Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 16 of 91
Found at i:5152915 original size:14 final size:14
Alignment explanation
Indices: 5152896--5152925 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5152886 AATTGTCTAT
*
5152896 TTATTTATTTATTA
1 TTATTTAATTATTA
5152910 TTATTTAATTATTA
1 TTATTTAATTATTA
5152924 TT
1 TT
5152926 TTCATTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATTTAATTATTA
Found at i:5154511 original size:35 final size:35
Alignment explanation
Indices: 5154450--5154545 Score: 158
Period size: 35 Copynumber: 2.7 Consensus size: 35
5154440 ACCCTTCAAC
*
5154450 TCTCCCTTT-GGGCACTGATCGGTCTCCTCCCCTTTT
1 TCTCCCTTTAGTGC-CTG-TCGGTCTCCTCCCCTTTT
5154486 TCTCCCTTTAGTGCCTGTCGGTCTCCTCCCCTTTT
1 TCTCCCTTTAGTGCCTGTCGGTCTCCTCCCCTTTT
5154521 TCTCCCTTTAGTGCCTGTCGGTCTC
1 TCTCCCTTTAGTGCCTGTCGGTCTC
5154546 ACCTGTTCTC
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
35 43 0.74
36 12 0.21
37 3 0.05
ACGTcount: A:0.04, C:0.39, G:0.17, T:0.41
Consensus pattern (35 bp):
TCTCCCTTTAGTGCCTGTCGGTCTCCTCCCCTTTT
Found at i:5155385 original size:38 final size:37
Alignment explanation
Indices: 5155327--5155934 Score: 441
Period size: 38 Copynumber: 15.7 Consensus size: 37
5155317 TTGTTTTTTT
* * * * *
5155327 AAATGAATTTCTCAAGATTGAGGTAATGACACTTTTAA
1 AAATGAACTCCTCAAAACTGAGGCAATGA-ACTTTTAA
* * *
5155365 GAATAAACTCCTCAAAATTGAGGCAATGAAAC-TTTAA
1 AAATGAACTCCTCAAAACTGAGGCAATG-AACTTTTAA
** * *
5155402 AAATGAACTCCTCAAGGCTGAGGTAATGGAACTTTAAA
1 AAATGAACTCCTCAAAACTGAGGCAAT-GAACTTTTAA
* *
5155440 AAATGAACTCCTCAAAGA-TGAGGCAACGGAACTTCTT-T
1 AAATGAACTCCTCAAA-ACTGAGGCAA-TGAACTT-TTAA
* *
5155478 AAACGAACTCCTCAAAGCTGAGGCAATGAAACTTTTAA
1 AAATGAACTCCTCAAAACTGAGGCAATG-AACTTTTAA
* * * *
5155516 AAATGAACTCCTCAAAGCGGAGGCAACGAAACTTCTT-T
1 AAATGAACTCCTCAAAACTGAGGCAATG-AACTT-TTAA
* * * *
5155554 AAACGAACTCCTCAAAGCTGAGGCAACGGAACTTTAAA
1 AAATGAACTCCTCAAAACTGAGGCAA-TGAACTTTTAA
* * *
5155592 AAATGAACTCCTCAAAGCTAAGGCAACGAGACTTTTTAA
1 AAATGAACTCCTCAAAACTGAGGCAATGA-AC-TTTTAA
* *
5155631 AAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAA
1 AAATGAACTCCTCAAAACTGAGGCAATG-AACTTTTAA
* ** *
5155669 AAATGAACTCCTCAAAGCTGAGGCAACCAAACTTTAAA
1 AAATGAACTCCTCAAAACTGAGGCAA-TGAACTTTTAA
** * **
5155707 AAATGAACTCCTCAAAGTTGAGGCAACGAGACTTTTTTTTTT
1 AAATGAACTCCTCAAAACTGAGGCAATGA-AC----TTTTAA
* * *
5155749 AAATGAACTCCTCAAAGCTGAGGCAACGGAACTTTAAA
1 AAATGAACTCCTCAAAACTGAGGCAA-TGAACTTTTAA
* * * *
5155787 AAATGAACTTCTCAAAGCTGAGGCAACGAGACTTTAAA
1 AAATGAACTCCTCAAAACTGAGGCAATGA-ACTTTTAA
* *
5155825 AAATGAACTCCTCAAAGCTGAGGCAACGAGACTTTTTTTTTTTTAA
1 AAATGAACTCCTCAAAACTGAGGCAATGA-AC--------TTTTAA
** *
5155871 AAATGAACTCCTCAAAGTTGAGGCAACGAAACTTTTAA
1 AAATGAACTCCTCAAAACTGAGGCAATG-AACTTTTAA
* *
5155909 AAATGAACTCCTCCAAGCTGAGGCAA
1 AAATGAACTCCTCAAAACTGAGGCAA
5155935 CAAAACTTTT
Statistics
Matches: 482, Mismatches: 56, Indels: 64
0.80 0.09 0.11
Matches are distributed among these distances:
37 39 0.08
38 335 0.70
39 40 0.08
40 1 0.00
42 30 0.06
43 2 0.00
46 34 0.07
47 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.24
Consensus pattern (37 bp):
AAATGAACTCCTCAAAACTGAGGCAATGAACTTTTAA
Found at i:5155512 original size:76 final size:75
Alignment explanation
Indices: 5155322--5155948 Score: 662
Period size: 76 Copynumber: 8.1 Consensus size: 75
5155312 TTTTTTTGTT
* * * * * * * * **
5155322 TTTTTAAATGAATTTCTC-AAGATTGAGGTAATGACACTTTTAAGAATAAACTCCTCAAAATTGA
1 TTTTTAAATGAACTCCTCAAAG-CTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGA
*
5155386 GGCAATGAAAC
65 GGCAACGAAAC
** * * * * * *
5155397 TTTAAAAATGAACTCCTCAAGGCTGAGGTAATGGAACTTTAAAAAATGAACTCCTCAAAGATGAG
1 TTTTTAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGAG
*
5155462 GCAACGGAAC
66 GCAACGAAAC
* * *
5155472 TTCTTTAAACGAACTCCTCAAAGCTGAGGCAATGAAACTTTTAAAAATGAACTCCTCAAAGCGGA
1 TT-TTTAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGA
5155537 GGCAACGAAAC
65 GGCAACGAAAC
* * * *
5155548 TTCTTTAAACGAACTCCTCAAAGCTGAGGCAACGGAACTTTAAAAAATGAACTCCTCAAAGCTAA
1 TT-TTTAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGA
*
5155613 GGCAACGAGAC
65 GGCAACGAAAC
5155624 TTTTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAGCTG
1 TTTTT--AAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAGCTG
*
5155689 AGGCAACCAAAC
64 AGGCAACGAAAC
** * * **
5155701 TTTAAAAAATGAACTCCTCAAAGTTGAGGCAACGAGACTTTTTTTTTTAAATGAACTCCTCAAAG
1 TTT-TTAAATGAACTCCTCAAAGCTGAGGCAACGAAAC----TTTTAAAAATGAACTCCTCAAAG
*
5155766 CTGAGGCAACGGAAC
61 CTGAGGCAACGAAAC
** * * *
5155781 TTTAAAAAATGAACTTCTCAAAGCTGAGGCAACGAGACTTTAAAAAATGAACTCCTCAAAGCTGA
1 TTT-TTAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGA
*
5155846 GGCAACGAGAC
65 GGCAACGAAAC
*
5155857 TTTTTTTTTTTTAAAAATGAACTCCTCAAAGTTGAGGCAACGAAACTTTTAAAAATGAACTCCTC
1 -------TTTTT--AAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTC
* *
5155922 CAAGCTGAGGCAACAAAAC
57 AAAGCTGAGGCAACGAAAC
5155941 TTTTTAAA
1 TTTTTAAA
5155949 GTCTTGAAAC
Statistics
Matches: 473, Mismatches: 61, Indels: 36
0.83 0.11 0.06
Matches are distributed among these distances:
75 65 0.14
76 200 0.42
77 72 0.15
80 70 0.15
83 3 0.01
84 63 0.13
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (75 bp):
TTTTTAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGAG
GCAACGAAAC
Found at i:5155684 original size:115 final size:116
Alignment explanation
Indices: 5155397--5155935 Score: 712
Period size: 118 Copynumber: 4.6 Consensus size: 116
5155387 GCAATGAAAC
* * * * * *
5155397 TTTAAAAATGAACTCCTCAAGGCTGAGGTAATGGAACTTTAAAAAATGAACTCCTCAAAGATGAG
1 TTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGAG
** * * *
5155462 GCAACGGAACTTCT-TTAAACGAACTCCTCAAAGCTGAGGCAATGAAAC--T
66 GCAACGGAACTT-TAAAAAATGAACTCCTCAAAGCTGAGGCAACGAGACTTT
* * *
5155511 TTTAAAAATGAACTCCTCAAAGCGGAGGCAACGAAACTTCTT-TAAACGAACTCCTCAAAGCTGA
1 TTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAAACTT-TTAAAAATGAACTCCTCAAAGCTGA
*
5155575 GGCAACGGAACTTTAAAAAATGAACTCCTCAAAGCTAAGGCAACGAGAC-TT
65 GGCAACGGAACTTTAAAAAATGAACTCCTCAAAGCTGAGGCAACGAGACTTT
5155626 TTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGAG
1 TTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGAG
** *
5155691 GCAACCAAACTTTAAAAAATGAACTCCTCAAAGTTGAGGCAACGAGACTTTTT
66 GCAACGGAACTTTAAAAAATGAACTCCTCAAAGCTGAGGCAACGAGAC--TTT
** * * *
5155744 TTTTTAAATGAACTCCTCAAAGCTGAGGCAACGGAACTTTAAAAAATGAACTTCTCAAAGCTGAG
1 TTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGAG
5155809 GCAAC-GAGACTTTAAAAAATGAACTCCTCAAAGCTGAGGCAACGAGACTTTTTTTTT
66 GCAACGGA-ACTTTAAAAAATGAACTCCTCAAAGCTGAGGCAACGAGAC------TTT
* *
5155866 TTTAAAAATGAACTCCTCAAAGTTGAGGCAACGAAACTTTTAAAAATGAACTCCTCCAAGCTGAG
1 TTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGAG
5155931 GCAAC
66 GCAAC
5155936 AAAACTTTTT
Statistics
Matches: 377, Mismatches: 36, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
113 1 0.00
114 96 0.25
115 105 0.28
117 1 0.00
118 106 0.28
122 68 0.18
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.23
Consensus pattern (116 bp):
TTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGAG
GCAACGGAACTTTAAAAAATGAACTCCTCAAAGCTGAGGCAACGAGACTTT
Found at i:5155886 original size:84 final size:84
Alignment explanation
Indices: 5155785--5155945 Score: 259
Period size: 84 Copynumber: 1.9 Consensus size: 84
5155775 CGGAACTTTA
* *
5155785 AAAAATGAACTTCTCAAAGCTGAGGCAACGAGACTTTAAAAAATGAACTCCTCAAAGCTGAGGCA
1 AAAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTAAAAAATGAACTCCTCAAAGCTGAGGCA
* *
5155850 ACGAGACTTTTTTTTTTTT
66 ACAAAACTTTTTTTTTTTT
* * *
5155869 AAAAATGAACTCCTCAAAGTTGAGGCAACGAAACTTTTAAAAATGAACTCCTCCAAGCTGAGGCA
1 AAAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTAAAAAATGAACTCCTCAAAGCTGAGGCA
5155934 ACAAAACTTTTT
66 ACAAAACTTTTT
5155946 AAAGTCTTGA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 70 1.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (84 bp):
AAAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTAAAAAATGAACTCCTCAAAGCTGAGGCA
ACAAAACTTTTTTTTTTTT
Found at i:5155935 original size:38 final size:38
Alignment explanation
Indices: 5155865--5155944 Score: 133
Period size: 38 Copynumber: 2.1 Consensus size: 38
5155855 ACTTTTTTTT
* *
5155865 TTTTAAAAATGAACTCCTCAAAGTTGAGGCAACGAAAC
1 TTTTAAAAATGAACTCCTCAAAGCTGAGGCAACAAAAC
*
5155903 TTTTAAAAATGAACTCCTCCAAGCTGAGGCAACAAAAC
1 TTTTAAAAATGAACTCCTCAAAGCTGAGGCAACAAAAC
5155941 TTTT
1 TTTT
5155945 TAAAGTCTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (38 bp):
TTTTAAAAATGAACTCCTCAAAGCTGAGGCAACAAAAC
Found at i:5168194 original size:11 final size:11
Alignment explanation
Indices: 5168174--5168202 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5168164 GTCTTAGATT
5168174 TTTA-TTATTA
1 TTTATTTATTA
5168184 TTTATTTATTA
1 TTTATTTATTA
5168195 TTTATTTA
1 TTTATTTA
5168203 ATGTCATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:5168313 original size:17 final size:18
Alignment explanation
Indices: 5168277--5168314 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5168267 TTTTATCATC
*
5168277 ATTTTTTTATCTATTGTT
1 ATTTATTTATCTATTGTT
*
5168295 ATTTATTTAT-TATTTTT
1 ATTTATTTATCTATTGTT
5168312 ATT
1 ATT
5168315 GAATAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
ATTTATTTATCTATTGTT
Found at i:5168868 original size:18 final size:16
Alignment explanation
Indices: 5168831--5168861 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5168821 CTATATGCCT
5168831 TTATTTTTATAGTATA
1 TTATTTTTATAGTATA
5168847 TTATTTTTATA-TATA
1 TTATTTTTATAGTATA
5168862 GAGTTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTATTTTTATAGTATA
Found at i:5171215 original size:21 final size:20
Alignment explanation
Indices: 5171190--5171230 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
5171180 CTTCCTTCTA
*
5171190 TGATTTTTGACTGTTAAAGAC
1 TGATTTTAGACT-TTAAAGAC
*
5171211 TGATTTTAGCCTTTAAAGAC
1 TGATTTTAGACTTTAAAGAC
5171231 AGTTTTTAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.41
Consensus pattern (20 bp):
TGATTTTAGACTTTAAAGAC
Found at i:5171226 original size:20 final size:20
Alignment explanation
Indices: 5171203--5171241 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5171193 TTTTTGACTG
*
5171203 TTAAAGACTGATTTTAGCCT
1 TTAAAGACAGATTTTAGCCT
*
5171223 TTAAAGACAGTTTTTAGCC
1 TTAAAGACAGATTTTAGCC
5171242 GTTATTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
TTAAAGACAGATTTTAGCCT
Found at i:5174886 original size:2 final size:2
Alignment explanation
Indices: 5174879--5174907 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5174869 GATTGAAGTC
5174879 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5174908 GTTTCTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5175754 original size:28 final size:27
Alignment explanation
Indices: 5175680--5175778 Score: 180
Period size: 28 Copynumber: 3.6 Consensus size: 27
5175670 TACTTTCAAC
5175680 TTAAGTTGGGTAGCTTTTAGATTAGAG
1 TTAAGTTGGGTAGCTTTTAGATTAGAG
5175707 TTAAGTTGGGTAGCTTTTAGATTAGAG
1 TTAAGTTGGGTAGCTTTTAGATTAGAG
5175734 TTAAGTTGGGGTAGCTTTTAGATTAGAG
1 TTAAGTT-GGGTAGCTTTTAGATTAGAG
5175762 TTAAGTTGGGGTAGCTT
1 TTAAGTT-GGGTAGCTT
5175779 CTTTACTTCA
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
27 34 0.48
28 37 0.52
ACGTcount: A:0.24, C:0.04, G:0.31, T:0.40
Consensus pattern (27 bp):
TTAAGTTGGGTAGCTTTTAGATTAGAG
Found at i:5176574 original size:14 final size:14
Alignment explanation
Indices: 5176555--5176581 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5176545 AATCAAAGAA
5176555 ATATACCAAAAAAT
1 ATATACCAAAAAAT
5176569 ATATACCAAAAAA
1 ATATACCAAAAAA
5176582 AATTCAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.19
Consensus pattern (14 bp):
ATATACCAAAAAAT
Found at i:5176732 original size:69 final size:67
Alignment explanation
Indices: 5176650--5177098 Score: 382
Period size: 69 Copynumber: 6.5 Consensus size: 67
5176640 TGGTTGATTT
* * * * * *
5176650 TTAAGAGCGATAAAGCTTGGATATTTGTCGCCGGTGAGAGTGGGTAAAGCTTGGGTTGTTTGCCG
1 TTAAGAGGGGTAAAGCTTGGTTATTTGCCGCCGGTTAGAG-GGGTAAAGCTTGGG-TATTTGCCG
*
5176715 CCAG
64 CCGG
* * * * *
5176719 TTAAGAGGGATAAAGCTTGGGTTTTTTGCCACCGGTTAGGAGGGGTAAAGCTTGGGTATTTACTG
1 TTAAGAGGGGTAAAGCTT-GGTTATTTGCCGCCGGTTA-GAGGGGTAAAGCTTGGGTATTTGCCG
*
5176784 TCGG
64 CCGG
* * *
5176788 -TGAGAGTGGGTAAAGCTTGGGTTATTTACCGCCGGTTAGGAGGGATAAAGCTTGGGTATTTGCC
1 TTAAGAG-GGGTAAAGCTT-GGTTATTTGCCGCCGGTTA-GAGGGGTAAAGCTTGGGTATTTGCC
* *
5176852 ACCTG
63 GCCGG
* * * * *
5176857 -TGAGAGTGGGTAAAGCTTGGGTTGTTTGCCGCCAGTTAAGAGGGATAAAGCTTGGGTTTTTTGC
1 TTAAGAG-GGGTAAAGCTT-GGTTATTTGCCGCCGGTT-AGAGGGGTAAAGCTTGGG-TATTTGC
*
5176921 CACCGG
62 CGCCGG
* * * *
5176927 TTAGGAGGGGTAAAGCTTGGGTATTTGCTGCCGGTTAGAGTGGGTAAAGCTTGGGTATTTGCTGC
1 TTAAGAGGGGTAAAGCTTGGTTATTTGCCGCCGGTTAGAG-GGGTAAAGCTTGGGTATTTGCCGC
5176992 CGG
65 CGG
* * * *
5176995 TT-AGAGTGGGTAAAGCTTGGGTATTTGCCACCTGTGAGAGTGGGTAAAGCTTGGGCTATTTGCC
1 TTAAGAG-GGGTAAAGCTTGGTTATTTGCCGCCGGTTAGAG-GGGTAAAGCTTGGG-TATTTGCC
*
5177059 GCCCG
63 GCCGG
* * ** * *
5177064 TTAGGAAGAATAAAGCTTGGGCTATTTGCTGCCGG
1 TTAAGAGGGGTAAAGCTT-GGTTATTTGCCGCCGG
5177099 CAAAGGAAAG
Statistics
Matches: 317, Mismatches: 52, Indels: 21
0.81 0.13 0.05
Matches are distributed among these distances:
67 3 0.01
68 65 0.21
69 177 0.56
70 65 0.21
71 7 0.02
ACGTcount: A:0.21, C:0.14, G:0.35, T:0.30
Consensus pattern (67 bp):
TTAAGAGGGGTAAAGCTTGGTTATTTGCCGCCGGTTAGAGGGGTAAAGCTTGGGTATTTGCCGCC
GG
Found at i:5176947 original size:173 final size:172
Alignment explanation
Indices: 5176658--5177084 Score: 685
Period size: 173 Copynumber: 2.5 Consensus size: 172
5176648 TTTTAAGAGC
* * * *
5176658 GATAAAGCTTGGATATTTGTCGCCGGTGAGAGTGGGTAAAGCTTGGGTTGTTTGCCGCCAGTTAA
1 GATAAAGCTTGGGTATTTGCCACCTGTGAGAGTGGGTAAAGCTTGGGTTGTTTGCCGCCAGTTAA
*
5176723 GAGGGATAAAGCTTGGGTTTTTTGCCACCGGTTAGGAGGGGTAAAGCTTGGGTATTTACTGTCGG
66 GAGGGATAAAGCTTGGGTTTTTTGCCACCGGTTAGGAGGGGTAAAGCTTGGGTATTTACTGCCGG
5176788 TGAGAGTGGGTAAAGCTTGGGTTATTTACCGCCGGTTAGGAG-G
131 TGAGAGTGGGTAAAGCTTGGG-TATTTACCGCCGGTTA-GAGTG
5176831 GATAAAGCTTGGGTATTTGCCACCTGTGAGAGTGGGTAAAGCTTGGGTTGTTTGCCGCCAGTTAA
1 GATAAAGCTTGGGTATTTGCCACCTGTGAGAGTGGGTAAAGCTTGGGTTGTTTGCCGCCAGTTAA
*
5176896 GAGGGATAAAGCTTGGGTTTTTTGCCACCGGTTAGGAGGGGTAAAGCTTGGGTATTTGCTGCCGG
66 GAGGGATAAAGCTTGGGTTTTTTGCCACCGGTTAGGAGGGGTAAAGCTTGGGTATTTACTGCCGG
* * *
5176961 TTAGAGTGGGTAAAGCTTGGGTATTTGCTGCCGGTTAGAGTG
131 TGAGAGTGGGTAAAGCTTGGGTATTTACCGCCGGTTAGAGTG
* * * * *
5177003 GGTAAAGCTTGGGTATTTGCCACCTGTGAGAGTGGGTAAAGCTTGGGCTATTTGCCGCCCGTTAG
1 GATAAAGCTTGGGTATTTGCCACCTGTGAGAGTGGGTAAAGCTTGGGTTGTTTGCCGCCAGTTAA
* *
5177068 GAAGAATAAAGCTTGGG
66 GAGGGATAAAGCTTGGG
5177085 CTATTTGCTG
Statistics
Matches: 237, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
171 3 0.01
172 90 0.38
173 144 0.61
ACGTcount: A:0.21, C:0.14, G:0.36, T:0.30
Consensus pattern (172 bp):
GATAAAGCTTGGGTATTTGCCACCTGTGAGAGTGGGTAAAGCTTGGGTTGTTTGCCGCCAGTTAA
GAGGGATAAAGCTTGGGTTTTTTGCCACCGGTTAGGAGGGGTAAAGCTTGGGTATTTACTGCCGG
TGAGAGTGGGTAAAGCTTGGGTATTTACCGCCGGTTAGAGTG
Found at i:5177085 original size:35 final size:34
Alignment explanation
Indices: 5176660--5177098 Score: 431
Period size: 35 Copynumber: 12.7 Consensus size: 34
5176650 TTAAGAGCGA
* * *
5176660 TAAAGCTTGGATATTTGTCGCCGGTGAGAGTGGG
1 TAAAGCTTGGGTATTTGCCGCCGGTTAGAGTGGG
* * *
5176694 TAAAGCTTGGGTTGTTTGCCGCCAGTTAAGAG-GGA
1 TAAAGCTTGGG-TATTTGCCGCCGGTT-AGAGTGGG
* *
5176729 TAAAGCTTGGGTTTTTTGCCACCGGTTAGGAG-GGG
1 TAAAGCTTGGG-TATTTGCCGCCGGTTA-GAGTGGG
* * * *
5176764 TAAAGCTTGGGTATTTACTGTCGGTGAGAGTGGG
1 TAAAGCTTGGGTATTTGCCGCCGGTTAGAGTGGG
* *
5176798 TAAAGCTTGGGTTATTTACCGCCGGTTAGGAG-GGA
1 TAAAGCTTGGG-TATTTGCCGCCGGTTA-GAGTGGG
* * *
5176833 TAAAGCTTGGGTATTTGCCACCTGTGAGAGTGGG
1 TAAAGCTTGGGTATTTGCCGCCGGTTAGAGTGGG
* * *
5176867 TAAAGCTTGGGTTGTTTGCCGCCAGTTAAGAG-GGA
1 TAAAGCTTGGG-TATTTGCCGCCGGTT-AGAGTGGG
* *
5176902 TAAAGCTTGGGTTTTTTGCCACCGGTTAGGAG-GGG
1 TAAAGCTTGGG-TATTTGCCGCCGGTTA-GAGTGGG
*
5176937 TAAAGCTTGGGTATTTGCTGCCGGTTAGAGTGGG
1 TAAAGCTTGGGTATTTGCCGCCGGTTAGAGTGGG
*
5176971 TAAAGCTTGGGTATTTGCTGCCGGTTAGAGTGGG
1 TAAAGCTTGGGTATTTGCCGCCGGTTAGAGTGGG
* * *
5177005 TAAAGCTTGGGTATTTGCCACCTGTGAGAGTGGG
1 TAAAGCTTGGGTATTTGCCGCCGGTTAGAGTGGG
* * **
5177039 TAAAGCTTGGGCTATTTGCCGCCCGTTAG-GAAGAA
1 TAAAGCTTGGG-TATTTGCCGCCGGTTAGAG-TGGG
*
5177074 TAAAGCTTGGGCTATTTGCTGCCGG
1 TAAAGCTTGGG-TATTTGCCGCCGG
5177099 CAAAGGAAAG
Statistics
Matches: 343, Mismatches: 49, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
33 9 0.03
34 153 0.45
35 170 0.50
36 11 0.03
ACGTcount: A:0.20, C:0.14, G:0.36, T:0.30
Consensus pattern (34 bp):
TAAAGCTTGGGTATTTGCCGCCGGTTAGAGTGGG
Found at i:5177909 original size:11 final size:11
Alignment explanation
Indices: 5177893--5177928 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
5177883 TTTTAATTTT
5177893 AAATAAATAAA
1 AAATAAATAAA
5177904 AAATAAATATAA
1 AAATAAATA-AA
5177916 AAA-AAATAAA
1 AAATAAATAAA
5177926 AAA
1 AAA
5177929 ATGATAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.21
11 14 0.58
12 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:5178245 original size:13 final size:13
Alignment explanation
Indices: 5178229--5178285 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
5178219 ATAAGAATAG
*
5178229 AAAATATGATAAT
1 AAAATATAATAAT
*
5178242 AAAAGATAATAAT
1 AAAATATAATAAT
*
5178255 AAAATAAAAATAAT
1 AAAAT-ATAATAAT
5178269 AATTAA-ATAATAAT
1 AA--AATATAATAAT
5178283 AAA
1 AAA
5178286 TGAGAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
12 1 0.03
13 15 0.42
14 18 0.50
16 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (13 bp):
AAAATATAATAAT
Found at i:5178268 original size:14 final size:15
Alignment explanation
Indices: 5178247--5178285 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
5178237 ATAATAAAAG
5178247 ATAATAATAAAATAA
1 ATAATAATAAAATAA
*
5178262 A-AATAAT-AATTAA
1 ATAATAATAAAATAA
5178275 ATAATAATAAA
1 ATAATAATAAA
5178286 TGAGAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 6 0.29
14 12 0.57
15 3 0.14
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAATAATAAAATAA
Found at i:5178269 original size:17 final size:17
Alignment explanation
Indices: 5178239--5178284 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
5178229 AAAATATGAT
5178239 AATAAAAGATAATAATAA
1 AATAAAA-ATAATAATAA
*
5178257 AATAAAAATAATAATTA
1 AATAAAAATAATAATAA
*
5178274 AATAATAATAA
1 AATAAAAATAA
5178285 ATGAGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 19 0.73
18 7 0.27
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
AATAAAAATAATAATAA
Found at i:5190365 original size:20 final size:20
Alignment explanation
Indices: 5190320--5190357 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5190310 TTTTGGCCCC
5190320 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
5190340 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
5190358 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:5197213 original size:20 final size:20
Alignment explanation
Indices: 5197168--5197205 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5197158 TTTTGGCCCC
5197168 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
5197188 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
5197206 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:5197289 original size:27 final size:27
Alignment explanation
Indices: 5197259--5197316 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
5197249 TTGGAGTAAA
*
5197259 AGGGTAAAATGGTAATTTTGCCACC-CC
1 AGGGCAAAATGGTAATTTT-CCACCACC
*
5197286 AGGGGCAAAATTGTAATTTTCCACCACC
1 A-GGGCAAAATGGTAATTTTCCACCACC
5197314 AGG
1 AGG
5197317 ACATTTTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (27 bp):
AGGGCAAAATGGTAATTTTCCACCACC
Found at i:5202766 original size:17 final size:17
Alignment explanation
Indices: 5202726--5202758 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5202716 ATGATAATAA
5202726 AAAATAATAATTAAATG
1 AAAATAATAATTAAATG
5202743 AAAATAATAATTAAAT
1 AAAATAATAATTAAAT
5202759 AATAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
AAAATAATAATTAAATG
Found at i:5202767 original size:27 final size:27
Alignment explanation
Indices: 5202719--5202770 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
5202709 AGAAAATATG
5202719 ATAATAAAAAATAATAATTAAATGAAA
1 ATAATAAAAAATAATAATTAAATGAAA
*
5202746 ATAATAATTAAATAATAA-TAAATGA
1 ATAATAA-AAAATAATAATTAAATGA
5202771 GAAAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (27 bp):
ATAATAAAAAATAATAATTAAATGAAA
Found at i:5203786 original size:23 final size:23
Alignment explanation
Indices: 5203760--5203861 Score: 75
Period size: 26 Copynumber: 4.3 Consensus size: 23
5203750 ATTTATTTTT
*
5203760 ATTTTATTTTTTAAATATTAATA
1 ATTTTATTATTTAAATATTAATA
*
5203783 ATTTATAATTAATTAAAATATTAATA
1 ATTT-T-ATT-ATTTAAATATTAATA
* *
5203809 A-TTAATAATTTAAATTATTAAT-
1 ATTTTATTATTTAAA-TATTAATA
*
5203831 ATTTTAGTATAATTTAATTATTAAT-
1 ATTTTA-T-T-ATTTAAATATTAATA
5203856 ATTTTA
1 ATTTTA
5203862 ATTAATAATA
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
22 7 0.11
23 16 0.25
24 2 0.03
25 18 0.29
26 20 0.32
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (23 bp):
ATTTTATTATTTAAATATTAATA
Found at i:5203787 original size:15 final size:15
Alignment explanation
Indices: 5203769--5203917 Score: 70
Period size: 15 Copynumber: 10.2 Consensus size: 15
5203759 TATTTTATTT
5203769 TTTAAATATTAATAA
1 TTTAAATATTAATAA
5203784 TTTATAATTAATTAA-AA
1 TTTA-AA-T-ATTAATAA
5203801 TATT-AATAATTAATAA
1 T-TTAAAT-ATTAATAA
5203817 TTTAAATTATTAAT-A
1 TTTAAA-TATTAATAA
*
5203832 TTT---TAGT-ATAA
1 TTTAAATATTAATAA
* *
5203843 TTTAATTATTAATAT
1 TTTAAATATTAATAA
* *
5203858 TTTAATTAATAAT-A
1 TTTAAATATTAATAA
*
5203872 TTT---TATTTATAA
1 TTTAAATATTAATAA
*
5203884 TTT-AATATTATTATGA
1 TTTAAATATTA--ATAA
*
5203900 TTAAAATATTAATAA
1 TTTAAATATTAATAA
5203915 TTT
1 TTT
5203918 TTTATTTTTT
Statistics
Matches: 104, Mismatches: 12, Indels: 36
0.68 0.08 0.24
Matches are distributed among these distances:
10 2 0.02
11 12 0.12
12 4 0.04
14 10 0.10
15 37 0.36
16 20 0.19
17 12 0.12
18 7 0.07
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (15 bp):
TTTAAATATTAATAA
Found at i:5203801 original size:26 final size:24
Alignment explanation
Indices: 5203772--5203867 Score: 97
Period size: 25 Copynumber: 3.9 Consensus size: 24
5203762 TTTATTTTTT
5203772 AAATATTAATAATTTATAATTAATTA
1 AAATATTAAT-ATTT-TAATTAATTA
*
5203798 AAATATTAATA-ATTAA-TAATTTA
1 AAATATTAATATTTTAATTAA-TTA
* * *
5203821 AATTATTAATATTTTAGTATAATTT
1 AAATATTAATATTTTAAT-TAATTA
*
5203846 AATTATTAATATTTTAATTAAT
1 AAATATTAATATTTTAATTAAT
5203868 AATATTTTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
22 3 0.05
23 16 0.27
24 8 0.13
25 20 0.33
26 13 0.22
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (24 bp):
AAATATTAATATTTTAATTAATTA
Found at i:5203862 original size:41 final size:42
Alignment explanation
Indices: 5203803--5203918 Score: 130
Period size: 41 Copynumber: 2.8 Consensus size: 42
5203793 AATTAAAATA
* *
5203803 TTAATAATTAATAATTTAAATTATTAATATTTTA-GTATAAT
1 TTAATTATTAATATTTTAAATTATTAATATTTTATGTATAAT
* *
5203844 TTAATTATTAATATTTT-AATTAATAATATTTTATTTATAAT
1 TTAATTATTAATATTTTAAATTATTAATATTTTATGTATAAT
* * *
5203885 TTAA-TATTATTATGATTAAAATATTAATAATTTT
1 TTAATTATTAATAT-TTTAAATTATTAAT-ATTTT
5203919 TTATTTTTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
40 23 0.37
41 27 0.43
42 8 0.13
43 5 0.08
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (42 bp):
TTAATTATTAATATTTTAAATTATTAATATTTTATGTATAAT
Found at i:5203957 original size:16 final size:16
Alignment explanation
Indices: 5203938--5204022 Score: 52
Period size: 16 Copynumber: 5.3 Consensus size: 16
5203928 ATTTATACTC
5203938 ATTAAAATTTTAATAT
1 ATTAAAATTTTAATAT
*
5203954 ATT-AATTATTTAATA-
1 ATTAAAAT-TTTAATAT
* **
5203969 AATAAAACATTAATAGT
1 ATTAAAATTTTAATA-T
*
5203986 -TTAAAATATTAATAT
1 ATTAAAATTTTAATAT
*
5204001 -TATAATATTTTAATCAT
1 AT-TAAAATTTTAAT-AT
5204018 ATTAA
1 ATTAA
5204023 TATTAATAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
15 13 0.25
16 34 0.64
17 5 0.09
18 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (16 bp):
ATTAAAATTTTAATAT
Found at i:5203958 original size:8 final size:8
Alignment explanation
Indices: 5203947--5204065 Score: 50
Period size: 8 Copynumber: 14.5 Consensus size: 8
5203937 CATTAAAATT
5203947 TTAATATA
1 TTAATATA
5203955 TTAAT-TA
1 TTAATATA
5203962 TTTAATA-A
1 -TTAATATA
* * *
5203970 ATAAAACA
1 TTAATATA
5203978 TTAATAGT-
1 TTAATA-TA
*
5203986 TTAAAATA
1 TTAATATA
5203994 TTAATAT-
1 TTAATATA
*
5204001 TATAATATT
1 T-TAATATA
5204010 TTAATCATA
1 TTAAT-ATA
5204019 TTAATATTA
1 TTAATA-TA
* *
5204028 ATAATGT-
1 TTAATATA
5204035 TTAAATTATA
1 TT-AA-TATA
*
5204045 TATAAAATA
1 T-TAATATA
*
5204054 TTAATATT
1 TTAATATA
5204062 TTAA
1 TTAA
5204066 ATTTGACAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 26
0.67 0.12 0.21
Matches are distributed among these distances:
7 9 0.11
8 50 0.60
9 20 0.24
10 3 0.04
11 1 0.01
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (8 bp):
TTAATATA
Found at i:5204078 original size:29 final size:29
Alignment explanation
Indices: 5204021--5204078 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
5204011 TAATCATATT
* *
5204021 AATATTAATAATGTTTAAATTATATATAA
1 AATATTAATAATGTTTAAATTACAAATAA
5204050 AATATTAAT-AT-TTTAAATTTGACAAATAA
1 AATATTAATAATGTTTAAA-TT-ACAAATAA
5204079 TTTTTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 6 0.24
28 4 0.16
29 15 0.60
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (29 bp):
AATATTAATAATGTTTAAATTACAAATAA
Found at i:5208293 original size:29 final size:26
Alignment explanation
Indices: 5208244--5208297 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
5208234 TTTTTTGAAT
*
5208244 TATTTAAAAATTTTTCTTTTTTATTA
1 TATTTAAAAATTTTTATTTTTTATTA
5208270 TATTTAATTAAATTTTTATATTTTTATT
1 TATTTAA--AAATTTTTAT-TTTTTATT
5208298 TTGAATCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 7 0.29
28 9 0.38
29 8 0.33
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (26 bp):
TATTTAAAAATTTTTATTTTTTATTA
Found at i:5208596 original size:27 final size:27
Alignment explanation
Indices: 5208539--5208599 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 27
5208529 TGATTTAAAA
5208539 TAAAAATATAAAATTAATTTAACATAAT
1 TAAAAATATAAAA-TAATTTAACATAAT
5208567 TAAACAATATAAAA-AATTTAA-ATAAT
1 TAAA-AATATAAAATAATTTAACATAAT
*
5208593 TTAAAAT
1 TAAAAAT
5208600 TTTTTTTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 3 0.10
26 8 0.26
27 7 0.23
28 4 0.13
29 9 0.29
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (27 bp):
TAAAAATATAAAATAATTTAACATAAT
Found at i:5213520 original size:42 final size:42
Alignment explanation
Indices: 5213453--5213572 Score: 168
Period size: 42 Copynumber: 2.9 Consensus size: 42
5213443 ATCATCATTG
**
5213453 GCTTATGCGCACTCCCACTAACACATAGCCGGGTCAGCATCA
1 GCTTATGCGCACTCCCACTCGCACATAGCCGGGTCAGCATCA
* * *
5213495 GCTTATGCGTACTCTCACTCGCACATAGCCGGGTCAGCATCG
1 GCTTATGCGCACTCCCACTCGCACATAGCCGGGTCAGCATCA
* * *
5213537 GCTTATGTGCACCCCCACTCGCACATAGCCAGGTCA
1 GCTTATGCGCACTCCCACTCGCACATAGCCGGGTCA
5213573 ATATCATTAA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.23, C:0.36, G:0.21, T:0.21
Consensus pattern (42 bp):
GCTTATGCGCACTCCCACTCGCACATAGCCGGGTCAGCATCA
Found at i:5217109 original size:67 final size:67
Alignment explanation
Indices: 5216973--5217124 Score: 171
Period size: 67 Copynumber: 2.3 Consensus size: 67
5216963 CTATTGTTGT
* * * * * * ** *
5216973 AGGTAGTGGTTGAACCTTTGAAAAAGCACTTTGGGTTTTGGTTGAGCCCGTGAAAAATCATTGTG
1 AGGTTGTGGTTGAGCCTTTGAAAAACCACTTGGGGTTTTAGTTGAGCCCGTAAAAAATCAGCGTA
5217038 AA
66 AA
* *
5217040 AGGTTGTGGTTGAGCTTTTGAAAAACCACTTGGGGTTTTAGTTTAGCCCGTAAAAAA-CTAGCGT
1 AGGTTGTGGTTGAGCCTTTGAAAAACCACTTGGGGTTTTAGTTGAGCCCGTAAAAAATC-AGCGT
5217104 AAA
65 AAA
* *
5217107 AGGTTTTGGCTGAGCCTT
1 AGGTTGTGGTTGAGCCTT
5217125 GTAAAAGCCA
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
66 1 0.01
67 69 0.99
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.32
Consensus pattern (67 bp):
AGGTTGTGGTTGAGCCTTTGAAAAACCACTTGGGGTTTTAGTTGAGCCCGTAAAAAATCAGCGTA
AA
Found at i:5223530 original size:5 final size:5
Alignment explanation
Indices: 5223522--5223554 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
5223512 ACCTAACCTG
5223522 ACTTA ACTTA AC-TA ACTTA ACTTA ACTTA ACTT
1 ACTTA ACTTA ACTTA ACTTA ACTTA ACTTA ACTT
5223555 GGGCCATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
ACTTA
Found at i:5223541 original size:14 final size:15
Alignment explanation
Indices: 5223522--5223554 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
5223512 ACCTAACCTG
5223522 ACTTAACTTAAC-TA
1 ACTTAACTTAACTTA
5223536 ACTTAACTTAACTTA
1 ACTTAACTTAACTTA
5223551 ACTT
1 ACTT
5223555 GGGCCATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (15 bp):
ACTTAACTTAACTTA
Found at i:5223609 original size:15 final size:15
Alignment explanation
Indices: 5223589--5223634 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
5223579 TTCTTAAAAC
*
5223589 AACTTTAAAACCAAA
1 AACTTTAAAATCAAA
*
5223604 AACTTTAAAATCTAA
1 AACTTTAAAATCAAA
*
5223619 AGCTTTAAAATCAAA
1 AACTTTAAAATCAAA
5223634 A
1 A
5223635 TCTCTGATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.57, C:0.15, G:0.02, T:0.26
Consensus pattern (15 bp):
AACTTTAAAATCAAA
Found at i:5227255 original size:17 final size:17
Alignment explanation
Indices: 5227225--5227257 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5227215 TTCTTGATAA
5227225 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
5227242 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
5227258 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:5227582 original size:29 final size:28
Alignment explanation
Indices: 5227431--5227573 Score: 178
Period size: 29 Copynumber: 5.0 Consensus size: 28
5227421 AAATATTTTA
* * *
5227431 TCTTGTCTAAATTTGAGACAAATATGTAT
1 TCTTGTCTAAA-TTAAGACAAACATGTTT
* * * *
5227460 TCTTGTCTAGATGAAGACAAAAATATTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
*
5227488 TCCTTGTCTTAAATTAAGACAAACATATTT
1 T-CTTGTC-TAAATTAAGACAAACATGTTT
5227518 TCTTGTCTAAATTAAGACCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATGTTT
5227547 TCTTGTCTAAATTAAGACAAACATGTT
1 TCTTGTCTAAATTAAGACAAACATGTT
5227574 AAAGTTGTCA
Statistics
Matches: 101, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
28 33 0.33
29 49 0.49
30 19 0.19
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.38
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATGTTT
Found at i:5227582 original size:58 final size:57
Alignment explanation
Indices: 5227413--5227574 Score: 184
Period size: 58 Copynumber: 2.8 Consensus size: 57
5227403 GATCGTAATT
* * *
5227413 AAGACAAAAAATATTTTATCTTGTCTAAATTTGAGACAAATATG-TATTCTTGTCTAGATG
1 AAGAC-AAAAATA-TTT-TCTTGTCTAAA-TTAAGACAAACATGTTATTCTTGTCTAAATG
* *
5227473 AAGACAAAAATATTTTCCTTGTCTTAAATTAAGACAAACATATT-TTCTTGTCTAAATT
1 AAGACAAAAATATTTT-CTTGTC-TAAATTAAGACAAACATGTTATTCTTGTCTAAATG
* *
5227531 AAGACCAAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTA
1 AAGA-CAAAAATATTTTCTTGTCTAAATTAAGACAAACATGTTA
5227575 AAGTTGTCAT
Statistics
Matches: 89, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
57 20 0.22
58 42 0.47
59 22 0.25
60 5 0.06
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (57 bp):
AAGACAAAAATATTTTCTTGTCTAAATTAAGACAAACATGTTATTCTTGTCTAAATG
Found at i:5227582 original size:87 final size:90
Alignment explanation
Indices: 5227409--5227582 Score: 203
Period size: 87 Copynumber: 2.0 Consensus size: 90
5227399 TCTTGATCGT
* * *
5227409 AATTAAGACAAAAAATATTTTATCTTGTCTAAATTTGAGACAAATATGTATTCTTGTCTAGATGA
1 AATTAAGACAAAAAATATTTTATCTTGTCTAAATTTAAGACAAACATGTATTCTTGTCTAAATGA
***
5227474 AGACAAAAATATTTTCCTTGTCTTA
66 AGACAAAAATATTAAACTTGTCTTA
* * *
5227499 AATTAAGAC-AAACATA-TTT-TCTTGTCTAAA-TTAAGACCAAACATGTTTTCTTGTCTAAATT
1 AATTAAGACAAAAAATATTTTATCTTGTCTAAATTTAAGA-CAAACATGTATTCTTGTCTAAATG
* * *
5227560 AAGACAAACATGTTAAAGTTGTC
65 AAGACAAAAATATTAAACTTGTC
5227583 ATTTTTGTAC
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
86 5 0.07
87 48 0.68
88 3 0.04
89 6 0.08
90 9 0.13
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (90 bp):
AATTAAGACAAAAAATATTTTATCTTGTCTAAATTTAAGACAAACATGTATTCTTGTCTAAATGA
AGACAAAAATATTAAACTTGTCTTA
Found at i:5231906 original size:22 final size:23
Alignment explanation
Indices: 5231867--5231913 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
5231857 ATTTCTATGT
5231867 ATTATTACAAAAACTAAG-TCAA
1 ATTATTACAAAAACTAAGCTCAA
*
5231889 ATTATTATC-AAAATTAAGCTCAA
1 ATTATTA-CAAAAACTAAGCTCAA
5231912 AT
1 AT
5231914 AATTCTATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
ATTATTACAAAAACTAAGCTCAA
Found at i:5236495 original size:19 final size:19
Alignment explanation
Indices: 5236471--5236508 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5236461 CCATTTGACT
5236471 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
5236490 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
5236509 GTTAAGAAGT
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:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:5237201 original size:11 final size:10
Alignment explanation
Indices: 5237171--5237207 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
5237161 GTAGTTGAAA
5237171 TTGATGATAT
1 TTGATGATAT
*
5237181 TTCATGATAT
1 TTGATGATAT
5237191 TTGAGTGATAT
1 TTGA-TGATAT
5237202 TTGATG
1 TTGATG
5237208 TTTGGTGAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.27, C:0.03, G:0.22, T:0.49
Consensus pattern (10 bp):
TTGATGATAT
Found at i:5240346 original size:19 final size:19
Alignment explanation
Indices: 5240300--5240337 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5240290 TTCACTCTTC
5240300 AAATCCTTTGTTAATGCAA
1 AAATCCTTTGTTAATGCAA
*
5240319 AAATCCTTTGTTAGTGCAA
1 AAATCCTTTGTTAATGCAA
5240338 GGATCCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (19 bp):
AAATCCTTTGTTAATGCAA
Found at i:5243752 original size:27 final size:27
Alignment explanation
Indices: 5243699--5243773 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 27
5243689 CTCTTAAGTA
* * * *
5243699 CTTCCGCACTTGGAACAACCTTGAGCG
1 CTTCTGCACTTGGAACGACCCTAAGCG
* * *
5243726 GTTTTGCACTTAGAACGACCCTAAGCG
1 CTTCTGCACTTGGAACGACCCTAAGCG
*
5243753 CTTCTGCGCTTGGAACGACCC
1 CTTCTGCACTTGGAACGACCC
5243774 CGGGCGCTTC
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.21, C:0.32, G:0.23, T:0.24
Consensus pattern (27 bp):
CTTCTGCACTTGGAACGACCCTAAGCG
Found at i:5251411 original size:24 final size:23
Alignment explanation
Indices: 5251379--5251438 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
5251369 CGAGTCGCTC
*
5251379 TTATATTTATGTTTATG-ATAATG
1 TTATGTTTATGTTTATGAAT-ATG
*
5251402 TTTATGTTTATGGATTATGAATATG
1 -TTATGTTTAT-GTTTATGAATATG
*
5251427 TTATGTTAATGT
1 TTATGTTTATGT
5251439 AGCTAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
23 1 0.03
24 18 0.60
25 9 0.30
26 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (23 bp):
TTATGTTTATGTTTATGAATATG
Found at i:5251428 original size:19 final size:18
Alignment explanation
Indices: 5251386--5251437 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
5251376 CTCTTATATT
**
5251386 TATGTTTATGATAATGTT
1 TATGTTTATGATAATGAA
*
5251404 TATGTTTATGGATTATGAA
1 TATGTTTAT-GATAATGAA
*
5251423 TATG-TTATGTTAATG
1 TATGTTTATGATAATG
5251438 TAGCTAATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 5 0.18
18 13 0.46
19 10 0.36
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (18 bp):
TATGTTTATGATAATGAA
Found at i:5252901 original size:18 final size:20
Alignment explanation
Indices: 5252863--5252906 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
5252853 ATTATAATAA
*
5252863 AAAATAAAATATATAAGATT
1 AAAATAAAATATATAAAATT
*
5252883 ATAATAAAA-A-ATAAAATT
1 AAAATAAAATATATAAAATT
5252901 AAAATA
1 AAAATA
5252907 CATAAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 12 0.57
19 1 0.05
20 8 0.38
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAATAAAATATATAAAATT
Found at i:5254228 original size:27 final size:27
Alignment explanation
Indices: 5254184--5254263 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
5254174 GTTTCACTCA
* * *
5254184 TGTCATGTTGTCATCACGACGTTCAATT
1 TGTCATGTT-TCACCACGACATTCAAAT
** *
5254212 TGTTTTGTTTCACCACGATATTCAAAT
1 TGTCATGTTTCACCACGACATTCAAAT
*
5254239 TGTCATCTTTCACCACGACATTCAA
1 TGTCATGTTTCACCACGACATTCAA
5254264 CTCATGTCGT
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
27 35 0.83
28 7 0.17
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (27 bp):
TGTCATGTTTCACCACGACATTCAAAT
Found at i:5260538 original size:2 final size:2
Alignment explanation
Indices: 5260531--5260561 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5260521 TTAAGTCACC
5260531 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5260562 ATGACAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5260722 original size:10 final size:10
Alignment explanation
Indices: 5260696--5260732 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
5260686 TATACATAGA
5260696 AAATTTGAAAT
1 AAATTTG-AAT
5260707 AAATTTGAAT
1 AAATTTGAAT
*
5260717 ATATTTGAAT
1 AAATTTGAAT
5260727 AAATTT
1 AAATTT
5260733 TCATACTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 17 0.71
11 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (10 bp):
AAATTTGAAT
Found at i:5262127 original size:22 final size:22
Alignment explanation
Indices: 5262081--5262488 Score: 127
Period size: 21 Copynumber: 18.7 Consensus size: 22
5262071 ATTTACCCAT
*
5262081 ATTAATTTTTATAAATA-AAAT-
1 ATTAATATTT-TAAATATAAATA
*
5262102 ATTAATATTTTAAATATTAATA
1 ATTAATATTTTAAATATAAATA
*
5262124 ATTAA-ATTATAAATA-AAAT-
1 ATTAATATTTTAAATATAAATA
* *
5262143 ATTAATA-TTTAAATAATCAATT
1 ATTAATATTTTAAAT-ATAAATA
*
5262165 ATTAATATTTTAAATATACTATAA
1 ATTAATATTTTAAATATA-AAT-A
*
5262189 ATTATTAATATTTAGAA-ATAAAATA
1 ATTAAT-AT-TTTA-AATAT-AAATA
**
5262214 A-TAA-ATAATAAATA-ACAATAA
1 ATTAATATTTTAAATATA-AAT-A
* *
5262235 CATTCAA-ATTATAAGTA-AAATA
1 -ATT-AATATTTTAAATATAAATA
* *
5262257 A-TAATATTTTATAATATTAATG
1 ATTAATATTTTA-AATATAAATA
*
5262279 ATTAA-ATTTTAAAGA-AAAT-
1 ATTAATATTTTAAATATAAATA
* *
5262298 ATTAATA-TTTAAATGATCAATT
1 ATTAATATTTTAAAT-ATAAATA
*
5262320 ATTAATATTTTAAATATATTAAAATT
1 ATTAATATTTT-AA-ATA-T-AAATA
* *
5262346 ATTAATATTTAAAAAATAAATA
1 ATTAATATTTTAAATATAAATA
* **
5262368 A-AAATA-AAT-AATCAT-AATA
1 ATTAATATTTTAAAT-ATAAATA
*
5262387 GCATTTAA-ATTATAAATA-AAAT-
1 --A-TTAATATTTTAAATATAAATA
*
5262409 ATTAATATTTTAAAATATTAATGA
1 ATTAATATTTT-AAATATAAAT-A
*
5262433 A-TAA-ATTATAAATA-AAAT-
1 ATTAATATTTTAAATATAAATA
* *
5262451 ATTAATA-TTTAAATTATCAATT
1 ATTAATATTTTAAA-TATAAATA
* *
5262473 ATTACTATTTTGAATA
1 ATTAATATTTTAAATA
5262489 AATTATAAAT
Statistics
Matches: 293, Mismatches: 43, Indels: 101
0.67 0.10 0.23
Matches are distributed among these distances:
18 1 0.00
19 43 0.15
20 40 0.14
21 56 0.19
22 56 0.19
23 36 0.12
24 27 0.09
25 9 0.03
26 22 0.08
27 3 0.01
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
ATTAATATTTTAAATATAAATA
Found at i:5262214 original size:26 final size:25
Alignment explanation
Indices: 5262112--5262214 Score: 88
Period size: 26 Copynumber: 4.1 Consensus size: 25
5262102 ATTAATATTT
* *
5262112 TAAA-TATTAATAATTAAATTATAAA
1 TAAATTATTAATATTTAAAATA-AAA
*
5262137 TAAAATATTAATATTT-AAAT--AA
1 TAAATTATTAATATTTAAAATAAAA
* **
5262159 TCAATTATTAATATTTTAAATATACTA
1 TAAATTATTAATA-TTTAAA-ATAAAA
5262186 TAAATTATTAATATTTAGAAATAAAA
1 TAAATTATTAATATTTA-AAATAAAA
5262212 TAA
1 TAA
5262215 TAAATAATAA
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
22 13 0.21
23 3 0.05
24 2 0.03
25 9 0.14
26 21 0.33
27 15 0.24
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (25 bp):
TAAATTATTAATATTTAAAATAAAA
Found at i:5262467 original size:26 final size:26
Alignment explanation
Indices: 5262269--5262370 Score: 65
Period size: 26 Copynumber: 4.1 Consensus size: 26
5262259 AATATTTTAT
* *
5262269 AATATTAATGA-TTAAATTTTAAAGAA
1 AATATTAAT-ATTTAAATTATAAATAA
* *
5262295 AATATTAATATTTAAATGATCAAT--
1 AATATTAATATTTAAATTATAAATAA
*
5262319 --TATTAATATTTTAAA-TAT-ATTAA
1 AATATTAATA-TTTAAATTATAAATAA
**
5262342 AATTATTAATATTTAAAAAATAAATAA
1 AA-TATTAATATTTAAATTATAAATAA
5262369 AA
1 AA
5262371 ATAAATAATC
Statistics
Matches: 59, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
21 2 0.03
22 10 0.17
23 6 0.10
25 7 0.12
26 28 0.47
27 6 0.10
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (26 bp):
AATATTAATATTTAAATTATAAATAA
Found at i:5262591 original size:151 final size:151
Alignment explanation
Indices: 5262089--5262676 Score: 813
Period size: 151 Copynumber: 3.9 Consensus size: 151
5262079 ATATTAATTT
*
5262089 TTATAAATAAAATATTAATATTTTA-AATATTAATAATTAAATTATAAATAAAATATTAATATTT
1 TTATAAATAAAATATTAATATTTTATAATATTAATGATTAAATTATAAATAAAATATTAATATTT
* * * *
5262153 AAATAATCAATTATTAATATTTTAAATATACTATAAATTATTAATATTTAGAAATAAA-ATAATA
66 AAATTATCAATTATTAATATTTTAAATAAATTATAAATTATTAATA-TTA-AAA-AAATAAAATA
* *
5262217 AATAATAAATAACAATAACATTCAAA
128 AA-AAT-AATCATAATAACATTCAAA
* * * *
5262243 TTATAAGTAAAATAATAATATTTTATAATATTAATGATTAAATTTTAAAGAAAATATTAATATTT
1 TTATAAATAAAATATTAATATTTTATAATATTAATGATTAAATTATAAATAAAATATTAATATTT
* * * *
5262308 AAATGATCAATTATTAATATTTTAAATATATTA-AAATTATTAATATTTAAAAAATAAATAAAAA
66 AAATTATCAATTATTAATATTTTAAATAAATTATAAATTATTAATATTAAAAAAAT-AA-AATAA
* *
5262372 TAAATAATCATAATAGCATTTAAA
129 -AAATAATCATAATAACATTCAAA
* *
5262396 TTATAAATAAAATATTAATATTTTAAAATATTAATGAATAAATTATAAATAAAATATTAATATTT
1 TTATAAATAAAATATTAATATTTTATAATATTAATGATTAAATTATAAATAAAATATTAATATTT
* *
5262461 AAATTATCAATTATTACTATTTTGAATAAATTATAAATTATTAATATTAAAAAAATAAAATAAAA
66 AAATTATCAATTATTAATATTTTAAATAAATTATAAATTATTAATATTAAAAAAATAAAATAAAA
* *
5262526 ATAATCATAATAACATTGAAT
131 ATAATCATAATAACATTCAAA
* * *
5262547 TTGTAAATAAAATATTAATATTTTATATTGTTAATGATTAAATTATAAATAAAATATTAATATTT
1 TTATAAATAAAATATTAATATTTTATAATATTAATGATTAAATTATAAATAAAATATTAATATTT
* * * *
5262612 AAATTATGAATTATAAATATTTTAAATAAATTATAAATTATTAAAATTCAAAAAATAAAATAAAA
66 AAATTATCAATTATTAATATTTTAAATAAATTATAAATTATTAATATTAAAAAAATAAAATAAAA
5262677 TAAAAATAAA
Statistics
Matches: 388, Mismatches: 40, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
151 142 0.37
152 7 0.02
153 108 0.28
154 63 0.16
155 68 0.18
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (151 bp):
TTATAAATAAAATATTAATATTTTATAATATTAATGATTAAATTATAAATAAAATATTAATATTT
AAATTATCAATTATTAATATTTTAAATAAATTATAAATTATTAATATTAAAAAAATAAAATAAAA
ATAATCATAATAACATTCAAA
Found at i:5262607 original size:26 final size:26
Alignment explanation
Indices: 5262577--5262649 Score: 71
Period size: 26 Copynumber: 2.7 Consensus size: 26
5262567 TTTTATATTG
5262577 TTAATGATTAAATTATAAATA-AAATA
1 TTAAT-ATTAAATTATAAATATAAATA
*
5262603 TTAATATTTAAATTATGAATTATAAATA
1 TTAATA-TTAAATTAT-AAATATAAATA
5262631 TTTTAA-A-TAAATTATAAAT
1 --TTAATATTAAATTATAAAT
5262650 TATTAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
25 1 0.03
26 17 0.43
27 12 0.30
28 5 0.12
29 1 0.03
30 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (26 bp):
TTAATATTAAATTATAAATATAAATA
Found at i:5262638 original size:42 final size:41
Alignment explanation
Indices: 5262544--5262659 Score: 115
Period size: 42 Copynumber: 2.7 Consensus size: 41
5262534 AATAACATTG
* * * *
5262544 AATTTGTAAATAAAATATTAATATTTTATATTGTTAATGATTA
1 AATTT-TAAATAAAATATTAATA-TTTAAATTATGAATGATAA
* *
5262587 AATTATAAATAAAATATTAATATTTAAATTATGAATTATAA
1 AATTTTAAATAAAATATTAATATTTAAATTATGAATGATAA
* * *
5262628 ATATTTTAAATAAATTATAAATTATTAAAATT
1 A-ATTTTAAATAAAATATTAA-TATTTAAATT
5262660 CAAAAAATAA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
41 15 0.25
42 33 0.54
43 13 0.21
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (41 bp):
AATTTTAAATAAAATATTAATATTTAAATTATGAATGATAA
Found at i:5262658 original size:20 final size:20
Alignment explanation
Indices: 5262593--5262658 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
5262583 ATTAAATTAT
* *
5262593 AAATAAAATATTAATATTTA
1 AAATAAATTATAAATATTTA
* *
5262613 AATTATGAATTATAAATATTTT
1 AA--ATAAATTATAAATATTTA
5262635 AAATAAATTATAAAT-TATTA
1 AAATAAATTATAAATAT-TTA
5262655 AAAT
1 AAAT
5262659 TCAAAAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.03
20 20 0.54
22 16 0.43
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
AAATAAATTATAAATATTTA
Found at i:5272503 original size:20 final size:23
Alignment explanation
Indices: 5272475--5272519 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
5272465 ATTTTTATTT
5272475 AAACTTATAATAC-T-AAATATA
1 AAACTTATAATACATAAAATATA
5272496 AAAC-TATAATACATAAAATATA
1 AAACTTATAATACATAAAATATA
5272518 AA
1 AA
5272520 TAGTTAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 5 0.23
22 9 0.41
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (23 bp):
AAACTTATAATACATAAAATATA
Found at i:5272627 original size:52 final size:51
Alignment explanation
Indices: 5272569--5272672 Score: 156
Period size: 52 Copynumber: 2.0 Consensus size: 51
5272559 TAGAATTAGG
5272569 ATTGTTTAAAGACTACATATTCAAGATAATTT-TCTTTCAACTAAAAATAAA
1 ATTGTTTAAAGACTACATATTCAAGATAATTTCT-TTTCAACTAAAAATAAA
* * *
5272620 NATTGTTTAAAGACTATATATTCAAGATAATTTCTTTTTAACTAAATATAAA
1 -ATTGTTTAAAGACTACATATTCAAGATAATTTCTTTTCAACTAAAAATAAA
5272672 A
1 A
5272673 CATAAAGCAC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
51 1 0.02
52 46 0.96
53 1 0.02
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.39
Consensus pattern (51 bp):
ATTGTTTAAAGACTACATATTCAAGATAATTTCTTTTCAACTAAAAATAAA
Found at i:5273479 original size:24 final size:24
Alignment explanation
Indices: 5273445--5273497 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
5273435 AAAAAGAGAA
* * *
5273445 AAAG-GAAAGAAAAAGAGAGGTAG
1 AAAGAGAAAGAAAAAAACAGATAG
5273468 AAAGAGAAAGAAAAAAACAGATAG
1 AAAGAGAAAGAAAAAAACAGATAG
5273492 AAAGAG
1 AAAGAG
5273498 GCTCGCATGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.66, C:0.02, G:0.28, T:0.04
Consensus pattern (24 bp):
AAAGAGAAAGAAAAAAACAGATAG
Found at i:5274484 original size:31 final size:31
Alignment explanation
Indices: 5274448--5274827 Score: 552
Period size: 31 Copynumber: 12.4 Consensus size: 31
5274438 CACGACATTG
* *
5274448 GTTATATGCATGGCGTGTTACAACATTGTAC
1 GTTATATGCATGGCGTGTTACCACATTTTAC
* *
5274479 GTTATATGCATGGCGTGTTACAACATTGTAC
1 GTTATATGCATGGCGTGTTACCACATTTTAC
* *
5274510 GTTATATGCATGGCGTGTTACAACATTGTAC
1 GTTATATGCATGGCGTGTTACCACATTTTAC
* *
5274541 GTTATATGCATGGCGTGTTACAATATTTTAC
1 GTTATATGCATGGCGTGTTACCACATTTTAC
* *
5274572 GTTATATGCATGGCGTATTACCACATTTTTC
1 GTTATATGCATGGCGTGTTACCACATTTTAC
*
5274603 GTTATATGCATGGCGTGTTACCCCATTTTAC
1 GTTATATGCATGGCGTGTTACCACATTTTAC
* *
5274634 GTTATATGCATGGTGTGTTACCACATTTTAT
1 GTTATATGCATGGCGTGTTACCACATTTTAC
*
5274665 GTTATATGCATGGCGTGTT---ACA-TTTAT
1 GTTATATGCATGGCGTGTTACCACATTTTAC
* * *
5274692 GCTATATGCATGGTGTGTTACCACATTTTAT
1 GTTATATGCATGGCGTGTTACCACATTTTAC
* *
5274723 GCTATATGCATGGCGTGTTACCACATTTTTAT
1 GTTATATGCATGGCGTGTTACCACA-TTTTAC
5274755 GTTATATGCATGGCGTGTTACCACATTTTAC
1 GTTATATGCATGGCGTGTTACCACATTTTAC
5274786 GTTATATGCATGGCGTGTTACCACATTTTAC
1 GTTATATGCATGGCGTGTTACCACATTTTAC
5274817 GTTATATGCAT
1 GTTATATGCAT
5274828 AGCATGTAAC
Statistics
Matches: 326, Mismatches: 18, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
27 22 0.07
28 3 0.01
30 3 0.01
31 268 0.82
32 30 0.09
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (31 bp):
GTTATATGCATGGCGTGTTACCACATTTTAC
Found at i:5279103 original size:80 final size:80
Alignment explanation
Indices: 5278970--5279208 Score: 320
Period size: 80 Copynumber: 3.0 Consensus size: 80
5278960 GATGCTGTCC
* * * *
5278970 TTCAACCACGAGCA-ACTGAAGATCCCCCTCCTCTCCCGTAGATGCATCGATAACCGAATCAGCC
1 TTCAACCACGAG-AGAGTGAAG-GCCCCCTCCCCTCCCGCAGATGCATCGATAACCGAATCAGCC
*
5279034 TCAAGAACATGGACTCT
64 TCAAGAACATGGACTCA
*
5279051 TTCAACCACGAGAGAGTGAAGGCCCCCTCCCCTCCCGCAGATGCATCCATAACCGAATCAGCCTC
1 TTCAACCACGAGAGAGTGAAGGCCCCCTCCCCTCCCGCAGATGCATCGATAACCGAATCAGCCTC
*
5279116 AGGAACATGGACTCA
66 AAGAACATGGACTCA
* * * * *
5279131 TTCAGCCACGAGCGAGTGAAGGTCCCCTTCCCCACCCTCAGATGCATCGATAACCGAATCAGCCT
1 TTCAACCACGAGAGAGTGAAGG-CCCCCTCCCCTCCCGCAGATGCATCGATAACCGAATCAGCCT
5279196 -AAGGAACATGGAC
65 CAA-GAACATGGAC
5279209 ACCTTTAGCA
Statistics
Matches: 141, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
80 75 0.53
81 66 0.47
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.17
Consensus pattern (80 bp):
TTCAACCACGAGAGAGTGAAGGCCCCCTCCCCTCCCGCAGATGCATCGATAACCGAATCAGCCTC
AAGAACATGGACTCA
Found at i:5281528 original size:31 final size:31
Alignment explanation
Indices: 5281490--5281578 Score: 133
Period size: 31 Copynumber: 2.9 Consensus size: 31
5281480 AGAAAGAAAT
* *
5281490 AAATGTTGTTACACACCATGCATATCAAGTC
1 AAATGTTGTAACACGCCATGCATATCAAGTC
5281521 AAATGTTGTAACACGCCATGCATATCAAGTC
1 AAATGTTGTAACACGCCATGCATATCAAGTC
* * *
5281552 AAATGTCGTGACACGCTATGCATATCA
1 AAATGTTGTAACACGCCATGCATATCA
5281579 GTGTTGTGAC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (31 bp):
AAATGTTGTAACACGCCATGCATATCAAGTC
Found at i:5281607 original size:18 final size:18
Alignment explanation
Indices: 5281584--5281633 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
5281574 TATCAGTGTT
5281584 GTGACACGCCATGCTGTC
1 GTGACACGCCATGCTGTC
*
5281602 GTGACATGCCATGCTGTC
1 GTGACACGCCATGCTGTC
* *
5281620 ATGACACTCCATGC
1 GTGACACGCCATGC
5281634 ATATCAGTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.20, C:0.32, G:0.24, T:0.24
Consensus pattern (18 bp):
GTGACACGCCATGCTGTC
Found at i:5281808 original size:55 final size:54
Alignment explanation
Indices: 5281719--5282175 Score: 500
Period size: 55 Copynumber: 8.3 Consensus size: 54
5281709 AAAAAAAAAA
* * *
5281719 AGTTAACACACAACACGCTAGGAACAGCCATGACACGCCAAAAACCAAAAAATCC
1 AGTTAACCCACAACACGCTAGGAACAGCCGTGACACGCTAAAAACCAAAAAA-CC
* * ** *
5281774 AGTTAACCCACAACACGCTCGGAATAGTTGTGACACTCTAAAAACCTAAAAAACC
1 AGTTAACCCACAACACGCTAGGAACAGCCGTGACACGCTAAAAACC-AAAAAACC
* * * * * *
5281829 AGTTAACCCACAACACGCCAGGAATAGTCGTGACATGCCAAAAACCAAAAAATCT
1 AGTTAACCCACAACACGCTAGGAACAGCCGTGACACGCTAAAAACCAAAAAA-CC
* * * * * * * **
5281884 AGTTAACCCACAACATGCCAAGAACGGCTGTGACACACCAAAAACCAAAAATGC
1 AGTTAACCCACAACACGCTAGGAACAGCCGTGACACGCTAAAAACCAAAAAACC
* *
5281938 AGTTAACCCACAACACGCCAAGAACAGCCGTGACACGCTAAAAACCCAAAAAACC
1 AGTTAACCCACAACACGCTAGGAACAGCCGTGACACGCTAAAAA-CCAAAAAACC
* * * * * *
5281993 AGTTAACCCATAACAAGCTAGGAACAACCATGATACACTAAAAACCCAAAAAACC
1 AGTTAACCCACAACACGCTAGGAACAGCCGTGACACGCTAAAAA-CCAAAAAACC
* * * * *
5282048 AGTTAACCCATAACACGCTAGGAACAACCTTGACACGGTAAAAACCTAAAAAACT
1 AGTTAACCCACAACACGCTAGGAACAGCCGTGACACGCTAAAAACC-AAAAAACC
* * *
5282103 AGTTAACCCACAACATGCTAGGAACAGTCGTGACACGCTAAAAACTCAAAAAATC
1 AGTTAACCCACAACACGCTAGGAACAGCCGTGACACGCTAAAAAC-CAAAAAACC
5282158 AGTTAACCCACAACACGC
1 AGTTAACCCACAACACGC
5282176 CATATGTAGA
Statistics
Matches: 341, Mismatches: 56, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
54 47 0.14
55 287 0.84
56 7 0.02
ACGTcount: A:0.45, C:0.29, G:0.13, T:0.13
Consensus pattern (54 bp):
AGTTAACCCACAACACGCTAGGAACAGCCGTGACACGCTAAAAACCAAAAAACC
Found at i:5281965 original size:219 final size:220
Alignment explanation
Indices: 5281719--5282177 Score: 577
Period size: 219 Copynumber: 2.1 Consensus size: 220
5281709 AAAAAAAAAA
* * *
5281719 AGTTAACACACAACACGCTAGGAACAGCCATGACACGCCAAAAA-CCAAAAAATCCAGTTAACCC
1 AGTTAACCCACAACACGCCAAGAACAGCCATGACACGCCAAAAACCCAAAAAA-CCAGTTAACCC
* * * **** * *
5281783 ACAACACGCTCGGAATAGTTGTGACACTCTAAAAACCTAAAAAACCAGTTAACCCACAACACGCC
65 ACAACAAGCTAGGAACAACCATGACACACTAAAAACCCAAAAAACCAGTTAACCCACAACACGCC
* ** * *
5281848 AGGAATAGTCGTGACATGCCAAAAACC-AAAAAATCTAGTTAACCCACAACATGCCAAGAAC-GG
130 AGGAACAACCGTGACACGCCAAAAACCTAAAAAA-CTAGTTAACCCACAACATGCCAAGAACAGT
5281911 CTGTGACACACCAAAAAC-C-AAAAATGC
194 C-GTGACACACCAAAAACTCAAAAAAT-C
* *
5281938 AGTTAACCCACAACACGCCAAGAACAGCCGTGACACGCTAAAAACCCAAAAAACCAGTTAACCCA
1 AGTTAACCCACAACACGCCAAGAACAGCCATGACACGCCAAAAACCCAAAAAACCAGTTAACCCA
* * * *
5282003 TAACAAGCTAGGAACAACCATGATACACTAAAAACCCAAAAAACCAGTTAACCCATAACACGCTA
66 CAACAAGCTAGGAACAACCATGACACACTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCA
* ** * *
5282068 GGAACAACCTTGACACGGTAAAAACCTAAAAAACTAGTTAACCCACAACATGCTAGGAACAGTCG
131 GGAACAACCGTGACACGCCAAAAACCTAAAAAACTAGTTAACCCACAACATGCCAAGAACAGTCG
* *
5282133 TGACACGCTAAAAACTCAAAAAATC
196 TGACACACCAAAAACTCAAAAAATC
5282158 AGTTAACCCACAACACGCCA
1 AGTTAACCCACAACACGCCA
5282178 TATGTAGACA
Statistics
Matches: 205, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
219 161 0.79
220 38 0.19
221 6 0.03
ACGTcount: A:0.45, C:0.29, G:0.13, T:0.13
Consensus pattern (220 bp):
AGTTAACCCACAACACGCCAAGAACAGCCATGACACGCCAAAAACCCAAAAAACCAGTTAACCCA
CAACAAGCTAGGAACAACCATGACACACTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCA
GGAACAACCGTGACACGCCAAAAACCTAAAAAACTAGTTAACCCACAACATGCCAAGAACAGTCG
TGACACACCAAAAACTCAAAAAATC
Found at i:5282642 original size:23 final size:22
Alignment explanation
Indices: 5282608--5282698 Score: 83
Period size: 23 Copynumber: 4.0 Consensus size: 22
5282598 CTCGCCTTCT
*
5282608 TTAATACCATGGCGTGTCACATA
1 TTAA-ACCATGGCGTGTCACACA
*
5282631 TTAAACCTATGGCATGTCACACA
1 TTAAACC-ATGGCGTGTCACACA
* * *
5282654 TTCAAGCCATGCCGTGTCACACG
1 TT-AAACCATGGCGTGTCACACA
* *
5282677 TTCAAGCCATGCCGTGTCACAC
1 TT-AAACCATGGCGTGTCACAC
5282699 GTCTGACCAT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
22 3 0.05
23 53 0.88
24 4 0.07
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (22 bp):
TTAAACCATGGCGTGTCACACA
Found at i:5282699 original size:23 final size:23
Alignment explanation
Indices: 5282645--5282700 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
5282635 ACCTATGGCA
*
5282645 TGTCACACATTCAAGCCATGCCG
1 TGTCACACGTTCAAGCCATGCCG
5282668 TGTCACACGTTCAAGCCATGCCG
1 TGTCACACGTTCAAGCCATGCCG
5282691 TGTCACACGT
1 TGTCACACGT
5282701 CTGACCATGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (23 bp):
TGTCACACGTTCAAGCCATGCCG
Found at i:5282952 original size:103 final size:99
Alignment explanation
Indices: 5282809--5283162 Score: 428
Period size: 103 Copynumber: 3.5 Consensus size: 99
5282799 CAAATTCCCT
* * *
5282809 CCATGGCGTGTCACACACTCTAAACCCTATTGTGTTACACCCGTGTCACACATTATCACTGTGTC
1 CCATGGCGTGTCACACACTCTAAACCCTA-CGTGTCACACCCGTGTCACACATTATCA-TGTGCC
*
5282874 GTTTCACACATTATGAACCTGTCGTGTCACACGTCTGA
64 GTTTCACACATTAT-AACCTG-CATGTCACACGTCTGA
* * * * *
5282912 CCATGGCGTGTTACACACTCTAAACGCTGGCGTGTCACACCCGTGTCACATATTCTCATTGTGCC
1 CCATGGCGTGTCACACACTCTAAACCCT-ACGTGTCACACCCGTGTCACACATTATCA-TGTGCC
* * * ***
5282977 ATCTCACACATTATCACCCTGCCATGTCACA-GATTCCCT
64 GTTTCACACATTAT-AACCTG-CATGTCACACG--TCTGA
5283016 CCATGGCGTGTCACACACTCTAAACCCTACCGTGTCACACCCGTGTCACACATTATCATGTGCCG
1 CCATGGCGTGTCACACACTCTAAACCCTA-CGTGTCACACCCGTGTCACACATTATCATGTGCCG
5283081 TTTCACACATTATAACCCTGCATGTCACACGTCTGA
65 TTTCACACATTATAA-CCTGCATGTCACACGTCTGA
*
5283117 CCATGGCGTGTCACACACTCTAAA--CT-CGTGTCACACCCTTGTCACA
1 CCATGGCGTGTCACACACTCTAAACCCTACGTGTCACACCCGTGTCACA
5283163 TTCTTACCAT
Statistics
Matches: 215, Mismatches: 30, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
97 19 0.09
99 2 0.01
101 26 0.12
102 11 0.05
103 103 0.48
104 54 0.25
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.27
Consensus pattern (99 bp):
CCATGGCGTGTCACACACTCTAAACCCTACGTGTCACACCCGTGTCACACATTATCATGTGCCGT
TTCACACATTATAACCTGCATGTCACACGTCTGA
Found at i:5283006 original size:207 final size:204
Alignment explanation
Indices: 5282689--5283196 Score: 642
Period size: 207 Copynumber: 2.5 Consensus size: 204
5282679 CAAGCCATGC
* * * * * *
5282689 CGTGTCACACGTCTGACCATGGCTTGTCCCACACTCAAAACGTTGTG-ATGTCACACCTGT-TCC
1 CGTGTCACACGTCTGACCATGGCGTGTCACACACTCTAAACGCTG-GCGTGTCACACCCGTGT-C
** * * * *
5282752 ACATATTCTCACCATGTCGTCTTACACATTTTCACCCTAGAATGTCACAAATTCCCTCCATGGCG
64 ACATATTCTCA-TGTGCCATCTCACACATTATCACCCTAGAATGTCACAAATTCCCTCCATGGCG
** * *
5282817 TGTCACACACTCTAAACCCTATTGTGTTACACCCGTGTCACACATTATCACTGTGTCGTTTCACA
128 TGTCACACACTCTAAACCCTACCGTGTCACACCCGTGTCACACATTATCA-TGTGCCGTTTCACA
5282882 CATTATGAA-CCTG
192 CATTAT-AACCCTG
*
5282895 TCGTGTCACACGTCTGACCATGGCGTGTTACACACTCTAAACGCTGGCGTGTCACACCCGTGTCA
1 -CGTGTCACACGTCTGACCATGGCGTGTCACACACTCTAAACGCTGGCGTGTCACACCCGTGTCA
* *
5282960 CATATTCTCATTGTGCCATCTCACACATTATCACCCT-GCCATGTCACAGATTCCCTCCATGGCG
65 CATATTCTCA-TGTGCCATCTCACACATTATCACCCTAG-AATGTCACAAATTCCCTCCATGGCG
5283024 TGTCACACACTCTAAACCCTACCGTGTCACACCCGTGTCACACATTATCATGTGCCGTTTCACAC
128 TGTCACACACTCTAAACCCTACCGTGTCACACCCGTGTCACACATTATCATGTGCCGTTTCACAC
5283089 ATTATAACCCTG
193 ATTATAACCCTG
* *
5283101 CATGTCACACGTCTGACCATGGCGTGTCACACACTCTAAA--CT--CGTGTCACACCCTTGTCAC
1 CGTGTCACACGTCTGACCATGGCGTGTCACACACTCTAAACGCTGGCGTGTCACACCCGTGTCAC
* *
5283162 ATTCTTAC-CATGT-CGA-CTCACACATTATCACCCTA
66 A-TATT-CTCATGTGCCATCTCACACATTATCACCCTA
5283197 ACGTGTCACA
Statistics
Matches: 269, Mismatches: 25, Indels: 21
0.85 0.08 0.07
Matches are distributed among these distances:
199 18 0.07
200 2 0.01
201 22 0.08
202 5 0.02
203 3 0.01
205 40 0.15
206 25 0.09
207 153 0.57
208 1 0.00
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.28
Consensus pattern (204 bp):
CGTGTCACACGTCTGACCATGGCGTGTCACACACTCTAAACGCTGGCGTGTCACACCCGTGTCAC
ATATTCTCATGTGCCATCTCACACATTATCACCCTAGAATGTCACAAATTCCCTCCATGGCGTGT
CACACACTCTAAACCCTACCGTGTCACACCCGTGTCACACATTATCATGTGCCGTTTCACACATT
ATAACCCTG
Found at i:5283374 original size:81 final size:81
Alignment explanation
Indices: 5283232--5283436 Score: 320
Period size: 81 Copynumber: 2.5 Consensus size: 81
5283222 TGTTACTTAT
* * * *
5283232 TCTCACCATGATGTGTCACACATTTCCACCATGCTGTGTCACAAACTCTATACCTTACCGTGTCA
1 TCTCACCATGACGTGTCACACATTCCCACCATGCCGTGTCACAAACTCTATACCCTACCGTGTCA
5283297 CACCCGTCTCACATAG
66 CACCCGTCTCACATAG
* * *
5283313 TCTCACCATGACGTGTCACACATTGCCACTATGCCGTGTCACAAACTCTATACCCTGCCGTGTCA
1 TCTCACCATGACGTGTCACACATTCCCACCATGCCGTGTCACAAACTCTATACCCTACCGTGTCA
*
5283378 CACCCGTCTCACATAT
66 CACCCGTCTCACATAG
* *
5283394 TCTTACCATGACGTGTCACACATTCCCACCATGCCATGTCACA
1 TCTCACCATGACGTGTCACACATTCCCACCATGCCGTGTCACA
5283437 CATTCCCACC
Statistics
Matches: 113, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 113 1.00
ACGTcount: A:0.24, C:0.36, G:0.13, T:0.27
Consensus pattern (81 bp):
TCTCACCATGACGTGTCACACATTCCCACCATGCCGTGTCACAAACTCTATACCCTACCGTGTCA
CACCCGTCTCACATAG
Found at i:5283459 original size:23 final size:23
Alignment explanation
Indices: 5283398--5283448 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
5283388 ACATATTCTT
* *
5283398 ACCATGACGTGTCACACATTCCC
1 ACCATGCCATGTCACACATTCCC
5283421 ACCATGCCATGTCACACATTCCC
1 ACCATGCCATGTCACACATTCCC
5283444 ACCAT
1 ACCAT
5283449 TCCGTTTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.41, G:0.10, T:0.22
Consensus pattern (23 bp):
ACCATGCCATGTCACACATTCCC
Found at i:5288403 original size:12 final size:12
Alignment explanation
Indices: 5288384--5288412 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5288374 ATATACTAAA
5288384 ATAT-TTTTAGT
1 ATATATTTTAGT
5288395 ATATATTTTAGT
1 ATATATTTTAGT
5288407 ATATAT
1 ATATAT
5288413 ATATACTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (12 bp):
ATATATTTTAGT
Found at i:5289011 original size:357 final size:359
Alignment explanation
Indices: 5288535--5289194 Score: 1044
Period size: 357 Copynumber: 1.8 Consensus size: 359
5288525 ACATATAAAC
* *
5288535 CTAAAGAGAAGTTGTGAGATTAGATTAGTTTTGAAACCTAGTTATTTTTTTTATAATTTCATGTA
1 CTAAAGAGAAGTTGTGAGATTAGAATAGTTTTGAAACCTAGTTATTTTTCTTATAATTTCATGTA
* *
5288600 ATTAAGGACAAACCCATATAGTTAATTAAATTAATTCATGAAATTATAATTATTAATTAACT-TG
66 ATTAAGGACAAACCCATATAGTTAATTAAATTAATTAATGAAACTATAATTATTAATTAACTAT-
* * * *
5288664 TAATGTCTTTTAATATATATACTTTATATATATTAAGTTTATTTATAAGGAATATAATTACTATT
130 TAATGTCTTTTAATATATATACTTTATATACATTAAGTTCATTTATAAGAAATACAATTACTATT
* **
5288729 ACGTATAT-TAAAATATTTTTAATGTATATATGTACTTTAAATATAAACATATTTACTTTCTATT
195 ACATATATATAAAATATTTTT-A-GTATATATACACTTTAAATATAAACATATTTACTTTCTATT
*
5288793 TTGTGTTAATATTACAAAAATTATAACTTATAAAATTATTAATTAGAATATATATACCATTTTTT
258 TTGTGTTAACATTACAAAAATTATAACTTATAAAATTATTAATTAGAATATATATACCATTTTTT
5288858 ATATAAAATTATAATATATATATATATATATATATAT
323 ATATAAAATTATAATATATATATATATATATATATAT
* *
5288895 CTAAAGGGAAGTTGTGAGATTAGAATAGTTTTGAAACTTAG-T-TTTTTCTT-TAATTTCATGTA
1 CTAAAGAGAAGTTGTGAGATTAGAATAGTTTTGAAACCTAGTTATTTTTCTTATAATTTCATGTA
* * *
5288957 ATTAAGGACAAATCCATATAGTTAATTAAATT-ATTAAATGAAACTATGATTATTAATTGACTAT
66 ATTAAGGACAAACCCATATAGTTAATTAAATTAATT-AATGAAACTATAATTATTAATTAACTAT
**
5289021 TAATGTCTTTTAATATATATACTTTATATACATTTGGTTCATTTATAAGAAATACAATTACTATT
130 TAATGTCTTTTAATATATATACTTTATATACATTAAGTTCATTTATAAGAAATACAATTACTATT
* *
5289086 ATATATATACTGAAATATTTTTAGTATATATACACTTTAAATATAAACATATTTACTTTCTATTT
195 ACATATATA-TAAAATATTTTTAGTATATATACACTTTAAATATAAACATATTTACTTTCTATTT
5289151 TGTGTTAACATTACAAAAATTATAACTTATAAAATTATTAATTA
259 TGTGTTAACATTACAAAAATTATAACTTATAAAATTATTAATTA
5289195 TGTTTGAGAT
Statistics
Matches: 275, Mismatches: 21, Indels: 11
0.90 0.07 0.04
Matches are distributed among these distances:
356 3 0.01
357 213 0.77
358 9 0.03
359 12 0.04
360 38 0.14
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (359 bp):
CTAAAGAGAAGTTGTGAGATTAGAATAGTTTTGAAACCTAGTTATTTTTCTTATAATTTCATGTA
ATTAAGGACAAACCCATATAGTTAATTAAATTAATTAATGAAACTATAATTATTAATTAACTATT
AATGTCTTTTAATATATATACTTTATATACATTAAGTTCATTTATAAGAAATACAATTACTATTA
CATATATATAAAATATTTTTAGTATATATACACTTTAAATATAAACATATTTACTTTCTATTTTG
TGTTAACATTACAAAAATTATAACTTATAAAATTATTAATTAGAATATATATACCATTTTTTATA
TAAAATTATAATATATATATATATATATATATAT
Found at i:5291625 original size:3 final size:3
Alignment explanation
Indices: 5291617--5291653 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5291607 CATGTACATA
5291617 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5291654 GTATCTCCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5299366 original size:39 final size:39
Alignment explanation
Indices: 5299322--5299440 Score: 95
Period size: 39 Copynumber: 3.0 Consensus size: 39
5299312 AATTAAGTAG
5299322 TCTCATTTCAGATAAGGCATTTATTCTTTTTTAAAGTTA
1 TCTCATTTCAGATAAGGCATTTATTCTTTTTTAAAGTTA
* *
5299361 TCTCATTAT-AGATGAGAAGC--TTATT-TATATTTAAAGTTA
1 TCTCATT-TCAGAT-A-AGGCATTTATTCT-TTTTTAAAGTTA
* * * *
5299400 CCTCATTCCAGATGAGG-ACTTTGTTCCTTTTTTAAAGTTA
1 TCTCATTTCAGATAAGGCA-TTTATT-CTTTTTTAAAGTTA
5299440 T
1 T
5299441 GTAGCTTCAA
Statistics
Matches: 61, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
37 2 0.03
38 1 0.02
39 41 0.67
40 13 0.21
41 4 0.07
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (39 bp):
TCTCATTTCAGATAAGGCATTTATTCTTTTTTAAAGTTA
Found at i:5308570 original size:2 final size:2
Alignment explanation
Indices: 5308563--5308595 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5308553 ACTTTCTATA
5308563 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5308596 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5308714 original size:37 final size:37
Alignment explanation
Indices: 5308673--5308754 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
5308663 AATGCAATAT
* * *
5308673 CATCATCATGTGTGTACTCTCTACTCGCACACTTCAA
1 CATCATCATGTGCGCACTCCCTACTCGCACACTTCAA
5308710 CATCATCATGTGCGCACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGCGCACTCCCTACTCGCACACTTCAA
5308747 CATCATCA
1 CATCATCA
5308755 CACAACATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.26, C:0.37, G:0.10, T:0.28
Consensus pattern (37 bp):
CATCATCATGTGCGCACTCCCTACTCGCACACTTCAA
Found at i:5310081 original size:24 final size:24
Alignment explanation
Indices: 5310035--5310085 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5310025 TGGAAAAGCG
*
5310035 TTTTCAACAAAATTCCATGGAAAA
1 TTTTCAACAAAATTCCATCGAAAA
* * *
5310059 TTTTCAACAGAATTTCGTCGAAAA
1 TTTTCAACAAAATTCCATCGAAAA
5310083 TTT
1 TTT
5310086 CCAATGGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (24 bp):
TTTTCAACAAAATTCCATCGAAAA
Found at i:5310750 original size:25 final size:24
Alignment explanation
Indices: 5310703--5310751 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
5310693 CTAAATTTCT
* *
5310703 TCATGTATTTCCCCACGTATTTTG
1 TCATGTATTTACCCAAGTATTTTG
*
5310727 TCATGTATATTACCCAAGTTTTTTG
1 TCATGTAT-TTACCCAAGTATTTTG
5310752 ATAGATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.47
Consensus pattern (24 bp):
TCATGTATTTACCCAAGTATTTTG
Found at i:5319972 original size:28 final size:30
Alignment explanation
Indices: 5319914--5319973 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
5319904 TTTTTGAAAT
*
5319914 TTACACTTTTGCCCCCATAAAAGTCAAAAA
1 TTACACTTTTGCCCCCATAAAACTCAAAAA
* *
5319944 TTACATTTTTG-CCCCA-AAAACTGAAAAA
1 TTACACTTTTGCCCCCATAAAACTCAAAAA
5319972 TT
1 TT
5319974 GCCCATAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 12 0.44
29 5 0.19
30 10 0.37
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (30 bp):
TTACACTTTTGCCCCCATAAAACTCAAAAA
Found at i:5320163 original size:19 final size:19
Alignment explanation
Indices: 5320139--5320176 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5320129 CTGCCAAACC
*
5320139 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
5320158 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
5320177 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:5322072 original size:18 final size:20
Alignment explanation
Indices: 5322050--5322098 Score: 75
Period size: 18 Copynumber: 2.5 Consensus size: 20
5322040 CTAAAAGTTT
5322050 ATTCATCTTCATCT-TTTTC
1 ATTCATCTTCATCTCTTTTC
5322069 -TTCATCTTCATCTCTTTTC
1 ATTCATCTTCATCTCTTTTC
5322088 ATGTCATCTTC
1 AT-TCATCTTC
5322099 TTCATCTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 13 0.48
19 5 0.19
20 1 0.04
21 8 0.30
ACGTcount: A:0.14, C:0.29, G:0.02, T:0.55
Consensus pattern (20 bp):
ATTCATCTTCATCTCTTTTC
Found at i:5322102 original size:30 final size:30
Alignment explanation
Indices: 5322066--5322134 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
5322056 CTTCATCTTT
* *
5322066 TTCTTCATCTTCATCTCTTTTCATGTCATC
1 TTCTTCATCTTCATCTCCTTGCATGTCATC
* *
5322096 TTCTTCATCTTCATTTCCTTGCATGTCATT
1 TTCTTCATCTTCATCTCCTTGCATGTCATC
5322126 TTCTTCATC
1 TTCTTCATC
5322135 CTCAATCAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.13, C:0.29, G:0.04, T:0.54
Consensus pattern (30 bp):
TTCTTCATCTTCATCTCCTTGCATGTCATC
Found at i:5324262 original size:82 final size:82
Alignment explanation
Indices: 5324140--5324700 Score: 1018
Period size: 82 Copynumber: 6.8 Consensus size: 82
5324130 GAGATTGCTT
* *
5324140 ATGTGCGCGATGT-GGGGGGAGCACATGATGGCATTAGTTGTGCACGATGTGGGGGTACACACAA
1 ATGTGCGCGATGTGGGGGGGAGCACATGATGGGATTAGTTGTGCTCGATGTGGGGGTACACACAA
5324204 TGATGATGATATATGCC
66 TGATGATGATATATGCC
5324221 ATGTGCGCGATGTGGGGGGGAGCACATGATGGGATTAGTTGTGCTCGATGTGGGGGTACACACAA
1 ATGTGCGCGATGTGGGGGGGAGCACATGATGGGATTAGTTGTGCTCGATGTGGGGGTACACACAA
5324286 TGATGATGATATATGCC
66 TGATGATGATATATGCC
5324303 ATGTGCGCGATGTGGGGGGGAGCACATGATGGGATTAGTTGTGCTCGATGTGGGGGTACACACAA
1 ATGTGCGCGATGTGGGGGGGAGCACATGATGGGATTAGTTGTGCTCGATGTGGGGGTACACACAA
5324368 TGATGATGATATATGCC
66 TGATGATGATATATGCC
5324385 ATGTGCGCGATGTGGGGGGGAGCACATGATGGGATTAGTTGTGCTCGATGTGGGGGTACACACAA
1 ATGTGCGCGATGTGGGGGGGAGCACATGATGGGATTAGTTGTGCTCGATGTGGGGGTACACACAA
5324450 TGATGATGATATATGCC
66 TGATGATGATATATGCC
5324467 ATGTGCGCGATGTGGGGGGGAGCACATGATGGGATTAGTTGTGCTCGATGTGGGGGTACACACAA
1 ATGTGCGCGATGTGGGGGGGAGCACATGATGGGATTAGTTGTGCTCGATGTGGGGGTACACACAA
5324532 TGATGATGATATATGCC
66 TGATGATGATATATGCC
*
5324549 ATGTGCGCGATGTGGGGGGGAGCACATGATGGGATTAGTTGTGCTCGATGTGGGGGTGCACACGA
1 ATGTGCGCGATGTGGGGGGGAGCACATGATGGGATTAGTTGTGCTCGATGTGGGGGTACACAC-A
5324614 TGATGATGATGATATATGCC
65 --ATGATGATGATATATGCC
* * * *
5324634 ATGTACGCGATGT-GGGGGGAGCACATGATGGCATTAGTTGTGCGCGATGTGGGGGTGCACACAA
1 ATGTGCGCGATGTGGGGGGGAGCACATGATGGGATTAGTTGTGCTCGATGTGGGGGTACACACAA
5324698 TGA
66 TGA
5324701 CTCCAGCTAT
Statistics
Matches: 470, Mismatches: 6, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
81 17 0.04
82 374 0.80
83 2 0.00
84 47 0.10
85 30 0.06
ACGTcount: A:0.23, C:0.14, G:0.38, T:0.25
Consensus pattern (82 bp):
ATGTGCGCGATGTGGGGGGGAGCACATGATGGGATTAGTTGTGCTCGATGTGGGGGTACACACAA
TGATGATGATATATGCC
Found at i:5344537 original size:16 final size:17
Alignment explanation
Indices: 5344509--5344544 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
5344499 TATTTTATTA
5344509 ATAAATAAAATTTAAAT
1 ATAAATAAAATTTAAAT
*
5344526 ATAAAT-AAATTTTAAT
1 ATAAATAAAATTTAAAT
5344542 ATA
1 ATA
5344545 TTTATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAATAAAATTTAAAT
Found at i:5345319 original size:23 final size:23
Alignment explanation
Indices: 5345293--5345337 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
5345283 TGTGAAACAG
*
5345293 CATGTTGGGAATGTGTGACACGA
1 CATGGTGGGAATGTGTGACACGA
5345316 CATGGTGGGAATGTGTGACACG
1 CATGGTGGGAATGTGTGACACG
5345338 GTTGTGACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.13, G:0.38, T:0.24
Consensus pattern (23 bp):
CATGGTGGGAATGTGTGACACGA
Found at i:5345648 original size:47 final size:47
Alignment explanation
Indices: 5345340--5345628 Score: 319
Period size: 47 Copynumber: 6.1 Consensus size: 47
5345330 GTGACACGGT
* * * * *
5345340 TGTGACATGGCAGGGTTCAGAGTTTGTGACACGCCATGAAGGGAGTC
1 TGTGACACGCCAGCGTTCAGAGTTTGTGACACGCCATGGAGGGAATC
* * * ** * * *
5345387 TGTGAGACGCCAACATTCAGAGTTAATGACATGACATGGAGGAAATC
1 TGTGACACGCCAGCGTTCAGAGTTTGTGACACGCCATGGAGGGAATC
* *
5345434 TGTGACACGCCAGCGTTTAGAGTTCT-TGACATGCCATGGAGGGAATC
1 TGTGACACGCCAGCGTTCAGAGTT-TGTGACACGCCATGGAGGGAATC
* *
5345481 TGTGACACACCAGCGTTCAGAGTTCGTGACACGCCATGGAGGGAATC
1 TGTGACACGCCAGCGTTCAGAGTTTGTGACACGCCATGGAGGGAATC
* * * **
5345528 TGTGAGATGCCAGCGTTCATAGTTCATGACACGCCATGGAGGGAATC
1 TGTGACACGCCAGCGTTCAGAGTTTGTGACACGCCATGGAGGGAATC
** * * *
5345575 TGTGACACATCAGTGTTCAGAGTTTGTGACGCGCTATGGAGGGAATC
1 TGTGACACGCCAGCGTTCAGAGTTTGTGACACGCCATGGAGGGAATC
5345622 TGTGACA
1 TGTGACA
5345629 TGGCAGGGTT
Statistics
Matches: 201, Mismatches: 39, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
47 201 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (47 bp):
TGTGACACGCCAGCGTTCAGAGTTTGTGACACGCCATGGAGGGAATC
Found at i:5345662 original size:141 final size:141
Alignment explanation
Indices: 5345340--5345648 Score: 386
Period size: 141 Copynumber: 2.2 Consensus size: 141
5345330 GTGACACGGT
* *
5345340 TGTGACATGGCAGGGTTCAGAGTTTGTGACACGCCATGAAGGGAGTCTGTGAGACGCCAACATTC
1 TGTGACATGGCAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGAGACGCCAACATTC
* * * *
5345405 AGAGTTAATGACATGACATGGAGGAAATCTGTGACACGCCAGCGTTTAGAGTTCTTGACATGCCA
66 AGAGTTAATGACACGACATGGAGGAAATCTGTGACACACCAGCGTTCAGAGTTCTTGACACGCCA
5345470 TGGAGGGAATC
131 TGGAGGGAATC
*** * * * * *
5345481 TGTGACACACCAGCGTTCAGAGTTCGTGACACGCCATGGAGGGAATCTGTGAGATGCCAGCGTTC
1 TGTGACATGGCAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGAGACGCCAACATTC
* * * * * * * *
5345546 ATAGTTCATGACACGCCATGGAGGGAATCTGTGACACATCAGTGTTCAGAGTT-TGTGACGCGCT
66 AGAGTTAATGACACGACATGGAGGAAATCTGTGACACACCAGCGTTCAGAGTTCT-TGACACGCC
5345610 ATGGAGGGAATC
130 ATGGAGGGAATC
**
5345622 TGTGACATGGCAGGGTTTGGAGTTTGT
1 TGTGACATGGCAGGGTTCAGAGTTTGT
5345649 CAGACTTCAT
Statistics
Matches: 138, Mismatches: 29, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
140 1 0.01
141 137 0.99
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (141 bp):
TGTGACATGGCAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGAGACGCCAACATTC
AGAGTTAATGACACGACATGGAGGAAATCTGTGACACACCAGCGTTCAGAGTTCTTGACACGCCA
TGGAGGGAATC
Found at i:5346550 original size:31 final size:31
Alignment explanation
Indices: 5346328--5346561 Score: 310
Period size: 31 Copynumber: 7.5 Consensus size: 31
5346318 GTGTCAGCAT
* *
5346328 TGGCGTGTTATAACATTTGAC-TTGATATGCA
1 TGGCGTGTTACAACATTTTACGTT-ATATGCA
* *
5346359 TGGAGTGTTACAACATTTTATGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
* *
5346390 TGGCGTGTTACAAAATTTTATGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
5346421 TGGCGTGTTACAACATTTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
*
5346452 TGACGTGTTACAACATTTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
*
5346483 TGACGTGTTATC-ACATTTTACGTTATATGCA
1 TGGCGTGTTA-CAACATTTTACGTTATATGCA
** **
5346514 TGGCGTGTTACCGCATTTTACGTTATATTTA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
* *
5346545 GGGCGTGTTACCACATT
1 TGGCGTGTTACAACATT
5346562 ATGGGTTAAC
Statistics
Matches: 185, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
30 1 0.01
31 181 0.98
32 3 0.02
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.40
Consensus pattern (31 bp):
TGGCGTGTTACAACATTTTACGTTATATGCA
Found at i:5348264 original size:144 final size:144
Alignment explanation
Indices: 5347939--5348284 Score: 392
Period size: 144 Copynumber: 2.4 Consensus size: 144
5347929 GAAGAGCCGG
* * *
5347939 TAAGGACGGTTCTAACGATTTGTGTTCAAACATTCCATATGTGATTATCGAATAACATATTTGTG
1 TAAGGACTGTTCTAACGATTTGTGTTCAAA-ATTTCATATGTGATTATCGAATAACATATTTGTA
* * * * * *
5348004 TTTGCAGTTGGACCATGCGACGACAGCTCCACAACCACCGAGAGGTCCTTTTTAGACTCATAGTG
65 TTTGCAGTTGAACCATGCGACGACAGCTCCACAACCACCGAGAGGTCCTCTTCAGACACACAATG
*
5348069 CTAACGACGAGCTGA
130 CTAACGACCAGCTGA
* * *
5348084 TAAGGACTGTTATAACGGTTTGTGTTTAACAATTTCATATGTGATTATCGAATAACATA-TTGTA
1 TAAGGACTGTTCTAACGATTTGTGTTCAA-AATTTCATATGTGATTATCGAATAACATATTTGTA
* * * * *
5348148 TTTGCAGTTGAACCATGCGATGACAGTTCCTCAACCACTGAGAGGTCCTCTTCAGACACACAATT
65 TTTGCAGTTGAACCATGCGACGACAGCTCCACAACCACCGAGAGGTCCTCTTCAGACACACAATG
* *
5348213 CTAACGACCCATC-GG
130 CTAACGA-CCAGCTGA
* * * * * *
5348228 TAA-GATCTGTTCTAATGATTTGTGTTCAATATTTTCACATATGTTTATCGAGTAACA
1 TAAGGA-CTGTTCTAACGATTTGTGTTCAA-AATTTCATATGTGATTATCGAATAACA
5348285 CAGTAATTTT
Statistics
Matches: 168, Mismatches: 30, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
143 2 0.01
144 110 0.65
145 55 0.33
146 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (144 bp):
TAAGGACTGTTCTAACGATTTGTGTTCAAAATTTCATATGTGATTATCGAATAACATATTTGTAT
TTGCAGTTGAACCATGCGACGACAGCTCCACAACCACCGAGAGGTCCTCTTCAGACACACAATGC
TAACGACCAGCTGA
Found at i:5350202 original size:118 final size:118
Alignment explanation
Indices: 5350025--5350359 Score: 508
Period size: 118 Copynumber: 2.8 Consensus size: 118
5350015 GGGGCATGTC
* * * * * *
5350025 GTGTCACCCCACAATACTGTAAGAAGTCAGTGTGTCACCATAGAAATCTGTATGCACTCAGCATG
1 GTGTCACCCCACAATAATGCAAGAAGTCAGCGTGTCACCACAGAAATCTGCATGCACTCAGCGTG
5350090 TCATGCCAACTATCTGCTTCCACTCAGCGTGTCACCACAAGATGGGACGTGCA
66 TCATGCCAACTATCTGCTTCCACTCAGCGTGTCACCACAAGATGGGACGTGCA
* *
5350143 GTGTCACCCCACAATAATGCAAGAAGTCAGCGTGTCACCACAGAAATCTGCATGTACTCAACGTG
1 GTGTCACCCCACAATAATGCAAGAAGTCAGCGTGTCACCACAGAAATCTGCATGCACTCAGCGTG
* ** * * *
5350208 TCACGCCAACTATCTGCTTCCACTCAATGTGTCACCACAATATGGGGCGTGCC
66 TCATGCCAACTATCTGCTTCCACTCAGCGTGTCACCACAAGATGGGACGTGCA
* * * *
5350261 GTGTCACCCTATAATAATGCAAGAAGTCAGCGTGTCACCACAAAAATCTGCATGCATTCAGCGTG
1 GTGTCACCCCACAATAATGCAAGAAGTCAGCGTGTCACCACAGAAATCTGCATGCACTCAGCGTG
5350326 TCATGCCAACTATCTGCTTCCACTCAGCGTGTCA
66 TCATGCCAACTATCTGCTTCCACTCAGCGTGTCA
5350360 TGCCAACTAT
Statistics
Matches: 194, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
118 194 1.00
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (118 bp):
GTGTCACCCCACAATAATGCAAGAAGTCAGCGTGTCACCACAGAAATCTGCATGCACTCAGCGTG
TCATGCCAACTATCTGCTTCCACTCAGCGTGTCACCACAAGATGGGACGTGCA
Found at i:5350341 original size:31 final size:31
Alignment explanation
Indices: 5350318--5350390 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
5350308 CTGCATGCAT
5350318 TCAGCGTGTCATGCCAACTATCTGCTTCCAC
1 TCAGCGTGTCATGCCAACTATCTGCTTCCAC
5350349 TCAGCGTGTCATGCCAACTATCTGCTTCCAC
1 TCAGCGTGTCATGCCAACTATCTGCTTCCAC
5350380 TCAGCGTGTCA
1 TCAGCGTGTCA
5350391 CCACAATGGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.19, C:0.34, G:0.18, T:0.29
Consensus pattern (31 bp):
TCAGCGTGTCATGCCAACTATCTGCTTCCAC
Found at i:5350459 original size:31 final size:31
Alignment explanation
Indices: 5350407--5350476 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
5350397 TGGGGCATGC
* *
5350407 CGTGTCACCCCATAATACTGCAAGAAATCAG
1 CGTGTCACCACAAAATACTGCAAGAAATCAG
* * *
5350438 CGTGTCACCACAGAAAT-CTGCATGCACTCAG
1 CGTGTCACCACA-AAATACTGCAAGAAATCAG
5350469 CGTGTCAC
1 CGTGTCAC
5350477 GCCAACTATC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 30 0.91
32 3 0.09
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (31 bp):
CGTGTCACCACAAAATACTGCAAGAAATCAG
Found at i:5350469 original size:147 final size:149
Alignment explanation
Indices: 5350198--5350507 Score: 489
Period size: 147 Copynumber: 2.1 Consensus size: 149
5350188 ATCTGCATGT
* *
5350198 ACTCAACGTGTCACGCCAACTATCTGCTTCCACTCAATGTGTCACCACAATATGGGGCGTGCCGT
1 ACTCAACGTGTCACGCCAACTATCTGCTTCCACTCAACGTGTCACCACAATATGGGGCATGCCGT
* * *
5350263 GTCACCCTATAATAATGCAAGAAGTCAGCGTGTCACCACAAAAATCTGCATGCATTCAGCGTGTC
66 GTCACCCCATAATAATGCAAGAAATCAGCGTGTCACCACAAAAATCTGCATGCACTCAGCGTGTC
*
5350328 ATGCCAACTATCTGCTTCC
131 ACGCCAACTATCTGCTTCC
* * *
5350347 ACTCAGCGTGTCATGCCAACTATCTGCTTCCACTCAGCGTGTCACCAC-A-ATGGGGCATGCCGT
1 ACTCAACGTGTCACGCCAACTATCTGCTTCCACTCAACGTGTCACCACAATATGGGGCATGCCGT
* *
5350410 GTCACCCCATAATACTGCAAGAAATCAGCGTGTCACCACAGAAATCTGCATGCACTCAGCGTGTC
66 GTCACCCCATAATAATGCAAGAAATCAGCGTGTCACCACAAAAATCTGCATGCACTCAGCGTGTC
*
5350475 ACGCCAACTATCTGTTTCC
131 ACGCCAACTATCTGCTTCC
*
5350494 ACTCAATGTGTCAC
1 ACTCAACGTGTCAC
5350508 CACAAGATGT
Statistics
Matches: 146, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
147 101 0.69
148 1 0.01
149 44 0.30
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.24
Consensus pattern (149 bp):
ACTCAACGTGTCACGCCAACTATCTGCTTCCACTCAACGTGTCACCACAATATGGGGCATGCCGT
GTCACCCCATAATAATGCAAGAAATCAGCGTGTCACCACAAAAATCTGCATGCACTCAGCGTGTC
ACGCCAACTATCTGCTTCC
Found at i:5357385 original size:63 final size:63
Alignment explanation
Indices: 5357312--5357434 Score: 183
Period size: 63 Copynumber: 2.0 Consensus size: 63
5357302 CCACAACCCA
*
5357312 ATGACAATGGTGCTCAACAAAGAGTTGACAAAGCTCATACAATTCAGAGAGCTAAGAGAGCTG
1 ATGACAATGGTGCTCAACAAAGAGTTGACAAAGCTCAGACAATTCAGAGAGCTAAGAGAGCTG
* * * * * *
5357375 ATGACGATGGTGGTCAACAAAGAGTTGACAGAGTTGAGACAATTCAGAGAGCTGAGAGAG
1 ATGACAATGGTGCTCAACAAAGAGTTGACAAAGCTCAGACAATTCAGAGAGCTAAGAGAG
5357435 AAAGATGAGC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.19
Consensus pattern (63 bp):
ATGACAATGGTGCTCAACAAAGAGTTGACAAAGCTCAGACAATTCAGAGAGCTAAGAGAGCTG
Found at i:5363783 original size:22 final size:22
Alignment explanation
Indices: 5363716--5363784 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
5363706 ATTTAATTTT
* ** *
5363716 ATTAATGTATTTTCTATAAAAT
1 ATTAATATATTTTAAATAAAAA
*
5363738 ATTAATA-ATATTTAAAAAAAAA
1 ATTAATATAT-TTTAAATAAAAA
5363760 ATTAATATATTTTAAATAAAAA
1 ATTAATATATTTTAAATAAAAA
5363782 ATT
1 ATT
5363785 TTAAAAATAG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 2 0.05
22 35 0.90
23 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (22 bp):
ATTAATATATTTTAAATAAAAA
Found at i:5363788 original size:24 final size:23
Alignment explanation
Indices: 5363733--5363793 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
5363723 TATTTTCTAT
5363733 AAAATATTAATAATATTTAAAAA
1 AAAATATTAATAATATTTAAAAA
5363756 AAAA-ATTAAT-ATATTTTAAATAA
1 AAAATATTAATAATA-TTTAAA-AA
* *
5363779 AAAATTTTAAAAATA
1 AAAATATTAATAATA
5363794 GTAATACTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 3 0.09
22 12 0.38
23 10 0.31
24 4 0.12
25 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATATTAATAATATTTAAAAA
Found at i:5378841 original size:3 final size:3
Alignment explanation
Indices: 5378833--5378909 Score: 61
Period size: 3 Copynumber: 25.3 Consensus size: 3
5378823 ATATTTTTTG
* *
5378833 TTA TTA TTAA TTA TTT TTA TT- TTA TTA TCA -TA TT- TCCTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA T--TA TTA TTA
* *
5378878 TTTC TTA TTA TTA TTA TTA TTA TTA TTT TTA T
1 -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5378910 ACTTTACATT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
2 4 0.07
3 48 0.81
4 6 0.10
5 1 0.02
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5378866 original size:13 final size:14
Alignment explanation
Indices: 5378833--5378910 Score: 56
Period size: 13 Copynumber: 5.8 Consensus size: 14
5378823 ATATTTTTTG
5378833 TTATTATTA-ATTA
1 TTATTATTATATTA
* *
5378846 TTTTTATTTTATTA
1 TTATTATTATATTA
* **
5378860 TCA-TATT-TCCTA
1 TTATTATTATATTA
*
5378872 TTATTATT-TCTTA
1 TTATTATTATATTA
5378885 TTATTATTATTATTA
1 TTATTATTA-TATTA
*
5378900 TTATTTTTATA
1 TTATTATTATA
5378911 CTTTACATTT
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
12 5 0.10
13 27 0.53
14 7 0.14
15 12 0.24
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATTATATTA
Found at i:5379043 original size:8 final size:9
Alignment explanation
Indices: 5379020--5379061 Score: 52
Period size: 8 Copynumber: 4.8 Consensus size: 9
5379010 TTTATCGTAC
5379020 TATTTTTAT
1 TATTTTTAT
5379029 GTATTTTTA-
1 -TATTTTTAT
5379038 TATTTTTAT
1 TATTTTTAT
*
5379047 TATTATTA-
1 TATTTTTAT
5379055 TATTTTT
1 TATTTTT
5379062 CATAAGCGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 14 0.48
9 7 0.24
10 8 0.28
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (9 bp):
TATTTTTAT
Found at i:5379043 original size:17 final size:17
Alignment explanation
Indices: 5379020--5379061 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
5379010 TTTATCGTAC
*
5379020 TATTTTTATGTATTTTTA
1 TATTTTTAT-TATTATTA
5379038 TATTTTTATTATTATTA
1 TATTTTTATTATTATTA
5379055 TATTTTT
1 TATTTTT
5379062 CATAAGCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (17 bp):
TATTTTTATTATTATTA
Found at i:5379300 original size:20 final size:20
Alignment explanation
Indices: 5379277--5379335 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
5379267 TTTCAAATTT
5379277 ATTATTTATTA-TATGTTTGA
1 ATTATTTATTATTAT-TTTGA
*
5379297 ATTA-TTATTATTTATTTTTA
1 ATTATTTATTA-TTATTTTGA
5379317 ATTATTTATTTATTATTTT
1 ATTATTTA-TTATTATTTT
5379336 TATCAAGTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
19 6 0.18
20 12 0.35
21 13 0.38
22 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
ATTATTTATTATTATTTTGA
Found at i:5379311 original size:26 final size:24
Alignment explanation
Indices: 5379259--5379312 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 24
5379249 ATGTCATGTA
5379259 TATTATATTTTCAAATTTATTATT
1 TATTATATTTTCAAATTTATTATT
* *
5379283 TATTATATGTTTGAATTATTATTATT
1 TATTATAT-TTTCAAAT-TTATTATT
5379309 TATT
1 TATT
5379313 TTTAATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 8 0.31
25 6 0.23
26 12 0.46
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (24 bp):
TATTATATTTTCAAATTTATTATT
Found at i:5379872 original size:18 final size:18
Alignment explanation
Indices: 5379849--5379891 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
5379839 AACAAAAGCA
5379849 CAAGATTTAAAACTTACC
1 CAAGATTTAAAACTTACC
5379867 CAAGATTTAAAACTTACC
1 CAAGATTTAAAACTTACC
5379885 CAAGATT
1 CAAGATT
5379892 CAAGCCCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (18 bp):
CAAGATTTAAAACTTACC
Found at i:5380598 original size:22 final size:22
Alignment explanation
Indices: 5380568--5380623 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
5380558 GTCGACTTTT
*
5380568 GGTCAGCCTCTCAACTACCGTC
1 GGTCGGCCTCTCAACTACCGTC
5380590 GGTCGGCCTCTCAACTACCGTC
1 GGTCGGCCTCTCAACTACCGTC
*
5380612 GGTCGGCTTCTC
1 GGTCGGCCTCTC
5380624 CCCATTGCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.12, C:0.39, G:0.23, T:0.25
Consensus pattern (22 bp):
GGTCGGCCTCTCAACTACCGTC
Found at i:5381034 original size:17 final size:17
Alignment explanation
Indices: 5381014--5381058 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
5381004 TTTTTTCATT
*
5381014 TTTTCATTTTTTATATA
1 TTTTCAATTTTTATATA
*
5381031 TTTTTAATTTTTATATA
1 TTTTCAATTTTTATATA
*
5381048 TTTTAAATTTT
1 TTTTCAATTTT
5381059 CTTGTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTCAATTTTTATATA
Found at i:5381035 original size:19 final size:18
Alignment explanation
Indices: 5381011--5381051 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5381001 TTCTTTTTTC
*
5381011 ATTTTTTCATTTTT-TAT
1 ATTTTTTAATTTTTATAT
5381028 ATATTTTTAATTTTTATAT
1 AT-TTTTTAATTTTTATAT
5381047 ATTTT
1 ATTTT
5381052 AAATTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 14 0.67
19 5 0.24
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTTTTAATTTTTATAT
Found at i:5383418 original size:21 final size:21
Alignment explanation
Indices: 5383392--5383433 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5383382 TATGGGTTTA
*
5383392 CAGGTATCAATATTTGTTCAT
1 CAGGTATCAATACTTGTTCAT
**
5383413 CAGGTATTGATACTTGTTCAT
1 CAGGTATCAATACTTGTTCAT
5383434 TAAGATGTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (21 bp):
CAGGTATCAATACTTGTTCAT
Found at i:5394086 original size:237 final size:237
Alignment explanation
Indices: 5393618--5394098 Score: 711
Period size: 237 Copynumber: 2.0 Consensus size: 237
5393608 GGATAATACA
* * *
5393618 TGTCTTACATTTAAAAATAGTTTGTATAATATTTTAGTGTATGTTTAGCTTGATTTTTTTAATTT
1 TGTCTTACATTTAAAAATAGCTGGTATAATATTTTAGTGTATGTTGAGCTTGATTTTTTTAATTT
* *
5393683 ATTTACTTTTTAAAAATAAAAATCATGTCAAACAAGATTTGAAGAAACTTTTTAAAAAAACTAAT
66 ATTTACCTTTTAAAAATAAAAATCATGTCAAACAAGATTTGAAGAAACTCTTTAAAAAAACTAAT
5393748 GTTTTTTAAGGAACACAATTTAGAAAAAAAAAACTTAAAGAAAAACTCTAGATAAAAGTTTTTTC
131 GTTTTTTAAGGAACACAATTTA-AAAAAAAAAACTTAAAGAAAAACTCTAGATAAAAGTTTTTTC
5393813 TTTTTTGCTTTTAAAAACATATAAGATTTTTAGGAAATACCTT
195 TTTTTTGCTTTTAAAAACATATAAGATTTTTAGGAAATACCTT
* * *
5393856 TGTCTTACATTTAAAAATAGCTGGTATGATATTTTGGTGTTTGTTGAGCTTGATTTCTTTTTTAA
1 TGTCTTACATTTAAAAATAGCTGGTATAATATTTTAGTGTATGTTGAGCTTGA--T-TTTTTTAA
* *
5393921 TTTATTTACCTTTTAAAAGTAAAAATCATGTCAAACAAGATTTTTAA-AAACTCTTTAAAAAAA-
63 TTTATTTACCTTTTAAAAATAAAAATCATGTCAAACAAGA-TTTGAAGAAACTCTTTAAAAAAAC
* * *** *
5393984 TAGTTTTTTTTAAGGAACACAATTT-AAAAAAAATGTTTAAAG-AAAACTCTAGATAAGAGTTTT
127 TAATGTTTTTTAAGGAACACAATTTAAAAAAAAAAACTTAAAGAAAAACTCTAGATAAAAGTTTT
*
5394047 TTCTTCTTTT-CTTTTAAAAACATATCAGATTTTTAGGAAATACCTT
192 TTCTT-TTTTGCTTTTAAAAACATATAAGATTTTTAGGAAATACCTT
*
5394093 TCTCTT
1 TGTCTT
5394099 GCAATCGATC
Statistics
Matches: 220, Mismatches: 18, Indels: 11
0.88 0.07 0.04
Matches are distributed among these distances:
237 65 0.30
238 65 0.30
240 24 0.11
241 61 0.28
242 5 0.02
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.42
Consensus pattern (237 bp):
TGTCTTACATTTAAAAATAGCTGGTATAATATTTTAGTGTATGTTGAGCTTGATTTTTTTAATTT
ATTTACCTTTTAAAAATAAAAATCATGTCAAACAAGATTTGAAGAAACTCTTTAAAAAAACTAAT
GTTTTTTAAGGAACACAATTTAAAAAAAAAAACTTAAAGAAAAACTCTAGATAAAAGTTTTTTCT
TTTTTGCTTTTAAAAACATATAAGATTTTTAGGAAATACCTT
Found at i:5403008 original size:20 final size:20
Alignment explanation
Indices: 5402979--5403021 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
5402969 ATTAGGTTAC
5402979 TTTTAAGTTAGTT-ATTTTAA
1 TTTTAAGTTA-TTCATTTTAA
* *
5402999 TTTTATGTTATTCCTTTTAA
1 TTTTAAGTTATTCATTTTAA
5403019 TTT
1 TTT
5403022 GGTTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTAAGTTATTCATTTTAA
Found at i:5404145 original size:14 final size:13
Alignment explanation
Indices: 5404125--5404161 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
5404115 GTTGGTTTTA
5404125 ATTTTAGTTAATT
1 ATTTTAGTTAATT
5404138 AGTTTTAGTTAATT
1 A-TTTTAGTTAATT
*
5404152 AATTTAGTTA
1 ATTTTAGTTA
5404162 TTCAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (13 bp):
ATTTTAGTTAATT
Found at i:5410325 original size:31 final size:31
Alignment explanation
Indices: 5410267--5410329 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
5410257 ACGTGCACTA
*
5410267 TGCAATAGGATTATACATTGCCAGCCCAAGG
1 TGCAATAGGACTATACATTGCCAGCCCAAGG
* * * *
5410298 TGCAATAGGACTGTATATTGTCGGCCCAAGG
1 TGCAATAGGACTATACATTGCCAGCCCAAGG
5410329 T
1 T
5410330 TGATGGGGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (31 bp):
TGCAATAGGACTATACATTGCCAGCCCAAGG
Found at i:5414719 original size:61 final size:61
Alignment explanation
Indices: 5414617--5414906 Score: 357
Period size: 61 Copynumber: 4.8 Consensus size: 61
5414607 GTGACAAATG
* * * * * * *
5414617 CAACCATGCATGTGCGAAATGGGTAGTGCATATGCCAGTAATGATGCAGTCGTGATAATTA
1 CAACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGCAGTCATGATAATTA
* * *
5414678 TAACCGTGCATGTGCAGAGTGGGCAGTGCACATGCCGGTAATGATGCTGTCATGATAATTA
1 CAACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGCAGTCATGATAATTA
* * *
5414739 CAACCGTGCATGTGCGGAGTGGGCAGTGCACATGTCGATAATGATG-ATGTCGTGATAATTA
1 CAACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGCA-GTCATGATAATTA
* * * **
5414800 TAATCGTGCATGTGCGGAGTGGGCAGTGCACATGTCGGTAATGATGCTTTCATGATAATTA
1 CAACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGCAGTCATGATAATTA
* * * * *
5414861 CAATCGTGCATATGCTGAGTGGGTAGTGCACATGCCGGTGATGATG
1 CAACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATG
5414907 TACATGAACT
Statistics
Matches: 199, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
61 199 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (61 bp):
CAACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGCAGTCATGATAATTA
Done.