Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold226
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1071921
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.31
Warning! 95108 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:5680 original size:49 final size:48
Alignment explanation
Indices: 5622--5719 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 48
5612 CGCTTTGAAT
5622 ACAGATCGGACTTTAATTTTTGCAATTTATATTCGCACTCCCATAAGG
1 ACAGATCGGACTTTAATTTTTGCAATTTATATTCGCACTCCCATAAGG
*
5670 ANCAGATCGGACTTTAATTTTTGCAATTTATATTCGCCCTCCCATAAGG
1 A-CAGATCGGACTTTAATTTTTGCAATTTATATTCGCACTCCCATAAGG
5719 A
1 A
5720 TGCTTTGTGC
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 1 0.02
49 47 0.98
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.35
Consensus pattern (48 bp):
ACAGATCGGACTTTAATTTTTGCAATTTATATTCGCACTCCCATAAGG
Found at i:5806 original size:4 final size:4
Alignment explanation
Indices: 5793--5854 Score: 72
Period size: 4 Copynumber: 15.8 Consensus size: 4
5783 AAAGTTTACA
* * * * *
5793 GACG GACA GACA GACG GACA GACG GACA GACG GACG GACG GACG GACA
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
5841 GACG GAC- GACG GAC
1 GACG GACG GACG GAC
5855 AAAAAGTGAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
3 3 0.06
4 46 0.94
ACGTcount: A:0.34, C:0.26, G:0.40, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:5815 original size:20 final size:20
Alignment explanation
Indices: 5790--5848 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
5780 TAAAAAGTTT
*
5790 ACAGACGGACAGACAGACGG
1 ACAGACGGACAGACGGACGG
5810 ACAGACGGACAGACGGACGG
1 ACAGACGGACAGACGGACGG
*
5830 ACGGACGGACAGACGGACG
1 ACAGACGGACAGACGGACG
5849 ACGGACAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.36, C:0.25, G:0.39, T:0.00
Consensus pattern (20 bp):
ACAGACGGACAGACGGACGG
Found at i:10988 original size:7 final size:7
Alignment explanation
Indices: 10976--11042 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
10966 GAGAAGGATC
10976 ATTCGAG
1 ATTCGAG
10983 ATTCGAG
1 ATTCGAG
*
10990 ATTCGAA
1 ATTCGAG
*
10997 ATACGAG
1 ATTCGAG
*
11004 ATTCGAA
1 ATTCGAG
*
11011 ATACGAG
1 ATTCGAG
11018 ATTCGAG
1 ATTCGAG
*
11025 ATTCGAA
1 ATTCGAG
11032 ATTCGAG
1 ATTCGAG
11039 ATTC
1 ATTC
11043 AATATCTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:37641 original size:55 final size:56
Alignment explanation
Indices: 37530--37642 Score: 133
Period size: 55 Copynumber: 2.0 Consensus size: 56
37520 GGCCGGAATG
* * * * *
37530 TAAAAAAGGGGGAAAATCCACTATATAGTAGGTTTTCCGTGGGGGTAATCTGGCTA
1 TAAAAAAGGGGGAAAACCCACTATATAGTAGGCTTTCCCTGGGGGAAAACTGGCTA
*
37586 TAAAAAA-GGGGAAAGCCCACTATATAGTCA-GCTTTCCCTGGGGGAAAAACT-GCTA
1 TAAAAAAGGGGGAAAACCCACTATATAGT-AGGCTTTCCCTGGGGG-AAAACTGGCTA
37641 TA
1 TA
37643 TAGCCATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
55 37 0.76
56 12 0.24
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.24
Consensus pattern (56 bp):
TAAAAAAGGGGGAAAACCCACTATATAGTAGGCTTTCCCTGGGGGAAAACTGGCTA
Found at i:37642 original size:33 final size:32
Alignment explanation
Indices: 37605--37696 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 32
37595 GGAAAGCCCA
* *
37605 CTATATAGTCAGCTTTCCCTGGGGGAAAAACTG
1 CTATATAGCCA-CTTTCCCGGGGGGAAAAACTG
* * *
37638 CTATATAGCCATTTTTCCGGGGGGAAGAACTG
1 CTATATAGCCACTTTCCCGGGGGGAAAAACTG
* *
37670 CTATATAGCCATTTTTCCGGGGGGAAA
1 CTATATAGCCACTTTCCCGGGGGGAAA
37697 GATGGCTAGG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 43 0.81
33 10 0.19
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (32 bp):
CTATATAGCCACTTTCCCGGGGGGAAAAACTG
Found at i:37669 original size:32 final size:32
Alignment explanation
Indices: 37625--37696 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
37615 AGCTTTCCCT
37625 GGGGGAAAAACTGCTATATAGCCATTTTTCCG
1 GGGGGAAAAACTGCTATATAGCCATTTTTCCG
*
37657 GGGGGAAGAACTGCTATATAGCCATTTTTCCG
1 GGGGGAAAAACTGCTATATAGCCATTTTTCCG
37689 GGGGGAAA
1 GGGGGAAA
37697 GATGGCTAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.25
Consensus pattern (32 bp):
GGGGGAAAAACTGCTATATAGCCATTTTTCCG
Found at i:43131 original size:15 final size:15
Alignment explanation
Indices: 43111--43140 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43101 AGTGGGGCCT
*
43111 CAGATATCCGGACGC
1 CAGATAACCGGACGC
43126 CAGATAACCGGACGC
1 CAGATAACCGGACGC
43141 TTCAGTTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.33, G:0.27, T:0.10
Consensus pattern (15 bp):
CAGATAACCGGACGC
Found at i:44474 original size:11 final size:11
Alignment explanation
Indices: 44448--44559 Score: 66
Period size: 11 Copynumber: 10.1 Consensus size: 11
44438 ACTAAACCCT
44448 GGGTTTACTTTTG
1 GGGTTTAC--TTG
44461 GGGTTTACTTG
1 GGGTTTACTTG
44472 GGGTTTACTCT-
1 GGGTTTACT-TG
*
44483 GGGTTTACTTT
1 GGGTTTACTTG
** ** * *
44494 TTG-AAAATTT
1 GGGTTTACTTG
** *
44504 GGGTCCACTCG
1 GGGTTTACTTG
*
44515 GGGTTTACTTT
1 GGGTTTACTTG
*
44526 GGGTTTACTCG
1 GGGTTTACTTG
*
44537 GGGTTTACTTT
1 GGGTTTACTTG
44548 GGGTTTACTTG
1 GGGTTTACTTG
44559 G
1 G
44560 AAATTGCTTT
Statistics
Matches: 75, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
10 6 0.08
11 60 0.80
12 1 0.01
13 8 0.11
ACGTcount: A:0.12, C:0.12, G:0.30, T:0.46
Consensus pattern (11 bp):
GGGTTTACTTG
Found at i:44489 original size:22 final size:22
Alignment explanation
Indices: 44448--44559 Score: 100
Period size: 22 Copynumber: 5.0 Consensus size: 22
44438 ACTAAACCCT
44448 GGGTTTACTTTTGGGGTTTACTTG
1 GGGTTTAC-TTT-GGGTTTACTTG
* *
44472 GGGTTTACTCTGGGTTTACTTT
1 GGGTTTACTTTGGGTTTACTTG
** ** * ** *
44494 TTG-AAAATTTGGGTCCACTCG
1 GGGTTTACTTTGGGTTTACTTG
*
44515 GGGTTTACTTTGGGTTTACTCG
1 GGGTTTACTTTGGGTTTACTTG
44537 GGGTTTACTTTGGGTTTACTTG
1 GGGTTTACTTTGGGTTTACTTG
44559 G
1 G
44560 AAATTGCTTT
Statistics
Matches: 67, Mismatches: 20, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
21 11 0.16
22 46 0.69
23 2 0.03
24 8 0.12
ACGTcount: A:0.12, C:0.12, G:0.30, T:0.46
Consensus pattern (22 bp):
GGGTTTACTTTGGGTTTACTTG
Found at i:44741 original size:11 final size:11
Alignment explanation
Indices: 44723--44764 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
44713 CTCTGTGTCC
44723 ACTCTGGGTTT
1 ACTCTGGGTTT
*
44734 ACTTTGGGTTT
1 ACTCTGGGTTT
44745 ACTCTGGGTTT
1 ACTCTGGGTTT
*
44756 ACTCAGGGT
1 ACTCTGGGT
44765 CCACTCTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.12, C:0.17, G:0.29, T:0.43
Consensus pattern (11 bp):
ACTCTGGGTTT
Found at i:44770 original size:22 final size:22
Alignment explanation
Indices: 44719--44771 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
44709 TACTCTCTGT
**
44719 GTCCACTCTGGGTTTACTTTGG
1 GTCCACTCTGGGTTTACTCAGG
**
44741 GTTTACTCTGGGTTTACTCAGG
1 GTCCACTCTGGGTTTACTCAGG
44763 GTCCACTCT
1 GTCCACTCT
44772 AGTAAACCCG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.40
Consensus pattern (22 bp):
GTCCACTCTGGGTTTACTCAGG
Found at i:80294 original size:14 final size:14
Alignment explanation
Indices: 80277--80312 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
80267 TAAAATTTGA
*
80277 TACTAGTAACTGGC
1 TACTAGAAACTGGC
80291 TACTAGAAACTGGC
1 TACTAGAAACTGGC
*
80305 TACGAGAA
1 TACTAGAA
80313 GTAAGAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (14 bp):
TACTAGAAACTGGC
Found at i:80377 original size:37 final size:37
Alignment explanation
Indices: 80292--80370 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
80282 GTAACTGGCT
*
80292 ACTAGAAACTGGCTACGAGAAGTAAGAAAAGCTAGCC
1 ACTAGAAACTAGCTACGAGAAGTAAGAAAAGCTAGCC
* *
80329 GCTAGAAACTAGCTACGAGAAGTAAGAAAATCTAGCC
1 ACTAGAAACTAGCTACGAGAAGTAAGAAAAGCTAGCC
80366 ACTAG
1 ACTAG
80371 TCACTAGTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (37 bp):
ACTAGAAACTAGCTACGAGAAGTAAGAAAAGCTAGCC
Found at i:82166 original size:2 final size:2
Alignment explanation
Indices: 82161--82214 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
82151 ATTTTTCAGT
*
82161 TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
82203 TC TC TC TC TC TC
1 TC TC TC TC TC TC
82215 ATTAGATTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:97407 original size:3 final size:3
Alignment explanation
Indices: 97401--97438 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
97391 TTGTTGTTGT
97401 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
97439 TACCTTTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:100853 original size:14 final size:14
Alignment explanation
Indices: 100834--100866 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
100824 GGTAAAGTTA
100834 GCTACTAGTAACTG
1 GCTACTAGTAACTG
100848 GCTACTAGTAACTG
1 GCTACTAGTAACTG
100862 GCTAC
1 GCTAC
100867 GAGAAGTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (14 bp):
GCTACTAGTAACTG
Found at i:100900 original size:37 final size:37
Alignment explanation
Indices: 100850--100940 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 37
100840 AGTAACTGGC
*
100850 TACTAGTAACTGGCTACGAGAAGT-AAGAAAAGATAGT
1 TACTAGTAACTGGCTACGAG-AGTAAAGAAAAGATAGG
* * * *
100887 TACTAGTAACTGGCTACGAGATTAAATAAAAGTTGGG
1 TACTAGTAACTGGCTACGAGAGTAAAGAAAAGATAGG
100924 TACTAGTAACTGGCTAC
1 TACTAGTAACTGGCTAC
100941 TAGTAACTGG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 2 0.04
37 46 0.96
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.25
Consensus pattern (37 bp):
TACTAGTAACTGGCTACGAGAGTAAAGAAAAGATAGG
Found at i:100942 original size:51 final size:51
Alignment explanation
Indices: 100887--100991 Score: 149
Period size: 51 Copynumber: 2.1 Consensus size: 51
100877 AAAAGATAGT
* * * * *
100887 TACTAGTAACTGGCTACGAG-ATTAAATAAAAGTTGGGTACTAGTAACTGGC
1 TACTAGTAACTGGCTACGAGAAGT-AAGAAAAGCTAGCTACTAGTAACTGGC
100938 TACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTAGTAACTGGC
1 TACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTAGTAACTGGC
100989 TAC
1 TAC
100992 GAGAAGTAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
51 46 0.96
52 2 0.04
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (51 bp):
TACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTAGTAACTGGC
Found at i:100943 original size:14 final size:14
Alignment explanation
Indices: 100924--100954 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
100914 AAAAGTTGGG
100924 TACTAGTAACTGGC
1 TACTAGTAACTGGC
100938 TACTAGTAACTGGC
1 TACTAGTAACTGGC
100952 TAC
1 TAC
100955 GAGAAGTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (14 bp):
TACTAGTAACTGGC
Found at i:101006 original size:88 final size:88
Alignment explanation
Indices: 100836--101006 Score: 290
Period size: 88 Copynumber: 1.9 Consensus size: 88
100826 TAAAGTTAGC
*
100836 TACTAGTAACTGGCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGATAGTTACTAGTAACTGGC
1 TACTAGTAACTGGCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGATAGCTACTAGTAACTGGC
* *
100901 TACGAGATTAAATAAAAGTTGGG
66 TACGAGAGTAAAGAAAAGTTGGG
*
100924 TACTAGTAACTGGCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTAGTAACTGGC
1 TACTAGTAACTGGCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGATAGCTACTAGTAACTGGC
100989 TACGAGAAGT-AAGAAAAG
66 TACGAG-AGTAAAGAAAAG
101007 CTAGCTACAT
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
88 76 0.97
89 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (88 bp):
TACTAGTAACTGGCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGATAGCTACTAGTAACTGGC
TACGAGAGTAAAGAAAAGTTGGG
Found at i:101047 original size:43 final size:37
Alignment explanation
Indices: 100936--101014 Score: 158
Period size: 37 Copynumber: 2.1 Consensus size: 37
100926 CTAGTAACTG
100936 GCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTA
1 GCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTA
100973 GCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTA
1 GCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTA
101010 GCTAC
1 GCTAC
101015 ATGTATTAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (37 bp):
GCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTA
Found at i:101440 original size:177 final size:176
Alignment explanation
Indices: 101144--101542 Score: 618
Period size: 177 Copynumber: 2.3 Consensus size: 176
101134 TCACTGTCAA
* * * *
101144 TTGTCAATATATCTCAAGTAGCTGTATATATAAACTAAAGATATATGCCCGACTTGCTAAAATCA
1 TTGTCAATATATCTCAAGTAGCTGTATATATAGATTGAAGATATATGCCCGACATGCTAAAATCA
* *
101209 ACATTCTGTCAAGTCATCCACATAATATTACGACACAATTACTCAGATATCTCTCTTTATGTAGT
66 ACATTCTGTCAAGTCATCCACATAATATAACGACACAATCACTCAGATATCTCTCTTTATGTAGT
* *
101274 CAGCTACTTGTGCGTTTCGTTCCAAATATCTTTATGTTTTGGAGGTT
131 CAGCTACTTGTGCATTTCGTTACAAATATCTTTAT-TTTTGGAGGTT
* * * *
101321 TTGTCAATATATCTCAAGTAGTTGTTTATATAGATTGAAGATATATGCCGGACATGCTAATATCA
1 TTGTCAATATATCTCAAGTAGCTGTATATATAGATTGAAGATATATGCCCGACATGCTAAAATCA
* *
101386 ACATTCTGTGAAGTCATCCACTTAATATAACGACACAATCACTCAGATATCTCTCTTTATGTAGT
66 ACATTCTGTCAAGTCATCCACATAATATAACGACACAATCACTCAGATATCTCTCTTTATGTAGT
* **
101451 CAGCTACTTGTGCATTTCGTTACAAATATCTTTATTTTTTGCTGTT
131 CAGCTACTTGTGCATTTCGTTACAAATATCTTTATTTTTGGAGGTT
* *
101497 GTGTCTATATATCTCAAGTAGCTGTATATATAGATTGAAGATATAT
1 TTGTCAATATATCTCAAGTAGCTGTATATATAGATTGAAGATATAT
101543 AGTGTTGTGC
Statistics
Matches: 201, Mismatches: 21, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
176 50 0.25
177 151 0.75
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (176 bp):
TTGTCAATATATCTCAAGTAGCTGTATATATAGATTGAAGATATATGCCCGACATGCTAAAATCA
ACATTCTGTCAAGTCATCCACATAATATAACGACACAATCACTCAGATATCTCTCTTTATGTAGT
CAGCTACTTGTGCATTTCGTTACAAATATCTTTATTTTTGGAGGTT
Found at i:102391 original size:2 final size:2
Alignment explanation
Indices: 102384--102426 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
102374 CCCCCTTCCC
*
102384 AG AG AG AG AG AG AG AG AG AG AT AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
102426 A
1 A
102427 CCGGAACCTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02
Consensus pattern (2 bp):
AG
Found at i:102976 original size:22 final size:22
Alignment explanation
Indices: 102926--102978 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
102916 TATAAGTATT
*
102926 GCTTAAAGGTGGCTTAAAGAAA
1 GCTTAAAGATGGCTTAAAGAAA
* **
102948 GCGTAAAGATGGCTTAAAGGCA
1 GCTTAAAGATGGCTTAAAGAAA
102970 GCTTAAAGA
1 GCTTAAAGA
102979 CTATCTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21
Consensus pattern (22 bp):
GCTTAAAGATGGCTTAAAGAAA
Found at i:102999 original size:11 final size:11
Alignment explanation
Indices: 102983--103011 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
102973 TAAAGACTAT
102983 CTTTAAGCCAC
1 CTTTAAGCCAC
102994 CTTTAAGCCAC
1 CTTTAAGCCAC
103005 CTTTAAG
1 CTTTAAG
103012 GACAACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:103059 original size:11 final size:11
Alignment explanation
Indices: 103043--103096 Score: 99
Period size: 11 Copynumber: 4.9 Consensus size: 11
103033 GTCCAAACTT
103043 CTTTAAGCCAC
1 CTTTAAGCCAC
103054 CTTTAAGCCAC
1 CTTTAAGCCAC
*
103065 CTTTAAGCTAC
1 CTTTAAGCCAC
103076 CTTTAAGCCAC
1 CTTTAAGCCAC
103087 CTTTAAGCCA
1 CTTTAAGCCA
103097 TTAAAAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 41 1.00
ACGTcount: A:0.28, C:0.33, G:0.09, T:0.30
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:104443 original size:2 final size:2
Alignment explanation
Indices: 104436--104483 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
104426 CTGATGAACT
104436 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
104478 GA GA GA
1 GA GA GA
104484 TTTTTTTCAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:104892 original size:11 final size:11
Alignment explanation
Indices: 104869--104918 Score: 75
Period size: 11 Copynumber: 4.6 Consensus size: 11
104859 GTAAATGCCA
*
104869 CTTAAAGAT-G
1 CTTAAAGGTGG
104879 CTTAAAGGTGG
1 CTTAAAGGTGG
104890 CTTAAAGGTGG
1 CTTAAAGGTGG
*
104901 CTTAAAGGTAG
1 CTTAAAGGTGG
104912 CTTAAAG
1 CTTAAAG
104919 AAGTTTGGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
10 8 0.22
11 29 0.78
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:105004 original size:10 final size:11
Alignment explanation
Indices: 104989--105028 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
104979 GGTTGTATAG
*
104989 CCTTTAAG-CT
1 CCTTTAAGCCA
*
104999 CCTTTAAGTCA
1 CCTTTAAGCCA
105010 CCTTTAAGCCA
1 CCTTTAAGCCA
105021 CCTTTAAG
1 CCTTTAAG
105029 GACTTGCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.25, C:0.30, G:0.10, T:0.35
Consensus pattern (11 bp):
CCTTTAAGCCA
Found at i:114705 original size:2 final size:2
Alignment explanation
Indices: 114698--114747 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
114688 ATTAATATAC
114698 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
114740 GA GA GA GA
1 GA GA GA GA
114748 AAATAAGTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:118970 original size:95 final size:95
Alignment explanation
Indices: 118801--118982 Score: 249
Period size: 95 Copynumber: 1.9 Consensus size: 95
118791 TCAATAAGTG
* * * *
118801 CCAAAATTAAGTACTTTACTTAACAAGCAATCTTTGTTCCATTCCCACACGTGCAGCTCTATAAG
1 CCAAAATTAAGTACTATAATTAACAAGCAACCTTTGCTCCATTCCCACACGTGCAGCTCTATAAG
118866 TTAAACATTCTCAAAACATTTGGAATGGTA
66 TTAAACATTCTCAAAACATTTGGAATGGTA
* * * * * *
118896 CCAAAATTAAGTGCTATAATTCACAAGCGACCTTTGCTCCATTCCCATACGTGCAGGTCTTTGAA
1 CCAAAATTAAGTACTATAATTAACAAGCAACCTTTGCTCCATTCCCACACGTGCAGCTCTAT-AA
*
118961 -TTAAGCATTCTCAAAACATTTG
65 GTTAAACATTCTCAAAACATTTG
118983 TAATAATAAG
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
95 73 0.97
96 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (95 bp):
CCAAAATTAAGTACTATAATTAACAAGCAACCTTTGCTCCATTCCCACACGTGCAGCTCTATAAG
TTAAACATTCTCAAAACATTTGGAATGGTA
Found at i:119006 original size:31 final size:31
Alignment explanation
Indices: 118971--119032 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
118961 TTAAGCATTC
118971 TCAAAACATTTGTAATAATAAGGCAATGGTG
1 TCAAAACATTTGTAATAATAAGGCAATGGTG
*
119002 TCAAAACATTTGTAATATTAAGGCAATGGTG
1 TCAAAACATTTGTAATAATAAGGCAATGGTG
119033 GTGTCCATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (31 bp):
TCAAAACATTTGTAATAATAAGGCAATGGTG
Found at i:121989 original size:3 final size:3
Alignment explanation
Indices: 121983--122009 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
121973 TTGTTGTTGT
121983 TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA
122010 AGATTTACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:124142 original size:16 final size:16
Alignment explanation
Indices: 124121--124155 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
124111 ATCTGAATTT
*
124121 ATTCTTTCATAATGTC
1 ATTCTTACATAATGTC
124137 ATTCTTACATAATGTC
1 ATTCTTACATAATGTC
124153 ATT
1 ATT
124156 TTCTCACAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.49
Consensus pattern (16 bp):
ATTCTTACATAATGTC
Found at i:129747 original size:40 final size:40
Alignment explanation
Indices: 129692--129770 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
129682 AGCGATCAAA
129692 TAGTAAACTAGACTCTTGTTACAAATACAACAAAATGTTT
1 TAGTAAACTAGACTCTTGTTACAAATACAACAAAATGTTT
129732 TAGTAAACTAGACTCTTGTTACAAATACAACAAAATGTT
1 TAGTAAACTAGACTCTTGTTACAAATACAACAAAATGTT
129771 CTTCCGTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (40 bp):
TAGTAAACTAGACTCTTGTTACAAATACAACAAAATGTTT
Found at i:133295 original size:23 final size:24
Alignment explanation
Indices: 133263--133309 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
133253 CGCTATACGT
133263 TTATAACGAATTCG-TAAAAAATA
1 TTATAACGAATTCGTTAAAAAATA
* *
133286 TTATAGCGAATTCGTTATAAAATA
1 TTATAACGAATTCGTTAAAAAATA
133310 ATTAAGGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.34
Consensus pattern (24 bp):
TTATAACGAATTCGTTAAAAAATA
Found at i:133583 original size:15 final size:16
Alignment explanation
Indices: 133546--133586 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
133536 TTAAAATTAC
133546 TTCGTTATAGCCGTAAA
1 TTCGTTATAGCCGT-AA
*
133563 TTCGTTATAGCCGT-G
1 TTCGTTATAGCCGTAA
133578 TTCGTTATA
1 TTCGTTATA
133587 TACATCAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
17 14 0.61
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (16 bp):
TTCGTTATAGCCGTAA
Found at i:146723 original size:6 final size:6
Alignment explanation
Indices: 146712--146736 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
146702 TTGCAATAAA
146712 GAAATT GAAATT GAAATT GAAATT G
1 GAAATT GAAATT GAAATT GAAATT G
146737 TATGAGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (6 bp):
GAAATT
Found at i:148306 original size:20 final size:19
Alignment explanation
Indices: 148269--148309 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
148259 ATACTCCACT
148269 AAAACAAAAAACCAAAACC
1 AAAACAAAAAACCAAAACC
148288 AAAACAACAACAA-CAAAACC
1 AAAACAA-AA-AACCAAAACC
148308 AA
1 AA
148310 CAACCATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 11 0.55
21 2 0.10
ACGTcount: A:0.73, C:0.27, G:0.00, T:0.00
Consensus pattern (19 bp):
AAAACAAAAAACCAAAACC
Found at i:148312 original size:15 final size:15
Alignment explanation
Indices: 148271--148313 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 15
148261 ACTCCACTAA
148271 AACAA-AAAACCAA-
1 AACAACAAAACCAAC
148284 AAC--CAAAA-CAAC
1 AACAACAAAACCAAC
148296 AACAACAAAACCAAC
1 AACAACAAAACCAAC
148311 AAC
1 AAC
148314 CATGTACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 3 0.12
12 7 0.28
13 3 0.12
14 5 0.20
15 7 0.28
ACGTcount: A:0.70, C:0.30, G:0.00, T:0.00
Consensus pattern (15 bp):
AACAACAAAACCAAC
Found at i:159659 original size:254 final size:257
Alignment explanation
Indices: 159206--159704 Score: 916
Period size: 254 Copynumber: 1.9 Consensus size: 257
159196 GTTTTCATAT
159206 TTTTTACATTTAATATTTATTTAAAAAAAAAAAAACCCTCACATTTCTGTTTTTCAGTCTAGGTG
1 TTTTTACATTTAATATTTATTT-AAAAAAAAAAAACCCTCACATTTCTGTTTTTCAGTCTAGGTG
159271 TGTATAAGTGTAATAAAGTCACACATGAAAATATTTTTTTTTGGTCATTATTGCCATTGATTTTT
65 TGTATAAGTGTAATAAAGTCACACATGAAAATATTTTTTTTTGGTCATTATTGCCATTGATTTTT
159336 ACCTTGTCTTACATTATCATTAGATCGATCTTTGATAGTATCTATTTCCATTGAAAAGTAAAGGT
130 ACCTTGTCTTACATTATCATTAGATCGATCTTTGATAGTATCTATTTCCATTGAAAAGTAAAGGT
* *
159401 GTGTTATTTTTCTTCCTATAA-TTTTTTTTTATTTTTTTAAACTGAAAAAAGCCGGNTTTCAAA
195 GTGTTATTTTTCTTCCTATAATTTTTTTTTTATTATTTAAAACTGAAAAAAGCCGG-TTTCAAA
* *
159464 TTTTTACATTTAATATTTATTT-TAAGAAAAAAACCCTCACATTTCTG-TTTTCAGTCTAGGTGT
1 TTTTTACATTTAATATTTATTTAAAAAAAAAAAACCCTCACATTTCTGTTTTTCAGTCTAGGTGT
159527 GTATAAGTGTAATAAAGTCACACATGAAAATA-TTTTTTTTGGTCATTATTGCCATTGATTTTTA
66 GTATAAGTGTAATAAAGTCACACATGAAAATATTTTTTTTTGGTCATTATTGCCATTGATTTTTA
159591 CCTTGTCTTACATTATCATTAGATCGATCTTTGATAGTATCTATTTCCATTGAAAAGTAAAGGTG
131 CCTTGTCTTACATTATCATTAGATCGATCTTTGATAGTATCTATTTCCATTGAAAAGTAAAGGTG
159656 TGTTATTTTTCTTCCTATAATTTTTTTTTTATTATTTAAAACTGAAAAA
196 TGTTATTTTTCTTCCTATAATTTTTTTTTTATTATTTAAAACTGAAAAA
159705 TCCAGGTCAA
Statistics
Matches: 236, Mismatches: 4, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
254 117 0.50
255 74 0.31
256 23 0.10
258 22 0.09
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.45
Consensus pattern (257 bp):
TTTTTACATTTAATATTTATTTAAAAAAAAAAAACCCTCACATTTCTGTTTTTCAGTCTAGGTGT
GTATAAGTGTAATAAAGTCACACATGAAAATATTTTTTTTTGGTCATTATTGCCATTGATTTTTA
CCTTGTCTTACATTATCATTAGATCGATCTTTGATAGTATCTATTTCCATTGAAAAGTAAAGGTG
TGTTATTTTTCTTCCTATAATTTTTTTTTTATTATTTAAAACTGAAAAAAGCCGGTTTCAAA
Found at i:160533 original size:12 final size:12
Alignment explanation
Indices: 160513--160548 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
160503 TAGTGTTCCA
160513 AATAATAACAAT
1 AATAATAACAAT
160525 -ATAAATAACAAT
1 AAT-AATAACAAT
160537 AATAATAACAAT
1 AATAATAACAAT
160549 CTTAACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.09
12 18 0.82
13 2 0.09
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (12 bp):
AATAATAACAAT
Found at i:184747 original size:19 final size:19
Alignment explanation
Indices: 184723--184760 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
184713 ATATGCTACT
184723 ATACAGTAATGATACTGAA
1 ATACAGTAATGATACTGAA
184742 ATACAGTAATGATACTGAA
1 ATACAGTAATGATACTGAA
184761 TTGTTTTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (19 bp):
ATACAGTAATGATACTGAA
Found at i:184857 original size:11 final size:11
Alignment explanation
Indices: 184841--184871 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
184831 ATAAAAACTT
184841 TTATTATTGTA
1 TTATTATTGTA
184852 TTATTATTGTA
1 TTATTATTGTA
184863 TTATT-TTGT
1 TTATTATTGT
184872 TTTTTGTAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (11 bp):
TTATTATTGTA
Found at i:194665 original size:17 final size:16
Alignment explanation
Indices: 194643--194684 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 16
194633 TTTGGTCGTG
194643 TGTTTTTTTATTTTGTT
1 TGTTTTTTTATTTT-TT
194660 TGTTTTATTTATTTTTT
1 TGTTTT-TTTATTTTTT
194677 TGTGTTTT
1 TGT-TTTT
194685 ATTCATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.07, C:0.00, G:0.12, T:0.81
Consensus pattern (16 bp):
TGTTTTTTTATTTTTT
Found at i:194682 original size:19 final size:19
Alignment explanation
Indices: 194641--194697 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
194631 TCTTTGGTCG
*
194641 TGTGTTTT-TTTATTTTGT
1 TGTGTTTTATTTATTTTTT
194659 T-TGTTTTATTTATTTTTT
1 TGTGTTTTATTTATTTTTT
*
194677 TGTGTTTTATTCATTTATTT
1 TGTGTTTTATTTATTT-TTT
194697 T
1 T
194698 TTCGGGGGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.18
18 11 0.32
19 13 0.38
20 4 0.12
ACGTcount: A:0.11, C:0.02, G:0.11, T:0.77
Consensus pattern (19 bp):
TGTGTTTTATTTATTTTTT
Found at i:197248 original size:20 final size:20
Alignment explanation
Indices: 197219--197268 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
197209 TTGTCTTTAT
197219 TATTTAGATTGCCCTGACTA
1 TATTTAGATTGCCCTGACTA
* * *
197239 TATTTGGATTGTCTTGACTA
1 TATTTAGATTGCCCTGACTA
*
197259 TTTTTA-ATTG
1 TATTTAGATTG
197269 TCTTGGCTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (20 bp):
TATTTAGATTGCCCTGACTA
Found at i:197261 original size:38 final size:37
Alignment explanation
Indices: 197200--197299 Score: 103
Period size: 38 Copynumber: 2.6 Consensus size: 37
197190 ACTGTCGTGA
* * *
197200 ATATTTTGATTGTCTTTATTATTTAGATTGCCCTGACT
1 ATATTTGGATTGTCTTGACTATTTA-ATTGCCCTGACT
* * *
197238 ATATTTGGATTGTCTTGACTATTTTTAATTGTCTTGGCT
1 ATATTTGGATTGTCTTGACTA--TTTAATTGCCCTGACT
*
197277 ATTTTTGG-TTGTCTTGACTATTT
1 ATATTTGGATTGTCTTGACTATTT
197300 TTATTTGTCT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
36 3 0.06
38 30 0.57
39 16 0.30
40 4 0.08
ACGTcount: A:0.18, C:0.11, G:0.16, T:0.55
Consensus pattern (37 bp):
ATATTTGGATTGTCTTGACTATTTAATTGCCCTGACT
Found at i:197270 original size:19 final size:19
Alignment explanation
Indices: 197246--197354 Score: 123
Period size: 19 Copynumber: 5.8 Consensus size: 19
197236 CTATATTTGG
197246 ATTGTCTTGACTATTTTTA
1 ATTGTCTTGACTATTTTTA
* *
197265 ATTGTCTTGGCTATTTTTG
1 ATTGTCTTGACTATTTTTA
*
197284 GTTGTCTTGACTATTTTTA
1 ATTGTCTTGACTATTTTTA
* *
197303 TTTGTCTTGACTATTCTT-
1 ATTGTCTTGACTATTTTTA
* * * *
197321 ATTTTCCTGAATA-TTTTG
1 ATTGTCTTGACTATTTTTA
197339 ATTGTCTTGACTATTT
1 ATTGTCTTGACTATTT
197355 GGATTATACG
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
17 3 0.04
18 19 0.26
19 51 0.70
ACGTcount: A:0.17, C:0.12, G:0.14, T:0.58
Consensus pattern (19 bp):
ATTGTCTTGACTATTTTTA
Found at i:197300 original size:18 final size:18
Alignment explanation
Indices: 197155--197359 Score: 178
Period size: 18 Copynumber: 11.1 Consensus size: 18
197145 TTTCGACTAC
*
197155 TTGTCTTGACTATTTTGC
1 TTGTCTTGACTATTTTGA
* *
197173 TTGTATTGTCTATTTTGA
1 TTGTCTTGACTATTTTGA
* * *
197191 CTGTCGTGAATATTTTGA
1 TTGTCTTGACTATTTTGA
* * *
197209 TTGTCTTTATTATTTAGA
1 TTGTCTTGACTATTTTGA
* *
197227 TTGCCCTGACTATATTTGGA
1 TTGTCTTGACTAT-TTT-GA
*
197247 TTGTCTTGACTATTTTTAA
1 TTGTCTTGACTA-TTTTGA
* *
197266 TTGTCTTGGCTATTTTTGG
1 TTGTCTTGACTA-TTTTGA
*
197285 TTGTCTTGACTATTTTTA
1 TTGTCTTGACTATTTTGA
197303 TTTGTCTTGACTATTCTT-A
1 -TTGTCTTGACTATT-TTGA
* * *
197322 TTTTCCTGAATATTTTGA
1 TTGTCTTGACTATTTTGA
*
197340 TTGTCTTGACTATTTGGA
1 TTGTCTTGACTATTTTGA
197358 TT
1 TT
197360 ATACGATTGT
Statistics
Matches: 147, Mismatches: 34, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
17 2 0.01
18 82 0.56
19 45 0.31
20 17 0.12
21 1 0.01
ACGTcount: A:0.17, C:0.12, G:0.16, T:0.55
Consensus pattern (18 bp):
TTGTCTTGACTATTTTGA
Found at i:197308 original size:57 final size:55
Alignment explanation
Indices: 197247--197354 Score: 144
Period size: 55 Copynumber: 1.9 Consensus size: 55
197237 TATATTTGGA
* * ** *
197247 TTGTCTTGACTATTTTTAATTGTCTTGGCTATTTTTGGTTGTCTTGACTATTTTTAT
1 TTGTCTTGACTATTCTT-ATTGTCCTGAATA-TTTTGATTGTCTTGACTATTTTTAT
*
197304 TTGTCTTGACTATTCTTATTTTCCTGAATATTTTGATTGTCTTGACTATTT
1 TTGTCTTGACTATTCTTATTGTCCTGAATATTTTGATTGTCTTGACTATTT
197355 GGATTATACG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
55 20 0.44
56 9 0.20
57 16 0.36
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.58
Consensus pattern (55 bp):
TTGTCTTGACTATTCTTATTGTCCTGAATATTTTGATTGTCTTGACTATTTTTAT
Found at i:202573 original size:168 final size:168
Alignment explanation
Indices: 202317--202732 Score: 649
Period size: 168 Copynumber: 2.5 Consensus size: 168
202307 AAAAACTGGT
* * *
202317 TGCATGGTTATGATGTCCAT-AAGGCCCTCTACCAAAATTGTG--AATTATTGGCCCCTGGGTCA
1 TGCATGGTTATGATGTCCATGAA-GCCCTCTACCTAAATTGTGAAAATCA-TGACCCCTGGGTCA
* * *
202379 GGGGTTCTGGGTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAGAAAA
64 GGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAGAAAA
* *
202444 TCTTCTTCTCTACTACCATATATATTTTTTGAAAACTAAA
129 TCTTCTTCTCTACTACCATATATATTTGTTAAAAACTAAA
* *
202484 TGCATGATTATGATGTCCATGAAGCCCTGTACCTAAATTGTGAAAATCATGACCCCTGGGTCAGG
1 TGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAAATCATGACCCCTGGGTCAGG
202549 GGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAGAAAATC
66 GGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAGAAAATC
* *
202614 TTCTTCTCTTCTATCATATATATTTGTTAAAAACTAAA
131 TTCTTCTCTACTACCATATATATTTGTTAAAAACTAAA
* * * *
202652 TGTATGGTTATGATGTCCATGAAGCCCTCAACCTAAATTGTGAAATTCATGACCCCTTGGTCAGG
1 TGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAAATCATGACCCCTGGGTCAGG
202717 GGTTCAGGCTCTAGGG
66 GGTTCAGGCTCTAGGG
202733 NNNNNNNNNN
Statistics
Matches: 228, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
167 36 0.16
168 188 0.82
169 4 0.02
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (168 bp):
TGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAAATCATGACCCCTGGGTCAGG
GGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAGAAAATC
TTCTTCTCTACTACCATATATATTTGTTAAAAACTAAA
Found at i:207084 original size:49 final size:49
Alignment explanation
Indices: 207029--208203 Score: 1538
Period size: 49 Copynumber: 24.0 Consensus size: 49
207019 ACCAGGTAAG
*
207029 TACTATGTCAAGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
* **
207078 TACTATGTCAAGTCTTACAC--TGTCAGAATAAAAGTCAACATGTAGTC
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
* * * * *
207125 TAATTTGTCAGGTCTTACACTTTGTCAGAATAGTAGTCAACATATGGTC
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
* * *
207174 TTCTATGTCAGGTCTTACACTGTGT-TGTAATAGTAGTCAACATAT-GTTC
1 TACTATGTCAGGTCTTACACTGTGTCAG-AATAGTAGTCAACATGTAG-TC
*
207223 TACTATGTCAGGCCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
* ** * *
207272 TACTATGTCAGGTCTTACACTTTGTCAGAATAGTAGTCTTCGTGTGGT-
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
* * * *
207320 TGTCTATGTCAGGTCTTACACTGTGTTATAATAGTAGTCAACATAT-GTTC
1 T-ACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAG-TC
* *
207370 TACTATGTCAGGTCTTACATTGTGTCAGAATAGTAATCAACATGTAGTC
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
* * * * *
207419 TACTATGTCAGGTCTTACACTGTGTTAGAATAATAGTCATCGTGTGGTC
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
*
207468 TACTATGTCAGGT-TTACACTGTGTTAGAATAGTAGTCAACATGTAGTC
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
* * *
207516 TACTATGTCATGTCTTACACTGTGTCAGAATAGTAGTCAATAAGTAGTC
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
* * *
207565 T-GTAATGTCAGGTCTTACACTGTGTCAAAATAGTAGTCAAGATGTAGTC
1 TACT-ATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
* * *
207614 TACTATGTCATGTTTTACACTGTGTCAGAATGGTAGTCAACATGTAGTC
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
* * *
207663 TACTAAGTCAGGTCTTACACTGTGTCGGAATAGTAGTCAAGATGTAGTC
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
*
207712 TACTATGTCATGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
* * *
207761 TACTATGTCATGTCTTACACTGTGTCGGAATAGTAGTCAAGATGTAGTC
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
* * *
207810 TACTATGCCATGTCTTACACTGTGTCAGAATGGTAGTCAACATGTAGTC
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
* * *
207859 TACTAAGTCAGGTCTTACACTGTGTCGGAATAGTAGTCAAGATGTAGTC
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
* * *
207908 TACTATGCCATGTCTTACACTGTGTCAGAATAGTAGTCAATATGTAGTC
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
* * ** *
207957 TACAATGTCATGTCTTACACTGTGTTGGAATAGTAGTCATCATGTAGTC
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
* * * *
208006 TTCTATGTCATGTCTTACTCTTTGTCAGAATAGTAGTCAACATGTAGTC
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
* * *
208055 TACTATGTCAGGTCTTACACTGTGTTAGAAAAAGTAGTCATCATGTAGTC
1 TACTATGTCAGGTCTTACACTGTGTCAG-AATAGTAGTCAACATGTAGTC
* * * * ** *
208105 TTCTATGTCATGTCTTACTCTGTGTCAGAATAGTAGTCAACATCTTTTT
1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
* * *
208154 TACTATGTCAGGTCTTACACTGTGTTAGAAAAAGTAGTTAACATGTAGTC
1 TACTATGTCAGGTCTTACACTGTGTCAG-AATAGTAGTCAACATGTAGTC
208204 GGTTGTTCAA
Statistics
Matches: 980, Mismatches: 131, Indels: 29
0.86 0.11 0.03
Matches are distributed among these distances:
47 42 0.04
48 48 0.05
49 827 0.84
50 63 0.06
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (49 bp):
TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC
Found at i:210552 original size:65 final size:65
Alignment explanation
Indices: 210465--210614 Score: 273
Period size: 65 Copynumber: 2.3 Consensus size: 65
210455 GTTTTCATTC
* *
210465 CAAGAAAAGAGAAAAGAAGTATGCCTAACAATGAAGTATTCTACACTGTTTGTGATGTTTGATTT
1 CAAGTAAAGAGAAAAGAAGTATGCCTAACAATGAAGTATTCTACACTGTTTGGGATGTTTGATTT
210530 CAAGTAAAGAGAAAAGAAGTATGCCTAACAATGAAGTATTCTACACTGTTTGGGATGTTTGATTT
1 CAAGTAAAGAGAAAAGAAGTATGCCTAACAATGAAGTATTCTACACTGTTTGGGATGTTTGATTT
*
210595 CAAGTAAAGAAAAAAGAAGT
1 CAAGTAAAGAGAAAAGAAGT
210615 TTTTGTGAAG
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 82 1.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (65 bp):
CAAGTAAAGAGAAAAGAAGTATGCCTAACAATGAAGTATTCTACACTGTTTGGGATGTTTGATTT
Found at i:211355 original size:49 final size:49
Alignment explanation
Indices: 211279--211726 Score: 680
Period size: 49 Copynumber: 9.1 Consensus size: 49
211269 CATGGAGATT
* * *
211279 ACATGTAGTTTACTATGTCATGCCTTACACTGTGTCAGAATAGTAGTCA
1 ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA
* * * *
211328 ACATGTAGTCTACTCTTTCAAGTCTTACACTGTGTCAGAATAGTAGTGA
1 ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA
* * *
211377 ACATGTAGCCTACTATGTCATGCCTTACACTGTGTCAGAATAGTAGTCA
1 ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA
*
211426 ACATGTAGTCTACTATGTCAGGTGTTACACTGTGTCAGAATAGTAGTCA
1 ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA
* *
211475 ACATGTGGTCTTCTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA
1 ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA
* * * *
211524 ACATGTAGTCTACTCTTTCAAGTCTTACACTGTGTCAGAATAGTAGTGA
1 ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA
* *
211573 ACATGTAGCCTACTATGTCAGGTCTTACACTGTGTCAGAATAATAGTCA
1 ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA
* *
211622 ACATGTAGTCTACTATGCCATGTCTTACACTGTGTCAGAATAGTAGTCA
1 ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA
* * *
211671 ACATGTAGTCTACTATGTCAGGTGTTACACTGTGTTAAAATAGTAGTCA
1 ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA
211720 ACATGTA
1 ACATGTA
211727 TATATTTTAT
Statistics
Matches: 359, Mismatches: 40, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 359 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (49 bp):
ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA
Found at i:217374 original size:448 final size:448
Alignment explanation
Indices: 216539--217435 Score: 1733
Period size: 448 Copynumber: 2.0 Consensus size: 448
216529 CATATGTTAT
216539 GATCTCTACTGTAAAAAAAACTGTAAAATGGTCTTTTCATTTGACTCGTTTGGTCCGAAACAAAA
1 GATCTCTACTGTAAAAAAAACTGTAAAATGGTCTTTTCATTTGACTCGTTTGGTCCGAAACAAAA
216604 ATTAACACATAATTTTGATTGCACCATCTAAGTTTGACCAGTTTCACTGCATAATAGTTTAACAT
66 ATTAACACATAATTTTGATTGCACCATCTAAGTTTGACCAGTTTCACTGCATAATAGTTTAACAT
*
216669 AACAAGCCTTGATTACAGAGAAGCACTAATCTGTGACTAATGAGTATTAAAGGGACTGATGGCGT
131 AACAAGCCTTGATTACAAAGAAGCACTAATCTGTGACTAATGAGTATTAAAGGGACTGATGGCGT
216734 GTCAGATTCACTAACTATGAAGTGAATAATTAAACACTGTACAAAAATAATGTTTGGAAAATATA
196 GTCAGATTCACTAACTATGAAGTGAATAATTAAACACTGTACAAAAATAATGTTTGGAAAATATA
216799 AAGTATTGCATCTTGTATGCTTTCACAAGCATGGAGTATTCTATGAAGTACATCTACAAATGATA
261 AAGTATTGCATCTTGTATGCTTTCACAAGCATGGAGTATTCTATGAAGTACATCTACAAATGATA
216864 AATTGAAATCATCTAGCGGGCTGTTATATGTTCAAATGGATTTCTTAGATCTGGGATCC-ATATA
326 AATTGAAATCATCTAGCGGGCTGTTATATGTTCAAATGGATTTCTTAGATCTGGGATCCAATATA
*
216928 TATATTGCTGGGTTAAGATCTATGACAACAAACTGAGACATTTTCAGATCTTTAAGNAG
391 TATATTGCTGGGTTAAAATCTATGACAACAAACTGAGACATTTTCAGATCTTTAAG-AG
216987 GATCTCTACTGTAAAAAAAACTGTAAAATGGTCTTTTCATTTGACTCGTTTGGTCCGAAACAAAA
1 GATCTCTACTGTAAAAAAAACTGTAAAATGGTCTTTTCATTTGACTCGTTTGGTCCGAAACAAAA
217052 ATTAACACATAATTTTGATTGCACCATCTAAGTTTGACCAGTTTCACTGCATAATAGTTTAACAT
66 ATTAACACATAATTTTGATTGCACCATCTAAGTTTGACCAGTTTCACTGCATAATAGTTTAACAT
217117 AACAAGCCTTGATTACAAAGAAGCACTAATCTGTGACTAATGAGTATTAAAGGGACTGATGGCGT
131 AACAAGCCTTGATTACAAAGAAGCACTAATCTGTGACTAATGAGTATTAAAGGGACTGATGGCGT
217182 GTCAGATTCACTAACTATGAAGTGAATAATTAAACACTGTACAAAAATAATGTTTGGAAAATATA
196 GTCAGATTCACTAACTATGAAGTGAATAATTAAACACTGTACAAAAATAATGTTTGGAAAATATA
217247 AAGTATTGCATCTTGTATGCTTTCACAAGCATGGAGTATTCTATGAAGTACATCTACAAATGATA
261 AAGTATTGCATCTTGTATGCTTTCACAAGCATGGAGTATTCTATGAAGTACATCTACAAATGATA
217312 AATTGAAATCATCTAGCGGGCTGTTATATGTTCAAATGGATTTCTTAGATCTGGGATCCATATAT
326 AATTGAAATCATCTAGCGGGCTGTTATATGTTCAAATGGATTTCTTAGATCTGGGATCC--A-AT
217377 ATATATATTGCTGGGTTAAAATCTATGACAACAAACTGAGACATTTTCAGATCTTTAAG
388 ATATATATTGCTGGGTTAAAATCTATGACAACAAACTGAGACATTTTCAGATCTTTAAG
217436 GGTAACTTAC
Statistics
Matches: 443, Mismatches: 2, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
448 383 0.86
452 60 0.14
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (448 bp):
GATCTCTACTGTAAAAAAAACTGTAAAATGGTCTTTTCATTTGACTCGTTTGGTCCGAAACAAAA
ATTAACACATAATTTTGATTGCACCATCTAAGTTTGACCAGTTTCACTGCATAATAGTTTAACAT
AACAAGCCTTGATTACAAAGAAGCACTAATCTGTGACTAATGAGTATTAAAGGGACTGATGGCGT
GTCAGATTCACTAACTATGAAGTGAATAATTAAACACTGTACAAAAATAATGTTTGGAAAATATA
AAGTATTGCATCTTGTATGCTTTCACAAGCATGGAGTATTCTATGAAGTACATCTACAAATGATA
AATTGAAATCATCTAGCGGGCTGTTATATGTTCAAATGGATTTCTTAGATCTGGGATCCAATATA
TATATTGCTGGGTTAAAATCTATGACAACAAACTGAGACATTTTCAGATCTTTAAGAG
Found at i:233800 original size:5 final size:5
Alignment explanation
Indices: 233799--233833 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
233789 AAAAAAACAA
233799 AAAAC AAAAC AAAAC AAAAAC AAAAC AAAAC AAAA
1 AAAAC AAAAC AAAAC -AAAAC AAAAC AAAAC AAAA
233834 AACGACGCCG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:233819 original size:16 final size:16
Alignment explanation
Indices: 233792--233834 Score: 77
Period size: 16 Copynumber: 2.6 Consensus size: 16
233782 CCCCCCCAAA
233792 AAAACAAAAAACAAAAC
1 AAAAC-AAAAACAAAAC
233809 AAAACAAAAACAAAAC
1 AAAACAAAAACAAAAC
233825 AAAACAAAAA
1 AAAACAAAAA
233835 ACGACGCCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 21 0.81
17 5 0.19
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAACAAAAACAAAAC
Found at i:233834 original size:11 final size:11
Alignment explanation
Indices: 233791--233833 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
233781 CCCCCCCCAA
*
233791 AAAAACAAAAA
1 AAAAACAAAAC
233802 ACAAAACAAAAC
1 A-AAAACAAAAC
233814 AAAAACAAAAC
1 AAAAACAAAAC
233825 -AAAACAAAA
1 AAAAACAAAA
233834 AACGACGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 9 0.30
11 11 0.37
12 10 0.33
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:238384 original size:16 final size:16
Alignment explanation
Indices: 238363--238394 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
238353 CCGAATTAAA
*
238363 TTGATTTTATTTATTT
1 TTGATTTGATTTATTT
238379 TTGATTTGATTTATTT
1 TTGATTTGATTTATTT
238395 GATCCATCTA
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:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (16 bp):
TTGATTTGATTTATTT
Found at i:250427 original size:18 final size:18
Alignment explanation
Indices: 250404--250453 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
250394 TGCAATATGG
250404 TCAAAGTTCAATCAGAGT
1 TCAAAGTTCAATCAGAGT
250422 TCAAAGTTCAATCAGAGT
1 TCAAAGTTCAATCAGAGT
250440 TCAAAGTTCAATCA
1 TCAAAGTTCAATCA
250454 AAGCTGCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (18 bp):
TCAAAGTTCAATCAGAGT
Found at i:251285 original size:18 final size:18
Alignment explanation
Indices: 251262--251311 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
251252 TGCAATATGG
251262 TCAAAGTTCAATCAGAGT
1 TCAAAGTTCAATCAGAGT
251280 TCAAAGTTCAATCAGAGT
1 TCAAAGTTCAATCAGAGT
251298 TCAAAGTTCAATCA
1 TCAAAGTTCAATCA
251312 AAGCTGCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (18 bp):
TCAAAGTTCAATCAGAGT
Found at i:256406 original size:16 final size:16
Alignment explanation
Indices: 256385--256415 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
256375 GCCTGAAGTG
256385 GGACAGACAGACGGAC
1 GGACAGACAGACGGAC
256401 GGACAGACAGACGGA
1 GGACAGACAGACGGA
256416 GTGACGGACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.23, G:0.39, T:0.00
Consensus pattern (16 bp):
GGACAGACAGACGGAC
Found at i:266092 original size:16 final size:17
Alignment explanation
Indices: 266073--266107 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
266063 TATGTATTGA
*
266073 ATAGGTATTGTAT-GGT
1 ATAGGTATAGTATAGGT
266089 ATAGGTATAGTATAGGT
1 ATAGGTATAGTATAGGT
266106 AT
1 AT
266108 CGTATAAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (17 bp):
ATAGGTATAGTATAGGT
Found at i:266096 original size:27 final size:27
Alignment explanation
Indices: 266061--266112 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
266051 AGATATCGTA
* * *
266061 TATATGTATTGAATAGGTATTGTATGG
1 TATAGGTATAGAATAGGTATCGTATGG
*
266088 TATAGGTATAGTATAGGTATCGTAT
1 TATAGGTATAGAATAGGTATCGTAT
266113 AAGTGTCGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.31, C:0.02, G:0.25, T:0.42
Consensus pattern (27 bp):
TATAGGTATAGAATAGGTATCGTATGG
Found at i:272375 original size:18 final size:18
Alignment explanation
Indices: 272352--272473 Score: 172
Period size: 18 Copynumber: 6.8 Consensus size: 18
272342 ACCATCAAGA
*
272352 ACCACAAGACGTCCGTAC
1 ACCACACGACGTCCGTAC
*
272370 ACCACAAGACGTCCGTAC
1 ACCACACGACGTCCGTAC
*
272388 ACCACACGGCGTCCGTAC
1 ACCACACGACGTCCGTAC
*
272406 ACCACTCGACGTCCGTAC
1 ACCACACGACGTCCGTAC
* *
272424 ACCACTCGACGTCCTTAC
1 ACCACACGACGTCCGTAC
*
272442 ACCACTCGACGTCCGTAC
1 ACCACACGACGTCCGTAC
*
272460 ACCACTCGACGTCC
1 ACCACACGACGTCC
272474 TTACCCCAGG
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 98 1.00
ACGTcount: A:0.25, C:0.43, G:0.16, T:0.15
Consensus pattern (18 bp):
ACCACACGACGTCCGTAC
Found at i:275557 original size:2 final size:2
Alignment explanation
Indices: 275550--275607 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
275540 GTAAGGTTTT
275550 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
275592 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
275608 AGTATTTGAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:276139 original size:17 final size:18
Alignment explanation
Indices: 276114--276151 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
276104 AATTGATTTT
*
276114 TTAATTTTTTTCA-TAAA
1 TTAACTTTTTTCATTAAA
*
276131 TTAACTTTTTTGATTAAA
1 TTAACTTTTTTCATTAAA
276149 TTA
1 TTA
276152 GTAATGTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (18 bp):
TTAACTTTTTTCATTAAA
Found at i:277826 original size:50 final size:50
Alignment explanation
Indices: 277687--277826 Score: 181
Period size: 50 Copynumber: 2.8 Consensus size: 50
277677 TGTACCTTCA
*** * * * *
277687 TAACGCACTTTGAAAATTTTTTTCAAAGTGGGTTAACTTGGTCCAAAATT
1 TAACGCACTTTGAAAAAAATTTTCAAAGTGCGTTAATTTTGTCCAAAACT
* *
277737 TAACGCACTTTGAAAAAAAATTTCAAAGTGCGTTGATTTTGTCCAAAACT
1 TAACGCACTTTGAAAAAAATTTTCAAAGTGCGTTAATTTTGTCCAAAACT
* *
277787 TAACGCAATTTGAAAAAAATTTTCAAAGTGCGTAAATTTT
1 TAACGCACTTTGAAAAAAATTTTCAAAGTGCGTTAATTTT
277827 TCAAAGTGCG
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 77 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (50 bp):
TAACGCACTTTGAAAAAAATTTTCAAAGTGCGTTAATTTTGTCCAAAACT
Found at i:284352 original size:12 final size:13
Alignment explanation
Indices: 284335--284372 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
284325 GATAATACCA
284335 TCAATGAAT-TTT
1 TCAATGAATGTTT
284347 TCAATG-ATGTTT
1 TCAATGAATGTTT
*
284359 TCAATGAACGTTT
1 TCAATGAATGTTT
284372 T
1 T
284373 TTTAATGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 2 0.09
12 15 0.65
13 6 0.26
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (13 bp):
TCAATGAATGTTT
Found at i:286251 original size:12 final size:12
Alignment explanation
Indices: 286234--286259 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
286224 TGTCTTTCTA
286234 AAAAAAAAAAAC
1 AAAAAAAAAAAC
286246 AAAAAAAAAAAC
1 AAAAAAAAAAAC
286258 AA
1 AA
286260 CCAAACAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:297889 original size:2 final size:2
Alignment explanation
Indices: 297882--297917 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
297872 AATATCAAAT
297882 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
297918 GTTAAGTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:309869 original size:28 final size:28
Alignment explanation
Indices: 309829--309927 Score: 126
Period size: 28 Copynumber: 3.5 Consensus size: 28
309819 AAATCAGTGA
309829 ATATCGCCAATGTGTGATTATCCTATTG
1 ATATCGCCAATGTGTGATTATCCTATTG
* *
309857 ATATCTCCAATGTGTGATTATCTTATTG
1 ATATCGCCAATGTGTGATTATCCTATTG
* * * **
309885 ATATCACCAATGTTTGAATATCGAATTG
1 ATATCGCCAATGTGTGATTATCCTATTG
*
309913 ATATCGCCATTGTGT
1 ATATCGCCAATGTGT
309928 AAGCTCTCTG
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 61 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (28 bp):
ATATCGCCAATGTGTGATTATCCTATTG
Found at i:315899 original size:2 final size:2
Alignment explanation
Indices: 315886--315923 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
315876 ACCAAATAAT
*
315886 GA GA GC GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
315924 AAATAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:327412 original size:21 final size:21
Alignment explanation
Indices: 327385--327830 Score: 460
Period size: 21 Copynumber: 20.9 Consensus size: 21
327375 ATACATAATC
* * *
327385 ATCTCGTTATTACGAGATCTT
1 ATCTCGTAATAACGAGATATT
*
327406 TTCTCGTAATAACGAGATAATT
1 ATCTCGTAATAACGAGAT-ATT
* *
327428 AACTCGTAATAACGAGATCTT
1 ATCTCGTAATAACGAGATATT
*
327449 TTCTCGTAATAACGAGATAATT
1 ATCTCGTAATAACGAGAT-ATT
* *
327471 AACTCGTAATAACGAGATCTT
1 ATCTCGTAATAACGAGATATT
* *
327492 TTCTCGTTATAACGAGATAATT
1 ATCTCGTAATAACGAGAT-ATT
* *
327514 AACTCGTAATAACGAGATCTT
1 ATCTCGTAATAACGAGATATT
* *
327535 TTCTCGTTATAACGAGATAATT
1 ATCTCGTAATAACGAGAT-ATT
* *
327557 AACTCGTAATAACGAGATCTT
1 ATCTCGTAATAACGAGATATT
* *
327578 TTCTCGTAATAACGAGATCTT
1 ATCTCGTAATAACGAGATATT
* *
327599 AACTCGTTATAACGAGATAATT
1 ATCTCGTAATAACGAGAT-ATT
*
327621 AACTCGTAATAACGAGATATT
1 ATCTCGTAATAACGAGATATT
* * *
327642 AACTCGTAATTACGAGATCTT
1 ATCTCGTAATAACGAGATATT
*
327663 TTCTCGTAATAACGAGATATT
1 ATCTCGTAATAACGAGATATT
* * *
327684 AACTCGTTATAATGAGATAATT
1 ATCTCGTAATAACGAGAT-ATT
* *
327706 AACTCGTAATAACGAGATCTT
1 ATCTCGTAATAACGAGATATT
*
327727 TTCTCGTAATAACGAGATAATT
1 ATCTCGTAATAACGAGAT-ATT
* * *
327749 AACTCGTTATAACGAGATCTT
1 ATCTCGTAATAACGAGATATT
* *
327770 TTCTCGTAATTACGAGATATT
1 ATCTCGTAATAACGAGATATT
* *
327791 TTCTCGTAATAACGAGATCTT
1 ATCTCGTAATAACGAGATATT
* *
327812 TTCTCGTAATTACGAGATA
1 ATCTCGTAATAACGAGATA
327831 AAAATATTTT
Statistics
Matches: 353, Mismatches: 65, Indels: 14
0.82 0.15 0.03
Matches are distributed among these distances:
21 228 0.65
22 125 0.35
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (21 bp):
ATCTCGTAATAACGAGATATT
Found at i:327443 original size:43 final size:42
Alignment explanation
Indices: 327396--327829 Score: 544
Period size: 43 Copynumber: 10.2 Consensus size: 42
327386 TCTCGTTATT
327396 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATA
1 ACGAGATCTTTTCTCGTAATAACGAGAT-ATTAACTCGTAATA
327439 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATA
1 ACGAGATCTTTTCTCGTAATAACGAGAT-ATTAACTCGTAATA
*
327482 ACGAGATCTTTTCTCGTTATAACGAGATAATTAACTCGTAATA
1 ACGAGATCTTTTCTCGTAATAACGAGAT-ATTAACTCGTAATA
*
327525 ACGAGATCTTTTCTCGTTATAACGAGATAATTAACTCGTAATA
1 ACGAGATCTTTTCTCGTAATAACGAGAT-ATTAACTCGTAATA
* *
327568 ACGAGATCTTTTCTCGTAATAACGAGATCTTAACTCGTTATA
1 ACGAGATCTTTTCTCGTAATAACGAGATATTAACTCGTAATA
* ** *
327610 ACGAGATAATTAACTCGTAATAACGAGATATTAACTCGTAATT
1 ACGAGAT-CTTTTCTCGTAATAACGAGATATTAACTCGTAATA
*
327653 ACGAGATCTTTTCTCGTAATAACGAGATATTAACTCGTTATA
1 ACGAGATCTTTTCTCGTAATAACGAGATATTAACTCGTAATA
* * ** * **
327695 ATGAGATAATTAACTCGTAATAACGAGATCTTTTCTCGTAATA
1 ACGAGAT-CTTTTCTCGTAATAACGAGATATTAACTCGTAATA
* ** * * ** *
327738 ACGAGATAATTAACTCGTTATAACGAGATCTTTTCTCGTAATT
1 ACGAGAT-CTTTTCTCGTAATAACGAGATATTAACTCGTAATA
* * ** *
327781 ACGAGATATTTTCTCGTAATAACGAGATCTTTTCTCGTAATT
1 ACGAGATCTTTTCTCGTAATAACGAGATATTAACTCGTAATA
327823 ACGAGAT
1 ACGAGAT
327830 AAAAATATTT
Statistics
Matches: 360, Mismatches: 29, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
42 94 0.26
43 266 0.74
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (42 bp):
ACGAGATCTTTTCTCGTAATAACGAGATATTAACTCGTAATA
Found at i:327498 original size:64 final size:64
Alignment explanation
Indices: 327396--327830 Score: 552
Period size: 64 Copynumber: 6.8 Consensus size: 64
327386 TCTCGTTATT
* **
327396 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATCTTTTCTCGTAATA
1 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATATTAACTCGTAATA
* ** * ** *
327460 ACGAGATAATTAACTCGTAATAACGAGAT-CTTTTCTCGTTATAACGAGATAATTAACTCGTAAT
1 ACGAGAT-CTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGAT-ATTAACTCGTAAT
327524 A
64 A
* * **
327525 ACGAGATCTTTTCTCGTTATAACGAGATAATTAACTCGTAATAACGAGATCTTTTCTCGTAATA
1 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATATTAACTCGTAATA
** * *
327589 ACGAGATCTTAACTCGTTATAACGAGATAATTAACTCGTAATAACGAGATATTAACTCGTAATT
1 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATATTAACTCGTAATA
* *
327653 ACGAGATCTTTTCTCGTAATAACGAGAT-ATTAACTCGTTATAATGAGATAATTAACTCGTAATA
1 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGAT-ATTAACTCGTAATA
* * ** *
327717 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTTATAACGAGATCTTTTCTCGTAATT
1 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATATTAACTCGTAATA
* * ** *
327781 ACGAGATATTTTCTCGTAATAACGAGAT-CTTTTCTCGTAATTACGAGATA
1 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATA
327831 AAAATATTTT
Statistics
Matches: 321, Mismatches: 45, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
63 35 0.11
64 213 0.66
65 73 0.23
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (64 bp):
ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATATTAACTCGTAATA
Found at i:340490 original size:2 final size:2
Alignment explanation
Indices: 340485--340528 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
340475 TTAACCAGAA
340485 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
340527 TC
1 TC
340529 ATGTGTTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:341843 original size:11 final size:11
Alignment explanation
Indices: 341823--341869 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
341813 TCAGAAGACA
341823 TTGAATCAACG
1 TTGAATCAACG
*
341834 TTGAAACAACG
1 TTGAATCAACG
*
341845 TCAGAATTCAACG
1 T-TGAA-TCAACG
341858 TTGAATCAACG
1 TTGAATCAACG
341869 T
1 T
341870 CGGAATTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
11 18 0.60
12 6 0.20
13 6 0.20
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (11 bp):
TTGAATCAACG
Found at i:341856 original size:24 final size:25
Alignment explanation
Indices: 341828--341883 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 25
341818 AGACATTGAA
341828 TCAACGTTGAAACAACGTCAGAA-T
1 TCAACGTTGAAACAACGTCAGAATT
* *
341852 TCAACGTTGAATCAACGTCGGAATT
1 TCAACGTTGAAACAACGTCAGAATT
341877 TCAACGT
1 TCAACGT
341884 CCATTCAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 21 0.72
25 8 0.28
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (25 bp):
TCAACGTTGAAACAACGTCAGAATT
Found at i:341891 original size:25 final size:24
Alignment explanation
Indices: 341840--341892 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
341830 AACGTTGAAA
**
341840 CAACGTCAGAATTCAACGTTGAAT
1 CAACGTCAGAATTCAACGTCCAAT
* *
341864 CAACGTCGGAATTTCAACGTCCATT
1 CAACGTCAGAA-TTCAACGTCCAAT
341889 CAAC
1 CAAC
341893 TTTCATATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (24 bp):
CAACGTCAGAATTCAACGTCCAAT
Found at i:343812 original size:4 final size:4
Alignment explanation
Indices: 343797--343853 Score: 53
Period size: 4 Copynumber: 14.2 Consensus size: 4
343787 TGATAGAGAG
* ** * *
343797 AGAC AGAG AGAC AGAC AGAC CTAC ATAC AGA- AGGAC AGAC AGAC GGAC
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC A-GAC AGAC AGAC AGAC
343845 AGAC AGAC A
1 AGAC AGAC A
343854 TACAAAACAT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
3 1 0.02
4 41 0.95
5 1 0.02
ACGTcount: A:0.47, C:0.23, G:0.26, T:0.04
Consensus pattern (4 bp):
AGAC
Found at i:343852 original size:12 final size:12
Alignment explanation
Indices: 343797--343852 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
343787 TGATAGAGAG
343797 AGACAGA-GAGAC
1 AGACAGACG-GAC
**
343809 AGACAGACCTAC
1 AGACAGACGGAC
* *
343821 ATACAGAAGGAC
1 AGACAGACGGAC
343833 AGACAGACGGAC
1 AGACAGACGGAC
343845 AGACAGAC
1 AGACAGAC
343853 ATACAAAACA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.46, C:0.23, G:0.27, T:0.04
Consensus pattern (12 bp):
AGACAGACGGAC
Found at i:344150 original size:25 final size:25
Alignment explanation
Indices: 344116--344658 Score: 753
Period size: 25 Copynumber: 22.1 Consensus size: 25
344106 TATCGATCAA
* *
344116 TGCTAGTATCACTTTTGTACTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
344141 TGCTAATATCA-TTTTGTACTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
*
344165 TGCTCATATCATTTTTGTACTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
* *
344190 TGTTAATATCACTTTTGTACTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
*
344215 TGCTAATAT-AATTTTGTACTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
*
344239 TGCTCATATCATTTTTGTACTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
* *
344264 TGTTAATATCACTTTTGTACTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
344289 TGCTAATATCA-TTTTGTACTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
344313 TG---ATATCATTTTTGTACTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
* * *
344335 TGTTAATATCACTTTTGTACTGTGC
1 TGCTAATATCATTTTTGTACTTTGC
344360 TGCTAATATCA-TTTTGTACTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
* *
344384 TGCTCATATCAATTTTGTACTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
* *
344409 TGTTAATATCACTTTTGTACTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
*
344434 TGCTCATATCATTTTTGTACTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
* *
344459 TGTTAATATCACTTTTGTACTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
344484 TGCTAATATCA-TTTTGTACTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
*
344508 TGCTCATATCATTTTTGTACTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
* *
344533 TGCTAATATCACTTTTGTACTTTTC
1 TGCTAATATCATTTTTGTACTTTGC
344558 TGCTAATATCATTTTTGTACTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
* *
344583 TGTTAATATCA-TTTTGTGCTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
* * *
344607 TGCTCATATCATTTTTGCACGTTGC
1 TGCTAATATCATTTTTGTACTTTGC
* * *
344632 TGTTAATATCATTTTTGAATTTTGC
1 TGCTAATATCATTTTTGTACTTTGC
344657 TG
1 TG
344659 ATATTTGGTA
Statistics
Matches: 463, Mismatches: 46, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
21 6 0.01
22 15 0.03
24 126 0.27
25 316 0.68
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.51
Consensus pattern (25 bp):
TGCTAATATCATTTTTGTACTTTGC
Found at i:344243 original size:74 final size:74
Alignment explanation
Indices: 344122--344658 Score: 839
Period size: 74 Copynumber: 7.3 Consensus size: 74
344112 TCAATGCTAG
344122 TATCACTTTTGTACTTTGCTGCTAATATCATTTTGTACTTTGCTGCTCATATCATTTTTGTACTT
1 TATCACTTTTGTACTTTGCTGCTAATATCATTTTGTACTTTGCTGCTCATATCATTTTTGTACTT
344187 TGCTGTTAA
66 TGCTGTTAA
*
344196 TATCACTTTTGTACTTTGCTGCTAATATAATTTTGTACTTTGCTGCTCATATCATTTTTGTACTT
1 TATCACTTTTGTACTTTGCTGCTAATATCATTTTGTACTTTGCTGCTCATATCATTTTTGTACTT
344261 TGCTGTTAA
66 TGCTGTTAA
344270 TATCACTTTTGTACTTTGCTGCTAATATCATTTTGTACTTTGCTG---ATATCATTTTTGTACTT
1 TATCACTTTTGTACTTTGCTGCTAATATCATTTTGTACTTTGCTGCTCATATCATTTTTGTACTT
344332 TGCTGTTAA
66 TGCTGTTAA
* *
344341 TATCACTTTTGTACTGTGCTGCTAATATCATTTTGTACTTTGCTGCTCATATCAATTTTGTACTT
1 TATCACTTTTGTACTTTGCTGCTAATATCATTTTGTACTTTGCTGCTCATATCATTTTTGTACTT
344406 TGCTGTTAA
66 TGCTGTTAA
* * * *
344415 TATCACTTTTGTACTTTGCTGCTCATATCATTTTTGTACTTTGCTGTTAATATCACTTTTGTACT
1 TATCACTTTTGTACTTTGCTGCTAATATCA-TTTTGTACTTTGCTGCTCATATCATTTTTGTACT
*
344480 TTGCTGCTAA
65 TTGCTGTTAA
* * *
344490 TATCA-TTTTGTACTTTGCTGCTCATATCATTTTTGTACTTTGCTGCTAATATCACTTTTGTACT
1 TATCACTTTTGTACTTTGCTGCTAATATCA-TTTTGTACTTTGCTGCTCATATCATTTTTGTACT
* *
344554 TTTCTGCTAA
65 TTGCTGTTAA
* * * * *
344564 TATCATTTTTGTACTTTGCTGTTAATATCATTTTGTGCTTTGCTGCTCATATCATTTTTGCACGT
1 TATCACTTTTGTACTTTGCTGCTAATATCATTTTGTACTTTGCTGCTCATATCATTTTTGTACTT
344629 TGCTGTTAA
66 TGCTGTTAA
* * *
344638 TATCATTTTTGAATTTTGCTG
1 TATCACTTTTGTACTTTGCTG
344659 ATATTTGGTA
Statistics
Matches: 435, Mismatches: 23, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
71 70 0.16
74 298 0.69
75 67 0.15
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.51
Consensus pattern (74 bp):
TATCACTTTTGTACTTTGCTGCTAATATCATTTTGTACTTTGCTGCTCATATCATTTTTGTACTT
TGCTGTTAA
Found at i:344287 original size:99 final size:99
Alignment explanation
Indices: 344116--344658 Score: 774
Period size: 99 Copynumber: 5.5 Consensus size: 99
344106 TATCGATCAA
* * * *
344116 TGCTAGTATCACTTTTGTACTTTGCTGCTAATATCA-TTTTGTACTTTGCTGCTCATATCATTTT
1 TGCTAATATCATTTTTGTACTTTGCTGCTAATATCATTTTTGTACTTTGCTGCTAATATCACTTT
*
344180 TGTACTTTGCTGTTAATATCACTTTTGTACTTTGC
66 TGTACTTTGCTGCTAATATCA-TTTTGTACTTTGC
* * *
344215 TGCTAATAT-AATTTTGTACTTTGCTGCTCATATCATTTTTGTACTTTGCTGTTAATATCACTTT
1 TGCTAATATCATTTTTGTACTTTGCTGCTAATATCATTTTTGTACTTTGCTGCTAATATCACTTT
344279 TGTACTTTGCTGCTAATATCATTTTGTACTTTGC
66 TGTACTTTGCTGCTAATATCATTTTGTACTTTGC
* * *
344313 TG---ATATCATTTTTGTACTTTGCTGTTAATATCACTTTTGTACTGTGCTGCTAATATCA-TTT
1 TGCTAATATCATTTTTGTACTTTGCTGCTAATATCATTTTTGTACTTTGCTGCTAATATCACTTT
*
344374 TGTACTTTGCTGCTCATATCAATTTTGTACTTTGC
66 TGTACTTTGCTGCTAATATC-ATTTTGTACTTTGC
* * * *
344409 TGTTAATATCACTTTTGTACTTTGCTGCTCATATCATTTTTGTACTTTGCTGTTAATATCACTTT
1 TGCTAATATCATTTTTGTACTTTGCTGCTAATATCATTTTTGTACTTTGCTGCTAATATCACTTT
344474 TGTACTTTGCTGCTAATATCATTTTGTACTTTGC
66 TGTACTTTGCTGCTAATATCATTTTGTACTTTGC
* * * *
344508 TGCTCATATCATTTTTGTACTTTGCTGCTAATATCACTTTTGTACTTTTCTGCTAATATCATTTT
1 TGCTAATATCATTTTTGTACTTTGCTGCTAATATCATTTTTGTACTTTGCTGCTAATATCACTTT
* *
344573 TGTACTTTGCTGTTAATATCATTTTGTGCTTTGC
66 TGTACTTTGCTGCTAATATCATTTTGTACTTTGC
* * * * * *
344607 TGCTCATATCATTTTTGCACGTTGCTGTTAATATCATTTTTGAATTTTGCTG
1 TGCTAATATCATTTTTGTACTTTGCTGCTAATATCATTTTTGTACTTTGCTG
344659 ATATTTGGTA
Statistics
Matches: 399, Mismatches: 38, Indels: 14
0.88 0.08 0.03
Matches are distributed among these distances:
95 26 0.07
96 61 0.15
98 39 0.10
99 251 0.63
100 22 0.06
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.51
Consensus pattern (99 bp):
TGCTAATATCATTTTTGTACTTTGCTGCTAATATCATTTTTGTACTTTGCTGCTAATATCACTTT
TGTACTTTGCTGCTAATATCATTTTGTACTTTGC
Found at i:356751 original size:14 final size:14
Alignment explanation
Indices: 356732--356775 Score: 70
Period size: 14 Copynumber: 3.0 Consensus size: 14
356722 GTACGGTAAT
356732 AAACTCTCTCTCTC
1 AAACTCTCTCTCTC
356746 AAACTCTCTCTCTCTC
1 AAA--CTCTCTCTCTC
356762 AAACTCTCTCTCTC
1 AAACTCTCTCTCTC
356776 TCAATTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.50
16 14 0.50
ACGTcount: A:0.20, C:0.43, G:0.00, T:0.36
Consensus pattern (14 bp):
AAACTCTCTCTCTC
Found at i:356756 original size:16 final size:16
Alignment explanation
Indices: 356735--356779 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
356725 CGGTAATAAA
356735 CTCTCTCTCTCAAACT
1 CTCTCTCTCTCAAACT
356751 CTCTCTCTCTCAAACT
1 CTCTCTCTCTCAAACT
356767 CTCTCTCTCTCAA
1 CTCTCTCTCTCAA
356780 TTTGATAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.18, C:0.44, G:0.00, T:0.38
Consensus pattern (16 bp):
CTCTCTCTCTCAAACT
Found at i:359488 original size:15 final size:15
Alignment explanation
Indices: 359468--359497 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
359458 AGTGGAGCCT
359468 CAGATATCCGGACGC
1 CAGATATCCGGACGC
359483 CAGATATCCGGACGC
1 CAGATATCCGGACGC
359498 TTCACTTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
CAGATATCCGGACGC
Found at i:361207 original size:11 final size:11
Alignment explanation
Indices: 361191--361241 Score: 77
Period size: 11 Copynumber: 4.7 Consensus size: 11
361181 TAAGCAAGTC
361191 CTTAAAGGTGG
1 CTTAAAGGTGG
361202 CTTAAAGGTGG
1 CTTAAAGGTGG
*
361213 CTTAAAGGTGA
1 CTTAAAGGTGG
*
361224 CTTAAAGG-AG
1 CTTAAAGGTGG
361234 CTTAAAGG
1 CTTAAAGG
361242 CTATACAACC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
10 8 0.22
11 29 0.78
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.25
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:361328 original size:11 final size:10
Alignment explanation
Indices: 361312--361361 Score: 64
Period size: 11 Copynumber: 4.7 Consensus size: 10
361302 GTCCAAACTT
361312 CTTTAAGCTAC
1 CTTTAAGC-AC
361323 CTTTAAGCCAC
1 CTTTAAG-CAC
361334 CTTTAAGCAAC
1 CTTTAAGC-AC
*
361345 CTTTAAGCAT
1 CTTTAAGCAC
361355 CTTTAAG
1 CTTTAAG
361362 TGGCATTTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
10 9 0.25
11 26 0.72
12 1 0.03
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34
Consensus pattern (10 bp):
CTTTAAGCAC
Found at i:361340 original size:22 final size:21
Alignment explanation
Indices: 361312--361361 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
361302 GTCCAAACTT
*
361312 CTTTAAGCTACCTTTAAGCCAC
1 CTTTAAGCAACCTTTAAG-CAC
*
361334 CTTTAAGCAACCTTTAAGCAT
1 CTTTAAGCAACCTTTAAGCAC
361355 CTTTAAG
1 CTTTAAG
361362 TGGCATTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34
Consensus pattern (21 bp):
CTTTAAGCAACCTTTAAGCAC
Found at i:361361 original size:10 final size:11
Alignment explanation
Indices: 361312--361353 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
361302 GTCCAAACTT
*
361312 CTTTAAGCTAC
1 CTTTAAGCAAC
*
361323 CTTTAAGCCAC
1 CTTTAAGCAAC
361334 CTTTAAGCAAC
1 CTTTAAGCAAC
361345 CTTTAAGCA
1 CTTTAAGCA
361354 TCTTTAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.31
Consensus pattern (11 bp):
CTTTAAGCAAC
Found at i:361411 original size:22 final size:22
Alignment explanation
Indices: 361354--361414 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
361344 CCTTTAAGCA
* *
361354 TCTTTAAGTGGCATTTACGCTC
1 TCTTTAAGTGGCCTTTACACTC
* *
361376 TCTTTACACT-GCCTTTACACTG
1 TCTTTA-AGTGGCCTTTACACTC
361398 TCTTTAAGTGGCCTTTA
1 TCTTTAAGTGGCCTTTA
361415 AGTCAATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.43
Consensus pattern (22 bp):
TCTTTAAGTGGCCTTTACACTC
Found at i:361752 original size:2 final size:2
Alignment explanation
Indices: 361745--361810 Score: 114
Period size: 2 Copynumber: 33.0 Consensus size: 2
361735 CGGTGAAAAA
361745 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
361787 TC TT TC TC TT TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC
361811 AATCGGTCAC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:367638 original size:167 final size:166
Alignment explanation
Indices: 367189--368206 Score: 1734
Period size: 166 Copynumber: 6.1 Consensus size: 166
367179 AACATTACAT
** * *
367189 TTCTTGAGAAGAA-AACTTTTAAACATTTTTCAC-ATGTAGTTCTATGTTAAACTTTAAACCCCG
1 TTCTTGAGAAGAAGATTTTTTAAACA-TTTTC-CTATGTATTTCTATGTTAAACTTTGAACCCCG
* * * * *
367252 CCTGTGGCCCCAGTTTTGGTCCGGGGGTCACTATTTTTACAATTTAGAATCTTCACTATATATAA
64 CATGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATAC
367317 AAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG
129 AAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG
*
367355 TTCTTGAGAAAAAGATTTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCA
1 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCA
* * *
367420 TGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTCTACAATTTAGAATCTTCATTATACATACAA
66 TGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAA
367485 GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG
131 GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG
* *
367521 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTAAGGTATTTCTATGTTAAACTTTTAACCCCGC
1 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCT-ATGTATTTCTATGTTAAACTTTGAACCCCGC
* *
367586 ATGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTCTACAATTTAGAATCTTCACTATACATACA
65 ATGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACA
367651 AGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG
130 AGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG
*
367688 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATTGTATTTCTATGTTAAACTTTTAACCCCGC
1 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTA-TGTATTTCTATGTTAAACTTTGAACCCCGC
*
367753 ATGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATGTATACA
65 ATGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACA
367818 AGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG
130 AGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG
* * *
367855 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGGTAAAATTTGAACCCCGCC
1 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCA
* *
367920 TGGGGCCCCAGTTTTGGCCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATAAAA
66 TGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAA
367985 GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG
131 GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG
* * *
368021 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGGTAAAATTTGAACCCCGCC
1 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCA
*
368086 TGGGGCCCCAGTTTTGGCCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAA
66 TGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAA
368151 GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG
131 GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG
368187 TTCTTGAGAAGAAGATTTTT
1 TTCTTGAGAAGAAGATTTTT
368207 AAAAACATGC
Statistics
Matches: 819, Mismatches: 29, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
165 1 0.00
166 483 0.59
167 335 0.41
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (166 bp):
TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCA
TGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAA
GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG
Found at i:367896 original size:333 final size:332
Alignment explanation
Indices: 367189--368206 Score: 1752
Period size: 333 Copynumber: 3.1 Consensus size: 332
367179 AACATTACAT
** *
367189 TTCTTGAGAAGAA-AACTTTTAAACATTTTTCAC-ATGTAGTTCTATGTTAAACTTTAAACCCCG
1 TTCTTGAGAAGAAGATTTTTTAAACA-TTTTC-CTATGTATTTCTATGTTAAACTTTAAACCCCG
* * *
367252 CCTGTGGCCCCAGTTTTGGTCCGGGGGTCACTATTTTTACAATTTAGAATCTTCACTATATATAA
64 CCTGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATAA
*
367317 AAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTGAGAAAAAGATTTTTTAAACAT
129 AAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTGAGAAGAAGATTTTTTAAACAT
367382 TTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCATGGGGCCCCAGTTTTGGTCCGAGGGTC
194 TTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCATGGGGCCCCAGTTTTGGTCCGAGGGTC
* * *
367447 ACGATTTCTACAATTTAGAATCTTCATTATACATACAAGCTTTTGTGTAAATATTGGCATTTCTG
259 ACGATTTTTACAATTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTG
367512 GTGCAGTGG
324 GTGCAGTGG
* *
367521 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTAAGGTATTTCTATGTTAAACTTTTAACCCCGC
1 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCT-ATGTATTTCTATGTTAAACTTTAAACCCCGC
* * * *
367586 ATGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTCTACAATTTAGAATCTTCACTATACATACA
65 CTGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATAAA
367651 AGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTGAGAAGAAGATTTTTTAAACATT
130 AGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTGAGAAGAAGATTTTTTAAACATT
*
367716 TTCCTATTGTATTTCTATGTTAAACTTTTAACCCCGCATGGGGCCCCAGTTTTGGTCCGAGGGTC
195 TTCCTA-TGTATTTCTATGTTAAACTTTGAACCCCGCATGGGGCCCCAGTTTTGGTCCGAGGGTC
*
367781 ACGATTTTTACAATTTAGAATCTTCACTATGTATACAAGCTTTTGTGTAAATATTGGCATTTCTG
259 ACGATTTTTACAATTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTG
367846 GTGCAGTGG
324 GTGCAGTGG
* * *
367855 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGGTAAAATTTGAACCCCGCC
1 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTAAACCCCGCC
*
367920 TGGGGCCCCAGTTTTGGCCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATAAAA
66 TGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATAAAA
367985 GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTGAGAAGAAGATTTTTTAAACATTT
131 GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTGAGAAGAAGATTTTTTAAACATTT
* * * *
368050 TCCTATGTATTTCTATGGTAAAATTTGAACCCCGCCTGGGGCCCCAGTTTTGGCCCGAGGGTCAC
196 TCCTATGTATTTCTATGTTAAACTTTGAACCCCGCATGGGGCCCCAGTTTTGGTCCGAGGGTCAC
368115 GATTTTTACAATTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGT
261 GATTTTTACAATTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGT
368180 GCAGTGG
326 GCAGTGG
368187 TTCTTGAGAAGAAGATTTTT
1 TTCTTGAGAAGAAGATTTTT
368207 AAAAACATGC
Statistics
Matches: 649, Mismatches: 33, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
331 1 0.00
332 164 0.25
333 324 0.50
334 160 0.25
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (332 bp):
TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTAAACCCCGCC
TGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATAAAA
GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTGAGAAGAAGATTTTTTAAACATTT
TCCTATGTATTTCTATGTTAAACTTTGAACCCCGCATGGGGCCCCAGTTTTGGTCCGAGGGTCAC
GATTTTTACAATTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGT
GCAGTGG
Found at i:368388 original size:4 final size:4
Alignment explanation
Indices: 368379--368424 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
368369 AAAGTTTACA
* * *
368379 GACG GACG GACA GACA GATG GACG GACG GACG GACG GAC- GACG GAC
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GAC
368425 AACGGGTGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 3 0.08
4 34 0.92
ACGTcount: A:0.30, C:0.24, G:0.43, T:0.02
Consensus pattern (4 bp):
GACG
Found at i:368393 original size:12 final size:12
Alignment explanation
Indices: 368376--368429 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
368366 TGAAAAGTTT
368376 ACAGACGGACGG
1 ACAGACGGACGG
* *
368388 ACAGACAGATGG
1 ACAGACGGACGG
*
368400 ACGGACGGACGG
1 ACAGACGGACGG
*
368412 ACGGAC-GACGG
1 ACAGACGGACGG
368423 ACA-ACGG
1 ACAGACGG
368430 GTGATCAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
10 2 0.06
11 8 0.23
12 25 0.71
ACGTcount: A:0.33, C:0.24, G:0.41, T:0.02
Consensus pattern (12 bp):
ACAGACGGACGG
Found at i:374484 original size:101 final size:100
Alignment explanation
Indices: 374309--374510 Score: 368
Period size: 101 Copynumber: 2.0 Consensus size: 100
374299 AGCATCATAA
*
374309 CAATTCTTTTTCAAATTTATATAAATCAGTGCACTAGCTAGCTTTTTTAAAAATTCAATTAATTT
1 CAATTCTTTTTCAAATTTATATAAATCAGTGCACTAGCTAGCTTTTTTAAAAATTCAATTAAATT
*
374374 CTTAAACTCCCACTTGTAATATAGCTCCTCAATGCT
66 CTTAAACTCCCACTTGTAA-ATAGCCCCTCAATGCT
*
374410 CAATTCTTTTTCAAATTTATATAAATCCGTGCACTAGCTAGCTTTTTTAAAAATTCAATTAAATT
1 CAATTCTTTTTCAAATTTATATAAATCAGTGCACTAGCTAGCTTTTTTAAAAATTCAATTAAATT
374475 CTTAAACTCCCACTTGTAAATAGCCCCTCAATGCT
66 CTTAAACTCCCACTTGTAAATAGCCCCTCAATGCT
374510 C
1 C
374511 CTATTGGTCA
Statistics
Matches: 98, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
100 16 0.16
101 82 0.84
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (100 bp):
CAATTCTTTTTCAAATTTATATAAATCAGTGCACTAGCTAGCTTTTTTAAAAATTCAATTAAATT
CTTAAACTCCCACTTGTAAATAGCCCCTCAATGCT
Found at i:380443 original size:62 final size:61
Alignment explanation
Indices: 380363--380490 Score: 238
Period size: 62 Copynumber: 2.1 Consensus size: 61
380353 ATCCGCCAAA
*
380363 CTTAAACAAATACAAAAATAAATTAATGAAGTTAGGAATTTTTACCATATGCATTTGTCAT
1 CTTAAACAAATACAAAAATAAATTAATGAAGTTAGGAATTTTTACCATATACATTTGTCAT
380424 CTTANAACAAATACAAAAATAAATTAATGAAGTTAGGAATTTTTACCATATACATTTGTCAT
1 CTTA-AACAAATACAAAAATAAATTAATGAAGTTAGGAATTTTTACCATATACATTTGTCAT
380486 CTTAA
1 CTTAA
380491 GTTCGTAATT
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
61 5 0.08
62 60 0.92
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (61 bp):
CTTAAACAAATACAAAAATAAATTAATGAAGTTAGGAATTTTTACCATATACATTTGTCAT
Found at i:380734 original size:33 final size:32
Alignment explanation
Indices: 380646--380724 Score: 140
Period size: 32 Copynumber: 2.4 Consensus size: 32
380636 CCTAGCCATC
380646 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
*
380678 CTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
380710 TTTCCCCCACGGAAA
1 TTTCCCCC-CGGAAA
380725 GCTGACTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 38 0.86
33 6 0.14
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (32 bp):
TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
Found at i:381888 original size:13 final size:13
Alignment explanation
Indices: 381870--381919 Score: 72
Period size: 13 Copynumber: 4.2 Consensus size: 13
381860 AGGGTAATTA
381870 AAAAAAAACAACC
1 AAAAAAAACAACC
381883 -AAAAAAA-AA--
1 AAAAAAAACAACC
381892 AAAAAAAACAACC
1 AAAAAAAACAACC
381905 AAAAAAAACAACC
1 AAAAAAAACAACC
381918 AA
1 AA
381920 CACATATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 7 0.21
11 4 0.12
12 7 0.21
13 15 0.45
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAACAACC
Found at i:381897 original size:22 final size:22
Alignment explanation
Indices: 381869--381912 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
381859 AAGGGTAATT
381869 AAAAAAAAACAACCAAAAAAAA
1 AAAAAAAAACAACCAAAAAAAA
381891 AAAAAAAAACAACCAAAAAAAA
1 AAAAAAAAACAACCAAAAAAAA
381913 CAACCAACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (22 bp):
AAAAAAAAACAACCAAAAAAAA
Found at i:391040 original size:1 final size:1
Alignment explanation
Indices: 391036--391064 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
391026 TAGCCATCTT
391036 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
391065 GGAAAAATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:391095 original size:32 final size:32
Alignment explanation
Indices: 391059--391134 Score: 134
Period size: 32 Copynumber: 2.3 Consensus size: 32
391049 CCCCCCCCCC
391059 CCCCCCGGAAAAATGGCTATATAGCAGTTCTT
1 CCCCCCGGAAAAATGGCTATATAGCAGTTCTT
*
391091 CCCCCCGGAAAAATGGCTATATAGCAGTTTTT
1 CCCCCCGGAAAAATGGCTATATAGCAGTTCTT
391123 CCCCCACGGAAA
1 CCCCC-CGGAAA
391135 GCTGACTATA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 36 0.86
33 6 0.14
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.22
Consensus pattern (32 bp):
CCCCCCGGAAAAATGGCTATATAGCAGTTCTT
Found at i:391144 original size:33 final size:32
Alignment explanation
Indices: 391059--391147 Score: 124
Period size: 32 Copynumber: 2.8 Consensus size: 32
391049 CCCCCCCCCC
*
391059 CCCCCCGGAAAAATGGCTATATAGCAGTTCTT
1 CCCCCCGGAAAAATGACTATATAGCAGTTCTT
* *
391091 CCCCCCGGAAAAATGGCTATATAGCAGTTTTT
1 CCCCCCGGAAAAATGACTATATAGCAGTTCTT
**
391123 CCCCCACGGAAAGCTGACTATATAG
1 CCCCC-CGGAAAAATGACTATATAG
391148 TGGGCTTTCC
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 36 0.69
33 16 0.31
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (32 bp):
CCCCCCGGAAAAATGACTATATAGCAGTTCTT
Found at i:392312 original size:12 final size:12
Alignment explanation
Indices: 392297--392322 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
392287 ACCAAAAAAA
392297 AAAAAAACAACC
1 AAAAAAACAACC
392309 AAAAAAACAACC
1 AAAAAAACAACC
392321 AA
1 AA
392323 CACATATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAACAACC
Found at i:392323 original size:16 final size:15
Alignment explanation
Indices: 392280--392324 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
392270 AGGGTAATTT
*
392280 AAAAAAAACCAAAAA
1 AAAAAAAACCAACAA
*
392295 AAAAAAAAACAACCAA
1 AAAAAAAACCAA-CAA
*
392311 AAAAACAACCAACA
1 AAAAAAAACCAACA
392325 CATATATTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAACCAACAA
Found at i:392324 original size:19 final size:19
Alignment explanation
Indices: 392280--392315 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
392270 AGGGTAATTT
392280 AAAAAA-AACCAAAAAAAA
1 AAAAAACAACCAAAAAAAA
392298 AAAAAACAACCAAAAAAA
1 AAAAAACAACCAAAAAAA
392316 CAACCAACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (19 bp):
AAAAAACAACCAAAAAAAA
Found at i:393187 original size:17 final size:17
Alignment explanation
Indices: 393154--393187 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
393144 GGTTTTCCGG
*
393154 GGGGGAAAAGCTACTAT
1 GGGGGAAAAACTACTAT
*
393171 GGGGGAAAAACTGCTAT
1 GGGGGAAAAACTACTAT
393188 ACAACACCGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.35, T:0.18
Consensus pattern (17 bp):
GGGGGAAAAACTACTAT
Found at i:394119 original size:2 final size:2
Alignment explanation
Indices: 394112--394163 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
394102 AGCACATACA
*
394112 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
394154 AG AG AG AG AG
1 AG AG AG AG AG
394164 TGGGTGGGTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:397045 original size:2 final size:2
Alignment explanation
Indices: 397038--397069 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
397028 TAGCCGATTT
397038 TA TA TA TA TA TA TA NTA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA T
397070 TTCATCATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:397058 original size:15 final size:14
Alignment explanation
Indices: 397038--397069 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
397028 TAGCCGATTT
397038 TATATATATATATA
1 TATATATATATATA
397052 NTATATATATATATA
1 -TATATATATATATA
397067 TAT
1 TAT
397070 TTCATCATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATATATATATA
Found at i:403090 original size:22 final size:22
Alignment explanation
Indices: 403040--403092 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
403030 TATACGTGTT
*
403040 GCTTAAAGGTGGCTTAAAGAAA
1 GCTTAAAGATGGCTTAAAGAAA
* **
403062 GCGTAAAGATGGCTTAAAGGCA
1 GCTTAAAGATGGCTTAAAGAAA
403084 GCTTAAAGA
1 GCTTAAAGA
403093 CTATCTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21
Consensus pattern (22 bp):
GCTTAAAGATGGCTTAAAGAAA
Found at i:403113 original size:11 final size:11
Alignment explanation
Indices: 403097--403125 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
403087 TAAAGACTAT
403097 CTTTAAGCCAC
1 CTTTAAGCCAC
403108 CTTTAAGCCAC
1 CTTTAAGCCAC
403119 CTTTAAG
1 CTTTAAG
403126 GACAACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:403173 original size:11 final size:11
Alignment explanation
Indices: 403157--403210 Score: 99
Period size: 11 Copynumber: 4.9 Consensus size: 11
403147 GTCCAAACTT
403157 CTTTAAGCCAC
1 CTTTAAGCCAC
403168 CTTTAAGCCAC
1 CTTTAAGCCAC
*
403179 CTTTAAGCTAC
1 CTTTAAGCCAC
403190 CTTTAAGCCAC
1 CTTTAAGCCAC
403201 CTTTAAGCCA
1 CTTTAAGCCA
403211 TTAAAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 41 1.00
ACGTcount: A:0.28, C:0.33, G:0.09, T:0.30
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:406570 original size:6 final size:6
Alignment explanation
Indices: 406559--406583 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
406549 GAATAAAGAA
406559 ATTGTC ATTGTC ATTGTC ATTGTC A
1 ATTGTC ATTGTC ATTGTC ATTGTC A
406584 AATATATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (6 bp):
ATTGTC
Found at i:412798 original size:15 final size:15
Alignment explanation
Indices: 412774--412803 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
412764 GCGTTAATCT
412774 CAATCCCATAGCATA
1 CAATCCCATAGCATA
*
412789 CAATCTCATAGCATA
1 CAATCCCATAGCATA
412804 TTATTAGACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.30, G:0.07, T:0.23
Consensus pattern (15 bp):
CAATCCCATAGCATA
Done.