Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 54 of 203
Found at i:17644868 original size:18 final size:19
Alignment explanation
Indices: 17644808--17644869 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
17644798 TTTCATTAAT
*
17644808 TTATTGATTAATTGACTATTT
1 TTATTG-TT-ATTGACTATTA
*
17644829 TTATTTTTATT-ACTATTTA
1 TTATTGTTATTGACTA-TTA
17644848 TTATTGTTATTGAC-ATTA
1 TTATTGTTATTGACTATTA
17644866 TTAT
1 TTAT
17644870 ATTTGATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 11 0.31
19 16 0.44
20 4 0.11
21 5 0.14
ACGTcount: A:0.27, C:0.05, G:0.06, T:0.61
Consensus pattern (19 bp):
TTATTGTTATTGACTATTA
Found at i:17646618 original size:16 final size:13
Alignment explanation
Indices: 17646585--17646611 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17646575 ATATTTTTTA
17646585 AAAATATAATATT
1 AAAATATAATATT
17646598 AAAATATAATATT
1 AAAATATAATATT
17646611 A
1 A
17646612 CTAAAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAATATAATATT
Found at i:17650027 original size:30 final size:31
Alignment explanation
Indices: 17649993--17650148 Score: 121
Period size: 30 Copynumber: 5.2 Consensus size: 31
17649983 TAAAAAAATG
** *
17649993 CATTTTGACCCCTGTA-CTTTTCGAAATTTA
1 CATTTTGACCCCTAAACCTTTTCAAAATTTA
*
17650023 CATTTTGA-CCCTAAACCTTTTTAAAATTTA
1 CATTTTGACCCCTAAACCTTTTCAAAATTTA
* *
17650053 CATTTTGACCAC-AAA-ATTTTCTAAAA-TTA
1 CATTTTGACCCCTAAACCTTTTC-AAAATTTA
** * *
17650082 CATTTCAACCCTTAAACTTTTTCAAAATTT-
1 CATTTTGACCCCTAAACCTTTTCAAAATTTA
* * *
17650112 CACTTTAACCCCTAAA-C-TTTCAAGAAATTA
1 CATTTTGACCCCTAAACCTTTTCAA-AATTTA
17650142 CATTTTG
1 CATTTTG
17650149 GCCCATATTT
Statistics
Matches: 99, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
28 6 0.06
29 24 0.24
30 60 0.61
31 9 0.09
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.40
Consensus pattern (31 bp):
CATTTTGACCCCTAAACCTTTTCAAAATTTA
Found at i:17650142 original size:60 final size:60
Alignment explanation
Indices: 17650015--17650146 Score: 144
Period size: 59 Copynumber: 2.2 Consensus size: 60
17650005 TGTACTTTTC
** * * * *
17650015 GAAATTTACATTTTGACCCTAAACCTTTTTAAAATTTACATTTTGACCACAAAATTTTCTA
1 GAAA-TTACATTTCAACCCTAAACCTTTTTAAAATTTACACTTTAACCACAAAACTTTCAA
* *
17650076 -AAATTACATTTCAACCCTTAAA-CTTTTTCAAAATTT-CACTTTAACCCCTAAACTTTCAA
1 GAAATTACATTTCAACCC-TAAACCTTTTT-AAAATTTACACTTTAACCACAAAACTTTCAA
17650135 GAAATTACATTT
1 GAAATTACATTT
17650147 TGGCCCATAT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
59 35 0.58
60 25 0.42
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.39
Consensus pattern (60 bp):
GAAATTACATTTCAACCCTAAACCTTTTTAAAATTTACACTTTAACCACAAAACTTTCAA
Found at i:17650584 original size:15 final size:15
Alignment explanation
Indices: 17650560--17650592 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
17650550 AAAAAGAACC
17650560 AAAAACAGCAACCAA
1 AAAAACAGCAACCAA
*
17650575 AAAAATAGCAACCAA
1 AAAAACAGCAACCAA
17650590 AAA
1 AAA
17650593 GAAAGAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.70, C:0.21, G:0.06, T:0.03
Consensus pattern (15 bp):
AAAAACAGCAACCAA
Found at i:17650717 original size:9 final size:9
Alignment explanation
Indices: 17650703--17650781 Score: 52
Period size: 8 Copynumber: 9.6 Consensus size: 9
17650693 GTTCGGCCTA
17650703 AAAAAGAAG
1 AAAAAGAAG
17650712 AAAAAG--G
1 AAAAAGAAG
17650719 AAAAAGGAA-
1 AAAAA-GAAG
*
17650728 AAAAA-TAG
1 AAAAAGAAG
17650736 AAAAA-ATAG
1 AAAAAGA-AG
17650745 --AAAGAA-
1 AAAAAGAAG
17650751 AAAATAGAAG
1 AAAA-AGAAG
17650761 AAAAAG-AG
1 AAAAAGAAG
17650769 AAAAAGAA-
1 AAAAAGAAG
17650777 AAAAA
1 AAAAA
17650782 AATTAAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 23
0.70 0.02 0.28
Matches are distributed among these distances:
7 11 0.19
8 22 0.39
9 20 0.35
10 4 0.07
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:17650737 original size:24 final size:24
Alignment explanation
Indices: 17650702--17650781 Score: 81
Period size: 24 Copynumber: 3.2 Consensus size: 24
17650692 GGTTCGGCCT
17650702 AAAAAAGAAGAAAAAGGAAAAAGG
1 AAAAAAGAAGAAAAAGGAAAAAGG
** * *
17650726 AAAAAA-ATAGAAAAAATAGAAAGA
1 AAAAAAGA-AGAAAAAGGAAAAAGG
*
17650750 AAAAATAGAAGAAAAAGAGAAAAAGA
1 AAAAA-AGAAGAAAAAG-GAAAAAGG
17650776 AAAAAA
1 AAAAAA
17650782 AATTAAAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
23 1 0.02
24 23 0.51
25 9 0.20
26 12 0.27
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (24 bp):
AAAAAAGAAGAAAAAGGAAAAAGG
Found at i:17650752 original size:13 final size:13
Alignment explanation
Indices: 17650734--17650780 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
17650724 GGAAAAAAAT
17650734 AGAAAAAATAGAA
1 AGAAAAAATAGAA
17650747 AGAAAAAATAG-A
1 AGAAAAAATAGAA
* *
17650759 AGAAAAAGAGAAAA
1 AGAAAAA-ATAGAA
17650773 AGAAAAAA
1 AGAAAAAA
17650781 AAATTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.27
13 14 0.47
14 8 0.27
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (13 bp):
AGAAAAAATAGAA
Found at i:17651510 original size:23 final size:23
Alignment explanation
Indices: 17651452--17651545 Score: 131
Period size: 23 Copynumber: 4.2 Consensus size: 23
17651442 TCGCATTTTC
*
17651452 AAAAGTTTTCGTGTTTTAAAA--
1 AAAAATTTTCGTGTTTTAAAATG
* *
17651473 AAAAA-TTCCGCGTTTTAAAATG
1 AAAAATTTTCGTGTTTTAAAATG
*
17651495 AAAAATTTTCGTGTTTTCAAATG
1 AAAAATTTTCGTGTTTTAAAATG
17651518 AAAAATTTTCGTGTTTTAAAATG
1 AAAAATTTTCGTGTTTTAAAATG
17651541 AAAAA
1 AAAAA
17651546 AAAAACAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
20 13 0.21
21 4 0.06
22 5 0.08
23 41 0.65
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.38
Consensus pattern (23 bp):
AAAAATTTTCGTGTTTTAAAATG
Found at i:17651684 original size:20 final size:19
Alignment explanation
Indices: 17651657--17651699 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
17651647 GTATTTTATC
17651657 AAAAAAA-TTTATGTTTTCA
1 AAAAAAATTTTATGTTTT-A
*
17651676 AAAACAAATTTTCTGTTTTA
1 AAAA-AAATTTTATGTTTTA
17651696 AAAA
1 AAAA
17651700 TTTTCGTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 8 0.38
21 9 0.43
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (19 bp):
AAAAAAATTTTATGTTTTA
Found at i:17651699 original size:37 final size:37
Alignment explanation
Indices: 17651659--17651738 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
17651649 ATTTTATCAA
*
17651659 AAAAATTTAT-GT-TTTCAAAAACAAATTTTC-TGTTTT
1 AAAAATTT-TCGTGTTTCAAAAACAAA-ATTCGTGTTTT
*
17651695 AAAAATTTTCGTGTTTCAAAAATAAAATTCGTGTTTT
1 AAAAATTTTCGTGTTTCAAAAACAAAATTCGTGTTTT
17651732 CAAAAAT
1 -AAAAAT
17651739 AAAAATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
35 1 0.03
36 13 0.34
37 18 0.47
38 6 0.16
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.42
Consensus pattern (37 bp):
AAAAATTTTCGTGTTTCAAAAACAAAATTCGTGTTTT
Found at i:17651702 original size:16 final size:17
Alignment explanation
Indices: 17651681--17651717 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
17651671 TTTCAAAAAC
*
17651681 AAATTTTC-TGTTTTAA
1 AAATTTTCGTGTTTCAA
17651697 AAATTTTCGTGTTTCAA
1 AAATTTTCGTGTTTCAA
17651714 AAAT
1 AAAT
17651718 AAAATTCGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (17 bp):
AAATTTTCGTGTTTCAA
Found at i:17651727 original size:20 final size:21
Alignment explanation
Indices: 17651702--17651742 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
17651692 TTTAAAAATT
17651702 TTCGTG-TTTCAAAAATAAAA
1 TTCGTGTTTTCAAAAATAAAA
17651722 TTCGTGTTTTCAAAAATAAAA
1 TTCGTGTTTTCAAAAATAAAA
17651743 ATAAAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (21 bp):
TTCGTGTTTTCAAAAATAAAA
Found at i:17651767 original size:15 final size:16
Alignment explanation
Indices: 17651747--17651777 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17651737 ATAAAAATAA
17651747 AAAATC-TCATGTTTT
1 AAAATCTTCATGTTTT
17651762 AAAATCTTCATGTTTT
1 AAAATCTTCATGTTTT
17651778 TTTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.48
Consensus pattern (16 bp):
AAAATCTTCATGTTTT
Found at i:17651833 original size:16 final size:15
Alignment explanation
Indices: 17651785--17651838 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
17651775 TTTTTTAAAA
17651785 AAAAGTTTTGTGTTTCT
1 AAAA-TTTTGTGTTT-T
*
17651802 AAAATTCTTGTATTTT
1 AAAATT-TTGTGTTTT
17651818 AAAATTTTCGTGTTTT
1 AAAATTTT-GTGTTTT
17651834 CAAAA
1 -AAAA
17651839 AAGGAAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 2 0.06
16 15 0.47
17 15 0.47
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.50
Consensus pattern (15 bp):
AAAATTTTGTGTTTT
Found at i:17658881 original size:1 final size:1
Alignment explanation
Indices: 17658877--17658982 Score: 68
Period size: 1 Copynumber: 106.0 Consensus size: 1
17658867 AAAAGTAAAC
* * * * * * * * *
17658877 AAAAAACAAAAAAAAACAACAAAAAAAACAACAAAAAAACAAAACAAAAAAACAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
17658942 CAAAACAAAAAAAGAAAAAACAAAGAAAAGAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17658983 TCAAGATGAA
Statistics
Matches: 73, Mismatches: 32, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:17658882 original size:13 final size:13
Alignment explanation
Indices: 17658879--17658959 Score: 121
Period size: 13 Copynumber: 6.3 Consensus size: 13
17658869 AAGTAAACAA
17658879 AAAACAAAAAAA-
1 AAAACAAAAAAAC
17658891 AACAACAAAAAAA-
1 AA-AACAAAAAAAC
*
17658904 ACAACAAAAAAAC
1 AAAACAAAAAAAC
17658917 AAAACAAAAAAAC
1 AAAACAAAAAAAC
17658930 AAAACAAAAAAAC
1 AAAACAAAAAAAC
*
17658943 AAAACAAAAAAAG
1 AAAACAAAAAAAC
17658956 AAAA
1 AAAA
17658960 AACAAAGAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
12 12 0.19
13 52 0.81
ACGTcount: A:0.85, C:0.14, G:0.01, T:0.00
Consensus pattern (13 bp):
AAAACAAAAAAAC
Found at i:17658914 original size:33 final size:34
Alignment explanation
Indices: 17658873--17658964 Score: 118
Period size: 33 Copynumber: 2.7 Consensus size: 34
17658863 GAAAAAAAGT
17658873 AAAC-AAAAAACAAAAAAAAACAACAAAA-AAAA
1 AAACAAAAAAACAAAAAAAAACAACAAAACAAAA
*
17658905 CAACAAAAAAACAAAACAAAAA-AACAAAACAAAA
1 AAACAAAAAAACAAAA-AAAAACAACAAAACAAAA
*
17658939 AAACAAAACAAAAAAAGAAAAAACAA
1 AAACAAAA-AAACAAA-AAAAAACAA
17658965 AGAAAAGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
32 3 0.06
33 18 0.35
34 16 0.31
35 11 0.22
36 3 0.06
ACGTcount: A:0.85, C:0.14, G:0.01, T:0.00
Consensus pattern (34 bp):
AAACAAAAAAACAAAAAAAAACAACAAAACAAAA
Found at i:17658931 original size:46 final size:44
Alignment explanation
Indices: 17658864--17658965 Score: 127
Period size: 46 Copynumber: 2.2 Consensus size: 44
17658854 ATTATGCCTG
**
17658864 AAAAAAAGTAAACAAAAAACAAAA-AAAAACAACAAAA-AAAACAA
1 AAAAAAACAAAACAAAAAACAAAACAAAAA-AACAAAACAAAA-AA
17658908 CAAAAAAACAAAACAAAAAAACAAAACAAAAAAACAAAACAAAAAA
1 -AAAAAAACAAAAC-AAAAAACAAAACAAAAAAACAAAACAAAAAA
17658954 AGAAAAAACAAA
1 A-AAAAAACAAA
17658966 GAAAAGAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
45 12 0.24
46 30 0.59
47 9 0.18
ACGTcount: A:0.84, C:0.13, G:0.02, T:0.01
Consensus pattern (44 bp):
AAAAAAACAAAACAAAAAACAAAACAAAAAAACAAAACAAAAAA
Found at i:17658936 original size:38 final size:39
Alignment explanation
Indices: 17658879--17658959 Score: 121
Period size: 38 Copynumber: 2.1 Consensus size: 39
17658869 AAGTAAACAA
*
17658879 AAAACAAAAAAAAACAACAAAAAAA-ACAACAAAAAAAC
1 AAAACAAAAAAAAACAACAAAAAAACAAAACAAAAAAAC
*
17658917 AAAACAAAAAAACAA-AACAAAAAAACAAAACAAAAAAAG
1 AAAACAAAAAAA-AACAACAAAAAAACAAAACAAAAAAAC
17658956 AAAA
1 AAAA
17658960 AACAAAGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
38 22 0.56
39 17 0.44
ACGTcount: A:0.85, C:0.14, G:0.01, T:0.00
Consensus pattern (39 bp):
AAAACAAAAAAAAACAACAAAAAAACAAAACAAAAAAAC
Found at i:17658959 original size:26 final size:25
Alignment explanation
Indices: 17658877--17658982 Score: 126
Period size: 25 Copynumber: 4.2 Consensus size: 25
17658867 AAAAGTAAAC
17658877 AAAAAACAAAAAAA-AACAACAAAAA
1 AAAAAACAAAAAAACAA-AACAAAAA
*
17658902 AAACAACAAAAAAACAAAACAAAAA
1 AAAAAACAAAAAAACAAAACAAAAA
17658927 AACAAAACAAAAAAACAAAACAAAAA
1 AA-AAAACAAAAAAACAAAACAAAAA
* * * *
17658953 AAGAAA-AAACAAAGAAAAGAAAAA
1 AAAAAACAAAAAAACAAAACAAAAA
*
17658977 GAAAAA
1 AAAAAA
17658983 TCAAGATGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
24 19 0.27
25 26 0.37
26 26 0.37
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (25 bp):
AAAAAACAAAAAAACAAAACAAAAA
Found at i:17659977 original size:81 final size:82
Alignment explanation
Indices: 17659853--17660006 Score: 283
Period size: 81 Copynumber: 1.9 Consensus size: 82
17659843 AAATTCTGTT
*
17659853 TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTTACGCTGAGGTA-TTT
1 TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
17659917 TTTTAATTTAATTTCTG
66 TTTTAATTTAATTTCTG
*
17659934 TTTTTTCAAAAACTCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
1 TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
17659999 TTTTAATT
66 TTTTAATT
17660007 NNNNNNNNNN
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
81 59 0.84
82 11 0.16
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (82 bp):
TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
TTTTAATTTAATTTCTG
Found at i:17661273 original size:30 final size:29
Alignment explanation
Indices: 17661231--17661393 Score: 150
Period size: 30 Copynumber: 5.5 Consensus size: 29
17661221 AAAAAAATAA
* *
17661231 AAAATTGCATTTTGACCCCTATACTTTTT
1 AAAATTACATTTTGACCCCTAAACTTTTT
*
17661260 AAAACTTATATTTTGACCCC-AAACCTTTTT
1 AAAA-TTACATTTTGACCCCTAAA-CTTTTT
17661290 AAAATTTACATTTTGA-CCCTAAACTTTTCT
1 AAAA-TTACATTTTGACCCCTAAACTTTT-T
** * *
17661320 AAAATTACATTTCAACCCTTAAACTTTCTC
1 AAAATTACATTTTGACCCCTAAACTTT-TT
* * * **
17661350 AAAATTTCACTTTAACCCCTAAACTTTCA
1 AAAATTACATTTTGACCCCTAAACTTTTT
17661379 AGAAATTACATTTTG
1 A-AAATTACATTTTG
17661394 GCCCATATTT
Statistics
Matches: 109, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
29 24 0.22
30 84 0.77
31 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCTAAACTTTTT
Found at i:17661354 original size:60 final size:59
Alignment explanation
Indices: 17661231--17661391 Score: 159
Period size: 59 Copynumber: 2.7 Consensus size: 59
17661221 AAAAAAATAA
* * * ** *
17661231 AAAATTGCATTTTGACCCCTATACTTTT-TAAAACTTATATTTTGACCCCAAACCTTTTT
1 AAAATTTCATTTTGACCCCTAAACTTTTCTAAAA-TTACATTTCAACCCCAAACCTTTTC
*
17661290 AAAATTTACATTTTGA-CCCTAAACTTTTCTAAAATTACATTTCAACCCTTAAA-CTTTCTC
1 AAAATTT-CATTTTGACCCCTAAACTTTTCTAAAATTACATTTCAACCC-CAAACCTTT-TC
* * *
17661350 AAAATTTCACTTTAACCCCTAAAC-TTTCAAGAAATTACATTT
1 AAAATTTCATTTTGACCCCTAAACTTTTCTA-AAATTACATTT
17661392 TGGCCCATAT
Statistics
Matches: 86, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
59 43 0.50
60 43 0.50
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (59 bp):
AAAATTTCATTTTGACCCCTAAACTTTTCTAAAATTACATTTCAACCCCAAACCTTTTC
Found at i:17661798 original size:10 final size:10
Alignment explanation
Indices: 17661779--17661812 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
17661769 CAAGCAAAGC
*
17661779 AACAAGCAAA
1 AACAAACAAA
17661789 AACAAACAAA
1 AACAAACAAA
*
17661799 AAGAAACAAA
1 AACAAACAAA
17661809 AACA
1 AACA
17661813 GCAACCAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.76, C:0.18, G:0.06, T:0.00
Consensus pattern (10 bp):
AACAAACAAA
Found at i:17661830 original size:15 final size:15
Alignment explanation
Indices: 17661806--17661838 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
17661796 AAAAAGAAAC
17661806 AAAAACAGCAACCAA
1 AAAAACAGCAACCAA
*
17661821 AAAAATAGCAACCAA
1 AAAAACAGCAACCAA
17661836 AAA
1 AAA
17661839 GAAAGAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.70, C:0.21, G:0.06, T:0.03
Consensus pattern (15 bp):
AAAAACAGCAACCAA
Found at i:17661983 original size:24 final size:25
Alignment explanation
Indices: 17661948--17662037 Score: 89
Period size: 24 Copynumber: 3.7 Consensus size: 25
17661938 GGTTCGGCCT
17661948 AAAAAAGA-AGAAAAAAGAAAAAGG
1 AAAAAAGATAGAAAAAAGAAAAAGG
* * *
17661972 AAAAAA-ATAGAAAAAATAGAAAGA
1 AAAAAAGATAGAAAAAAGAAAAAGG
*
17661996 AAAAATAGA-AGAAAAAGAGAAAAAGA
1 AAAAA-AGATAGAAAAA-AGAAAAAGG
*
17662022 AAAAAAAATA-AAAAAA
1 AAAAAAGATAGAAAAAA
17662038 CAGCAGGCTA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
23 1 0.02
24 25 0.45
25 15 0.27
26 14 0.25
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.04
Consensus pattern (25 bp):
AAAAAAGATAGAAAAAAGAAAAAGG
Found at i:17661985 original size:22 final size:22
Alignment explanation
Indices: 17661960--17662019 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
17661950 AAAAGAAGAA
17661960 AAAAGAAAAAGGAAAAAAATAG
1 AAAAGAAAAAGGAAAAAAATAG
*
17661982 AAAA-AATAGAAAG-AAAAAATAG
1 AAAAGAA-A-AAGGAAAAAAATAG
17662004 --AAGAAAAAGAGAAAAA
1 AAAAGAAAAAG-GAAAAA
17662020 GAAAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
19 2 0.06
20 4 0.13
21 8 0.26
22 14 0.45
23 3 0.10
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (22 bp):
AAAAGAAAAAGGAAAAAAATAG
Found at i:17661998 original size:13 final size:13
Alignment explanation
Indices: 17661980--17662026 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
17661970 GGAAAAAAAT
17661980 AGAAAAAATAGAA
1 AGAAAAAATAGAA
17661993 AGAAAAAATAG-A
1 AGAAAAAATAGAA
* *
17662005 AGAAAAAGAGAAAA
1 AGAAAAA-ATAGAA
17662019 AGAAAAAA
1 AGAAAAAA
17662027 AAATAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.27
13 14 0.47
14 8 0.27
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (13 bp):
AGAAAAAATAGAA
Found at i:17662019 original size:9 final size:8
Alignment explanation
Indices: 17661948--17662027 Score: 56
Period size: 8 Copynumber: 9.8 Consensus size: 8
17661938 GGTTCGGCCT
17661948 AAAAAAGA
1 AAAAAAGA
17661956 AGAAAAA-A
1 A-AAAAAGA
*
17661964 GAAAAAGGA
1 -AAAAAAGA
*
17661973 AAAAAATA
1 AAAAAAGA
*
17661981 GAAAAA-A
1 AAAAAAGA
* *
17661988 TAGAAAGA
1 AAAAAAGA
17661996 AAAAATAGA
1 AAAAA-AGA
17662005 AGAAAAAGA
1 A-AAAAAGA
*
17662014 GAAAAAGA
1 AAAAAAGA
17662022 AAAAAA
1 AAAAAA
17662028 AATAAAAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
7 5 0.09
8 33 0.59
9 14 0.25
10 4 0.07
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (8 bp):
AAAAAAGA
Found at i:17662028 original size:9 final size:9
Alignment explanation
Indices: 17661948--17662037 Score: 53
Period size: 9 Copynumber: 9.7 Consensus size: 9
17661938 GGTTCGGCCT
17661948 AAAAAAGAA
1 AAAAAAGAA
17661957 GAAAAAAGAA
1 -AAAAAAGAA
17661967 AAAGGAAA-AA
1 AAA--AAAGAA
17661977 AATAGAAA-AA
1 AA-A-AAAGAA
*
17661987 ATAGAAAGAA
1 A-AAAAAGAA
*
17661997 AAAATAGAA
1 AAAAAAGAA
*
17662006 GAAAAAG-A
1 AAAAAAGAA
*
17662014 GAAAAAGAA
1 AAAAAAGAA
17662023 AAAAAA-ATA
1 AAAAAAGA-A
17662032 AAAAAA
1 AAAAAA
17662038 CAGCAGGCTA
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
8 9 0.13
9 30 0.45
10 23 0.34
11 5 0.07
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.04
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:17662734 original size:18 final size:18
Alignment explanation
Indices: 17662700--17662734 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17662690 AATTTTTGAC
*
17662700 TTTTCGCGTTTTCAAAAG
1 TTTTCGCGTTTTAAAAAG
*
17662718 TTTTCGTGTTTTAAAAA
1 TTTTCGCGTTTTAAAAA
17662735 AAAAATTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (18 bp):
TTTTCGCGTTTTAAAAAG
Found at i:17662760 original size:23 final size:23
Alignment explanation
Indices: 17662719--17662808 Score: 112
Period size: 23 Copynumber: 4.0 Consensus size: 23
17662709 TTTCAAAAGT
17662719 TTTCGTGTTTTAAAA--AAAAAA
1 TTTCGTGTTTTAAAATGAAAAAA
* * *
17662740 TTCCGCGTTTTAAAATGAAAAAT
1 TTTCGTGTTTTAAAATGAAAAAA
* * *
17662763 TTTCATGTTTTCAAATGAAAAAT
1 TTTCGTGTTTTAAAATGAAAAAA
17662786 TTTCGTGTTTTAAAATGAAAAAA
1 TTTCGTGTTTTAAAATGAAAAAA
17662809 AAACAAAAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
21 13 0.23
23 44 0.77
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (23 bp):
TTTCGTGTTTTAAAATGAAAAAA
Found at i:17662943 original size:20 final size:19
Alignment explanation
Indices: 17662916--17662958 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
17662906 GTATTTTATC
17662916 AAAAAAA-TTTATGTTTTCA
1 AAAAAAATTTTATGTTTT-A
*
17662935 AAAACAAATTTTCTGTTTTA
1 AAAA-AAATTTTATGTTTTA
17662955 AAAA
1 AAAA
17662959 TTTTCGTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 8 0.38
21 9 0.43
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (19 bp):
AAAAAAATTTTATGTTTTA
Found at i:17662958 original size:37 final size:37
Alignment explanation
Indices: 17662918--17662997 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
17662908 ATTTTATCAA
*
17662918 AAAAATTTAT-GT-TTTCAAAAACAAATTTTC-TGTTTT
1 AAAAATTT-TCGTGTTTCAAAAACAAA-ATTCGTGTTTT
*
17662954 AAAAATTTTCGTGTTTCAAAAAGAAAATTCGTGTTTT
1 AAAAATTTTCGTGTTTCAAAAACAAAATTCGTGTTTT
17662991 CAAAAAT
1 -AAAAAT
17662998 AAAAATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
35 1 0.03
36 13 0.34
37 18 0.47
38 6 0.16
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (37 bp):
AAAAATTTTCGTGTTTCAAAAACAAAATTCGTGTTTT
Found at i:17662961 original size:16 final size:17
Alignment explanation
Indices: 17662940--17662975 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
17662930 TTTCAAAAAC
*
17662940 AAATTTTC-TGTTTTAA
1 AAATTTTCGTGTTTCAA
17662956 AAATTTTCGTGTTTCAA
1 AAATTTTCGTGTTTCAA
17662973 AAA
1 AAA
17662976 GAAAATTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.47
Consensus pattern (17 bp):
AAATTTTCGTGTTTCAA
Found at i:17662986 original size:20 final size:21
Alignment explanation
Indices: 17662961--17663001 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
17662951 TTTAAAAATT
17662961 TTCGTG-TTTCAAAAAGAAAA
1 TTCGTGTTTTCAAAAAGAAAA
*
17662981 TTCGTGTTTTCAAAAATAAAA
1 TTCGTGTTTTCAAAAAGAAAA
17663002 ATAAAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (21 bp):
TTCGTGTTTTCAAAAAGAAAA
Found at i:17663091 original size:16 final size:15
Alignment explanation
Indices: 17663043--17663096 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
17663033 TTTTTTTAAA
17663043 AAAAGTTTTGTGTTTCT
1 AAAA-TTTTGTGTTT-T
*
17663060 AAAATTCTTGTATTTT
1 AAAATT-TTGTGTTTT
17663076 AAAATTTTCGTGTTTT
1 AAAATTTT-GTGTTTT
17663092 CAAAA
1 -AAAA
17663097 AAGGAAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 2 0.06
16 15 0.47
17 15 0.47
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.50
Consensus pattern (15 bp):
AAAATTTTGTGTTTT
Found at i:17665052 original size:35 final size:35
Alignment explanation
Indices: 17665006--17665076 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
17664996 AATTGGGTCA
17665006 AAAACGAGGTATTGAGACCTCGATATTATAAACTG
1 AAAACGAGGTATTGAGACCTCGATATTATAAACTG
17665041 AAAACGAGGTATTGAGACCTCGATATTATAAACTG
1 AAAACGAGGTATTGAGACCTCGATATTATAAACTG
17665076 A
1 A
17665077 GCCGTAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (35 bp):
AAAACGAGGTATTGAGACCTCGATATTATAAACTG
Found at i:17665511 original size:5 final size:5
Alignment explanation
Indices: 17665501--17665546 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
17665491 TATGTTTTTA
*
17665501 ATATT ATATT ATATT ATTAAT ATATT ATATT ATATT ACTA-T ATATT
1 ATATT ATATT ATATT A-TATT ATATT ATATT ATATT A-TATT ATATT
17665547 TATAAAACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 2 0.06
5 28 0.78
6 6 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:17665549 original size:16 final size:16
Alignment explanation
Indices: 17665498--17665550 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 16
17665488 AAGTATGTTT
17665498 TTAATATTATATTATATTA
1 TTAATA-TATATT-TA-TA
17665517 TTAATATATTATATTATA
1 TTAATATA-TAT-TTATA
*
17665535 TTACTATATATTTATA
1 TTAATATATATTTATA
17665551 AAACAAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.16
17 3 0.10
18 11 0.35
19 11 0.35
20 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAATATATATTTATA
Found at i:17665550 original size:21 final size:21
Alignment explanation
Indices: 17665501--17665546 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
17665491 TATGTTTTTA
*
17665501 ATATTATATTATATTATTAAT
1 ATATTATATTATATTACTAAT
17665522 ATATTATATTATATTACT-AT
1 ATATTATATTATATTACTAAT
17665542 ATATT
1 ATATT
17665547 TATAAAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTATATTATATTACTAAT
Found at i:17665629 original size:35 final size:34
Alignment explanation
Indices: 17665572--17665638 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
17665562 AGAATAGATA
* *
17665572 TGAGAAAGAAAGAAACAGAGAAGCAAAACGAAATT
1 TGAGAAAGAAAGAAACAAAGAAG-AAAAAGAAATT
*
17665607 TGAGAAAGAAA-AAGAGAAAGAAGAAAAAGAAA
1 TGAGAAAGAAAGAA-ACAAAGAAGAAAAAGAAA
17665639 GAGAACCACG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 10 0.36
35 18 0.64
ACGTcount: A:0.66, C:0.04, G:0.24, T:0.06
Consensus pattern (34 bp):
TGAGAAAGAAAGAAACAAAGAAGAAAAAGAAATT
Found at i:17672990 original size:41 final size:41
Alignment explanation
Indices: 17672973--17673126 Score: 281
Period size: 41 Copynumber: 3.8 Consensus size: 41
17672963 ACTTATAGCA
17672973 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
1 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
* * *
17673014 TGATTCAAATCATCGGCACATAGCCTGCTAGGTTTATAACC
1 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
17673055 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
1 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
17673096 TGATTCAGATCACCGGCACGTAGCCTGCTAG
1 TGATTCAGATCACCGGCACGTAGCCTGCTAG
17673127 ACTTAAAGTC
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 107 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (41 bp):
TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
Found at i:17673082 original size:82 final size:82
Alignment explanation
Indices: 17672945--17673131 Score: 293
Period size: 82 Copynumber: 2.3 Consensus size: 82
17672935 ACAGATTCAA
* * *
17672945 CGGCACATAACCTGCTAAACTTATAGCATGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTAT
1 CGGCACATAGCCTGCTAGACTTATAACATGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTAT
*
17673010 AACCTGATTCAAATCAT
66 AACCTGATTCAAATCAC
** *
17673027 CGGCACATAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTAT
1 CGGCACATAGCCTGCTAGACTTATAACATGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTAT
*
17673092 AACCTGATTCAGATCAC
66 AACCTGATTCAAATCAC
*
17673109 CGGCACGTAGCCTGCTAGACTTA
1 CGGCACATAGCCTGCTAGACTTA
17673132 AAGTCTGAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 94 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (82 bp):
CGGCACATAGCCTGCTAGACTTATAACATGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTAT
AACCTGATTCAAATCAC
Found at i:17676318 original size:12 final size:12
Alignment explanation
Indices: 17676273--17676325 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
17676263 AATAACTTTT
**
17676273 ATATATATATGT
1 ATATATATATAC
*
17676285 ATATATATTCTAGC
1 ATATATA-TATA-C
17676299 ATTATATATATAC
1 A-TATATATATAC
17676312 ATATATATATAC
1 ATATATATATAC
17676324 AT
1 AT
17676326 GCTTATTCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 20 0.59
13 4 0.12
14 4 0.12
15 6 0.18
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (12 bp):
ATATATATATAC
Found at i:17680029 original size:40 final size:39
Alignment explanation
Indices: 17679969--17680109 Score: 117
Period size: 40 Copynumber: 3.6 Consensus size: 39
17679959 AACACACCAG
*
17679969 TTTGGCACCCAGTGCCTCATCAGATAATTCGAAGTAATAA
1 TTTGACACCCAGTGCCTCATC-GATAATTCGAAGTAATAA
* * **
17680009 TTTGACACCCAGTGTCTCATCGGCTAAACCGAAGT-A-AA
1 TTTGACACCCAGTGCCTCATC-GATAATTCGAAGTAATAA
* *
17680047 -TTGGCACCCAGTGCCTCATCGAATTAATTCGAAGTAGTAA
1 TTTGACACCCAGTGCCTCATCG-A-TAATTCGAAGTAATAA
* * * * *
17680087 ATTAACATCCAATGTCTCATCGA
1 TTTGACACCCAGTGCCTCATCGA
17680110 CTCGAAGTCA
Statistics
Matches: 79, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
36 1 0.01
37 18 0.23
38 11 0.14
39 1 0.01
40 32 0.41
41 16 0.20
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (39 bp):
TTTGACACCCAGTGCCTCATCGATAATTCGAAGTAATAA
Found at i:17680065 original size:37 final size:40
Alignment explanation
Indices: 17679969--17680067 Score: 123
Period size: 40 Copynumber: 2.5 Consensus size: 40
17679959 AACACACCAG
* **
17679969 TTTGGCACCCAGTGCCTCATCAGATAATTCGAAGTAATAA
1 TTTGGCACCCAGTGCCTCATCGGATAAACCGAAGTAATAA
* * *
17680009 TTTGACACCCAGTGTCTCATCGGCTAAACCGAAGT-A-AA
1 TTTGGCACCCAGTGCCTCATCGGATAAACCGAAGTAATAA
17680047 -TTGGCACCCAGTGCCTCATCG
1 TTTGGCACCCAGTGCCTCATCG
17680068 AATTAATTCG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
37 19 0.37
38 2 0.04
39 1 0.02
40 29 0.57
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (40 bp):
TTTGGCACCCAGTGCCTCATCGGATAAACCGAAGTAATAA
Found at i:17680946 original size:4 final size:4
Alignment explanation
Indices: 17680937--17680961 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
17680927 CCCTATTCTT
17680937 TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC T
17680962 ATTTCCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:17680997 original size:3 final size:3
Alignment explanation
Indices: 17680989--17681025 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
17680979 TTTATTTGTT
17680989 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
17681026 ACATACTTAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:17693718 original size:5 final size:5
Alignment explanation
Indices: 17693710--17693736 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
17693700 TTTAAATTAA
17693710 AATTT AATTT AATTT AATTT AATTT AA
1 AATTT AATTT AATTT AATTT AATTT AA
17693737 AAAAATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
AATTT
Found at i:17694653 original size:11 final size:11
Alignment explanation
Indices: 17694637--17694662 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17694627 CGTTGACTGA
17694637 AAAGTATCAAC
1 AAAGTATCAAC
17694648 AAAGTATCAAC
1 AAAGTATCAAC
17694659 AAAG
1 AAAG
17694663 CTTTGATCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (11 bp):
AAAGTATCAAC
Found at i:17695615 original size:17 final size:17
Alignment explanation
Indices: 17695593--17695626 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17695583 GCAGAAGAAA
17695593 GATGTTGTTTGGGTTAT
1 GATGTTGTTTGGGTTAT
17695610 GATGTTGTTTGGGTTAT
1 GATGTTGTTTGGGTTAT
17695627 TGTGAATCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.35, T:0.53
Consensus pattern (17 bp):
GATGTTGTTTGGGTTAT
Found at i:17701778 original size:19 final size:19
Alignment explanation
Indices: 17701733--17701778 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
17701723 AGTTCATGCT
*
17701733 TTCTATTCACATTTTCATA
1 TTCTATTCACATTTTCAAA
*
17701752 TTCAATTCACATTTTCAAA
1 TTCTATTCACATTTTCAAA
*
17701771 TTGTATTC
1 TTCTATTC
17701779 CACTTAGTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.28, C:0.20, G:0.02, T:0.50
Consensus pattern (19 bp):
TTCTATTCACATTTTCAAA
Found at i:17701991 original size:51 final size:51
Alignment explanation
Indices: 17701919--17702205 Score: 305
Period size: 51 Copynumber: 5.7 Consensus size: 51
17701909 GGTTCATATT
* * * **
17701919 GTAGCCTACACATAGTACTACACATGTGA-CCATTACCATCCGATACATGTA
1 GTAGCCTGCACATAGTACTACACACGTGATCCA-TACCATCCGGTACACATA
* * * * *
17701970 GTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCCGGCACGCATA
1 GTAGCCTGCACATAGTACTACACACGTGATCCATACCATCCGGTACACATA
* * * * *
17702021 GTAGCCTACACATAGTACTACACATGCGACCCAT--CATTCCGGTACACGTA
1 GTAGCCTGCACATAGTACTACACACGTGATCCATACCA-TCCGGTACACATA
**
17702071 GTAGCCTGCACATAGTACTACACACGTGA-CCATTACCATCCGACACACATA
1 GTAGCCTGCACATAGTACTACACACGTGATCCA-TACCATCCGGTACACATA
* * * * * *
17702122 GTAGCCTGCACATAGTACTACACATGTGATCGAAACTATCTGGTACGCATA
1 GTAGCCTGCACATAGTACTACACACGTGATCCATACCATCCGGTACACATA
17702173 GTAGCCTGCACATAGTACTACACACGTGA-CCAT
1 GTAGCCTGCACATAGTACTACACACGTGATCCAT
17702206 CACTTTCACT
Statistics
Matches: 193, Mismatches: 37, Indels: 13
0.79 0.15 0.05
Matches are distributed among these distances:
49 4 0.02
50 39 0.20
51 144 0.75
52 6 0.03
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (51 bp):
GTAGCCTGCACATAGTACTACACACGTGATCCATACCATCCGGTACACATA
Found at i:17702095 original size:101 final size:100
Alignment explanation
Indices: 17701919--17702205 Score: 355
Period size: 101 Copynumber: 2.8 Consensus size: 100
17701909 GGTTCATATT
* *
17701919 GTAGCCTACACATAGTACTACACATGTGACCATTACCA-TCCGATACATGTAGTAGCCTGCACAT
1 GTAGCCTACACATAGTACTACACATGTGACCA-T--CATTCCGGTACACGTAGTAGCCTGCACAT
* * * *
17701983 AGTACTACACACGTGATCGA-AACTATCCGGCACGCATA
63 AGTACTACACACGTGA-CCATAACCATCCGACACACATA
*
17702021 GTAGCCTACACATAGTACTACACATGCGACCCATCATTCCGGTACACGTAGTAGCCTGCACATAG
1 GTAGCCTACACATAGTACTACACATGTGA-CCATCATTCCGGTACACGTAGTAGCCTGCACATAG
*
17702086 TACTACACACGTGACCATTACCATCCGACACACATA
65 TACTACACACGTGACCATAACCATCCGACACACATA
* * * * * *
17702122 GTAGCCTGCACATAGTACTACACATGTGATCGA-AACTATCTGGTACGCATAGTAGCCTGCACAT
1 GTAGCCTACACATAGTACTACACATGTGA-CCATCA-T-TCCGGTACACGTAGTAGCCTGCACAT
17702186 AGTACTACACACGTGACCAT
63 AGTACTACACACGTGACCAT
17702206 CACTTTCACT
Statistics
Matches: 164, Mismatches: 16, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
100 5 0.03
101 84 0.51
102 72 0.44
103 3 0.02
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (100 bp):
GTAGCCTACACATAGTACTACACATGTGACCATCATTCCGGTACACGTAGTAGCCTGCACATAGT
ACTACACACGTGACCATAACCATCCGACACACATA
Found at i:17702195 original size:152 final size:152
Alignment explanation
Indices: 17701919--17702196 Score: 475
Period size: 152 Copynumber: 1.8 Consensus size: 152
17701909 GGTTCATATT
* * **
17701919 GTAGCCTACACATAGTACTACACATGTGACCATTACCATCCGATACATGTAGTAGCCTGCACATA
1 GTAGCCTACACATAGTACTACACACGTGACCATTACCATCCGACACACATAGTAGCCTGCACATA
17701984 GTACTACACACGTGATCGAAACTATCCGGCACGCATAGTAGCCTACACATAGTACTACACATGCG
66 GTACTACACACGTGATCGAAACTATCCGGCACGCATAGTAGCCTACACATAGTACTACACATGCG
17702049 ACCCATCATTCCGGTACACGTA
131 ACCCATCATTCCGGTACACGTA
*
17702071 GTAGCCTGCACATAGTACTACACACGTGACCATTACCATCCGACACACATAGTAGCCTGCACATA
1 GTAGCCTACACATAGTACTACACACGTGACCATTACCATCCGACACACATAGTAGCCTGCACATA
* * * *
17702136 GTACTACACATGTGATCGAAACTATCTGGTACGCATAGTAGCCTGCACATAGTACTACACA
66 GTACTACACACGTGATCGAAACTATCCGGCACGCATAGTAGCCTACACATAGTACTACACA
17702197 CGTGACCATC
Statistics
Matches: 117, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
152 117 1.00
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (152 bp):
GTAGCCTACACATAGTACTACACACGTGACCATTACCATCCGACACACATAGTAGCCTGCACATA
GTACTACACACGTGATCGAAACTATCCGGCACGCATAGTAGCCTACACATAGTACTACACATGCG
ACCCATCATTCCGGTACACGTA
Found at i:17704818 original size:26 final size:26
Alignment explanation
Indices: 17704788--17704863 Score: 125
Period size: 26 Copynumber: 2.9 Consensus size: 26
17704778 TAACTTACTT
* *
17704788 TAATTATAATTAATTAATCTTAATGC
1 TAATTATAATTAATTAATCATAATAC
*
17704814 TAATTATAATTAATTAATCGTAATAC
1 TAATTATAATTAATTAATCATAATAC
17704840 TAATTATAATTAATTAATCATAAT
1 TAATTATAATTAATTAATCATAAT
17704864 TAAATCATGG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (26 bp):
TAATTATAATTAATTAATCATAATAC
Found at i:17706964 original size:24 final size:25
Alignment explanation
Indices: 17706937--17706990 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
17706927 AAGTTCAAGC
* *
17706937 GAGCGAATATCAGGAAGCTC-CAAA
1 GAGCCAATAACAGGAAGCTCGCAAA
* *
17706961 GAGCCATTAACGGGAAGCTCGCAAA
1 GAGCCAATAACAGGAAGCTCGCAAA
17706986 GAGCC
1 GAGCC
17706991 TTTAATCAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.37, C:0.24, G:0.28, T:0.11
Consensus pattern (25 bp):
GAGCCAATAACAGGAAGCTCGCAAA
Found at i:17706989 original size:25 final size:24
Alignment explanation
Indices: 17706949--17706995 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
17706939 GCGAATATCA
17706949 GGAAGCTCCAAAGAGCCATTAACG
1 GGAAGCTCCAAAGAGCCATTAACG
*
17706973 GGAAGCTCGCAAAGAGCCTTTAA
1 GGAAGCTC-CAAAGAGCCATTAA
17706996 TCAAGACACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.36, C:0.23, G:0.26, T:0.15
Consensus pattern (24 bp):
GGAAGCTCCAAAGAGCCATTAACG
Found at i:17709409 original size:18 final size:19
Alignment explanation
Indices: 17709372--17709409 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
17709362 TAAGTAGTTA
* *
17709372 TTGACATTGATTTTTTGTT
1 TTGACAATGATTTTTGGTT
17709391 TTGACAATG-TTTTTGGTT
1 TTGACAATGATTTTTGGTT
17709409 T
1 T
17709410 GGGCAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.16, C:0.05, G:0.18, T:0.61
Consensus pattern (19 bp):
TTGACAATGATTTTTGGTT
Found at i:17710620 original size:43 final size:43
Alignment explanation
Indices: 17710541--17710624 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
17710531 GGTAATATGC
*
17710541 ATGAAGTTGATTACTTGATGTTGTAGTAATCTAGATGTTATAG
1 ATGAAGTTGATGACTTGATGTTGTAGTAATCTAGATGTTATAG
* *
17710584 ATGAA-TTGATGATCTT-ATGTTGTTATTAATGTAGATGTTAT
1 ATGAAGTTGATGA-CTTGATGTTG-TAGTAATCTAGATGTTAT
17710625 TAATGTGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 12 0.33
43 24 0.67
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.45
Consensus pattern (43 bp):
ATGAAGTTGATGACTTGATGTTGTAGTAATCTAGATGTTATAG
Found at i:17711635 original size:76 final size:76
Alignment explanation
Indices: 17711509--17711664 Score: 267
Period size: 76 Copynumber: 2.1 Consensus size: 76
17711499 TTCAACTTAC
*
17711509 TTAAGGTTAGTTTGGTAGACGATGTGACATCATGCATCTAGTCAGCTTTCGAGTCGAGTATAAGG
1 TTAAGGTTAGTTTGGTAGACGATGTGACATCATGCATCCAGTCAGCTTTCGAGTCGAGTATAAGG
17711574 TGTTATAAATA
66 TGTTATAAATA
* * * *
17711585 TTAAGGTTAGTTTGGTAGTCGATGTGACATCATGCATCCGGTCATCTTTCGAGTCGAGTGTAAGG
1 TTAAGGTTAGTTTGGTAGACGATGTGACATCATGCATCCAGTCAGCTTTCGAGTCGAGTATAAGG
17711650 TGTTATAAATA
66 TGTTATAAATA
17711661 TTAA
1 TTAA
17711665 AAAATGTAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (76 bp):
TTAAGGTTAGTTTGGTAGACGATGTGACATCATGCATCCAGTCAGCTTTCGAGTCGAGTATAAGG
TGTTATAAATA
Found at i:17714127 original size:18 final size:20
Alignment explanation
Indices: 17714087--17714129 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
17714077 ATATGTTGAA
*
17714087 TATT-TTTAAAATACTTTTT
1 TATTATTTAAAATACTTTTC
17714106 TATTATTTAAAA-A-TTTTC
1 TATTATTTAAAATACTTTTC
17714124 TATTAT
1 TATTAT
17714130 AATATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 5 0.23
20 7 0.32
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTATTTAAAATACTTTTC
Found at i:17715835 original size:18 final size:18
Alignment explanation
Indices: 17715792--17715825 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17715782 AGAAGTGGTG
17715792 ATAATTATACATTTAAAA
1 ATAATTATACATTTAAAA
17715810 ATAATTATA-ATTTAAA
1 ATAATTATACATTTAAA
17715826 CTATAGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAATTATACATTTAAAA
Found at i:17716066 original size:15 final size:17
Alignment explanation
Indices: 17716048--17716092 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 17
17716038 TTCTAAGCAT
17716048 ATTAATTATTA-A-TTA
1 ATTAATTATTAGACTTA
17716063 ATTAA-TATTAGACTTA
1 ATTAATTATTAGACTTA
17716079 ATTGAATTAATTAG
1 ATT-AATT-ATTAG
17716093 TTATTATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.20
15 6 0.24
16 6 0.24
17 2 0.08
18 1 0.04
19 5 0.20
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
ATTAATTATTAGACTTA
Found at i:17718096 original size:42 final size:42
Alignment explanation
Indices: 17718048--17718239 Score: 212
Period size: 42 Copynumber: 4.6 Consensus size: 42
17718038 CGTGTTTTAC
* * *
17718048 TTTCTGTTCAGCTTTTACGAGCTTCTATTTAACTCATACGAG
1 TTTCTGTTCAGCTCTTACGAGCTTCTATTCAACTCATATGAG
* * *
17718090 TTTCTGTTCAACCCTTACGAGCTTCTATTCAACTCTTATGAG
1 TTTCTGTTCAGCTCTTACGAGCTTCTATTCAACTCATATGAG
* * * *
17718132 TTTCTGTTAAGCTCTTACGAGCTTCTGTTCAACCCTTAT-AGG
1 TTTCTGTTCAGCTCTTACGAGCTTCTATTCAACTCATATGA-G
* * * *
17718174 TTTCTGTTTAGCTCTTATGAGCTTCTATTTAGCTC-TCATGAG
1 TTTCTGTTCAGCTCTTACGAGCTTCTATTCAACTCAT-ATGAG
17718216 TTTCTGTTCAGCT-TT-CGAGCTTCT
1 TTTCTGTTCAGCTCTTACGAGCTTCT
17718240 GAAACGATGT
Statistics
Matches: 128, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
40 8 0.06
41 4 0.03
42 115 0.90
43 1 0.01
ACGTcount: A:0.18, C:0.23, G:0.15, T:0.44
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTTACGAGCTTCTATTCAACTCATATGAG
Found at i:17718189 original size:63 final size:63
Alignment explanation
Indices: 17718048--17718225 Score: 198
Period size: 63 Copynumber: 2.8 Consensus size: 63
17718038 CGTGTTTTAC
* * * *
17718048 TTTCTGTTCAGCTTTTACGAGCTTCTATTTAA-CTCATACGAGTTTCTGTTCAACCCTTACGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTA-TTAAGCTCTTACGAGTTTCTGTTCAACCCTTAAGAG
* * * * * *
17718111 CTTCTATTCAACTCTTATGAGTTTCTGTTAAGCTCTTACGAGCTTCTGTTCAACCCTTATAG-G
1 TTTCTGTTCAGCTCTTATGAGCTTCTATTAAGCTCTTACGAGTTTCTGTTCAACCCTTA-AGAG
* * * *
17718174 TTTCTGTTTAGCTCTTATGAGCTTCTATTTAGCTCTCATGAGTTTCTGTTCA
1 TTTCTGTTCAGCTCTTATGAGCTTCTATTAAGCTCTTACGAGTTTCTGTTCA
17718226 GCTTTCGAGC
Statistics
Matches: 93, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
62 4 0.04
63 88 0.95
64 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (63 bp):
TTTCTGTTCAGCTCTTATGAGCTTCTATTAAGCTCTTACGAGTTTCTGTTCAACCCTTAAGAG
Found at i:17718190 original size:21 final size:21
Alignment explanation
Indices: 17718048--17718228 Score: 130
Period size: 21 Copynumber: 8.6 Consensus size: 21
17718038 CGTGTTTTAC
* *
17718048 TTTCTGTTCAGCTTTTACGAG
1 TTTCTGTTCAGCTCTTATGAG
* * * * * *
17718069 CTTCTATTTAACTCATACGAG
1 TTTCTGTTCAGCTCTTATGAG
* * *
17718090 TTTCTGTTCAACCCTTACGAG
1 TTTCTGTTCAGCTCTTATGAG
* * *
17718111 CTTCTATTCAACTCTTATGAG
1 TTTCTGTTCAGCTCTTATGAG
* *
17718132 TTTCTGTTAAGCTCTTACGAG
1 TTTCTGTTCAGCTCTTATGAG
* * *
17718153 CTTCTGTTCAACCCTTAT-AGG
1 TTTCTGTTCAGCTCTTATGA-G
*
17718174 TTTCTGTTTAGCTCTTATGAG
1 TTTCTGTTCAGCTCTTATGAG
* * * *
17718195 CTTCTATTTAGCTCTCATGAG
1 TTTCTGTTCAGCTCTTATGAG
17718216 TTTCTGTTCAGCT
1 TTTCTGTTCAGCT
17718229 TTCGAGCTTC
Statistics
Matches: 123, Mismatches: 35, Indels: 4
0.76 0.22 0.02
Matches are distributed among these distances:
20 1 0.01
21 121 0.98
22 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.44
Consensus pattern (21 bp):
TTTCTGTTCAGCTCTTATGAG
Found at i:17739901 original size:19 final size:21
Alignment explanation
Indices: 17739839--17739906 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
17739829 GTGTTTTGCT
17739839 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
* *
17739860 TCCTGTTCAGCTCTTATGAGC
1 TTCTGTTCAGCTCTTACGAGC
*
17739881 TTCTGTTTAGCT-TT-CGAGC
1 TTCTGTTCAGCTCTTACGAGC
17739900 TTCTGTT
1 TTCTGTT
17739907 GGTGTATTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 11 0.26
20 2 0.05
21 29 0.69
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTACGAGC
Found at i:17740752 original size:15 final size:15
Alignment explanation
Indices: 17740732--17740767 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
17740722 AGACACGGGC
17740732 ATGTGTCTCAGCCGT
1 ATGTGTCTCAGCCGT
17740747 ATGTGTCTCAGCCGT
1 ATGTGTCTCAGCCGT
*
17740762 GTGTGT
1 ATGTGT
17740768 TACACTGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.22, G:0.31, T:0.36
Consensus pattern (15 bp):
ATGTGTCTCAGCCGT
Found at i:17743210 original size:21 final size:20
Alignment explanation
Indices: 17743173--17743211 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17743163 TTAGGAATTA
*
17743173 ATTTAATTTTTAAAATTATT
1 ATTTAATTATTAAAATTATT
*
17743193 ATTTAATTAATTATAATTA
1 ATTTAATT-ATTAAAATTA
17743212 AATAATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTAATTATTAAAATTATT
Found at i:17749576 original size:42 final size:41
Alignment explanation
Indices: 17749472--17749584 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 41
17749462 ACACAGTCAG
* * *
17749472 GGACATGGGCGTGTGCTCAAGTCATGTAAGCCACATGGGCAA
1 GGACATGGGCGTGTGC-CAGGTCGTGTAAGCCACACGGGCAA
* *
17749514 GGACATGGGCGTGTGCCCAGGTCGTGTGAGCCATACGGGCAA
1 GGACATGGGCGTGTG-CCAGGTCGTGTAAGCCACACGGGCAA
* *
17749556 GGACATGGGCATGTGTCCAGGCCGTGTAA
1 GGACATGGGCGTGTG-CCAGGTCGTGTAA
17749585 CTCATTGTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 60 0.98
43 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.37, T:0.19
Consensus pattern (41 bp):
GGACATGGGCGTGTGCCAGGTCGTGTAAGCCACACGGGCAA
Found at i:17759442 original size:22 final size:22
Alignment explanation
Indices: 17759417--17759458 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17759407 GTAGGAACCC
*
17759417 AAGAAATTAAAGATAAAAAACG
1 AAGAAACTAAAGATAAAAAACG
* *
17759439 AAGAGACTAAAGCTAAAAAA
1 AAGAAACTAAAGATAAAAAA
17759459 TGAATATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.67, C:0.07, G:0.14, T:0.12
Consensus pattern (22 bp):
AAGAAACTAAAGATAAAAAACG
Found at i:17768093 original size:3 final size:3
Alignment explanation
Indices: 17768085--17768109 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17768075 CTACTTTTAT
17768085 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
17768110 AAGTCTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:17768170 original size:6 final size:6
Alignment explanation
Indices: 17768159--17768188 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
17768149 AGAGGCATCG
17768159 GCTTAT GCTTAT GCTTAT GCTTAT GCTTAT
1 GCTTAT GCTTAT GCTTAT GCTTAT GCTTAT
17768189 CTTCAATCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (6 bp):
GCTTAT
Found at i:17770215 original size:84 final size:84
Alignment explanation
Indices: 17770073--17770277 Score: 374
Period size: 84 Copynumber: 2.4 Consensus size: 84
17770063 AAGTTAAAGT
*
17770073 AGACACATAGAACATAGTTTTTTCCTTCAAATGCAAATAAAACAAGAAAGAAGCAAAAGACGGTG
1 AGACACATTGAACATAG-TTTTTCCTTCAAATGCAAATAAAACAAGAAAGAAGCAAAAGACGGTG
17770138 ATAAAACAATGCAAATAATC
65 ATAAAACAATGCAAATAATC
*
17770158 AGACACATTGAACATAGTTTTTCCTTCAAATGCAAATAAAACAAGAAAGAAGCAAAAGTCGGTGA
1 AGACACATTGAACATAGTTTTTCCTTCAAATGCAAATAAAACAAGAAAGAAGCAAAAGACGGTGA
17770223 TAAAACAATGCAAATAATC
66 TAAAACAATGCAAATAATC
*
17770242 AGACACATTGAACATAGTTTTTCATTCAAATGCAAA
1 AGACACATTGAACATAGTTTTTCCTTCAAATGCAAA
17770278 GAACAAAACA
Statistics
Matches: 117, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
84 101 0.86
85 16 0.14
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (84 bp):
AGACACATTGAACATAGTTTTTCCTTCAAATGCAAATAAAACAAGAAAGAAGCAAAAGACGGTGA
TAAAACAATGCAAATAATC
Found at i:17773591 original size:15 final size:16
Alignment explanation
Indices: 17773571--17773600 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17773561 TAGGATGAGG
17773571 GGTTTGAAAA-TGGAA
1 GGTTTGAAAAGTGGAA
17773586 GGTTTGAAAAGTGGA
1 GGTTTGAAAAGTGGA
17773601 GGGGTTGGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.27
Consensus pattern (16 bp):
GGTTTGAAAAGTGGAA
Found at i:17775760 original size:19 final size:19
Alignment explanation
Indices: 17775738--17775776 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
17775728 AATCAAAATC
17775738 AAAAACAAAAAAAAAGAAA
1 AAAAACAAAAAAAAAGAAA
** *
17775757 AAAAAGGAAGAAAAAGAAA
1 AAAAACAAAAAAAAAGAAA
17775776 A
1 A
17775777 TTCAAAATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.85, C:0.03, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAACAAAAAAAAAGAAA
Found at i:17775837 original size:14 final size:15
Alignment explanation
Indices: 17775815--17775843 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17775805 AAAAATAGAT
17775815 AAGGAAAAAAGAAAA
1 AAGGAAAAAAGAAAA
17775830 AAGG-AAAAAGAAAA
1 AAGGAAAAAAGAAAA
17775844 GGAAAGGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGGAAAAAAGAAAA
Found at i:17778165 original size:132 final size:132
Alignment explanation
Indices: 17777928--17778860 Score: 1350
Period size: 132 Copynumber: 7.1 Consensus size: 132
17777918 AATATTACAA
* * * *
17777928 ATCTTATCTCCCTAAGCAGTAGTAGAGTAGATCAAAGACGACAAATCTTATTTTTCCAAGATAGT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGT
* * * *
17777993 GGGATGCAGATTTAAGCCACCGAGCCTTATCTCCCTGAGCAGCAGAAGAGCAGGTTGAAGATAGC
66 GGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCAGAGTAGGTTGAAGATAGC
17778058 AG
131 AG
* * * * * * *
17778060 ATCTTATCTCCTTAAGCAGTAGTGGAGCAGATTGAAAACGAAAAATCTTATATTTTCAAGATATT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGT
* ** * *
17778125 GGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCAGAACAGGTTGAAGATTGT
66 GGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCAGAGTAGGTTGAAGATAGC
17778190 AG
131 AG
* * *
17778192 ATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGACAAATCTTATCTTTCCAAGATAGT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGT
* * * *
17778257 AGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGGAACAGTAGAGTAGGTTGAAGATAGC
66 GGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCAGAGTAGGTTGAAGATAGC
*
17778322 AT
131 AG
*
17778324 ATCTTATCTCCCTAAGCAGTAGTGGAGAAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGT
* * *
17778389 GGGAAGCAAATTTAAGCCACCGAGCCTTGTCTCCGTGAGCAGCAGCGGAGTAGGTTGAAGATAGC
66 GGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCAGAGTAGGTTGAAGATAGC
17778454 AG
131 AG
* *
17778456 ATATTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC-AGTAAATCTTATCTTTCCAAGATAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGA-CAAATCTTATCTTTCCAAGATAG
* *
17778520 TGGGAAGCAAATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATAG
65 TGGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCAGAGTAGGTTGAAGATAG
17778585 CAG
130 CAG
* * **
17778588 ATATTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAAGATAGT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGT
* * * *
17778653 GGGAAGCAAATTTAAGCCACCGAGCCTTGTCTCCCTGAGTAGCAGCGGAGTAGGTTGAAGATAAC
66 GGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCAGAGTAGGTTGAAGATAGC
17778718 AG
131 AG
* * *
17778720 ATATTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAAT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGT
** * *
17778785 GGGAAGCAGATTTAAGCCACTAAGCCTTATCTCCCTGAGCAGCA-CTAGAGTAGGTTGAAAATTA
66 GGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGC-AGAGTAGGTTGAAGA-TA
17778849 -CAG
129 GCAG
*
17778852 GTCTTATCT
1 ATCTTATCT
17778861 TTCTGAAGTT
Statistics
Matches: 726, Mismatches: 71, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
131 2 0.00
132 722 0.99
133 2 0.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (132 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGT
GGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCAGAGTAGGTTGAAGATAGC
AG
Found at i:17778493 original size:44 final size:44
Alignment explanation
Indices: 17778445--17778626 Score: 111
Period size: 44 Copynumber: 4.1 Consensus size: 44
17778435 GGAGTAGGTT
*
17778445 GAAGATAGCAGATATTATCTCCCTAAGCAGTAGTGGAGCAGATC
1 GAAGACAGCAGATATTATCTCCCTAAGCAGTAGTGGAGCAGATC
* * * * * *
17778489 GAAGACAGTAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAAATT
1 GAAGACAGCAGATATTATC-TCCCTAAGCAGTAGT-GG-AGCAGATC
* * * ** * * * * * * *
17778533 TAAGCCA-CCGAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTT
1 GAAGACAGCAGA-TATTATCTCCCTAAGCAGTAGTGGAGCAGATC
* *
17778577 GAAGATAGCAGATATTATCTCCCTAAGTAGTAGTGGAGCAGATC
1 GAAGACAGCAGATATTATCTCCCTAAGCAGTAGTGGAGCAGATC
17778621 GAAGAC
1 GAAGAC
17778627 GGTAAATCTT
Statistics
Matches: 94, Mismatches: 36, Indels: 16
0.64 0.25 0.11
Matches are distributed among these distances:
42 4 0.04
43 7 0.07
44 72 0.77
45 9 0.10
46 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.23
Consensus pattern (44 bp):
GAAGACAGCAGATATTATCTCCCTAAGCAGTAGTGGAGCAGATC
Found at i:17779030 original size:44 final size:44
Alignment explanation
Indices: 17778937--17779056 Score: 134
Period size: 44 Copynumber: 2.7 Consensus size: 44
17778927 GCTACAAATT
* * * *
17778937 TTATCTCTCTGAGGTTGTAGTGGGGCAGATCGAAGTCGATAATC
1 TTATCTCTCTGAAGTTGTAGTGGAGCAGATCAAAGTCAATAATC
* * * *
17778981 CTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGT-AATAGATC
1 TTATCTCTCTGAAGTTGTAGTGGAGCAGATCAAAGTCAATA-ATC
* *
17779025 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCA
1 TTATCTCTCTGAAGTTGTAGTGGAGCAGATCA
17779057 CATCAAGTTT
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
43 3 0.05
44 58 0.95
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (44 bp):
TTATCTCTCTGAAGTTGTAGTGGAGCAGATCAAAGTCAATAATC
Found at i:17780508 original size:3 final size:3
Alignment explanation
Indices: 17780500--17780542 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
17780490 ATTTTAATCC
17780500 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TCAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT T
17780543 GTTCCTTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 34 0.89
4 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:17780810 original size:194 final size:194
Alignment explanation
Indices: 17780609--17780995 Score: 756
Period size: 194 Copynumber: 2.0 Consensus size: 194
17780599 AGTTTTAAAT
17780609 TGAATTTAGTACTTATTTTAATATATTTATTTGTAACATATTTTAATATTTAGTTTGACATGCTC
1 TGAATTTAGTACTTATTTTAATATATTTATTTGTAACATATTTTAATATTTAGTTTGACATGCTC
17780674 TTTAAACTTATTATTAGTATAATTTTAAAATGTAATATATTATTATTTCAAATTATTATTAACAT
66 TTTAAACTTATTATTAGTATAATTTTAAAATGTAATATATTATTATTTCAAATTATTATTAACAT
17780739 GTACATTGTTTTAAAATTTATTACTTTTATTTTTAAATTCTATATTATTATAGGTTTCATTATC
131 GTACATTGTTTTAAAATTTATTACTTTTATTTTTAAATTCTATATTATTATAGGTTTCATTATC
17780803 TGAATTTAGTACTTATTTTAATATATTTATTTGTAACATATTTTAATATTTAGTTTGACATGCTC
1 TGAATTTAGTACTTATTTTAATATATTTATTTGTAACATATTTTAATATTTAGTTTGACATGCTC
*
17780868 TTTAAACTTATTATTAGTATAATTTTAAAATGTAATTTATTATTATTTCAAATTATTATTAACAT
66 TTTAAACTTATTATTAGTATAATTTTAAAATGTAATATATTATTATTTCAAATTATTATTAACAT
*
17780933 GTACATTGTTTTAAAATTTATTACTTTTATTTTTAAATTCTATATTATTATATGTTTCATTAT
131 GTACATTGTTTTAAAATTTATTACTTTTATTTTTAAATTCTATATTATTATAGGTTTCATTAT
17780996 AATTTTAATA
Statistics
Matches: 191, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
194 191 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (194 bp):
TGAATTTAGTACTTATTTTAATATATTTATTTGTAACATATTTTAATATTTAGTTTGACATGCTC
TTTAAACTTATTATTAGTATAATTTTAAAATGTAATATATTATTATTTCAAATTATTATTAACAT
GTACATTGTTTTAAAATTTATTACTTTTATTTTTAAATTCTATATTATTATAGGTTTCATTATC
Found at i:17784193 original size:27 final size:27
Alignment explanation
Indices: 17784155--17784210 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
17784145 TCTCTATTCC
17784155 CGTGTTTGGTTTAAAGTATTGGTAATA
1 CGTGTTTGGTTTAAAGTATTGGTAATA
17784182 CGTGTTTGGTTTAAAGTATTGGTAATA
1 CGTGTTTGGTTTAAAGTATTGGTAATA
17784209 CG
1 CG
17784211 GGTGTAATCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.05, G:0.27, T:0.43
Consensus pattern (27 bp):
CGTGTTTGGTTTAAAGTATTGGTAATA
Found at i:17784406 original size:15 final size:15
Alignment explanation
Indices: 17784386--17784415 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17784376 CTTTTTTGGC
*
17784386 CGATTTGCTTTCTGT
1 CGATTTGCTCTCTGT
17784401 CGATTTGCTCTCTGT
1 CGATTTGCTCTCTGT
17784416 TTTACCCTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.23, G:0.20, T:0.50
Consensus pattern (15 bp):
CGATTTGCTCTCTGT
Found at i:17787591 original size:91 final size:91
Alignment explanation
Indices: 17787453--17787660 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
17787443 TTGATTTTAG
* *
17787453 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
17787518 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
17787545 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
17787610 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
17787636 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
17787661 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 92 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:17787629 original size:26 final size:28
Alignment explanation
Indices: 17787575--17787635 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
17787565 TATTATCAAG
* *
17787575 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
17787603 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
17787629 AATTATA
1 AATTATA
17787636 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:17787635 original size:44 final size:43
Alignment explanation
Indices: 17787493--17787635 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
17787483 GAATTTTATG
* *
17787493 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
17787537 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
17787584 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
17787628 AAATTATA
1 AAATTATA
17787636 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:17787753 original size:59 final size:57
Alignment explanation
Indices: 17787687--17787875 Score: 152
Period size: 59 Copynumber: 3.2 Consensus size: 57
17787677 ATTTTATTAA
17787687 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT-TTTTATAGT
* * ** * *
17787746 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT-TTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATTTTTATAGT
* * * *
17787807 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
17787866 ATCATATATT
1 ATCATATATT
17787876 ATGATTTGAG
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
59 20 0.20
60 8 0.08
61 10 0.10
63 4 0.04
64 5 0.05
65 6 0.06
66 17 0.17
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATTTTTATAGT
Found at i:17787784 original size:66 final size:64
Alignment explanation
Indices: 17787714--17787912 Score: 186
Period size: 66 Copynumber: 3.2 Consensus size: 64
17787704 AAATATATTT
17787714 AATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
17787779 G
64 G
* * * * * **
17787780 AATATTAATTATTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* *
17787834 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
17787899 G
64 G
*
17787900 AATATTGATTATT
1 AATATTAATTATT
17787913 AAGAATTTTA
Statistics
Matches: 101, Mismatches: 18, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 5 0.05
65 7 0.07
66 27 0.27
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (64 bp):
AATATTAATTATTTAAATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:17787800 original size:120 final size:120
Alignment explanation
Indices: 17787676--17787973 Score: 517
Period size: 120 Copynumber: 2.5 Consensus size: 120
17787666 AATTATTTTA
* * *
17787676 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
17787740 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
17787796 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
*
17787861 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
17787916 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
17787974 ATGATTAAAT
Statistics
Matches: 168, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
120 161 0.96
121 7 0.04
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:17787816 original size:61 final size:61
Alignment explanation
Indices: 17787749--17787936 Score: 192
Period size: 61 Copynumber: 3.1 Consensus size: 61
17787739 TTATAGTATC
17787749 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * *
17787810 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
17787868 C
61 T
*
17787869 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
17787930 ATATATT
1 ATATATT
17787937 TTAATTAAAA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 18 0.19
60 16 0.17
61 25 0.26
62 7 0.07
63 11 0.11
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:17787836 original size:15 final size:15
Alignment explanation
Indices: 17787801--17787852 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
17787791 TTAAGAATTT
*
17787801 TATTAAATTAT-ATA
1 TATTTAATTATAATA
17787815 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
17787829 TATTTAATAATAAT-
1 TATTTAATTATAATA
17787843 TATGTTAATT
1 TAT-TTAATT
17787853 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:17787945 original size:18 final size:17
Alignment explanation
Indices: 17787917--17787951 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17787907 ATTATTAAGA
*
17787917 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
17787934 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
17787952 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:17788178 original size:44 final size:45
Alignment explanation
Indices: 17788113--17788203 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
17788103 ACCTCTATTG
* * *
17788113 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
*** *
17788157 CATTCAACCAAACAGTGGATTAGTTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
17788202 CA
1 CA
17788204 CCTCTAATCC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 19 0.49
45 20 0.51
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.29
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:17788205 original size:16 final size:16
Alignment explanation
Indices: 17788184--17788252 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
17788174 GATTAGTTAT
17788184 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
17788200 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
17788217 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
17788233 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
17788249 TACA
1 TACA
17788253 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:17788226 original size:33 final size:32
Alignment explanation
Indices: 17788184--17788252 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
17788174 GATTAGTTAT
17788184 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
17788217 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
17788249 TACA
1 TACA
17788253 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:17793240 original size:17 final size:17
Alignment explanation
Indices: 17793202--17793239 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
17793192 TAATTTTAAA
17793202 ATTTTAAAATTATGTTT
1 ATTTTAAAATTATGTTT
17793219 ATTTTAAAATTAT-TTT
1 ATTTTAAAATTATGTTT
17793235 ATTTT
1 ATTTT
17793240 TTAGAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
ATTTTAAAATTATGTTT
Found at i:17793696 original size:30 final size:30
Alignment explanation
Indices: 17793655--17793712 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
17793645 ATTTCACTAA
17793655 TATCAAATATTAACATATATATAATTATGC
1 TATCAAATATTAACATATATATAATTATGC
*
17793685 TATCCAATATTAACATATATATAATTAT
1 TATCAAATATTAACATATATATAATTAT
17793713 TTATACATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (30 bp):
TATCAAATATTAACATATATATAATTATGC
Found at i:17797895 original size:42 final size:41
Alignment explanation
Indices: 17797808--17798014 Score: 252
Period size: 42 Copynumber: 5.0 Consensus size: 41
17797798 GCGTTTATAG
* * * * *
17797808 AAAAAACGCCACTAAAGATTATGTTTTTTAACGGCACTTAA
1 AAAAAACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTAA
* *
17797849 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGGTTACA
1 AAAAAACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTA-A
* *
17797891 AAAAAATCGCCGCTAAAGATAATATTCTTTAGCGACGCTTAA
1 AAAAAA-CGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTAA
**
17797933 AGAAAAACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTGGT
1 A-AAAAACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTT-AA
* * *
17797976 AAAAAACGCCGCTATAGATCATGTTCTTTAGCAGCGCTT
1 AAAAAACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTT
17798015 TTATAAAAAA
Statistics
Matches: 145, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
41 34 0.23
42 75 0.52
43 36 0.25
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (41 bp):
AAAAAACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTAA
Found at i:17801572 original size:13 final size:13
Alignment explanation
Indices: 17801554--17801614 Score: 61
Period size: 13 Copynumber: 4.7 Consensus size: 13
17801544 TAAATTTTAG
*
17801554 TAAGTAATGTATT
1 TAAGTAATATATT
*
17801567 TAAGTAACATATT
1 TAAGTAATATATT
*
17801580 TAAGTAATAAATT
1 TAAGTAATATATT
* *
17801593 TAACTTATATATAT
1 TAAGTAATATAT-T
17801607 T-AGTAATA
1 TAAGTAATA
17801615 AGTTAAATTA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
13 36 0.95
14 2 0.05
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:17801691 original size:44 final size:43
Alignment explanation
Indices: 17801630--17801721 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 43
17801620 AATTAAATTG
17801630 TAAAAATATAAACATATA-TATTTTTAATATTAATAAGTTATGA
1 TAAAAATATAAACATATACT-TTTTTAATATTAATAAGTTATGA
* * *
17801673 TAAAATATATCAATATATACTTTTTTAATATTAATAAGTTA-AA
1 TAAAA-ATATAAACATATACTTTTTTAATATTAATAAGTTATGA
17801716 TAAAAA
1 TAAAAA
17801722 CTAAAATGTG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
42 1 0.02
43 11 0.25
44 31 0.70
45 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (43 bp):
TAAAAATATAAACATATACTTTTTTAATATTAATAAGTTATGA
Found at i:17802124 original size:7 final size:7
Alignment explanation
Indices: 17802117--17802165 Score: 71
Period size: 7 Copynumber: 6.9 Consensus size: 7
17802107 TTCATTCAAT
*
17802117 AGAAAAT
1 AGAAAAC
17802124 AGCAAAAC
1 AG-AAAAC
17802132 AGAAAAC
1 AGAAAAC
*
17802139 AGAAAAT
1 AGAAAAC
17802146 AGAAAAC
1 AGAAAAC
17802153 AGAAAAC
1 AGAAAAC
17802160 AGAAAA
1 AGAAAA
17802166 TAAAGAAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
7 32 0.84
8 6 0.16
ACGTcount: A:0.71, C:0.10, G:0.14, T:0.04
Consensus pattern (7 bp):
AGAAAAC
Found at i:17802153 original size:21 final size:22
Alignment explanation
Indices: 17802117--17802167 Score: 95
Period size: 21 Copynumber: 2.4 Consensus size: 22
17802107 TTCATTCAAT
17802117 AGAAAATAGCAAAACAGAAAAC
1 AGAAAATAGCAAAACAGAAAAC
17802139 AGAAAATAG-AAAACAGAAAAC
1 AGAAAATAGCAAAACAGAAAAC
17802160 AGAAAATA
1 AGAAAATA
17802168 AAGAAACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.71, C:0.10, G:0.14, T:0.06
Consensus pattern (22 bp):
AGAAAATAGCAAAACAGAAAAC
Found at i:17802211 original size:18 final size:19
Alignment explanation
Indices: 17802169--17802217 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
17802159 CAGAAAATAA
*
17802169 AGAAACATAAAAATGGTAC
1 AGAAACATAAAAATGCTAC
* *
17802188 AGAAACAT-AACATGCTAG
1 AGAAACATAAAAATGCTAC
*
17802206 AGAAACAGAAAA
1 AGAAACATAAAA
17802218 TTATGTGTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.59, C:0.12, G:0.16, T:0.12
Consensus pattern (19 bp):
AGAAACATAAAAATGCTAC
Found at i:17803046 original size:6 final size:6
Alignment explanation
Indices: 17803035--17803117 Score: 166
Period size: 6 Copynumber: 13.8 Consensus size: 6
17803025 TCAATTCTGT
17803035 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
17803083 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
17803118 TATAAATTTT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 77 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:17804500 original size:47 final size:49
Alignment explanation
Indices: 17804412--17804511 Score: 123
Period size: 47 Copynumber: 2.1 Consensus size: 49
17804402 GTTTTGTTAA
* * **
17804412 TTTAGGTAATATTTAAAAAAAATTAGATAAAATTATCAATTTCAGT-TT
1 TTTAAGTAATATTTAAAAAAAATTAGATAAAACTAAAAATTTCAGTGTT
* * *
17804460 TTTAAGTAATATTT-ATAAAAATTAGGTAAAACTAAAAATTTTAGTGTT
1 TTTAAGTAATATTTAAAAAAAATTAGATAAAACTAAAAATTTCAGTGTT
17804508 TTTA
1 TTTA
17804512 TTTCTTTTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 25 0.57
48 19 0.43
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (49 bp):
TTTAAGTAATATTTAAAAAAAATTAGATAAAACTAAAAATTTCAGTGTT
Found at i:17804528 original size:17 final size:17
Alignment explanation
Indices: 17804506--17804545 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
17804496 AATTTTAGTG
17804506 TTTTTATTTCT-TTTTAT
1 TTTTTATTT-TATTTTAT
17804523 TTTTTATTTTAATTTTAT
1 TTTTTATTTT-ATTTTAT
17804541 TTTTT
1 TTTTT
17804546 GTAATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.05
17 9 0.43
18 11 0.52
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTATTTTATTTTAT
Found at i:17804560 original size:9 final size:9
Alignment explanation
Indices: 17804548--17804591 Score: 54
Period size: 9 Copynumber: 4.7 Consensus size: 9
17804538 TATTTTTTGT
17804548 AATTTTTAC
1 AATTTTTAC
17804557 AATTTTTTTTAC
1 AA---TTTTTAC
17804569 AA-TTTTAC
1 AATTTTTAC
17804577 AATTTTTAC
1 AATTTTTAC
17804586 AATTTT
1 AATTTT
17804592 AAATTATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.26
9 14 0.45
12 9 0.29
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (9 bp):
AATTTTTAC
Found at i:17804562 original size:8 final size:8
Alignment explanation
Indices: 17804563--17804596 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
17804553 TTACAATTTT
17804563 TTTTACAA
1 TTTTACAA
17804571 TTTTACAA
1 TTTTACAA
17804579 TTTTTACAA
1 -TTTTACAA
17804588 TTTTA-AA
1 TTTTACAA
17804595 TT
1 TT
17804597 ATTATATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 4 0.16
8 13 0.52
9 8 0.32
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTTACAA
Found at i:17804567 original size:12 final size:12
Alignment explanation
Indices: 17804550--17804574 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17804540 TTTTTTGTAA
17804550 TTTTTACAATTT
1 TTTTTACAATTT
17804562 TTTTTACAATTT
1 TTTTTACAATTT
17804574 T
1 T
17804575 ACAATTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTACAATTT
Found at i:17804592 original size:17 final size:16
Alignment explanation
Indices: 17804562--17804596 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
17804552 TTTACAATTT
17804562 TTTTTACAATTTTACAA
1 TTTTTACAATTTTA-AA
17804579 TTTTTACAATTTTAAA
1 TTTTTACAATTTTAAA
17804595 TT
1 TT
17804597 ATTATATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTTACAATTTTAAA
Found at i:17804610 original size:21 final size:20
Alignment explanation
Indices: 17804585--17804639 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 20
17804575 ACAATTTTTA
17804585 CAATTTTAAATTATT-ATATT
1 CAATTTTAAATTATTCATA-T
*
17804605 CAAATTATTATA-TATTGCATAT
1 C-AATT-TTAAATTATT-CATAT
17804627 CAATTTTAAATTA
1 CAATTTTAAATTA
17804640 ATAATCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
20 5 0.18
21 14 0.50
22 6 0.21
23 3 0.11
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (20 bp):
CAATTTTAAATTATTCATAT
Found at i:17804838 original size:82 final size:86
Alignment explanation
Indices: 17804688--17804855 Score: 202
Period size: 82 Copynumber: 2.0 Consensus size: 86
17804678 TATAAAGAAC
* * *
17804688 TTATTTAATATATAAATTAAAAAGTACTAATTAATCCAAATCTTAAACCCTAACCCAACCCCAAA
1 TTATTTAATATATAAATTAAAAAG-AC-AACTAAT-CAAATCTTAAACCCTAAACCAAACCCAAA
17804753 TCCCTAACCCCTAACCCCTAAACT
63 TCCCTAACCCCTAACCCCTAAACT
* *
17804777 TTATTTAATATATAAATTAAAAA-AC-ACTAAT-TAATC-TAAACCCTAAACCATAACCC-GATC
1 TTATTTAATATATAAATTAAAAAGACAACTAATCAAATCTTAAACCCTAAACCA-AACCCAAATC
* *
17804837 CCTAGCCCCTAGCCCCTAA
65 CCTAACCCCTAACCCCTAA
17804856 TCCCTAACCC
Statistics
Matches: 71, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
82 33 0.46
83 8 0.11
85 5 0.07
87 2 0.03
89 23 0.32
ACGTcount: A:0.42, C:0.29, G:0.02, T:0.27
Consensus pattern (86 bp):
TTATTTAATATATAAATTAAAAAGACAACTAATCAAATCTTAAACCCTAAACCAAACCCAAATCC
CTAACCCCTAACCCCTAAACT
Found at i:17804926 original size:95 final size:96
Alignment explanation
Indices: 17804687--17804919 Score: 302
Period size: 89 Copynumber: 2.5 Consensus size: 96
17804677 ATATAAAGAA
** * * * *
17804687 CTTATTTAATATATAAATTAAAAAGTACTAATTAATCCAAATCTTAAACCCTAACCC-A-----A
1 CTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCATAACCCGATCCCTA
* **
17804746 -CCCCAAATCCCTAACCCCTAACCCCTAAAC
66 GCCCCTAGCCCCTAACCCCTAACCCCTAAAC
*
17804776 TTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCATAACCCGATCCCTA
1 CTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCATAACCCGATCCCTA
*
17804841 GCCCCTAGCCCCTAATCCCTAACCCCTAAAC
66 GCCCCTAGCCCCTAACCCCTAACCCCTAAAC
*
17804872 CTTATTTAATATAT-AATTAAAACACACTAATTAATCTAAACCCTAAAC
1 CTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAAC
17804920 TCTAACCTAA
Statistics
Matches: 124, Mismatches: 13, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
89 50 0.40
90 1 0.01
95 34 0.27
96 39 0.31
ACGTcount: A:0.42, C:0.28, G:0.02, T:0.27
Consensus pattern (96 bp):
CTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCATAACCCGATCCCTA
GCCCCTAGCCCCTAACCCCTAACCCCTAAAC
Found at i:17804949 original size:95 final size:96
Alignment explanation
Indices: 17804687--17804956 Score: 272
Period size: 95 Copynumber: 2.9 Consensus size: 96
17804677 ATATAAAGAA
** * * * *
17804687 CTTATTTAATATATAAATTAAAAAGTACTAATTAATCCAAATCTTAAACCCTAACCC-AA--C--
1 CTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCATAACCCGAACCCAA
* *
17804747 -CCCA-AATCCCTAACCCCTAACCCCTAAAC
66 ACCCATAAACCCTAATCCCTAACCCCTAAAC
* * *
17804776 TTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCATAACCCGATCCCTA
1 CTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCATAACCCGAACCCAA
* * **
17804841 GCCCCTAGCCCCTAATCCCTAACCCCTAAAC
66 ACCCATAAACCCTAATCCCTAACCCCTAAAC
* *
17804872 CTTATTTAATATAT-AATTAAAACACACTAATTAATCTAAACCCTAAACTC-TAA-CCTAACACC
1 CTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAAC-CATAACCCGAAC-CC
***
17804934 AAATTTATAAACCCTAATCCCTA
64 AAACCCATAAACCCTAATCCCTA
17804957 GCTCTTAACA
Statistics
Matches: 148, Mismatches: 24, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
89 50 0.34
90 1 0.01
92 1 0.01
94 4 0.03
95 56 0.38
96 36 0.24
ACGTcount: A:0.42, C:0.29, G:0.01, T:0.27
Consensus pattern (96 bp):
CTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCATAACCCGAACCCAA
ACCCATAAACCCTAATCCCTAACCCCTAAAC
Found at i:17804978 original size:7 final size:7
Alignment explanation
Indices: 17804968--17805018 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
17804958 CTCTTAACAT
17804968 CTAACCC
1 CTAACCC
17804975 CTAA--C
1 CTAACCC
*
17804980 CTAATCC
1 CTAACCC
17804987 CTAACCC
1 CTAACCC
17804994 CTAACCC
1 CTAACCC
*
17805001 TTAACCC
1 CTAACCC
* *
17805008 ATAAACC
1 CTAACCC
17805015 CTAA
1 CTAA
17805019 ATCACATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
5 5 0.14
7 32 0.86
ACGTcount: A:0.35, C:0.45, G:0.00, T:0.20
Consensus pattern (7 bp):
CTAACCC
Found at i:17805063 original size:14 final size:15
Alignment explanation
Indices: 17805041--17805074 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
17805031 CTTAAATCAG
*
17805041 AATCCCTAATT-CAT
1 AATCTCTAATTCCAT
17805055 AATCTCTAATTCCAT
1 AATCTCTAATTCCAT
17805070 AATCT
1 AATCT
17805075 ATAAAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.38
Consensus pattern (15 bp):
AATCTCTAATTCCAT
Done.