATTG
*
41348548 AAATGCTATGGAAATT
1 AAATGCTAGGGAAATT
41348564 CTCAAAGAGT
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:0.42, C:0.06, G:0.24, T:0.27
Consensus pattern (17 bp):
AAATGCTAGGGAAATTG
Found at i:41351035 original size:19 final size:19
Alignment explanation
Indices: 41351002--41351046 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
41350992 TTGTTTTTAC
* *
41351002 TTTTCATTTGCATATTTTT
1 TTTTCATTTGCATATGTGT
**
41351021 TTTTCATTTTTATATGTGT
1 TTTTCATTTGCATATGTGT
41351040 TTTTCAT
1 TTTTCAT
41351047 GCATTTATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.16, C:0.09, G:0.07, T:0.69
Consensus pattern (19 bp):
TTTTCATTTGCATATGTGT
Found at i:41354232 original size:20 final size:21
Alignment explanation
Indices: 41354209--41354254 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
41354199 CATAACAAGA
*
41354209 GCACCGAA-GTGCAAACAGGG
1 GCACCGAATGTACAAACAGGG
* *
41354229 GCA-CAAATGTACAAATAGGG
1 GCACCGAATGTACAAACAGGG
41354249 GCACCG
1 GCACCG
41354255 TAGAATGAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
19 3 0.15
20 16 0.80
21 1 0.05
ACGTcount: A:0.37, C:0.24, G:0.30, T:0.09
Consensus pattern (21 bp):
GCACCGAATGTACAAACAGGG
Found at i:41358575 original size:20 final size:20
Alignment explanation
Indices: 41358550--41358594 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
41358540 TAAATACACA
*
41358550 TAATTAAAATT-AGACATAAT
1 TAATT-AAATTAAGACACAAT
*
41358570 TAATTAAGTTAAGACACAAT
1 TAATTAAATTAAGACACAAT
41358590 TAATT
1 TAATT
41358595 CGGTTGGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (20 bp):
TAATTAAATTAAGACACAAT
Found at i:41360769 original size:14 final size:16
Alignment explanation
Indices: 41360750--41360856 Score: 57
Period size: 18 Copynumber: 6.7 Consensus size: 16
41360740 TTCTTTTTCA
41360750 ATTTTC-TTTTCT-TC
1 ATTTTCTTTTTCTCTC
41360764 ATTTTCTTTTTCTCTC
1 ATTTTCTTTTTCTCTC
41360780 ATTTT-TTTGGTT-TCT-
1 ATTTTCTTT--TTCTCTC
*
41360795 -TTTTCTTTTTCAATTTC
1 ATTTTCTTTTTC--TCTC
* *
41360812 TTTTTCTTTTTCACTTTC
1 ATTTTCTTTTT--CTCTC
*
41360830 TTTTTCTTTTTCT-TC
1 ATTTTCTTTTTCTCTC
*
41360845 TTTTTCATTTTT
1 ATTTTC-TTTTT
41360857 ATTACAATGT
Statistics
Matches: 79, Mismatches: 1, Indels: 24
0.76 0.01 0.23
Matches are distributed among these distances:
13 2 0.03
14 10 0.13
15 20 0.25
16 19 0.24
17 2 0.03
18 25 0.32
20 1 0.01
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.74
Consensus pattern (16 bp):
ATTTTCTTTTTCTCTC
Found at i:41360776 original size:6 final size:6
Alignment explanation
Indices: 41360739--41360843 Score: 70
Period size: 6 Copynumber: 17.0 Consensus size: 6
41360729 TGAATCTCAA
* * * **
41360739 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTCT CATT-TT TTTGGT
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCT-T -TTTCTT TTTCTT
** **
41360791 T-TCTT TTTCTT TTTCAA TTTCTT TTTCTT TTTCAC TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
41360838 TTTCTT
1 TTTCTT
41360844 CTTTTTCATT
Statistics
Matches: 75, Mismatches: 18, Indels: 12
0.71 0.17 0.11
Matches are distributed among these distances:
5 5 0.07
6 54 0.72
7 11 0.15
8 5 0.07
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.73
Consensus pattern (6 bp):
TTTCTT
Found at i:41360803 original size:18 final size:18
Alignment explanation
Indices: 41360790--41360841 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
41360780 ATTTTTTTGG
41360790 TTTCTTTTTCTTTTTCAA
1 TTTCTTTTTCTTTTTCAA
*
41360808 TTTCTTTTTCTTTTTCAC
1 TTTCTTTTTCTTTTTCAA
41360826 TTTCTTTTTCTTTTTC
1 TTTCTTTTTCTTTTTC
41360842 TTCTTTTTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTCTTTTTCTTTTTCAA
Found at i:41360855 original size:6 final size:6
Alignment explanation
Indices: 41360790--41360843 Score: 72
Period size: 6 Copynumber: 9.0 Consensus size: 6
41360780 ATTTTTTTGG
** **
41360790 TTTCTT TTTCTT TTTCAA TTTCTT TTTCTT TTTCAC TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
41360838 TTTCTT
1 TTTCTT
41360844 CTTTTTCATT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:41362986 original size:20 final size:20
Alignment explanation
Indices: 41362961--41363005 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
41362951 TAAATACACA
41362961 TAATTAAAATT-AGACACAAT
1 TAATT-AAATTAAGACACAAT
*
41362981 TAATTAAGTTAAGACACAAT
1 TAATTAAATTAAGACACAAT
41363001 TAATT
1 TAATT
41363006 CGATTGGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (20 bp):
TAATTAAATTAAGACACAAT
Found at i:41365385 original size:15 final size:15
Alignment explanation
Indices: 41365367--41365408 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
41365357 AGTTTCATTA
*
41365367 TCTACAGTTTCACAG
1 TCTATAGTTTCACAG
41365382 TCTATAGTTTCACAG
1 TCTATAGTTTCACAG
*
41365397 CCTATAGTTTCA
1 TCTATAGTTTCA
41365409 ATATATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (15 bp):
TCTATAGTTTCACAG
Found at i:41370262 original size:30 final size:30
Alignment explanation
Indices: 41370227--41370287 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
41370217 ATTATATAAG
*
41370227 TAAGATGATTTTATATGTGTATGAAATTGA
1 TAAGATGATTTTATATGCGTATGAAATTGA
*
41370257 TAAGATGATTTTATATGCGTATGAGATTGA
1 TAAGATGATTTTATATGCGTATGAAATTGA
41370287 T
1 T
41370288 TAAATTTGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.02, G:0.21, T:0.43
Consensus pattern (30 bp):
TAAGATGATTTTATATGCGTATGAAATTGA
Found at i:41373925 original size:20 final size:19
Alignment explanation
Indices: 41373875--41373926 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 19
41373865 AATAGTTCTG
*
41373875 TCTCTTGATAAACAGTTGTA
1 TCTCTTG-TGAACAGTTGTA
*
41373895 TGT-TT-TGAACAGTTGTA
1 TCTCTTGTGAACAGTTGTA
41373912 TCTCTTGGTGAACAG
1 TCTCTT-GTGAACAG
41373927 ATTCATTGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 13 0.50
18 2 0.08
19 2 0.08
20 9 0.35
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.40
Consensus pattern (19 bp):
TCTCTTGTGAACAGTTGTA
Found at i:41374196 original size:42 final size:44
Alignment explanation
Indices: 41374120--41374205 Score: 131
Period size: 42 Copynumber: 2.0 Consensus size: 44
41374110 CAAACAAAAA
41374120 CGCCGCTAAAGAACATGGTCTTTAGCGACA-TTTT-TTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGACATTTTTGTTTCTAAG
* * *
41374162 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTGTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGACATTTTTGTTTCTAAG
41374206 ATACAAAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
42 27 0.69
43 4 0.10
44 8 0.21
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (44 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGACATTTTTGTTTCTAAG
Found at i:41374558 original size:21 final size:21
Alignment explanation
Indices: 41374529--41374581 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
41374519 CTCTGCTCTG
* *
41374529 CTTCTCTCGCTACAGCCTCCA
1 CTTCCCTCGCTACAGCCGCCA
* * **
41374550 CTTCCCTCGTTGCAGCCGCTG
1 CTTCCCTCGCTACAGCCGCCA
41374571 CTTCCCTCGCT
1 CTTCCCTCGCT
41374582 TCCGCCTCTA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.08, C:0.47, G:0.15, T:0.30
Consensus pattern (21 bp):
CTTCCCTCGCTACAGCCGCCA
Found at i:41389677 original size:39 final size:39
Alignment explanation
Indices: 41389609--41389689 Score: 119
Period size: 39 Copynumber: 2.1 Consensus size: 39
41389599 CCTAACTCAT
*
41389609 AACCCCTAAATCCCCTTTAACCCTTAAAGCATAAACCCTA
1 AACCCCTAAATCCCC-TTAACCCCTAAAGCATAAACCCTA
*
41389649 AACCCCTAAATCTCCC-TAACCCCTAAAGCATAACCCCTA
1 AACCCCTAAATC-CCCTTAACCCCTAAAGCATAAACCCTA
41389688 AA
1 AA
41389690 AAATTTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 23 0.61
40 12 0.32
41 3 0.08
ACGTcount: A:0.38, C:0.40, G:0.02, T:0.20
Consensus pattern (39 bp):
AACCCCTAAATCCCCTTAACCCCTAAAGCATAAACCCTA
Found at i:41390780 original size:114 final size:112
Alignment explanation
Indices: 41390392--41390840 Score: 401
Period size: 114 Copynumber: 4.0 Consensus size: 112
41390382 TTATTAGCGG
* ** * * *
41390392 CCTGAGCATT--CGGCGCTTTTCTAAAAACACCGCTAAATCCCTGAAAGCACAGAAAACGATGAC
1 CCTGAGCATTAACGGCGCTTTT-TAAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGACGTC
* * * *
41390455 GTTGGGCTTAGTTTTTTTTGCGGCGCTATAC-CAAAAACGCAGCTAAATC
65 GTTGGGATTAG-GTTTTTTGCGGCGCT-TTCTCAAAAACGCCGCTAAATC
* * * *
41390504 CCTGAGCATTAGCGGCGCTTCTCTAGAAACGCCGCTAAATTCCCGAAAAGCTCAG-AAACG-CTG
1 CCTGAGCATTAACGGCGCTT-TTTAAAAACGCCGCTAAA-TCCCCAAAAGCTCAGAAAACGAC-G
* * * * *
41390567 TCGTT-GTACTTAGGTTTTTTGCGGTGCTTTTTCGAAAACGCCGCTAAAGC
63 TCGTTGGGA-TTAGGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAATC
* * * * * * * * *
41390617 CCTAAGAATTAACGACGCTTTAGTAAAAAAGCCACT-AATCACTCGAAAGCTCAGAAAAACGGCG
1 CCTGAGCATTAACGGCGCTTT-TTAAAAACGCCGCTAAATC-CCCAAAAGCTCAG-AAAACGACG
* *
41390681 TCGTTGGGATTAGGCTTTTTGCGGCGCTTGCTCAAAAACGCCGCTAAATC
63 TCGTTGGGATTAGGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAATC
* * * *
41390731 CCTGAGCATTAACGGCGCTTTATTAGAAACGCCGCTAAATCCCCAAAAGCTCGGCAATCGACGTC
1 CCTGAGCATTAACGGCGCTTT-TTAAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGACGTC
* **
41390796 GTTCGGATTAGGTTTTTTGAAGCGCTTTCT-ATAAAACGCCGCTAA
65 GTTGGGATTAGGTTTTTTGCGGCGCTTTCTCA-AAAACGCCGCTAA
41390841 TTCTTATCCT
Statistics
Matches: 269, Mismatches: 53, Indels: 29
0.77 0.15 0.08
Matches are distributed among these distances:
111 2 0.01
112 25 0.09
113 101 0.38
114 121 0.45
115 20 0.07
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (112 bp):
CCTGAGCATTAACGGCGCTTTTTAAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGACGTCG
TTGGGATTAGGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAATC
Found at i:41393690 original size:15 final size:15
Alignment explanation
Indices: 41393666--41393698 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
41393656 CAGGTCTTTC
41393666 TTTCTTTTCTATG-T
1 TTTCTTTTCTATGAT
41393680 TTTCATTTTCTATGAT
1 TTTC-TTTTCTATGAT
41393696 TTT
1 TTT
41393699 TTCAATTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 9 0.53
16 4 0.24
ACGTcount: A:0.12, C:0.12, G:0.06, T:0.70
Consensus pattern (15 bp):
TTTCTTTTCTATGAT
Found at i:41404973 original size:13 final size:13
Alignment explanation
Indices: 41404955--41405017 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
41404945 TCTTCATTGC
41404955 TTTTGAAAAGTAT
1 TTTTGAAAAGTAT
*
41404968 TTTTGAAAAGTGT
1 TTTTGAAAAGTAT
* *
41404981 TGTGGAAAAGTGA-
1 TTTTGAAAAGT-AT
* **
41404994 TTTTGAGAAGTGC
1 TTTTGAAAAGTAT
41405007 TTTTGAAAAGT
1 TTTTGAAAAGT
41405018 TTGGTTTAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.33, C:0.02, G:0.25, T:0.40
Consensus pattern (13 bp):
TTTTGAAAAGTAT
Found at i:41405014 original size:26 final size:26
Alignment explanation
Indices: 41404952--41405017 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 26
41404942 AGTTCTTCAT
41404952 TGCTTTTGAAAAGTATTTTTGAAAAG
1 TGCTTTTGAAAAGTATTTTTGAAAAG
* *
41404978 TG-TTGTGGAAAAGTGA-TTTTGAGAAG
1 TGCTT-TTGAAAAGT-ATTTTTGAAAAG
41405004 TGCTTTTGAAAAGT
1 TGCTTTTGAAAAGT
41405018 TTGGTTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 2 0.06
26 29 0.85
27 3 0.09
ACGTcount: A:0.32, C:0.03, G:0.26, T:0.39
Consensus pattern (26 bp):
TGCTTTTGAAAAGTATTTTTGAAAAG
Found at i:41413518 original size:13 final size:13
Alignment explanation
Indices: 41413500--41413541 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
41413490 AAGTACAGAA
41413500 TTCTCCTTGAGTT
1 TTCTCCTTGAGTT
**
41413513 TTCTCCAAGAGTT
1 TTCTCCTTGAGTT
*
41413526 CTCT-CTTGAGTT
1 TTCTCCTTGAGTT
41413538 TTCT
1 TTCT
41413542 TTAGAAGTTG
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.12, C:0.24, G:0.14, T:0.50
Consensus pattern (13 bp):
TTCTCCTTGAGTT
Found at i:41413550 original size:25 final size:24
Alignment explanation
Indices: 41413495--41413550 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
41413485 TGTTTAAGTA
41413495 CAGAA-TTCTCCTTGAGTTTTCTC
1 CAGAAGTTCTCCTTGAGTTTTCTC
*
41413518 CA-AGAGTTCTCTCTTGAGTTTTCTT
1 CAGA-AGTTCTC-CTTGAGTTTTCTC
*
41413543 TAGAAGTT
1 CAGAAGTT
41413551 GTTTTAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 1 0.04
23 3 0.11
24 5 0.19
25 17 0.63
26 1 0.04
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.45
Consensus pattern (24 bp):
CAGAAGTTCTCCTTGAGTTTTCTC
Found at i:41418745 original size:89 final size:90
Alignment explanation
Indices: 41418585--41418761 Score: 347
Period size: 89 Copynumber: 2.0 Consensus size: 90
41418575 AAAATTATTT
41418585 CAAGAATGAGGAAAAATCCCACTGGTTAAAAGAAAAATGAGAAAGAATGGAAATTAAAGAAGGTC
1 CAAGAATGAGGAAAAATCCCACTGGTTAAAAGAAAAATGAGAAAGAATGGAAATTAAAGAAGGTC
41418650 CCAAGTTCGAATCCCTTTCCTTGTC
66 CCAAGTTCGAATCCCTTTCCTTGTC
41418675 CAAGAATG-GGAAAAATCCCACTGGTTAAAAGAAAAATGAGAAAGAATGGAAATTAAAGAAGGTC
1 CAAGAATGAGGAAAAATCCCACTGGTTAAAAGAAAAATGAGAAAGAATGGAAATTAAAGAAGGTC
41418739 CCAAGTTCGAATCCCTTTCCTTG
66 CCAAGTTCGAATCCCTTTCCTTG
41418762 CGAAATAATT
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
89 79 0.91
90 8 0.09
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.21
Consensus pattern (90 bp):
CAAGAATGAGGAAAAATCCCACTGGTTAAAAGAAAAATGAGAAAGAATGGAAATTAAAGAAGGTC
CCAAGTTCGAATCCCTTTCCTTGTC
Found at i:41423834 original size:50 final size:50
Alignment explanation
Indices: 41423738--41423848 Score: 114
Period size: 50 Copynumber: 2.2 Consensus size: 50
41423728 CATGTATGCT
* * * * * *
41423738 TCATACGAGCTATGAATCGATATGCTCTCACAAGCTGGAAACTGGTAGGC
1 TCATACGAGCTAAGAATCGATAAGCTCTAACAACCTGCAAACTGGTAAGC
** * *
41423788 TCATACGAGCTAAGAATTTATAAGCTCTAACGACCTGCAAATTGGTAAGC
1 TCATACGAGCTAAGAATCGATAAGCTCTAACAACCTGCAAACTGGTAAGC
* *
41423838 TTATACAAGCT
1 TCATACGAGCT
41423849 GTGGTGTGTC
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (50 bp):
TCATACGAGCTAAGAATCGATAAGCTCTAACAACCTGCAAACTGGTAAGC
Found at i:41426934 original size:171 final size:170
Alignment explanation
Indices: 41426649--41426991 Score: 614
Period size: 171 Copynumber: 2.0 Consensus size: 170
41426639 TAAGGAATTA
*
41426649 AAAAATTTTATGGTTTGATTTTCACACTTTATTAAGAGTAACATTTATGTCATAGTTCAAATAAC
1 AAAAATTTTATGGTTTGATTTACACACTTTATTAAGAGTAACATTTATGTCATAGTTCAAATAAC
*
41426714 ATAGAAATTATTAAGATAATAAAACTTTATTTATACTAGAGTTTAGCATAATTAACAAAAATTCA
66 ATAGAAATTATTAAGATAATAAAACTTTATTTATACTAGAGTTTAGCATAATTAACAAAAAATCA
*
41426779 AATTTTTGAACAAAATATAACTTAATCATAATTATAAGAAT
131 AA-TTTTGAACAAAATATAACTTAATCAAAATTATAAGAAT
*
41426820 AAAAATTTTATGGTTTGATTTACACACTTTATTAAGAGTAACATTTATGTCATAGTTCAACTAAC
1 AAAAATTTTATGGTTTGATTTACACACTTTATTAAGAGTAACATTTATGTCATAGTTCAAATAAC
* * *
41426885 ATAGCAATTATTGAGATATTAAAACTTTATTTATACTAGAGTTTAGCATAATTAACAAAAAATCA
66 ATAGAAATTATTAAGATAATAAAACTTTATTTATACTAGAGTTTAGCATAATTAACAAAAAATCA
41426950 AATTTTGAACAAAATATAACTTAATCAAAATTATAAGAAT
131 AATTTTGAACAAAATATAACTTAATCAAAATTATAAGAAT
41426990 AA
1 AA
41426992 TGTATTCTAA
Statistics
Matches: 165, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
170 39 0.24
171 126 0.76
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.37
Consensus pattern (170 bp):
AAAAATTTTATGGTTTGATTTACACACTTTATTAAGAGTAACATTTATGTCATAGTTCAAATAAC
ATAGAAATTATTAAGATAATAAAACTTTATTTATACTAGAGTTTAGCATAATTAACAAAAAATCA
AATTTTGAACAAAATATAACTTAATCAAAATTATAAGAAT
Found at i:41429469 original size:29 final size:29
Alignment explanation
Indices: 41429437--41429600 Score: 168
Period size: 29 Copynumber: 5.7 Consensus size: 29
41429427 GGTCGTCACC
*
41429437 ATCCCTTTTCATAATCAATAGCCGAAGCT
1 ATCCCTTTTCATATTCAATAGCCGAAGCT
* *
41429466 ATCCCTTTTCATATTCGATAGTCGAAGCT
1 ATCCCTTTTCATATTCAATAGCCGAAGCT
* ** ** * *
41429495 ATCCCTCTTCATATTTGATAGTGGTCA-CC
1 ATCCCTTTTCATATTCAATAGCCG-AAGCT
* * *
41429524 ATCCCTTTTCATAATCAATATCTGAAGCT
1 ATCCCTTTTCATATTCAATAGCCGAAGCT
* *
41429553 ATCCCTTTTCATATTCGATACCCGAAGCT
1 ATCCCTTTTCATATTCAATAGCCGAAGCT
*
41429582 ATCCCTTTTCATACTCAAT
1 ATCCCTTTTCATATTCAAT
41429601 GATCGCCGAT
Statistics
Matches: 110, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
28 1 0.01
29 108 0.98
30 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.10, T:0.37
Consensus pattern (29 bp):
ATCCCTTTTCATATTCAATAGCCGAAGCT
Found at i:41429506 original size:58 final size:58
Alignment explanation
Indices: 41429437--41429600 Score: 188
Period size: 58 Copynumber: 2.8 Consensus size: 58
41429427 GGTCGTCACC
* * * *
41429437 ATCCCTTTTCATAATCAATAGCCGAAGCTATCCCTTTTCATATTCGATAGTC-GAAGCT
1 ATCCCTTTTCATATTCGATAGCCGAAGCTATCCCTTTTCATAATCAATA-TCTGAAGCT
* * ** * *
41429495 ATCCCTCTTCATATTTGATAGTGGTCA-CCATCCCTTTTCATAATCAATATCTGAAGCT
1 ATCCCTTTTCATATTCGATAGCCG-AAGCTATCCCTTTTCATAATCAATATCTGAAGCT
* *
41429553 ATCCCTTTTCATATTCGATACCCGAAGCTATCCCTTTTCATACTCAAT
1 ATCCCTTTTCATATTCGATAGCCGAAGCTATCCCTTTTCATAATCAAT
41429601 GATCGCCGAT
Statistics
Matches: 85, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
57 3 0.04
58 81 0.95
59 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.10, T:0.37
Consensus pattern (58 bp):
ATCCCTTTTCATATTCGATAGCCGAAGCTATCCCTTTTCATAATCAATATCTGAAGCT
Found at i:41429537 original size:87 final size:87
Alignment explanation
Indices: 41429431--41429594 Score: 283
Period size: 87 Copynumber: 1.9 Consensus size: 87
41429421 ATCGATGGTC
**
41429431 GTCACCATCCCTTTTCATAATCAATAGCCGAAGCTATCCCTTTTCATATTCGATAGTCGAAGCTA
1 GTCACCATCCCTTTTCATAATCAATAGCCGAAGCTATCCCTTTTCATATTCGATACCCGAAGCTA
41429496 TCCCTCTTCATATTTGATAGTG
66 TCCCTCTTCATATTTGATAGTG
* *
41429518 GTCACCATCCCTTTTCATAATCAATATCTGAAGCTATCCCTTTTCATATTCGATACCCGAAGCTA
1 GTCACCATCCCTTTTCATAATCAATAGCCGAAGCTATCCCTTTTCATATTCGATACCCGAAGCTA
*
41429583 TCCCTTTTCATA
66 TCCCTCTTCATA
41429595 CTCAATGATC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.26, C:0.28, G:0.10, T:0.36
Consensus pattern (87 bp):
GTCACCATCCCTTTTCATAATCAATAGCCGAAGCTATCCCTTTTCATATTCGATACCCGAAGCTA
TCCCTCTTCATATTTGATAGTG
Found at i:41430166 original size:21 final size:20
Alignment explanation
Indices: 41430138--41430181 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
41430128 GAATACTTTT
*
41430138 AATTATCAATCAACATTAAA
1 AATTATCAATCAACATAAAA
* *
41430158 AATTCATCATTTAACATAAAA
1 AATT-ATCAATCAACATAAAA
41430179 AAT
1 AAT
41430182 CACAAGATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.32
Consensus pattern (20 bp):
AATTATCAATCAACATAAAA
Found at i:41435325 original size:29 final size:29
Alignment explanation
Indices: 41435283--41435491 Score: 177
Period size: 29 Copynumber: 7.2 Consensus size: 29
41435273 ATTTGCTAAA
* *
41435283 CGATGGTTGTAACCATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * *
41435312 CGATGGTTGAAACCATCTCTTTTCATTAAT
1 CGATGGTCGAAACCATCCCTTTTCA-TATT
* *
41435342 CGATGGTC-ATCACCATCCCTTTTCATAAT
1 CGATGGTCGA-AACCATCCCTTTTCATATT
* * * *
41435371 CGATAGTCGAAGCTATCCCTTTTTATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * * * *
41435400 CGATAGCCGAAGCTATCCCTCTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* ** *
41435429 AGATGGTCGTCACCATCCCTTTTCATAAT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * * *
41435458 CGATAGCCGAAGCTATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
41435487 CGATG
1 CGATG
41435492 ATCACCGATA
Statistics
Matches: 144, Mismatches: 33, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
29 120 0.83
30 24 0.17
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (29 bp):
CGATGGTCGAAACCATCCCTTTTCATATT
Found at i:41439166 original size:15 final size:16
Alignment explanation
Indices: 41439139--41439168 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41439129 TAATACAATT
41439139 AATATATATTATATAA
1 AATATATATTATATAA
41439155 AATATA-ATTATATA
1 AATATATATTATATA
41439169 TTAGTTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATATTATATAA
Found at i:41447086 original size:27 final size:26
Alignment explanation
Indices: 41447043--41447280 Score: 264
Period size: 27 Copynumber: 8.8 Consensus size: 26
41447033 TGCAATTTGT
41447043 GGGTAAAATGA-CTGAAATACCCTCGAA
1 GGGTAAAATGATC-GAAATACCC-CGAA
41447070 GGGTAAAATGATCGAAATACCCCCGAA
1 GGGTAAAATGATCGAAATA-CCCCGAA
* * *
41447097 CGGTAAAATAATCGAAATACCCTCAAA
1 GGGTAAAATGATCGAAATACCC-CGAA
* *
41447124 GGATAAAATGATTGAAATACCCCTGAA
1 GGGTAAAATGATCGAAATACCCC-GAA
* * *
41447151 GGGTAAAATAACCGAAATATCCCCAAA
1 GGGTAAAATGATCGAAATA-CCCCGAA
* * *
41447178 AGGTAAAATGACCAAAATACCCCTGAA
1 GGGTAAAATGATCGAAATACCCC-GAA
*
41447205 GGGTAAAATGACCGAAATACCCCCGAA
1 GGGTAAAATGATCGAAATA-CCCCGAA
41447232 GGGTAAAATGATCGAAATAACCCCGAA
1 GGGTAAAATGATCGAAAT-ACCCCGAA
41447259 GGGTAAAATGAAT-GAAATACCC
1 GGGTAAAATG-ATCGAAATACCC
41447281 TCATAGGGTA
Statistics
Matches: 182, Mismatches: 20, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
26 12 0.07
27 155 0.85
28 15 0.08
ACGTcount: A:0.45, C:0.20, G:0.19, T:0.16
Consensus pattern (26 bp):
GGGTAAAATGATCGAAATACCCCGAA
Found at i:41447114 original size:54 final size:54
Alignment explanation
Indices: 41447043--41447296 Score: 305
Period size: 54 Copynumber: 4.7 Consensus size: 54
41447033 TGCAATTTGT
* * *
41447043 GGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCCCGAA
1 GGGTAAAATAACCGAAATACCCTCAAAGGGTAAAATGATCGAAATACCCCCGAA
* * * * *
41447097 CGGTAAAATAATCGAAATACCCTCAAAGGATAAAATGATTGAAATACCCCTGAA
1 GGGTAAAATAACCGAAATACCCTCAAAGGGTAAAATGATCGAAATACCCCCGAA
* * * *
41447151 GGGTAAAATAACCGAAATATCCC-CAAAAGGTAAAATGACCAAAATACCCCTGAA
1 GGGTAAAATAACCGAAATA-CCCTCAAAGGGTAAAATGATCGAAATACCCCCGAA
* * * *
41447205 GGGTAAAATGACCGAAATACCCCCGAAGGGTAAAATGATCGAAATAACCCCGAA
1 GGGTAAAATAACCGAAATACCCTCAAAGGGTAAAATGATCGAAATACCCCCGAA
* * *
41447259 GGGTAAAATGAA-TGAAATACCCTCATAGGGTAATATGA
1 GGGTAAAAT-AACCGAAATACCCTCAAAGGGTAAAATGA
41447297 CTACTATACC
Statistics
Matches: 169, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
53 3 0.02
54 162 0.96
55 4 0.02
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.17
Consensus pattern (54 bp):
GGGTAAAATAACCGAAATACCCTCAAAGGGTAAAATGATCGAAATACCCCCGAA
Found at i:41447183 original size:81 final size:81
Alignment explanation
Indices: 41447046--41447298 Score: 296
Period size: 81 Copynumber: 3.1 Consensus size: 81
41447036 AATTTGTGGG
* *
41447046 TAAAATGACTGAAATA-CCCTCGAAGGGTAAAATGATCGAAATACCCCCGAACGGTAAAATAATC
1 TAAAATGACTGAAATACCCCT-GAAGGGTAAAATGATCGAAATAACCCCGAAAGGTAAAATAATC
41447110 GAAATACCCTCAAAGGA
65 GAAATACCCTCAAAGGA
* * * * * * * *
41447127 TAAAATGATTGAAATACCCCTGAAGGGTAAAATAACCGAAATATCCCCAAAAGGTAAAATGACCA
1 TAAAATGACTGAAATACCCCTGAAGGGTAAAATGATCGAAATAACCCCGAAAGGTAAAATAATCG
* *
41447192 AAATACCC-CTGAAGGG
66 AAATACCCTC-AAAGGA
* * *
41447208 TAAAATGACCGAAATACCCCCGAAGGGTAAAATGATCGAAATAACCCCGAAGGGTAAAATGAAT-
1 TAAAATGACTGAAATACCCCTGAAGGGTAAAATGATCGAAATAACCCCGAAAGGTAAAAT-AATC
* *
41447272 GAAATACCCTCATAGGG
65 GAAATACCCTCAAAGGA
*
41447289 TAATATGACT
1 TAAAATGACT
41447299 ACTATACCCT
Statistics
Matches: 142, Mismatches: 26, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
80 1 0.01
81 135 0.95
82 6 0.04
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (81 bp):
TAAAATGACTGAAATACCCCTGAAGGGTAAAATGATCGAAATAACCCCGAAAGGTAAAATAATCG
AAATACCCTCAAAGGA
Found at i:41447669 original size:30 final size:31
Alignment explanation
Indices: 41447629--41447689 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
41447619 ACTGAATTGT
* *
41447629 ACTATTTACTGTATTGGGCTAAGGCCTACAC
1 ACTATTTACTGTAATGGGCTAAGGCCCACAC
41447660 ACTA-TTACTGTAATGGGCTAAGGCCCACAC
1 ACTATTTACTGTAATGGGCTAAGGCCCACAC
41447690 TGTACTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (31 bp):
ACTATTTACTGTAATGGGCTAAGGCCCACAC
Done.