Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 141 of 187
Found at i:42181846 original size:21 final size:20
Alignment explanation
Indices: 42181820--42181871 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
42181810 CTACAACTTA
*
42181820 AAGCAGAGGTAGCAGCGAGGG
1 AAGCAGAGGT-GCAGCGAGAG
*
42181841 AAGCAGAGGCTGTAGCGAGAG
1 AAGCAGAGG-TGCAGCGAGAG
42181862 AAGCAGAGGT
1 AAGCAGAGGT
42181872 TCAAAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.44, T:0.08
Consensus pattern (20 bp):
AAGCAGAGGTGCAGCGAGAG
Found at i:42182292 original size:34 final size:35
Alignment explanation
Indices: 42182248--42182314 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
42182238 CAGTAAAATA
*
42182248 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
42182282 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
42182315 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:42183020 original size:42 final size:41
Alignment explanation
Indices: 42182874--42183114 Score: 205
Period size: 41 Copynumber: 5.8 Consensus size: 41
42182864 TGTTTTTATA
* *
42182874 AAAGTGCCGCTAAAGAACATGAGCTTTAGCGGCGTTTGTTG-G
1 AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCG-TT-TTGAG
* * * * ** ** * *
42182916 TAGGTGCCGCTATAGGTCATGTTCTTTAGCGGCGTTTGTTACA
1 AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTT-TGA-G
*
42182959 AAAGCACCGCTAAAGAACATGACCTTTAGCGGCGTTTTCGAG
1 AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTT-GAG
* ***
42183001 AAAGTGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTT
1 AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTGAG
* * * ***
42183042 TATGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
1 AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTGAG
* *
42183083 TAAGCGCCGCTAAAGAACAAGACCTTTAGCGG
1 AAAGCGCCGCTAAAGAACATGACCTTTAGCGG
42183115 TATTTATTTC
Statistics
Matches: 163, Mismatches: 32, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
40 1 0.01
41 69 0.42
42 64 0.39
43 29 0.18
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (41 bp):
AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTGAG
Found at i:42183028 original size:85 final size:81
Alignment explanation
Indices: 42182880--42183114 Score: 245
Period size: 85 Copynumber: 2.8 Consensus size: 81
42182870 TATAAAAGTG
* * * ** **
42182880 CCGCTAAAGAACATGAGCTTTAGCGGCGTTTGTTGGTAGGTGCCGCTATAGGTCATGTTCTTTAG
1 CCGCTAAAGAACATGACCTTTAGCGGCG-TT-TTGGTAAGTGCCGCTAAAGAACATGACCTTTAG
42182945 CGGCGTTTGTTACAAAAGCA
64 CGGCGTTT-TT-CAAAAGCA
*
42182965 CCGCTAAAGAACATGACCTTTAGCGGCGTTTTCGAGAAAGTGCCGCTAAAGAACATGACCTTTAG
1 CCGCTAAAGAACATGACCTTTAGCGGCGTTTT-G-GTAAGTGCCGCTAAAGAACATGACCTTTAG
*** * *
42183030 CGGCGTTTTTTTTATGCG
64 CGGCGTTTTTCAAAAGCA
* ** * *
42183048 CCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTAAGCGCCGCTAAAGAACAAGACCTTTAGC
1 CCGCTAAAGAACATGACCTTTAGCGGCG-TTTTGGTAAGTGCCGCTAAAGAACATGACCTTTAGC
42183113 GG
65 GG
42183115 TATTTATTTC
Statistics
Matches: 128, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
82 29 0.23
83 32 0.25
84 9 0.07
85 58 0.45
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (81 bp):
CCGCTAAAGAACATGACCTTTAGCGGCGTTTTGGTAAGTGCCGCTAAAGAACATGACCTTTAGCG
GCGTTTTTCAAAAGCA
Found at i:42183063 original size:41 final size:41
Alignment explanation
Indices: 42182879--42183114 Score: 238
Period size: 42 Copynumber: 5.7 Consensus size: 41
42182869 TTATAAAAGT
* * * *
42182879 GCCGCTAAAGAACATGAGCTTTAGCGGCGTTTGTTGGTAGGT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGTTT-TTTGTAAGC
* ** ** ***
42182921 GCCGCTATAGGTCATGTTCTTTAGCGGCGTTTGTTACAAAAGC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGTTT-TT-TGTAAGC
* ** * *
42182964 ACCGCTAAAGAACATGACCTTTAGCGGCGTTTTCGAGAAAGT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGTTTT-TTGTAAGC
* *
42183006 GCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTTATGC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTGTAAGC
* *
42183047 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTAAGC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTGTAAGC
*
42183088 GCCGCTAAAGAACAAGACCTTTAGCGG
1 GCCGCTAAAGAACATGACCTTTAGCGG
42183115 TATTTATTTC
Statistics
Matches: 161, Mismatches: 31, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
41 66 0.41
42 67 0.42
43 28 0.17
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (41 bp):
GCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTGTAAGC
Found at i:42183315 original size:2 final size:2
Alignment explanation
Indices: 42183304--42183354 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
42183294 GATCATTGCT
42183304 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42183345 TA TA TA TA TA
1 TA TA TA TA TA
42183355 AAAGAAGCAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:42183834 original size:28 final size:28
Alignment explanation
Indices: 42183794--42183851 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
42183784 TTTGCATCAC
42183794 CTATTCCAGGTAATTTGTTCATTATTTT
1 CTATTCCAGGTAATTTGTTCATTATTTT
42183822 CTATTCCAGGTAATTTGTTCATTATTTT
1 CTATTCCAGGTAATTTGTTCATTATTTT
42183850 CT
1 CT
42183852 CTTATTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.21, C:0.16, G:0.10, T:0.53
Consensus pattern (28 bp):
CTATTCCAGGTAATTTGTTCATTATTTT
Found at i:42187783 original size:30 final size:30
Alignment explanation
Indices: 42187747--42187805 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
42187737 AGAGGTAGAT
42187747 TGGGAGGGAATAAAAGA-TTTAGGGAAAAAG
1 TGGGAGGGAATAAAA-ATTTTAGGGAAAAAG
* *
42187777 TGGGAGGGAGTAAAAATTTTGGGGAAAAA
1 TGGGAGGGAATAAAAATTTTAGGGAAAAA
42187806 TAAAATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.44, C:0.00, G:0.37, T:0.19
Consensus pattern (30 bp):
TGGGAGGGAATAAAAATTTTAGGGAAAAAG
Found at i:42187975 original size:21 final size:21
Alignment explanation
Indices: 42187941--42187981 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42187931 GGGGAAAAGT
*
42187941 GGGAAAGAGTAAAAGTTTTGA
1 GGGAAAGAGTAAAAGGTTTGA
42187962 GGGAAA-AGTAAAAAGGTTTG
1 GGGAAAGAGT-AAAAGGTTTG
42187982 GGAGTTTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.44, C:0.00, G:0.34, T:0.22
Consensus pattern (21 bp):
GGGAAAGAGTAAAAGGTTTGA
Found at i:42188404 original size:2 final size:2
Alignment explanation
Indices: 42188397--42188427 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
42188387 ATGCCTACAA
*
42188397 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42188428 AACAAACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:42190588 original size:23 final size:22
Alignment explanation
Indices: 42190537--42190588 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
42190527 AGGGACGAAA
42190537 AAAAAAGTTGAATTACAGGGAG
1 AAAAAAGTTGAATTACAGGGAG
* * *
42190559 AAGAAAATTTGACTTACATGGAGG
1 AA-AAAAGTTGAATTACAGGGA-G
42190583 AAAAAA
1 AAAAAA
42190589 AATGACATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 2 0.08
23 20 0.80
24 3 0.12
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (22 bp):
AAAAAAGTTGAATTACAGGGAG
Found at i:42190654 original size:78 final size:80
Alignment explanation
Indices: 42190535--42190687 Score: 186
Period size: 79 Copynumber: 1.9 Consensus size: 80
42190525 ATAGGGACGA
* * * ** *
42190535 AAAAAAAAGTTGAATTACAGGGAGAAGAAAATTTGACTTACATGGAGGAAAAAAA-ATGACATAC
1 AAAAAAAAGTTGAATTACAGGGACAAGAAAATTTAAATTACATGGACAAAAAAAAGATGAAATAC
*
42190599 ACGTAAAAAAATGAC
66 ACGGAAAAAAATGAC
* *
42190614 AAAAAAAA-TTAGAATTATAGGGACCA-AAAATTTAAATTACATGGACAAAAAAAAGATGAAATA
1 AAAAAAAAGTT-GAATTACAGGGACAAGAAAATTTAAATTACATGGACAAAAAAAAGATGAAATA
*
42190677 CATGGAAAAAA
65 CACGGAAAAAA
42190688 TGGACTAACA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
78 26 0.42
79 36 0.58
ACGTcount: A:0.58, C:0.08, G:0.16, T:0.18
Consensus pattern (80 bp):
AAAAAAAAGTTGAATTACAGGGACAAGAAAATTTAAATTACATGGACAAAAAAAAGATGAAATAC
ACGGAAAAAAATGAC
Found at i:42190659 original size:22 final size:23
Alignment explanation
Indices: 42190615--42190666 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
42190605 AAAAATGACA
*
42190615 AAAAAAATTAGAATTATAGGGAC
1 AAAAAAATTAGAATTACAGGGAC
* * *
42190638 CAAAAATTTA-AATTACATGGAC
1 AAAAAAATTAGAATTACAGGGAC
42190660 AAAAAAA
1 AAAAAAA
42190667 AGATGAAATA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.60, C:0.08, G:0.12, T:0.21
Consensus pattern (23 bp):
AAAAAAATTAGAATTACAGGGAC
Found at i:42198845 original size:5 final size:5
Alignment explanation
Indices: 42198835--42198879 Score: 72
Period size: 5 Copynumber: 8.8 Consensus size: 5
42198825 AAGTAAGTTG
*
42198835 TTATA TTATA TTATTA TAATA TTATA TTATA TTATA TTATA TTAT
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTAT
42198880 TATATATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 33 0.89
6 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:42198851 original size:8 final size:8
Alignment explanation
Indices: 42198838--42198884 Score: 62
Period size: 8 Copynumber: 6.0 Consensus size: 8
42198828 TAAGTTGTTA
42198838 TATTATAT
1 TATTATAT
*
42198846 TATTATAA
1 TATTATAT
42198854 TATTATAT
1 TATTATAT
42198862 TA-TAT-T
1 TATTATAT
42198868 ATATTATAT
1 -TATTATAT
42198877 TATTATAT
1 TATTATAT
42198885 ATAAAACAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 1 0.03
7 5 0.15
8 27 0.79
9 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTATAT
Found at i:42199999 original size:27 final size:25
Alignment explanation
Indices: 42199968--42200038 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 25
42199958 ACTTTAGCGC
* *
42199968 GCTCTCTGAGTTTTAGCACGTTAGT
1 GCTCTCTGACTATTAGCACGTTAGT
*
42199993 GCTCTCTGACTATTAGCACGTTGGT
1 GCTCTCTGACTATTAGCACGTTAGT
42200018 GCTCTCTGA-TATTTAGCACGT
1 GCTCTCTGACTA-TTAGCACGT
42200039 AATAATGCAC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
24 2 0.05
25 40 0.95
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (25 bp):
GCTCTCTGACTATTAGCACGTTAGT
Found at i:42202166 original size:24 final size:24
Alignment explanation
Indices: 42202134--42202180 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
42202124 GCCATAGTCG
42202134 AACTATGGTCTTACATGTAATCAT
1 AACTATGGTCTTACATGTAATCAT
42202158 AACTATGGTCTTACATGTAATCA
1 AACTATGGTCTTACATGTAATCA
42202181 CATATCACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (24 bp):
AACTATGGTCTTACATGTAATCAT
Found at i:42202933 original size:35 final size:35
Alignment explanation
Indices: 42202875--42203041 Score: 88
Period size: 35 Copynumber: 4.7 Consensus size: 35
42202865 CACTATGAAC
* * * *
42202875 GTAAGACCATGGTTGGACCATGGCAGTTTTTATAT
1 GTAAGACCATAGCTGGGCTATGGCAGTTTTTATAT
*
42202910 GTAAGACCATAGCTGGGCTATGGCA--TTTT-GAT
1 GTAAGACCATAGCTGGGCTATGGCAGTTTTTATAT
* * * * **** *
42202942 GATAAGACCATAACTGAGTTATGGTTATGGCACTATGAAC
1 G-TAAGACCATAGCTGGGCTATGG-CA-GTTTTTAT--AT
* * * * *
42202982 GTAAGACCATGGTTGGACCATGGCAGTGTTTATAT
1 GTAAGACCATAGCTGGGCTATGGCAGTTTTTATAT
*
42203017 GTAAGACCATAACTGGGCTATGGCA
1 GTAAGACCATAGCTGGGCTATGGCA
42203042 TTCTGATGAT
Statistics
Matches: 92, Mismatches: 32, Indels: 16
0.66 0.23 0.11
Matches are distributed among these distances:
32 3 0.03
33 23 0.25
34 1 0.01
35 42 0.46
37 5 0.05
38 1 0.01
39 15 0.16
40 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (35 bp):
GTAAGACCATAGCTGGGCTATGGCAGTTTTTATAT
Found at i:42202953 original size:33 final size:32
Alignment explanation
Indices: 42202908--42203072 Score: 105
Period size: 33 Copynumber: 4.8 Consensus size: 32
42202898 CAGTTTTTAT
*
42202908 ATGTAAGACCATAGCTGGGCTATGGCATTTTG
1 ATGTAAGACCATAACTGGGCTATGGCATTTTG
* * *
42202940 ATGATAAGACCATAACTGAGTTATGGTTATGGCACTATG
1 ATG-TAAGACCATAACT--G----GGCTATGGCATTTTG
* *** * * *
42202979 AACGTAAGACCATGGTTGGACCATGGCAGTGTTTAT
1 -ATGTAAGACCATAACTGGGCTATGGCA-T-TTT-G
*
42203015 ATGTAAGACCATAACTGGGCTATGGCATTCTG
1 ATGTAAGACCATAACTGGGCTATGGCATTTTG
*
42203047 ATGATAAGACCATAACTGGGTTATGG
1 ATG-TAAGACCATAACTGGGCTATGG
42203073 AACTACGAAT
Statistics
Matches: 98, Mismatches: 23, Indels: 23
0.68 0.16 0.16
Matches are distributed among these distances:
32 6 0.06
33 42 0.43
34 1 0.01
35 24 0.24
37 1 0.01
39 22 0.22
40 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (32 bp):
ATGTAAGACCATAACTGGGCTATGGCATTTTG
Found at i:42203022 original size:107 final size:107
Alignment explanation
Indices: 42202857--42203072 Score: 387
Period size: 107 Copynumber: 2.0 Consensus size: 107
42202847 ACCATAACTG
* *
42202857 GGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAGTTTTTATATGTAAGACCATAG
1 GGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAA
*
42202922 CTGGGCTATGGCATTTTGATGATAAGACCATAACTGAGTTAT
66 CTGGGCTATGGCATTCTGATGATAAGACCATAACTGAGTTAT
*
42202964 GGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAA
1 GGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAA
*
42203029 CTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTAT
66 CTGGGCTATGGCATTCTGATGATAAGACCATAACTGAGTTAT
42203071 GG
1 GG
42203073 AACTACGAAT
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 104 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (107 bp):
GGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAA
CTGGGCTATGGCATTCTGATGATAAGACCATAACTGAGTTAT
Found at i:42211417 original size:8 final size:8
Alignment explanation
Indices: 42211404--42211449 Score: 92
Period size: 8 Copynumber: 5.8 Consensus size: 8
42211394 ATGTAAGGGT
42211404 AATTCATA
1 AATTCATA
42211412 AATTCATA
1 AATTCATA
42211420 AATTCATA
1 AATTCATA
42211428 AATTCATA
1 AATTCATA
42211436 AATTCATA
1 AATTCATA
42211444 AATTCA
1 AATTCA
42211450 ACGAATTGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (8 bp):
AATTCATA
Found at i:42214081 original size:15 final size:16
Alignment explanation
Indices: 42214058--42214103 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
42214048 TTCCTTTATT
* *
42214058 TTATCTTTT-TATCCC
1 TTATATTTTATATACC
42214073 TTATATTTTTATATACC
1 TTATA-TTTTATATACC
42214090 TTATATTTTATATA
1 TTATATTTTATATA
42214104 TACGTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 4 0.15
16 13 0.48
17 10 0.37
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATATTTTATATACC
Found at i:42214093 original size:17 final size:18
Alignment explanation
Indices: 42214071--42214106 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
42214061 TCTTTTTATC
42214071 CCTTATATTTT-TATATA
1 CCTTATATTTTATATATA
42214088 CCTTATATTTTATATATA
1 CCTTATATTTTATATATA
42214106 C
1 C
42214107 GTATTTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.56
Consensus pattern (18 bp):
CCTTATATTTTATATATA
Found at i:42214203 original size:2 final size:2
Alignment explanation
Indices: 42214198--42214239 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
42214188 ACACACACAC
42214198 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42214240 GCATACATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42226107 original size:100 final size:100
Alignment explanation
Indices: 42225970--42226481 Score: 771
Period size: 100 Copynumber: 5.1 Consensus size: 100
42225960 GGTTGAAAAG
* * * *
42225970 TAAAAAGATTGAAGCCACAACGGCGGATTTTACTTCCTCAGCAGTACAGCGAAATAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGTGGAATAGATTGAAGC
* *
42226035 TACGACAGCGGATCTGGTTTCCCTGATATTGCAAT
66 TACGACGGCGGATCTAGTTTCCCTGATATTGCAAT
*
42226070 TAAAAAGATTGAAGCCACAACGGCGGATCTTAATTCCTTAGCAGTACAGTGGAATAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGTGGAATAGATTGAAGC
42226135 TACGACGGCGGATCTAGTTTCCCTGATATTGCAAT
66 TACGACGGCGGATCTAGTTTCCCTGATATTGCAAT
*
42226170 TAAAAAGATTGAAGCCACAACGGCGGATCTTAATTCCTTAGCAGTACAGTGGAATAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGTGGAATAGATTGAAGC
* *
42226235 TACGACGACGGATCTAGTTTCTCTGATATTGCAAT
66 TACGACGGCGGATCTAGTTTCCCTGATATTGCAAT
42226270 T-AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGTGGAATAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGTGGAATAGATTGAAGC
* **
42226334 TACAACGGCGGATCTAGTTTCCCTGATATTATAAT
66 TACGACGGCGGATCTAGTTTCCCTGATATTGCAAT
* * * *
42226369 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTT-GACGGTGCGGTGGAACAGATTGAAG
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAG-CAGTACAGTGGAATAGATTGAAG
* * * * *
42226433 CTACGGCGGCAGATCTGGTTT-CCTCGACATTGCAGT
65 CTACGACGGCGGATCTAGTTTCCCT-GATATTGCAAT
42226469 TAAATAA-ATTGAA
1 TAAA-AAGATTGAA
42226482 AATTTCAGAT
Statistics
Matches: 381, Mismatches: 27, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
99 97 0.25
100 282 0.74
101 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (100 bp):
TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGTGGAATAGATTGAAGC
TACGACGGCGGATCTAGTTTCCCTGATATTGCAAT
Found at i:42226428 original size:50 final size:50
Alignment explanation
Indices: 42225972--42226433 Score: 294
Period size: 50 Copynumber: 9.3 Consensus size: 50
42225962 TTGAAAAGTA
* * * *
42225972 AAAAGATTGAAGCCACAACGGCGGATTTTACTTCC-TCAGCAGTACAG-CG
1 AAAAGATTGAAGCCACAACGGCGGATCTTAATTCCTTGA-CAGTACAGTGG
* * * *** * * * * * **
42226021 AAATAGATTGAAGCTACGACAGCGGATCTGGTTTCCCTGATATTGCAATTA
1 AAA-AGATTGAAGCCACAACGGCGGATCTTAATTCCTTGACAGTACAGTGG
42226072 AAAAGATTGAAGCCACAACGGCGGATCTTAATTCCTT-AGCAGTACAGTGG
1 AAAAGATTGAAGCCACAACGGCGGATCTTAATTCCTTGA-CAGTACAGTGG
* * * * * * * * * **
42226122 AATAGATTGAAGCTACGACGGCGGATC-TAGTTTCCCTGATATTGCAATTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTA-ATTCCTTGACAGTACAGTGG
42226172 AAAAGATTGAAGCCACAACGGCGGATCTTAATTCCTT-AGCAGTACAGTGG
1 AAAAGATTGAAGCCACAACGGCGGATCTTAATTCCTTGA-CAGTACAGTGG
* * * * * * * * * * *
42226222 AATAGATTGAAGCTACGACGACGGATC-TAGTTTCTCTGATATTGCAAT-T
1 AAAAGATTGAAGCCACAACGGCGGATCTTAATTCCT-TGACAGTACAGTGG
*
42226271 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTT-AGCAGTACAGTGG
1 AAAAGATTGAAGCCACAACGGCGGATCTTAATTCCTTGA-CAGTACAGTGG
* * * * * * * * **
42226321 AATAGATTGAAGCTACAACGGCGGATC-TAGTTTCCCTGATATTATAATTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTA-ATTCCTTGACAGTACAGTGG
* * * *
42226371 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTGACGGTGCGGTGG
1 AAAAGATTGAAGCCACAACGGCGGATCTTAATTCCTTGACAGTACAGTGG
*
42226421 AACAGATTGAAGC
1 AAAAGATTGAAGC
42226434 TACGGCGGCA
Statistics
Matches: 302, Mismatches: 95, Indels: 31
0.71 0.22 0.07
Matches are distributed among these distances:
48 1 0.00
49 44 0.15
50 245 0.81
51 12 0.04
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (50 bp):
AAAAGATTGAAGCCACAACGGCGGATCTTAATTCCTTGACAGTACAGTGG
Found at i:42228477 original size:15 final size:16
Alignment explanation
Indices: 42228454--42228499 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
42228444 TTCCTTTATT
* *
42228454 TTATCTTTT-TATCCC
1 TTATATTTTATATACC
42228469 TTATATTTTTATATACC
1 TTATA-TTTTATATACC
42228486 TTATATTTTATATA
1 TTATATTTTATATA
42228500 TACGTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 4 0.15
16 13 0.48
17 10 0.37
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATATTTTATATACC
Found at i:42228489 original size:17 final size:18
Alignment explanation
Indices: 42228467--42228502 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
42228457 TCTTTTTATC
42228467 CCTTATATTTT-TATATA
1 CCTTATATTTTATATATA
42228484 CCTTATATTTTATATATA
1 CCTTATATTTTATATATA
42228502 C
1 C
42228503 GTATTTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.56
Consensus pattern (18 bp):
CCTTATATTTTATATATA
Found at i:42232855 original size:2 final size:2
Alignment explanation
Indices: 42232848--42232872 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42232838 CAATGCTATG
42232848 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
42232873 TATGAATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42233783 original size:22 final size:21
Alignment explanation
Indices: 42233753--42233795 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42233743 CAAGACACAT
*
42233753 TATTGGTTGGCTTATTTGATGA
1 TATTGGTTGG-ATATTTGATGA
*
42233775 TATTTGTTGGATATTTGATGA
1 TATTGGTTGGATATTTGATGA
42233796 AAGAAAGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.21, C:0.02, G:0.26, T:0.51
Consensus pattern (21 bp):
TATTGGTTGGATATTTGATGA
Found at i:42234101 original size:17 final size:17
Alignment explanation
Indices: 42234052--42234107 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
42234042 ACTCGCACAT
42234052 ATGAGTTTGCAGTTTTG
1 ATGAGTTTGCAGTTTTG
* * * *
42234069 GTAAGCTCGCAGTTTTG
1 ATGAGTTTGCAGTTTTG
*
42234086 ATGAGTTTGCACTTTTG
1 ATGAGTTTGCAGTTTTG
42234103 ATGAG
1 ATGAG
42234108 CTCGCAGTCT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.20, C:0.11, G:0.29, T:0.41
Consensus pattern (17 bp):
ATGAGTTTGCAGTTTTG
Found at i:42248571 original size:79 final size:79
Alignment explanation
Indices: 42248440--42248594 Score: 222
Period size: 79 Copynumber: 2.0 Consensus size: 79
42248430 TGTTAGTACG
* * *
42248440 CCTCTGCATTACTCTATTAATGAAGAATATTCGATATCTGAATATGTTAGATTGATTGTTACTAA
1 CCTCTACATTACTCTATTAATGAAGAATATTCGATATCTAAACATGTTAGATTGATTGTTACTAA
42248505 TTTTGATTTATGAT
66 TTTTGATTTATGAT
* * * *
42248519 CCTCTACATTACTTTTTTGATGAAGAATATAT-GATATCTAAACATGTTAGATTGATTGTTACTG
1 CCTCTACATTACTCTATTAATGAAGAATAT-TCGATATCTAAACATGTTAGATTGATTGTTACTA
*
42248583 ATTTTGGTTTAT
65 ATTTTGATTTAT
42248595 AACCGTGCAT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
79 66 0.99
80 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (79 bp):
CCTCTACATTACTCTATTAATGAAGAATATTCGATATCTAAACATGTTAGATTGATTGTTACTAA
TTTTGATTTATGAT
Found at i:42250319 original size:24 final size:24
Alignment explanation
Indices: 42250292--42250359 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
42250282 AAAAATTGTA
42250292 ATAATTATATATTTAAAAATAATT
1 ATAATTATATATTTAAAAATAATT
* *
42250316 ATAATT-T-TA--T-AAAATTATG
1 ATAATTATATATTTAAAAATAATT
* *
42250335 ATAATTACACATTTAAAAATAATT
1 ATAATTATATATTTAAAAATAATT
42250359 A
1 A
42250360 AAAATTAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
19 13 0.39
20 1 0.03
21 1 0.03
22 2 0.06
23 2 0.06
24 14 0.42
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (24 bp):
ATAATTATATATTTAAAAATAATT
Found at i:42250324 original size:18 final size:19
Alignment explanation
Indices: 42250291--42250340 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
42250281 AAAAAATTGT
42250291 AATAATTAT-ATATTTA-AA
1 AATAATTATAAT-TTTATAA
42250309 AATAATTATAATTTTATAA
1 AATAATTATAATTTTATAA
* *
42250328 AATTATGATAATT
1 AATAATTATAATT
42250341 ACACATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
AATAATTATAATTTTATAA
Found at i:42256092 original size:28 final size:29
Alignment explanation
Indices: 42256058--42256113 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
42256048 TGGTTTAATG
42256058 TGCAATTGTACACATG-AATTTTGATTTA
1 TGCAATTGTACACATGAAATTTTGATTTA
* * *
42256086 TGCAATTTTATATATGAAATTTTGATTT
1 TGCAATTGTACACATGAAATTTTGATTT
42256114 GACCCAGTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.48
Consensus pattern (29 bp):
TGCAATTGTACACATGAAATTTTGATTTA
Found at i:42256094 original size:15 final size:15
Alignment explanation
Indices: 42256074--42256113 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
42256064 TGTACACATG
*
42256074 AATTTTGATTTATGC
1 AATTTTGATTTATGA
*
42256089 AATTTT-ATATATGA
1 AATTTTGATTTATGA
42256103 AATTTTGATTT
1 AATTTTGATTT
42256114 GACCCAGTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.55
Consensus pattern (15 bp):
AATTTTGATTTATGA
Found at i:42260934 original size:3 final size:3
Alignment explanation
Indices: 42260926--42260962 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
42260916 GTCTCCTCTC
42260926 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
42260963 AGTCAATACA
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:42266850 original size:62 final size:62
Alignment explanation
Indices: 42266753--42266877 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
42266743 CTTTGAAGTA
*
42266753 TGAAATTTCGTTGTTGGATCGCAACACCAAATTTGTGTTGTGGCAGATAAAGATGCAGGCAG
1 TGAAATTTCGCTGTTGGATCGCAACACCAAATTTGTGTTGTGGCAGATAAAGATGCAGGCAG
42266815 TGAAATTTCGCTGTTGGATCGCAACACCAAATTTGTGTTGTGGCAGATAAAGATGCAGGCAG
1 TGAAATTTCGCTGTTGGATCGCAACACCAAATTTGTGTTGTGGCAGATAAAGATGCAGGCAG
42266877 T
1 T
42266878 TCTTGCACAG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (62 bp):
TGAAATTTCGCTGTTGGATCGCAACACCAAATTTGTGTTGTGGCAGATAAAGATGCAGGCAG
Found at i:42271544 original size:18 final size:20
Alignment explanation
Indices: 42271521--42271609 Score: 59
Period size: 19 Copynumber: 4.7 Consensus size: 20
42271511 TATAAAATAT
42271521 ATAAATT-AAA-AAGTTAAA
1 ATAAATTGAAAGAAGTTAAA
42271539 ATAAATTTGAATA-AA-TTAACA
1 ATAAA-TTGAA-AGAAGTTAA-A
* *
42271560 AT--ATTGAAATAAGTTGAA
1 ATAAATTGAAAGAAGTTAAA
*
42271578 ATAAATT-AAAGATGTTAAA
1 ATAAATTGAAAGAAGTTAAA
*
42271597 AT-ATTTGAAAGAA
1 ATAAATTGAAAGAA
42271610 ATAAAATATC
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
17 1 0.02
18 18 0.32
19 22 0.39
20 9 0.16
21 6 0.11
ACGTcount: A:0.57, C:0.01, G:0.10, T:0.31
Consensus pattern (20 bp):
ATAAATTGAAAGAAGTTAAA
Found at i:42271604 original size:28 final size:28
Alignment explanation
Indices: 42271521--42271616 Score: 99
Period size: 29 Copynumber: 3.4 Consensus size: 28
42271511 TATAAAATAT
*
42271521 ATAAATTAAAAAGTTAAAATAAATTTG-A
1 ATAAATTAAAATGTTAAAAT-AATTTGAA
* * *
42271549 ATAAATTAACAATATTGAAATAAGTTGAA
1 ATAAATTAA-AATGTTAAAATAATTTGAA
42271578 ATAAATTAAAGATGTTAAAAT-ATTTGAA
1 ATAAATTAAA-ATGTTAAAATAATTTGAA
*
42271606 AGAAA-TAAAAT
1 ATAAATTAAAAT
42271617 ATCTATATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
26 2 0.04
27 4 0.07
28 25 0.44
29 26 0.46
ACGTcount: A:0.58, C:0.01, G:0.09, T:0.31
Consensus pattern (28 bp):
ATAAATTAAAATGTTAAAATAATTTGAA
Found at i:42271658 original size:4 final size:4
Alignment explanation
Indices: 42271649--42271683 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
42271639 AACAATAGAT
42271649 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
42271684 AATGAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:42271947 original size:12 final size:12
Alignment explanation
Indices: 42271926--42271961 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
42271916 ATACCAATAA
42271926 TAAT-AATAAAT
1 TAATAAATAAAT
42271937 TAATAAATAAAT
1 TAATAAATAAAT
*
42271949 TAAAAAATAAAT
1 TAATAAATAAAT
42271961 T
1 T
42271962 TAAAAAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 4 0.17
12 19 0.83
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAATAAATAAAT
Found at i:42271966 original size:12 final size:12
Alignment explanation
Indices: 42271930--42271967 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
42271920 CAATAATAAT
42271930 AATAAA-TTAATA
1 AATAAATTTAA-A
*
42271942 AATAAATTAAAA
1 AATAAATTTAAA
42271954 AATAAATTTAAA
1 AATAAATTTAAA
42271966 AA
1 AA
42271968 AAGGATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 20 0.87
13 3 0.13
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAAATTTAAA
Found at i:42272386 original size:14 final size:14
Alignment explanation
Indices: 42272367--42272394 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42272357 ACTCCCTCAT
42272367 AACCCTAAAATCAG
1 AACCCTAAAATCAG
42272381 AACCCTAAAATCAG
1 AACCCTAAAATCAG
42272395 TTTGTTAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.29, G:0.07, T:0.14
Consensus pattern (14 bp):
AACCCTAAAATCAG
Found at i:42274305 original size:21 final size:21
Alignment explanation
Indices: 42274275--42274329 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
42274265 AACAGCGGTG
*
42274275 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
* *
42274296 GCGTTGAGATTGGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
42274317 GCGGTGAGATTAG
1 GCGGTGAGATTAG
42274330 AAACAATGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.09, G:0.38, T:0.31
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:42281387 original size:15 final size:15
Alignment explanation
Indices: 42281367--42281404 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
42281357 GACCCCTGTC
*
42281367 TCTTCTTTTTCTTTT
1 TCTTCTTCTTCTTTT
42281382 TCTTCTTCTTCTTTT
1 TCTTCTTCTTCTTTT
42281397 TCTTCTTC
1 TCTTCTTC
42281405 AGTCAATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TCTTCTTCTTCTTTT
Found at i:42282889 original size:91 final size:91
Alignment explanation
Indices: 42282704--42282892 Score: 231
Period size: 91 Copynumber: 2.1 Consensus size: 91
42282694 AGCAGAAAAA
*
42282704 TATGTTATTTTAAGGACTATTGTTTGGTGTATTAATGCAGCAGAAAAATTCTTGTTTAGTCGTCA
1 TATGTTATTTTAAGGACTATTGTTTGGTGTATTAAAGCAGCAGAAAAATTCTTGTTTAGTCGTCA
* * *
42282769 ATTAATGTTGTCTAAGTGACTGTATT
66 ATAAATGTGGTCTAAGTGACTGTAAT
* * * * *
42282795 TATGTTTTTTTAAGGATTATTGTTTGGTGTGTTAAAGCAGCAG-TAAATTGTTGTTTAGAT-GTC
1 TATGTTATTTTAAGGACTATTGTTTGGTGTATTAAAGCAGCAGAAAAATTCTTGTTTAG-TCGTC
* *
42282858 AATAAATGTGGTTTGAA-TGACTTTAAAT
65 AATAAATGTGGTCT-AAGTGACTGT-AAT
42282886 TATGTTA
1 TATGTTA
42282893 ATAATGGTCG
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
90 33 0.40
91 50 0.60
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (91 bp):
TATGTTATTTTAAGGACTATTGTTTGGTGTATTAAAGCAGCAGAAAAATTCTTGTTTAGTCGTCA
ATAAATGTGGTCTAAGTGACTGTAAT
Found at i:42283931 original size:43 final size:43
Alignment explanation
Indices: 42283870--42284038 Score: 164
Period size: 43 Copynumber: 4.0 Consensus size: 43
42283860 CATAGGATTT
* * * *
42283870 TCGATATGTGTTTTCGTGTAAGACCACGTATGGGACGTTGGCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCA
* * * *
42283913 TCGATTTGTGTTTACGTGTAAGACCATGTCTAGGACATTGGCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCA
* * * *
42283956 TCG-TATTTGATT-CGAGTAAGACC-CTCTCTGGGACAATGGCA
1 TCGATATGTGATTACGTGTAAGACCAC-GTCTGGGACATTGGCA
* * * *
42283997 TTGATATATGATTACATGTAAGACCACGTCTGGGACGTTGGC
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACATTGGC
42284039 GTTGTACGAG
Statistics
Matches: 101, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
41 25 0.25
42 14 0.14
43 61 0.60
44 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.32
Consensus pattern (43 bp):
TCGATATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCA
Found at i:42287167 original size:26 final size:27
Alignment explanation
Indices: 42287137--42287187 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
42287127 TTGAAGAAAC
42287137 AAACTCAG-AAGC-AAAAACAGAAAATG
1 AAACT-AGCAAGCGAAAAACAGAAAATG
*
42287163 AAACTAGCAAGCGAATAACAGAAAA
1 AAACTAGCAAGCGAAAAACAGAAAA
42287188 GAGAGATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 2 0.09
26 9 0.41
27 11 0.50
ACGTcount: A:0.61, C:0.16, G:0.16, T:0.08
Consensus pattern (27 bp):
AAACTAGCAAGCGAAAAACAGAAAATG
Found at i:42291264 original size:26 final size:27
Alignment explanation
Indices: 42291234--42291284 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
42291224 TTGAAGAAAC
42291234 AAACTCAG-AAGC-AAAAACAGAAAATG
1 AAACT-AGCAAGCGAAAAACAGAAAATG
*
42291260 AAACTAGCAAGCGAATAACAGAAAA
1 AAACTAGCAAGCGAAAAACAGAAAA
42291285 GAGAGATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 2 0.09
26 9 0.41
27 11 0.50
ACGTcount: A:0.61, C:0.16, G:0.16, T:0.08
Consensus pattern (27 bp):
AAACTAGCAAGCGAAAAACAGAAAATG
Found at i:42295238 original size:14 final size:14
Alignment explanation
Indices: 42295219--42295266 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 14
42295209 AAACATATCA
42295219 TTATATTAAATTAT
1 TTATATTAAATTAT
*
42295233 TTATATATAATTTAT
1 TTATAT-TAAATTAT
42295248 CATTATATTAAATTAT
1 --TTATATTAAATTAT
42295264 TTA
1 TTA
42295267 AATATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 9 0.31
15 7 0.24
16 7 0.24
17 6 0.21
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATATTAAATTAT
Found at i:42295250 original size:31 final size:31
Alignment explanation
Indices: 42295214--42295301 Score: 133
Period size: 31 Copynumber: 2.9 Consensus size: 31
42295204 TATTTAAACA
*
42295214 TATCATTATATTAAATTATTTATATATAATT
1 TATCATTATATTAAATTATTTAAATATAATT
*
42295245 TATCATTATATTAAATTATTTAAATATTATT
1 TATCATTATATTAAATTATTTAAATATAATT
* *
42295276 TATTATTATATTTAATT-TTTAAATAT
1 TATCATTATATTAAATTATTTAAATAT
42295302 TTTATATATC
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 9 0.17
31 44 0.83
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (31 bp):
TATCATTATATTAAATTATTTAAATATAATT
Found at i:42304522 original size:23 final size:22
Alignment explanation
Indices: 42304496--42304539 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
42304486 TATCCAATGT
* *
42304496 GTGGTGATAGAGTCCACTTATAA
1 GTGGTAATAGAATCC-CTTATAA
42304519 GTGGTAATAGAATCCCTTATA
1 GTGGTAATAGAATCCCTTATA
42304540 CGTTTCATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
GTGGTAATAGAATCCCTTATAA
Found at i:42304643 original size:17 final size:16
Alignment explanation
Indices: 42304601--42304651 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
42304591 TACGATGTGG
42304601 TATGAATGAATTATTA
1 TATGAATGAATTATTA
*
42304617 TATTGAATGAATTGTTA
1 TA-TGAATGAATTATTA
* *
42304634 TTATGCATGAACTATTA
1 -TATGAATGAATTATTA
42304651 T
1 T
42304652 TTCATATGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 3 0.10
17 24 0.83
18 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (16 bp):
TATGAATGAATTATTA
Found at i:42304644 original size:34 final size:34
Alignment explanation
Indices: 42304601--42304669 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
42304591 TACGATGTGG
* *
42304601 TATGAATGAATTATTATATTGA-ATGAATTGTTAT
1 TATGAATGAACTATTAT-TTCATATGAATTGTTAT
*
42304635 TATGCATGAACTATTATTTCATATGAATTGTTAT
1 TATGAATGAACTATTATTTCATATGAATTGTTAT
42304669 T
1 T
42304670 TTATGTGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 3 0.10
34 28 0.90
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (34 bp):
TATGAATGAACTATTATTTCATATGAATTGTTAT
Found at i:42304668 original size:17 final size:17
Alignment explanation
Indices: 42304648--42304681 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42304638 GCATGAACTA
42304648 TTATTTCATATGAATTG
1 TTATTTCATATGAATTG
* *
42304665 TTATTTTATGTGAATTG
1 TTATTTCATATGAATTG
42304682 CCTATTCTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.15, T:0.56
Consensus pattern (17 bp):
TTATTTCATATGAATTG
Found at i:42323953 original size:22 final size:22
Alignment explanation
Indices: 42323925--42323969 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
42323915 GTAATGTAAG
*
42323925 TTAGCTTAGACATTTCGGTGGC
1 TTAGCTTAGACATTTCAGTGGC
42323947 TTAGCTTAGACATTTCAGTGGC
1 TTAGCTTAGACATTTCAGTGGC
42323969 T
1 T
42323970 AATATAGCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (22 bp):
TTAGCTTAGACATTTCAGTGGC
Found at i:42336029 original size:18 final size:18
Alignment explanation
Indices: 42336006--42336041 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
42335996 TTTTATTACT
*
42336006 AGTGGTTTATCCATAACG
1 AGTGGTTTATCCACAACG
42336024 AGTGGTTTATCCACAACG
1 AGTGGTTTATCCACAACG
42336042 TGATGTAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (18 bp):
AGTGGTTTATCCACAACG
Found at i:42338858 original size:15 final size:15
Alignment explanation
Indices: 42338838--42338868 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42338828 TTACATATTG
*
42338838 CTCAAAATGAAGATA
1 CTCAAAATGAAAATA
42338853 CTCAAAATGAAAATA
1 CTCAAAATGAAAATA
42338868 C
1 C
42338869 ATATCGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (15 bp):
CTCAAAATGAAAATA
Found at i:42339003 original size:19 final size:17
Alignment explanation
Indices: 42338971--42339005 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
42338961 AACACCTAAT
42338971 AGAAAATGATTAGAAAA
1 AGAAAATGATTAGAAAA
42338988 AGAAATATGAATTAGAAA
1 AGAAA-ATG-ATTAGAAA
42339006 GAGTAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (17 bp):
AGAAAATGATTAGAAAA
Found at i:42340478 original size:5 final size:5
Alignment explanation
Indices: 42340470--42340522 Score: 56
Period size: 5 Copynumber: 10.8 Consensus size: 5
42340460 AACTTTTTAT
** *
42340470 TTTTC TTTTC -TTT- TTTTC TTCCC TTTTTC TTTTC TTTTC TTTTT TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC
42340519 TTTT
1 TTTT
42340523 TCCTCGCGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 6 0.15
5 30 0.77
6 3 0.08
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:42340483 original size:11 final size:11
Alignment explanation
Indices: 42340464--42340522 Score: 61
Period size: 10 Copynumber: 5.4 Consensus size: 11
42340454 ATTTGCAACT
*
42340464 TTTTATTTTTC
1 TTTTCTTTTTC
42340475 TTTTCTTTTT-
1 TTTTCTTTTTC
42340485 TTCTTCCCTTTTTC
1 TT-TT--CTTTTTC
42340499 TTTTC-TTTTC
1 TTTTCTTTTTC
42340509 TTTT-TTTTTC
1 TTTTCTTTTTC
42340519 TTTT
1 TTTT
42340523 TCCTCGCGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
10 20 0.48
11 12 0.29
13 8 0.19
14 2 0.05
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:42340502 original size:16 final size:15
Alignment explanation
Indices: 42340480--42340520 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
42340470 TTTTCTTTTC
42340480 TTTTTTTCTTCCCTT
1 TTTTTTTCTTCCCTT
**
42340495 TTTCTTTTCTTTTCTT
1 TTT-TTTTCTTCCCTT
42340511 TTTTTTTCTT
1 TTTTTTTCTT
42340521 TTTCCTCGCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTTCTTCCCTT
Found at i:42342312 original size:16 final size:16
Alignment explanation
Indices: 42342291--42342321 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42342281 ATAATATGAA
42342291 TTATTTATTAATTTTC
1 TTATTTATTAATTTTC
*
42342307 TTATTTATTTATTTT
1 TTATTTATTAATTTT
42342322 TTTCATATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTTATTAATTTTC
Found at i:42348736 original size:31 final size:31
Alignment explanation
Indices: 42348698--42348759 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
42348688 ATGTGTAGAC
42348698 TATAAATAGTTTACTTATTCTTCTAAAAGGT
1 TATAAATAGTTTACTTATTCTTCTAAAAGGT
* *
42348729 TATAAATAGTTTATTTATTCTTGTAAAAGGT
1 TATAAATAGTTTACTTATTCTTCTAAAAGGT
42348760 CAGACATCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.47
Consensus pattern (31 bp):
TATAAATAGTTTACTTATTCTTCTAAAAGGT
Found at i:42351520 original size:14 final size:14
Alignment explanation
Indices: 42351484--42351514 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
42351474 AAAACAGATT
42351484 TAACTATACTAAAA
1 TAACTATACTAAAA
42351498 TAACTATACTAAAA
1 TAACTATACTAAAA
42351512 TAA
1 TAA
42351515 TCATACATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (14 bp):
TAACTATACTAAAA
Found at i:42355435 original size:37 final size:37
Alignment explanation
Indices: 42355385--42355459 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
42355375 AAATAGTCCT
*
42355385 TCCTAGTTACCTTAATAAGCTTGTAGTAATCCATACA
1 TCCTAGTTACCTTAATAAGCTTGAAGTAATCCATACA
*
42355422 TCCTAGTTTCCTTAATAAGCTTGAAGTAATCCATACA
1 TCCTAGTTACCTTAATAAGCTTGAAGTAATCCATACA
42355459 T
1 T
42355460 ACTCTCCATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (37 bp):
TCCTAGTTACCTTAATAAGCTTGAAGTAATCCATACA
Found at i:42366809 original size:220 final size:220
Alignment explanation
Indices: 42366428--42367091 Score: 1114
Period size: 220 Copynumber: 3.0 Consensus size: 220
42366418 TGAATAAATA
* **
42366428 AATAACTATTATTAACATGATTACAATGATTGAACC-AAGATAAAGTACATAGTAACAACAACTG
1 AATAACTATCATTAACATGATTACAATGATTGAACCAAAGATAAAGTACATAGTAACAACAAGGG
* *
42366492 TAGTTAACACATTTTCTCTTACCATACTTTCATCATTCACTTATCTTTTATACACCACTCATGTT
66 TAGTTAACACATTTTCACTTACCATACTTTCATCATTCACTTATCTTTTATACACCACTCACGTT
* *
42366557 GCCCTTTGTAGAATCAAGTGAATAAGAAGGATATATGGAATGTAATCACAGAGCACAAGAGCATG
131 GCCCCTTGTAGAATCGAGTGAATAAGAAGGATATATGGAATGTAATCACAGAGCACAAGAGCATG
42366622 TAAATGCCAAATTATCACGAACACT
196 TAAATGCCAAATTATCACGAACACT
*
42366647 AATAACTATCATTAACATGATTGCAATGATTGAACCAAAGATAAAGTACATAGTAACAACAAGGG
1 AATAACTATCATTAACATGATTACAATGATTGAACCAAAGATAAAGTACATAGTAACAACAAGGG
*
42366712 TAGTTAACACATTTTCACTTACCATACTTTCATCATTCACTTATCTTTTATACACCACTCACGCT
66 TAGTTAACACATTTTCACTTACCATACTTTCATCATTCACTTATCTTTTATACACCACTCACGTT
*
42366777 ACCCCTTGTAGAATCGAGTGAATAAGAAGGATATATGGAATGTAATCACAGAGCACAAGAGCATG
131 GCCCCTTGTAGAATCGAGTGAATAAGAAGGATATATGGAATGTAATCACAGAGCACAAGAGCATG
42366842 TAAATGCCAAATTATCACGAACACT
196 TAAATGCCAAATTATCACGAACACT
* *
42366867 AATAACTATCATTAACATGATTAAAATGATTGAACCAAAGATAAATTACATAGTAACAACAAGGG
1 AATAACTATCATTAACATGATTACAATGATTGAACCAAAGATAAAGTACATAGTAACAACAAGGG
* * * *
42366932 TAGTTAACACGTTTTCACTTACCATACTTTCATCATTCACTTAACTTTTATATACCACTCACATT
66 TAGTTAACACATTTTCACTTACCATACTTTCATCATTCACTTATCTTTTATACACCACTCACGTT
* * * * * *
42366997 GCTCCTTATCGACTCGAGTGAACAAGAAGGATATATGGAATGTAATCACAAAGCACAAGAGCATG
131 GCCCCTTGTAGAATCGAGTGAATAAGAAGGATATATGGAATGTAATCACAGAGCACAAGAGCATG
*
42367062 TAAGTGCCAAATTATCACGAACACT
196 TAAATGCCAAATTATCACGAACACT
42367087 AATAA
1 AATAA
42367092 TGTTAGAACA
Statistics
Matches: 418, Mismatches: 26, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
219 34 0.08
220 384 0.92
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.28
Consensus pattern (220 bp):
AATAACTATCATTAACATGATTACAATGATTGAACCAAAGATAAAGTACATAGTAACAACAAGGG
TAGTTAACACATTTTCACTTACCATACTTTCATCATTCACTTATCTTTTATACACCACTCACGTT
GCCCCTTGTAGAATCGAGTGAATAAGAAGGATATATGGAATGTAATCACAGAGCACAAGAGCATG
TAAATGCCAAATTATCACGAACACT
Found at i:42376019 original size:18 final size:17
Alignment explanation
Indices: 42375987--42376020 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
42375977 TCCTGGGATG
*
42375987 TTATTGCTAATATTATT
1 TTATTGCTAACATTATT
42376004 TTATTAGCTAACATTAT
1 TTATT-GCTAACATTAT
42376021 CATATAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (17 bp):
TTATTGCTAACATTATT
Found at i:42379149 original size:19 final size:19
Alignment explanation
Indices: 42379116--42379165 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
42379106 ATTAATTATT
*
42379116 TATAAAATTTAATTTGAATA
1 TATAAAATAT-ATTTGAATA
* *
42379136 TATAAATTATATTTTAATA
1 TATAAAATATATTTGAATA
*
42379155 TTTAAAATATA
1 TATAAAATATA
42379166 ATCCATAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TATAAAATATATTTGAATA
Found at i:42379230 original size:35 final size:34
Alignment explanation
Indices: 42379174--42379264 Score: 96
Period size: 33 Copynumber: 2.7 Consensus size: 34
42379164 TAATCCATAA
* * * *
42379174 AAATTTAAATATATAAT-ATTATATATTTAAAAT
1 AAATTTTAATATAAAATAATTATATACTCAAAAT
*
42379207 AAATTTTAATAGTAAAATAATTATATACTCAAGAT
1 AAATTTTAATA-TAAAATAATTATATACTCAAAAT
* *
42379242 AAATATT-ATATAAAATATTTATA
1 AAATTTTAATATAAAATAATTATA
42379265 AGGGTTAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
33 22 0.45
34 8 0.16
35 19 0.39
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (34 bp):
AAATTTTAATATAAAATAATTATATACTCAAAAT
Found at i:42379256 original size:33 final size:34
Alignment explanation
Indices: 42379181--42379264 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 34
42379171 TAAAAATTTA
* * * *
42379181 AATATATAAT-ATTATATATTTAAAATAAATTTT
1 AATATAAAATAATTATATACTCAAAATAAATATT
*
42379214 AATAGTAAAATAATTATATACTCAAGATAAATATT
1 AATA-TAAAATAATTATATACTCAAAATAAATATT
*
42379249 -ATATAAAATATTTATA
1 AATATAAAATAATTATA
42379265 AGGGTTAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
33 16 0.37
34 8 0.19
35 19 0.44
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (34 bp):
AATATAAAATAATTATATACTCAAAATAAATATT
Found at i:42380046 original size:3 final size:3
Alignment explanation
Indices: 42380038--42380079 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
42380028 ACTTACGCCC
42380038 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42380080 TTCTTTCTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:42384084 original size:41 final size:41
Alignment explanation
Indices: 42384025--42384133 Score: 184
Period size: 41 Copynumber: 2.7 Consensus size: 41
42384015 CTTTCGGGGA
*
42384025 TTTAGCGGC-ATTTTAAGAAAGCGCCGCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
42384065 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
**
42384106 TTTAGCGGCGTTTTTGGGAAAGCGCCGC
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGC
42384134 AAAACAACCT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
40 9 0.14
41 56 0.86
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:42388149 original size:114 final size:114
Alignment explanation
Indices: 42387669--42388224 Score: 638
Period size: 114 Copynumber: 4.9 Consensus size: 114
42387659 AAAATAAGCA
** * * *
42387669 TTAGCGGCGTTTTCCATAAAGCGCCGC-AAAATACCTAATCCCAACGACGCCATTTT-TCGAGCT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTCT-GAGCT
* * * * *
42387732 TTCAGGGATTTAGCGACATTTTTTAAGAAAGCGCCGCTAAAGCTCAAGGCT
65 TTCGGGGATTTAGCGAC-GTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
* * * ** * *
42387783 TTAGCGGCGTTTTTGAAAAAGCGCCACAAAAAAATGTAAGCCCAACGACGCTG-TTTCTGACCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * * *
42387847 TCGGGGATTTGGCGGCGTTTTTAAGTAAGCACCGCTAACGCTCAGGGCT
66 TCGGGGATTTAGCGACGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
* * * *
42387896 TTAGCGGCGTTTATG-GTAAAGCGCCGCAAAAAAACCTAAGCCCAGCGATGCCGTTTTCTGAGCT
1 TTAGCGGCGTTTTTGAG-AAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGC-
* *
42387960 TTTCGGGGATTTAGCGGCGTTTTT-AGTCAAGTGCCGCTAATGCTCAGGGCT
64 TTTCGGGGATTTAGCGACGTTTTTAAGT-AAGCGCCGCTAATGCTCAGGGCT
* * * * *
42388011 TTAGCGGCGTTTTTGTGAATGCGCCGCGAAAATACCTAAGCCTAACGACGCCGTTTTTTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * * * *
42388076 TTGGCGATTTAGTGACGTTTTTAAGTAAGCGCCGCTAATGCCCAGGGAT
66 TCGGGGATTTAGCGACGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
** * *
42388125 TTAGCGGCGTTCGTGAGAAAGCGCCGCAAAAATACCTAAGCCCAACAACGTCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
*
42388190 TCGGGGATTTAG-TAGCGTTTTTAAGTAAGCGCCGC
66 TCGGGGATTTAGCGA-CGTTTTTAAGTAAGCGCCGC
42388225 AAAAATACCT
Statistics
Matches: 374, Mismatches: 59, Indels: 18
0.83 0.13 0.04
Matches are distributed among these distances:
113 73 0.20
114 181 0.48
115 119 0.32
116 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.27
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGCGACGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
Found at i:42388239 original size:73 final size:73
Alignment explanation
Indices: 42388143--42388297 Score: 240
Period size: 73 Copynumber: 2.1 Consensus size: 73
42388133 GTTCGTGAGA
* * *
42388143 AAGCGCCGCAAAAATACCTAAGCCCAACAACGTCGTTTTCTGAGCTTTCGGGGATTTAGTAGCGT
1 AAGCGCCGCAAAAATACCTAAGCCCAACAACGTCGTTTTCTGAGATTTCAGGGATTTAGCAGCGT
42388208 TTTTAAGT-
66 TTTT-AGTC
* * *
42388216 AAGCGCCGCAAAAATACCTAAGCCCAACGACGTTGTTTTCTGAGATTTCAGGGATTTAGCGGCGT
1 AAGCGCCGCAAAAATACCTAAGCCCAACAACGTCGTTTTCTGAGATTTCAGGGATTTAGCAGCGT
42388281 TTTTAGTC
66 TTTTAGTC
42388289 AAGCGCCGC
1 AAGCGCCGC
42388298 TAATGCTCAG
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
72 3 0.04
73 72 0.96
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27
Consensus pattern (73 bp):
AAGCGCCGCAAAAATACCTAAGCCCAACAACGTCGTTTTCTGAGATTTCAGGGATTTAGCAGCGT
TTTTAGTC
Found at i:42388340 original size:187 final size:186
Alignment explanation
Indices: 42388017--42388533 Score: 660
Period size: 187 Copynumber: 2.8 Consensus size: 186
42388007 GGCTTTAGCG
** * * * *
42388017 GCGTTTTTGTGAATGCGCCGCGAAAATACCTAAGCCTAACGACGCCGTTTTTTGAGCTTT-TGGC
1 GCGTTTTTAAGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTTTGAGCTTTCAGG-
* * **
42388081 GATTTAGTGACGTTTTTAAGTAAGCGCCGCTAATGCCCAGGGATTTAGCGGCGTTCGTGAGAAAG
65 GATTTAGTGGCGTTTTT-AGTAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGAAAG
*
42388146 CGCCGCAAAAATACCTAAGCCCAACAACGTCGTTTTCTGAGCTTTCGGGGATTTAGTA
129 CGCCGCAAAAATACCTAAGCCCAACAACGCCGTTTTCTGAGCTTTCGGGGATTTAGTA
* ** * *
42388204 GCGTTTTTAAGTAAGCGCCGCAAAAATACCTAAGCCCAACGACGTTGTTTTCTGAGATTTCAGGG
1 GCGTTTTTAAGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTTTGAGCTTTCAGGG
* * * * * *
42388269 ATTTAGCGGCGTTTTTAGTCAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCATTTTTGGGAATGT
66 ATTTAGTGGCGTTTTTAGT-AAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGAAAGC
* * *
42388334 GCCGCAAAAATACCTAAGCCTAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTG
130 GCCGCAAAAATACCTAAGCCCAACAACGCCGTTTTCTGAGCTTTCGGGGATTTAGTA
* * *
42388391 GCGTTTTTGAGAAAGCGTCGCAAAAATACCTAAGCCCAACGACGCCGTTTTTTGAGCTTTCGGGG
1 GCGTTTTTAAGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTTTGAGCTTTC-AGG
** * * * *
42388456 GATTTAGTGGCGTTTATGGGTAAGTGCCGCTAATGTTC-GGGTTTTTAGCGGCGTTTTTGACAAA
65 GATTTAGTGGCGTTT-TTAGTAAGCGCCGCTAATGCTCAGGG-ATTTAGCGGCGTTTTTGAGAAA
42388520 GCGCCGCAAAAATA
128 GCGCCGCAAAAATA
42388534 ATTTTATCTT
Statistics
Matches: 281, Mismatches: 44, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
186 3 0.01
187 212 0.75
188 63 0.22
189 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (186 bp):
GCGTTTTTAAGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTTTGAGCTTTCAGGG
ATTTAGTGGCGTTTTTAGTAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGAAAGCG
CCGCAAAAATACCTAAGCCCAACAACGCCGTTTTCTGAGCTTTCGGGGATTTAGTA
Found at i:42390514 original size:337 final size:331
Alignment explanation
Indices: 42389987--42390969 Score: 1098
Period size: 337 Copynumber: 2.9 Consensus size: 331
42389977 GCTAATGCTT
* * * * * *
42389987 AAGCAATAGCGGCGTTTGTACAAGAAACGCCGCAAAAGTGACTTAAAATTTTGGTTGAACGACGC
1 AAGC-ATAGCGGCGTTTGTTCAAGAAACGCCGCAAAATTGTCTTAAAATTTTTGCTAAACGACGC
* ** **
42390052 CGTTTCTGTCCACGATTTTTAACTTAGCATTTTCTCTATATTAATTAAACGGCGCCGTTTAAGTT
65 CGTTTCTGTACACG-TTTTT-ACTTAGCATTTTCTCTATATTAATCCAACGGCGCCGTTTCTGTT
** * * * *
42390117 AATTTTTAGTGGCGTTTGTTCAGGAAACGCCGCAAAAGTGACTTGAAATATTGGCTAAACGTCGA
128 AATTTTTAGTGGCGTTT-TTCACAAAACGCCGCAAAAGTGACTTAAAATATTGCCTAAACGACCA
* * * * *
42390182 CGTCTAACTTAAGCAAATTAATTTCTAGTGGCGTTTTAAAGGAAAACGCCAGAAATATGCATGAA
192 CGTATAGCTTAAGCAAATTAATTTTTACTGGCGTTTTAAA-GAAAACGCCAGAAATATGCATTAA
* *
42390247 ATCTTAACAAAACGGCGCCGTTTCGGATTAGAACCTTT-ATTCTTTGTGGCGCTTCTCTAG-AAA
256 AGCTTAATAAAACGGCGCCGTTTCGGATTAGAA-CTTTAATT-TTTGTGGCGCTT-TCTAGAAAA
42390310 CGCCGTAAATACAC
318 CGCCGTAAATACAC
* * *
42390324 AAGCTATAGTGGCGTTTGTTCAATAAACGCCGCTAAATTGTCTTAAAATTTTTGCTAAACGACGC
1 AAGC-ATAGCGGCGTTTGTTCAAGAAACGCCGCAAAATTGTCTTAAAATTTTTGCTAAACGACGC
* * *
42390389 CGTCTCTGTACACGCTTTTATACTTAGCATTTTCTCTATATTAATCCAATGGCGCAGTTTCTGTT
65 CGTTTCTGTACACG-TTTT-TACTTAGCATTTTCTCTATATTAATCCAACGGCGCCGTTTCTGTT
* * * * * **
42390454 AATTTTTTGTGGCGTTTTTATACCAAACGCCGCAAAAGTGACATAAAATATTGCCTAAACGGCTT
128 AATTTTTAGTGGCGTTTTT-CACAAAACGCCGCAAAAGTGACTTAAAATATTGCCTAAACGACCA
* *
42390519 CGTTTAGCTTAAGCAAATTAATTTTTACTGGCG-TTTAATCAAAAAACGCCAGAAATATGCATTA
192 CGTATAGCTTAAGCAAATTAATTTTTACTGGCGTTTTAA--AGAAAACGCCAGAAATATGCATTA
* * * * *
42390583 CAGCTTAATAAAACGGCACCGTTTTGGATTAGAACTTTAAATTTTAGTGGCGCTTTTTAGAAAAC
255 AAGCTTAATAAAACGGCGCCGTTTCGGATTAGAACTTT-AATTTTTGTGGCGCTTTCTAGAAAAC
**
42390648 GCCGTAAATGTAC
319 GCCGTAAATACAC
* * ** * *
42390661 AAGCAGTAGCGACGTTTGTTCAGGATGCACCGCAAAATTGTCTTAAAA-TTTTGTCTAAACGATG
1 AAGCA-TAGCGGCGTTTGTTCAAGAAACGCCGCAAAATTGTCTTAAAATTTTTG-CTAAACGACG
* * *
42390725 CCGTTTCTGTACTA-GTTTTTTATCTTAGCATTTTCTCTAAATTAATCCAACGGTGCCGTTTCTC
64 CCGTTTCTGTAC-ACG-TTTTTA-CTTAGCATTTTCTCTATATTAATCCAACGGCGCCGTTTCTG
* * *
42390789 TTAATTTATAGTGGCGTTTTTGCACAAAACGCCACAAAA-TGACTTAAAATATTGTCTAAACGAC
126 TTAATTTTTAGTGGCGTTTTT-CACAAAACGCCGCAAAAGTGACTTAAAATATTGCCTAAACGAC
* * *** * * *
42390853 CCCATATAGCTTAAGCAAATTAATTTTTACTGTAATTTTTACAGAAAACGCCAGAACTGTGCATT
190 CACGTATAGCTTAAGCAAATTAATTTTTACTG-GCGTTTTAAAGAAAACGCCAGAAATATGCATT
* *
42390918 AAAGCTTAATTAAACGGCGCCGTTTCGG-TTTGAACTTTAATTTTTAGTGGCG
254 AAAGCTTAATAAAACGGCGCCGTTTCGGATTAGAACTTTAATTTTT-GTGGCG
42390970 TTTTTGCAAA
Statistics
Matches: 546, Mismatches: 86, Indels: 30
0.82 0.13 0.05
Matches are distributed among these distances:
334 6 0.01
335 15 0.03
336 117 0.21
337 398 0.73
338 10 0.02
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (331 bp):
AAGCATAGCGGCGTTTGTTCAAGAAACGCCGCAAAATTGTCTTAAAATTTTTGCTAAACGACGCC
GTTTCTGTACACGTTTTTACTTAGCATTTTCTCTATATTAATCCAACGGCGCCGTTTCTGTTAAT
TTTTAGTGGCGTTTTTCACAAAACGCCGCAAAAGTGACTTAAAATATTGCCTAAACGACCACGTA
TAGCTTAAGCAAATTAATTTTTACTGGCGTTTTAAAGAAAACGCCAGAAATATGCATTAAAGCTT
AATAAAACGGCGCCGTTTCGGATTAGAACTTTAATTTTTGTGGCGCTTTCTAGAAAACGCCGTAA
ATACAC
Found at i:42391132 original size:14 final size:13
Alignment explanation
Indices: 42391094--42391145 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 13
42391084 GAAACAGAAC
*
42391094 AAAGGAGAAAACG
1 AAAGGAAAAAACG
*
42391107 AAATGGGTAAAAACG
1 AAA--GGAAAAAACG
42391122 AAAGAGAAAAAACG
1 AAAG-GAAAAAACG
42391136 -AAGGAAAAAA
1 AAAGGAAAAAA
42391146 GGGAGAGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 7 0.21
13 7 0.21
14 8 0.24
15 11 0.33
ACGTcount: A:0.65, C:0.06, G:0.25, T:0.04
Consensus pattern (13 bp):
AAAGGAAAAAACG
Found at i:42392382 original size:15 final size:16
Alignment explanation
Indices: 42392354--42392386 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42392344 TAACTTACAT
42392354 ATTTATATACATTTTTA
1 ATTTATATA-ATTTTTA
42392371 ATTTATAT-ATTTTTA
1 ATTTATATAATTTTTA
42392386 A
1 A
42392387 AATCTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATATAATTTTTA
Found at i:42392394 original size:17 final size:18
Alignment explanation
Indices: 42392374--42392407 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
42392364 ATTTTTAATT
42392374 TATATATTTTT-AAAATC
1 TATATATTTTTCAAAATC
*
42392391 TATATTTTTTTCAAAAT
1 TATATATTTTTCAAAAT
42392408 TTATCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATTTTTCAAAATC
Found at i:42392537 original size:9 final size:9
Alignment explanation
Indices: 42392511--42392895 Score: 421
Period size: 9 Copynumber: 44.4 Consensus size: 9
42392501 TAATAACATA
*
42392511 ATAACTAAC
1 ATAACTTAC
42392520 AT-AC-TAC
1 ATAACTTAC
*
42392527 ATAACCTAC
1 ATAACTTAC
42392536 ATAACTTAC
1 ATAACTTAC
42392545 ATAACTTAC
1 ATAACTTAC
* *
42392554 ATAAATTAA
1 ATAACTTAC
42392563 ATAACTTAC
1 ATAACTTAC
42392572 ATAACTTAC
1 ATAACTTAC
*
42392581 ATAACTTAA
1 ATAACTTAC
42392590 ATAACTTAC
1 ATAACTTAC
42392599 ATAA--TAC
1 ATAACTTAC
*
42392606 ATAACCTTTC
1 ATAA-CTTAC
42392616 -TAACTTAC
1 ATAACTTAC
42392624 ATAACTTAC
1 ATAACTTAC
42392633 ATAACTTAC
1 ATAACTTAC
42392642 ATAACTTAC
1 ATAACTTAC
42392651 ATAACTTAC
1 ATAACTTAC
* *
42392660 ATAAATTAA
1 ATAACTTAC
42392669 ATAACTTAC
1 ATAACTTAC
42392678 ATAACTTAC
1 ATAACTTAC
* *
42392687 ATAAATTAA
1 ATAACTTAC
42392696 ATAACTTAC
1 ATAACTTAC
42392705 ATAACTTAC
1 ATAACTTAC
42392714 ATAACTTAC
1 ATAACTTAC
*
42392723 ATAACTTAA
1 ATAACTTAC
42392732 ATAACTTAC
1 ATAACTTAC
*
42392741 ATAACTTAA
1 ATAACTTAC
42392750 ATAACTTAC
1 ATAACTTAC
42392759 ATAA--TAC
1 ATAACTTAC
42392766 ATAACCTT-C
1 ATAA-CTTAC
*
42392775 TTAACTTAC
1 ATAACTTAC
*
42392784 ATTA--TAC
1 ATAACTTAC
* *
42392791 ACAACGTAC
1 ATAACTTAC
42392800 ATAA--TAC
1 ATAACTTAC
*
42392807 ATTACTTAC
1 ATAACTTAC
*
42392816 ATTACTTAC
1 ATAACTTAC
42392825 AGTAA--TAC
1 A-TAACTTAC
*
42392833 ATTACTTAC
1 ATAACTTAC
*
42392842 ATTACTTAC
1 ATAACTTAC
42392851 AGT-ACTTAC
1 A-TAACTTAC
42392860 ATAA--TAC
1 ATAACTTAC
42392867 ATAA--TAC
1 ATAACTTAC
42392874 ATAACTTAC
1 ATAACTTAC
42392883 ATAACTTAC
1 ATAACTTAC
42392892 ATAA
1 ATAA
42392896 TACATAAAAA
Statistics
Matches: 324, Mismatches: 31, Indels: 42
0.82 0.08 0.11
Matches are distributed among these distances:
7 45 0.14
8 16 0.05
9 257 0.79
10 6 0.02
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.33
Consensus pattern (9 bp):
ATAACTTAC
Found at i:42392833 original size:26 final size:26
Alignment explanation
Indices: 42392797--42392854 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
42392787 ATACACAACG
42392797 TACA-TAATACATTACTTACATTACT
1 TACAGTAATACATTACTTACATTACT
42392822 TACAGTAATACATTACTTACATTACT
1 TACAGTAATACATTACTTACATTACT
42392848 TACAGTA
1 TACAGTA
42392855 CTTACATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.12
26 28 0.88
ACGTcount: A:0.40, C:0.19, G:0.03, T:0.38
Consensus pattern (26 bp):
TACAGTAATACATTACTTACATTACT
Found at i:42392869 original size:7 final size:7
Alignment explanation
Indices: 42392857--42392902 Score: 56
Period size: 7 Copynumber: 6.0 Consensus size: 7
42392847 TTACAGTACT
42392857 TACATAA
1 TACATAA
42392864 TACATAA
1 TACATAA
42392871 TACATAA
1 TACATAA
42392878 CTTACATAA
1 --TACATAA
42392887 CTTACATAA
1 --TACATAA
42392896 TACATAA
1 TACATAA
42392903 AAATATATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 21 0.57
9 16 0.43
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.30
Consensus pattern (7 bp):
TACATAA
Found at i:42398427 original size:21 final size:21
Alignment explanation
Indices: 42398392--42398465 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
42398382 CTACAACTTA
** *
42398392 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGTTGCAGCGAGAG
*
42398413 AAGTAGAGGTTGCAGCGAGAG
1 AAGCAGAGGTTGCAGCGAGAG
* * *
42398434 AAGCAGAGGCTACAACGAGAG
1 AAGCAGAGGTTGCAGCGAGAG
42398455 AAGCAGAGGTT
1 AAGCAGAGGTT
42398466 CAAAAGAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.35, C:0.15, G:0.42, T:0.08
Consensus pattern (21 bp):
AAGCAGAGGTTGCAGCGAGAG
Found at i:42398897 original size:43 final size:44
Alignment explanation
Indices: 42398849--42398965 Score: 107
Period size: 43 Copynumber: 2.7 Consensus size: 44
42398839 GTTTTTTATA
* * *
42398849 AAAGCGCCGCTAAA-AGTCATGTTC-TATAGCGGCGTTTGTGAAG
1 AAAGCGCCGCTAAAGA-ACATGATCTTATAGCGACGTTTGTGAAG
* ****
42398892 AAAGCGCCGGTAAAGAACATGATCTTATAGCGACGTTTGTCTTC
1 AAAGCGCCGCTAAAGAACATGATCTTATAGCGACGTTTGTGAAG
* *
42398936 AAA-CACCACTAAAGAACATGATCTT-TAGCG
1 AAAGCGCCGCTAAAGAACATGATCTTATAGCG
42398966 GCGACTTTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
42 5 0.08
43 38 0.62
44 18 0.30
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (44 bp):
AAAGCGCCGCTAAAGAACATGATCTTATAGCGACGTTTGTGAAG
Found at i:42398980 original size:42 final size:40
Alignment explanation
Indices: 42398902--42399017 Score: 142
Period size: 42 Copynumber: 2.8 Consensus size: 40
42398892 AAAGCGCCGG
*
42398902 TAAAGAACATGATCTTATAGCGACGTTTGTCTTCAAACACCAC
1 TAAAGAACATGATCTT-TAGCGGCGTTT-T-TTCAAACACCAC
* *
42398945 TAAAGAACATGATCTTTAGCGGCGACTTTTTTCAAACGCCGC
1 TAAAGAACATGATCTTTAGCGGCG--TTTTTTCAAACACCAC
* *
42398987 TAAAGACCATGATCTTTAGTGGCGTTTTTTC
1 TAAAGAACATGATCTTTAGCGGCGTTTTTTC
42399018 TAAGCGCCGC
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
40 7 0.11
42 39 0.59
43 17 0.26
44 3 0.05
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (40 bp):
TAAAGAACATGATCTTTAGCGGCGTTTTTTCAAACACCAC
Found at i:42405877 original size:18 final size:18
Alignment explanation
Indices: 42405854--42405888 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42405844 CTCTCGTCTT
* *
42405854 CTAAGGGGAAGTAGAAAG
1 CTAAGGGAAAGAAGAAAG
42405872 CTAAGGGAAAGAAGAAA
1 CTAAGGGAAAGAAGAAA
42405889 CTGACTAAGT
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:0.51, C:0.06, G:0.34, T:0.09
Consensus pattern (18 bp):
CTAAGGGAAAGAAGAAAG
Found at i:42410946 original size:10 final size:10
Alignment explanation
Indices: 42410931--42410959 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
42410921 GAATTTTTTG
42410931 ATGATATAAT
1 ATGATATAAT
42410941 ATGATATAAT
1 ATGATATAAT
42410951 A-GATATAAT
1 ATGATATAAT
42410960 TGTTTATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (10 bp):
ATGATATAAT
Found at i:42411243 original size:37 final size:37
Alignment explanation
Indices: 42411202--42411273 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
42411192 TCGGAGTAAT
*
42411202 TGGCATGATATCGGGTGGATTAGCTCTTATGAGCATC
1 TGGCATGATATCGGGTGGATTAGCTCTTACGAGCATC
* *
42411239 TGGCATGTTATTGGGTGGATTAGCTCTTACGAGCA
1 TGGCATGATATCGGGTGGATTAGCTCTTACGAGCA
42411274 ATTGGTGTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.33
Consensus pattern (37 bp):
TGGCATGATATCGGGTGGATTAGCTCTTACGAGCATC
Found at i:42413475 original size:45 final size:45
Alignment explanation
Indices: 42413411--42413708 Score: 361
Period size: 45 Copynumber: 6.6 Consensus size: 45
42413401 ACACAATCCA
*
42413411 CATGTATGAGTTCGCCATATCTATGAATTTTCTAT-TATGAATCTG
1 CATGTATGAGTTCGCCATATCTATGAATCTTCT-TCTATGAATCTG
*
42413456 CATGTATGATTTCGCCATATCTATGAATCTTCTTCTATGAATCTG
1 CATGTATGAGTTCGCCATATCTATGAATCTTCTTCTATGAATCTG
* * *
42413501 TAT-TATGAGTTCACCATATCTATGAATCTTCTTCTATGAATCCG
1 CATGTATGAGTTCGCCATATCTATGAATCTTCTTCTATGAATCTG
* **** * *
42413545 CATGTATGAATTTATGATATCTATGAATCTTCTACTATGAATTTG
1 CATGTATGAGTTCGCCATATCTATGAATCTTCTTCTATGAATCTG
* * *
42413590 CATGTATGAGTTCGCCATATTTATGAATATTCTTATATGAATCTG
1 CATGTATGAGTTCGCCATATCTATGAATCTTCTTCTATGAATCTG
* *
42413635 CATGTATGAGTTTGCTATATCTATGAATCTTCTAT-TATGAAT-TCG
1 CATGTATGAGTTCGCCATATCTATGAATCTTCT-TCTATGAATCT-G
* * *
42413680 CATCTATGAATTAGCCATATCTATGAATC
1 CATGTATGAGTTCGCCATATCTATGAATC
42413709 CACTTCTACA
Statistics
Matches: 217, Mismatches: 32, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
44 42 0.19
45 174 0.80
46 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (45 bp):
CATGTATGAGTTCGCCATATCTATGAATCTTCTTCTATGAATCTG
Found at i:42413767 original size:42 final size:44
Alignment explanation
Indices: 42413674--42413778 Score: 108
Period size: 42 Copynumber: 2.4 Consensus size: 44
42413664 TTCTATTATG
* * *
42413674 AATTCGCATCTATGAATTAGCCATATCTATGAATCCACTTCTACA
1 AATTCGCATGTATGAGTTAGCCATA-CTAAGAATCCACTTCTACA
* *
42413719 AGTTCGCATGTATGAGTTAG-CATA-TAAGAATCCACATT-TAGA
1 AATTCGCATGTATGAGTTAGCCATACTAAGAATCCAC-TTCTACA
* *
42413761 AATTCGCACGTAAGAGTT
1 AATTCGCATGTATGAGTT
42413779 TGTAGGAATG
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 28 0.55
43 2 0.04
44 4 0.08
45 17 0.33
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31
Consensus pattern (44 bp):
AATTCGCATGTATGAGTTAGCCATACTAAGAATCCACTTCTACA
Found at i:42415695 original size:30 final size:29
Alignment explanation
Indices: 42415656--42415722 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
42415646 ACCAAAAAAA
42415656 GCCACTTTTTTTAAAAAATTACCGAAATGG
1 GCCA-TTTTTTTAAAAAATTACCGAAATGG
* ** * *
42415686 GCCAGTTTTTTAATTATTTACCGGAATGG
1 GCCATTTTTTTAAAAAATTACCGAAATGG
42415715 GCCATTTT
1 GCCATTTT
42415723 CCCCGAAATC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (29 bp):
GCCATTTTTTTAAAAAATTACCGAAATGG
Found at i:42416323 original size:124 final size:123
Alignment explanation
Indices: 42416101--42416355 Score: 368
Period size: 125 Copynumber: 2.1 Consensus size: 123
42416091 AAATAGTGGG
** * * * *
42416101 AAATCGCTTCTACCAGGATGCTATTTGAGAAAAATTGTGAAATAGTGGCCTCGTGGACGCGATTT
1 AAATCGCTGATACCAGGATGCTATATGAGAAAAATTGTGAAATAGCGCCCTCGTGGACGCGATAT
* *
42416166 CGCTACAGTGGTCATGTAAGAAATAATTTTTTTTTGACTTTTACTGAGCAAATAGTATA
66 CGCTACAGTGGTCATGTAAGAAATAATATTTTTTTGACGTTT-CTGAGCAAATAGTATA
*
42416225 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATA
1 AAATCGCTGATACCAGGATGCTATATGAGAA-AAATTGTGAAATAGCGCCCTCGTGGACGCGATA
* * *
42416290 TCGCTACAGTTGGTCATGTAGGAAATAA-ATTTTTTTGACGTTTCTGAGCAAATAGTGTC
65 TCGCTACAG-TGGTCATGTAAGAAATAATATTTTTTTGACGTTTCTGAGCAAATAGTATA
42416349 AAATCGC
1 AAATCGC
42416356 GCCCTCGTGG
Statistics
Matches: 117, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
124 49 0.42
125 51 0.44
126 17 0.15
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (123 bp):
AAATCGCTGATACCAGGATGCTATATGAGAAAAATTGTGAAATAGCGCCCTCGTGGACGCGATAT
CGCTACAGTGGTCATGTAAGAAATAATATTTTTTTGACGTTTCTGAGCAAATAGTATA
Found at i:42419624 original size:14 final size:15
Alignment explanation
Indices: 42419607--42419640 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
42419597 AATAAATATC
42419607 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
42419621 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
42419636 TAAAA
1 TAAAA
42419641 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:42419902 original size:22 final size:22
Alignment explanation
Indices: 42419877--42419946 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
42419867 ATTTGAGAGT
* *
42419877 TTGAGAGAATTTTGGAAGAAAA
1 TTGAGAGAATTTTTGAAGGAAA
*
42419899 TTGAGAGAATTTTTGAAGGGAA
1 TTGAGAGAATTTTTGAAGGAAA
42419921 TTGAGAGAATTTTTGAAGGAAA
1 TTGAGAGAATTTTTGAAGGAAA
42419943 TTGA
1 TTGA
42419947 TATTGAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (22 bp):
TTGAGAGAATTTTTGAAGGAAA
Found at i:42420079 original size:11 final size:11
Alignment explanation
Indices: 42420063--42420093 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
42420053 TGTTCACGCG
42420063 CGCGACCACAT
1 CGCGACCACAT
42420074 CGCGACCACAT
1 CGCGACCACAT
*
42420085 CGCGTCCAC
1 CGCGACCAC
42420094 GTCAGCGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.48, G:0.19, T:0.10
Consensus pattern (11 bp):
CGCGACCACAT
Found at i:42423399 original size:3 final size:3
Alignment explanation
Indices: 42423391--42423431 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
42423381 TGCTTTACCT
42423391 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42423432 GTACTTCAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:42438177 original size:54 final size:54
Alignment explanation
Indices: 42438119--42438232 Score: 165
Period size: 54 Copynumber: 2.1 Consensus size: 54
42438109 GATTATGGAC
** * * * *
42438119 ATCTTGTAAGTATAAGGCTGTTATCTTAAATCGGTGAGCTGCAAGATTTTAAAA
1 ATCTTGTAAGTATAAGGCTGGGATCTTAAATCAGTAAACTGCAAGATTTGAAAA
*
42438173 ATCTTGTAAGTATAAGGTTGGGATCTTAAATCAGTAAACTGCAAGATTTGAAAA
1 ATCTTGTAAGTATAAGGCTGGGATCTTAAATCAGTAAACTGCAAGATTTGAAAA
42438227 ATCTTG
1 ATCTTG
42438233 CAATCTTAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (54 bp):
ATCTTGTAAGTATAAGGCTGGGATCTTAAATCAGTAAACTGCAAGATTTGAAAA
Found at i:42438320 original size:54 final size:54
Alignment explanation
Indices: 42438235--42438656 Score: 342
Period size: 54 Copynumber: 7.8 Consensus size: 54
42438225 AAATCTTGCA
* * *
42438235 ATCTTAAATTGGCGAGCCGCAATATTCGAAAAATCTTGTAAGTATAAGGCTGCG
1 ATCTTAAATCGGCGAGCCACAAGATTCGAAAAATCTTGTAAGTATAAGGCTGCG
* * * * * * *
42438289 ATATTAAATTGGCGAGTCACAAGATTTGAAAAATCCTATAAGTATAAGGCTACG
1 ATCTTAAATCGGCGAGCCACAAGATTCGAAAAATCTTGTAAGTATAAGGCTGCG
* * * * * * * *
42438343 A-CTTAAATCAGTGAGCCGCAAGACTCAAAAAATCTTGTAAGTATAAGGTTACA
1 ATCTTAAATCGGCGAGCCACAAGATTCGAAAAATCTTGTAAGTATAAGGCTGCG
* * * * ** * * * * *
42438396 ATCTTAAACCAGCAAACTGCAATATTAGGAAGATCTTATAAGTATAAGGCTGCG
1 ATCTTAAATCGGCGAGCCACAAGATTCGAAAAATCTTGTAAGTATAAGGCTGCG
* * * * ** **
42438450 ATCTTAAATCGACGAGTCACAAGATTCGAAAGATCTTGTAAATATAAGATTATG
1 ATCTTAAATCGGCGAGCCACAAGATTCGAAAAATCTTGTAAGTATAAGGCTGCG
* ** * * *
42438504 ATCTTAAATCAGTAAACCATAAGATTCAAAAAAATCTTGTAAGTATAAGGCTGCG
1 ATCTTAAATCGGCGAGCCACAAGATTC-GAAAAATCTTGTAAGTATAAGGCTGCG
* * * * * * *
42438559 ATCTTAAATCGACAAACCACAAGATTTGGAAAATCTTATAAGTATAAGGCTGCA
1 ATCTTAAATCGGCGAGCCACAAGATTCGAAAAATCTTGTAAGTATAAGGCTGCG
* ***
42438613 ATCTTAAATCGGCAAGCTGTAAGATTCGAAAAATCTTGTAAGTA
1 ATCTTAAATCGGCGAGCCACAAGATTCGAAAAATCTTGTAAGTA
42438657 GTGAATTGAG
Statistics
Matches: 282, Mismatches: 84, Indels: 4
0.76 0.23 0.01
Matches are distributed among these distances:
53 40 0.14
54 200 0.71
55 42 0.15
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (54 bp):
ATCTTAAATCGGCGAGCCACAAGATTCGAAAAATCTTGTAAGTATAAGGCTGCG
Found at i:42438619 original size:109 final size:108
Alignment explanation
Indices: 42438428--42438656 Score: 271
Period size: 109 Copynumber: 2.1 Consensus size: 108
42438418 TATTAGGAAG
* * ** *
42438428 ATCTTATAAGTATAAGGCTGCGATCTTAAATCGACGAGTCACAAGATTCGAAAGATCTTGTAAAT
1 ATCTTGTAAGTATAAGGCTGCGATCTTAAATCGACAAACCACAAGATTCGAAAGATCTTATAAAT
* ** *
42438493 ATAAGATTATGATCTTAAATCAGTAAACCATAAGATTCAAAAAA
66 ATAAGACTACAATCTTAAATCAGCAAACCATAAGATTC-AAAAA
* *
42438537 ATCTTGTAAGTATAAGGCTGCGATCTTAAATCGACAAACCACAAGATTTGGAAA-ATCTTATAAG
1 ATCTTGTAAGTATAAGGCTGCGATCTTAAATCGACAAACCACAAGA-TTCGAAAGATCTTATAAA
* * * * ** *
42438601 TATAAGGCTGCAATCTTAAATCGGCAAGCTGTAAGATTCGAAAA
65 TATAAGACTACAATCTTAAATCAGCAAACCATAAGATTCAAAAA
42438645 ATCTTGTAAGTA
1 ATCTTGTAAGTA
42438657 GTGAATTGAG
Statistics
Matches: 101, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
108 16 0.16
109 79 0.78
110 6 0.06
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (108 bp):
ATCTTGTAAGTATAAGGCTGCGATCTTAAATCGACAAACCACAAGATTCGAAAGATCTTATAAAT
ATAAGACTACAATCTTAAATCAGCAAACCATAAGATTCAAAAA
Found at i:42438639 original size:163 final size:161
Alignment explanation
Indices: 42438264--42438653 Score: 460
Period size: 163 Copynumber: 2.4 Consensus size: 161
42438254 CAATATTCGA
* * * * * *
42438264 AAAATCTTGTAAGTATAAGGCTGCGATATTAAATTGGCGAGTCACAAGATTTGAAAAATCCTATA
1 AAAATCTTATAAGTATAAGGCTGCGATCTTAAATCGGCGAGTCACAAGATTCGAAAAATCTTGTA
* * * * * *
42438329 AGTATAAGGCTACGACTTAAATCAGTGAGCCGCAAGACTCAAAAAATCTTGTAAGTATAAGGTTA
66 AATATAAGACTACGACTTAAATCAGTAAACCACAAGACTCAAAAAATCTTGTAAGTATAAGGCTA
** *
42438394 CAATCTTAAACCAGCAAACTGCAATATTAGG
131 CAATCTTAAACCAGCAAACCACAAGATTAGG
* * *
42438425 AAGATCTTATAAGTATAAGGCTGCGATCTTAAATCGACGAGTCACAAGATTCGAAAGATCTTGTA
1 AAAATCTTATAAGTATAAGGCTGCGATCTTAAATCGGCGAGTCACAAGATTCGAAAAATCTTGTA
* * * *
42438490 AATATAAGATTATGATCTTAAATCAGTAAACCATAAGATTCAAAAAAATCTTGTAAGTATAAGGC
66 AATATAAGACTACGA-CTTAAATCAGTAAACCACAAGACTC-AAAAAATCTTGTAAGTATAAGGC
* * * *
42438555 TGCGATCTTAAATC-GACAAACCACAAGATTTGG
129 TACAATCTTAAACCAG-CAAACCACAAGATTAGG
* * **
42438588 AAAATCTTATAAGTATAAGGCTGCAATCTTAAATCGGCAAG-CTGTAAGATTCGAAAAATCTTGT
1 AAAATCTTATAAGTATAAGGCTGCGATCTTAAATCGGCGAGTC-ACAAGATTCGAAAAATCTTGT
42438652 AA
65 AA
42438654 GTAGTGAATT
Statistics
Matches: 192, Mismatches: 33, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
161 67 0.35
162 22 0.11
163 103 0.54
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (161 bp):
AAAATCTTATAAGTATAAGGCTGCGATCTTAAATCGGCGAGTCACAAGATTCGAAAAATCTTGTA
AATATAAGACTACGACTTAAATCAGTAAACCACAAGACTCAAAAAATCTTGTAAGTATAAGGCTA
CAATCTTAAACCAGCAAACCACAAGATTAGG
Found at i:42438908 original size:21 final size:21
Alignment explanation
Indices: 42438884--42438946 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
42438874 AAGCAAGCTT
42438884 GATATATTAAATCAAGTTTTG
1 GATATATTAAATCAAGTTTTG
* * *
42438905 GATACA-TAAGT-AAG-CTT-
1 GATATATTAAATCAAGTTTTG
42438922 GATATATTAAATCAAGTTTTG
1 GATATATTAAATCAAGTTTTG
42438943 GATA
1 GATA
42438947 CATACCTTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 5 0.16
18 6 0.19
19 6 0.19
20 6 0.19
21 9 0.28
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (21 bp):
GATATATTAAATCAAGTTTTG
Found at i:42438929 original size:38 final size:38
Alignment explanation
Indices: 42438878--42438950 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
42438868 AACAAAAAGC
42438878 AAGCTTGATATATTAAATCAAGTTTTGGATACATAAGT
1 AAGCTTGATATATTAAATCAAGTTTTGGATACATAAGT
42438916 AAGCTTGATATATTAAATCAAGTTTTGGATACATA
1 AAGCTTGATATATTAAATCAAGTTTTGGATACATA
42438951 CCTTCTCGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (38 bp):
AAGCTTGATATATTAAATCAAGTTTTGGATACATAAGT
Found at i:42452672 original size:19 final size:19
Alignment explanation
Indices: 42452637--42452687 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
42452627 GATATAGATG
42452637 AATT-AAAATATAATAAT-T
1 AATTAAAAAT-TAATAATAT
*
42452655 CAATTAAAAATTATTAATAT
1 -AATTAAAAATTAATAATAT
42452675 AATATAAAAATTA
1 AAT-TAAAAATTA
42452688 GTGGCATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AATTAAAAATTAATAATAT
Found at i:42457794 original size:85 final size:85
Alignment explanation
Indices: 42457638--42457798 Score: 207
Period size: 85 Copynumber: 1.9 Consensus size: 85
42457628 AGATAAAAAC
* * * * * *
42457638 ATTTGCAGTTATTACCACTTGTTGTGAGTGCACAACATGGTTGTAGATTAAACAAACTACCACTG
1 ATTTACAGTTACTACCACTTATTGTGAGTGCACAACATGATTGCAGATGAAACAAACTACCACTG
42457703 GGTTTGTGGACAAGCCACAT
66 GGTTTGTGGACAAGCCACAT
* * * *
42457723 ATTTACAGTTACTGCCACTTATTGTGAGTGCACAACAT-ATTCGCATATGAAACAAACTGCCATT
1 ATTTACAGTTACTACCACTTATTGTGAGTGCACAACATGATT-GCAGATGAAACAAACTACCACT
*
42457787 GGTTTTGTGGAC
65 GGGTTTGTGGAC
42457799 GAGCTACCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
84 2 0.03
85 62 0.97
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (85 bp):
ATTTACAGTTACTACCACTTATTGTGAGTGCACAACATGATTGCAGATGAAACAAACTACCACTG
GGTTTGTGGACAAGCCACAT
Found at i:42458662 original size:521 final size:518
Alignment explanation
Indices: 42457684--42458727 Score: 1579
Period size: 521 Copynumber: 2.0 Consensus size: 518
42457674 ATGGTTGTAG
*
42457684 ATTAAACAAACTACCACTGGGTTTGTGGACAAGCCACATATTTACAGTTACTGCCACTTATTGTG
1 ATTAAACAAACTACCACTGGGTTTGTGGACAAGCCACATATTTACAGTTACTACCACTTATTGTG
* * *
42457749 AGTGCACAACATATTCGCATATGAAACAAACTGCCATTGGTTTTGTGGACGAGCTACCACTTATT
66 AGTGCACAACATATTCGCAAATGAAACAAACTGCCACTGGTTTTGTGGACGAGCCACCACTTATT
* * * * *
42457814 TGTAGATATAATAAACTGTCACTCTTCCTTCGTACAATGTCTCATCCCATGCAATGCACTATGTC
131 TGTAGATATAATAAACTGTCACTCTTCCTTCATACAATGTCCCACCCCATGCAATACACTATATC
*
42457879 ATGCTATGTAACAAATAAACACTAGTACTAGATATGTAACATGTACTCAATTCACTAACACTTAA
196 ATACTATGTAACAAATAAACACTAGTACTAGATATGTAACATGTACTCAATTCACTAACACTTAA
* * * * *
42457944 CATATATTTCATGTTCTTCGCAGGGCGGTAATAATATTATCACTTTCAATTTAATAGTTTCACTT
261 CATATATTTCATGTTCTTCGCACGACGGTAACAATATTATCACTTTAAATTTAACAGTTTCACTT
* * ** *
42458009 TATTAGAAAACACATAACGTTTATGTATCATGCGAAGTAATAAGGGCATTTAAGGCATTAAACAC
326 TATCAGAAAACACATAACGTTCACATATCATGCGAAGTAATAAGGGCACTTAAGGCATTAAACAC
*
42458074 AAATTTCAAAATTCACCCAATATCAGGGACCTAACTGAGCAAGGATAAACTGTAAAAATAATTTA
391 AAATTTCAAAATTCACCCAATATCAGGGACCTAACTGAGCAAAGATAAACTGTAAAAATAATTTA
* * * *
42458139 GGGAATGTACAGGGATTAAACTGAACATTTCATACTTCTACATAATATTAGTAATTTCAATCA
456 GGGAATGTACAAGGATTAAACTGAACACTTCATAATTCTACATAATATTAATAATTTCAATCA
* **
42458202 ATTAAACAAACTACCACT-GGTTTGTGGACGAGCCACATATTTGTAGTTACTACCACTTATTGTG
1 ATTAAACAAACTACCACTGGGTTTGTGGACAAGCCACATATTTACAGTTACTACCACTTATTGTG
* * *
42458266 AGTGCACAACATATTCGCAAATTAAACAAACTGCCACTGGATTTTGTGGATGAGCCACCACTTGT
66 AGTGCACAACATATTCGCAAATGAAACAAACTGCCACTGG-TTTTGTGGACGAGCCACCACTTAT
*
42458331 TTGTAGATTTAATAAACTGTCACTCTTCCTTCATACAATGTCCCACCCCATGCAATACACTATAT
130 TTGTAGATATAATAAACTGTCACTCTTCCTTCATACAATGTCCCACCCCATGCAATACACTATAT
* * * *
42458396 CATACTATGTAAGAAATCATCACTAGTAGTAGATATGTAACATGTACTCAATTTATCACTAACAC
195 CATACTATGTAACAAATAAACACTAGTACTAGATATGTAACATGTACTCAA--T-TCACTAACAC
* *
42458461 TTAACATGGT-TTTCATGTTCTTCGCACGACGGTAACAATATTATCACTTTAAATTTAACATTTT
257 TTAACAT-ATATTTCATGTTCTTCGCACGACGGTAACAATATTATCACTTTAAATTTAACAGTTT
* *
42458525 CACTTTATCAGAAAACACATAATGTTCACATATCATGCGATGTAATAAGGGCACTTAAGGCATTA
321 CACTTTATCAGAAAACACATAACGTTCACATATCATGCGAAGTAATAAGGGCACTTAAGGCATTA
* * ** * *
42458590 AACCCAAATTTCATAATTCACCCAATATCAGGGATTTAACTGAGTAAAGATAAACTTTAAAAATA
386 AACACAAATTTCAAAATTCACCCAATATCAGGGACCTAACTGAGCAAAGATAAACTGTAAAAATA
* * * *
42458655 ATTTAGGGAATGTATAAGGATTAAATTGAACACTTCATAATTTTACATATTATTAATAATTTCAA
451 ATTTAGGGAATGTACAAGGATTAAACTGAACACTTCATAATTCTACATAATATTAATAATTTCAA
42458720 TCA
516 TCA
42458723 ATTAA
1 ATTAA
42458728 TCATTTATTC
Statistics
Matches: 471, Mismatches: 50, Indels: 7
0.89 0.09 0.01
Matches are distributed among these distances:
517 79 0.17
518 144 0.31
520 1 0.00
521 246 0.52
522 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (518 bp):
ATTAAACAAACTACCACTGGGTTTGTGGACAAGCCACATATTTACAGTTACTACCACTTATTGTG
AGTGCACAACATATTCGCAAATGAAACAAACTGCCACTGGTTTTGTGGACGAGCCACCACTTATT
TGTAGATATAATAAACTGTCACTCTTCCTTCATACAATGTCCCACCCCATGCAATACACTATATC
ATACTATGTAACAAATAAACACTAGTACTAGATATGTAACATGTACTCAATTCACTAACACTTAA
CATATATTTCATGTTCTTCGCACGACGGTAACAATATTATCACTTTAAATTTAACAGTTTCACTT
TATCAGAAAACACATAACGTTCACATATCATGCGAAGTAATAAGGGCACTTAAGGCATTAAACAC
AAATTTCAAAATTCACCCAATATCAGGGACCTAACTGAGCAAAGATAAACTGTAAAAATAATTTA
GGGAATGTACAAGGATTAAACTGAACACTTCATAATTCTACATAATATTAATAATTTCAATCA
Found at i:42462204 original size:18 final size:17
Alignment explanation
Indices: 42462174--42462207 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
42462164 GAATTAATAC
42462174 CAATTTTCAAGAAAAGT
1 CAATTTTCAAGAAAAGT
*
42462191 CAATATTTCGAGAAAAG
1 CAAT-TTTCAAGAAAAG
42462208 CCGACAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (17 bp):
CAATTTTCAAGAAAAGT
Found at i:42474721 original size:19 final size:20
Alignment explanation
Indices: 42474699--42474751 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
42474689 AAAAGGGAGG
* **
42474699 AAATCAGTGTAAAGTG-GGA
1 AAATCAGTGTAAAGAGAAAA
42474718 AAATCAGTGTAAAGAGAAAA
1 AAATCAGTGTAAAGAGAAAA
42474738 AAATCAGTGTAAAG
1 AAATCAGTGTAAAG
42474752 GGAGGAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.51, C:0.06, G:0.25, T:0.19
Consensus pattern (20 bp):
AAATCAGTGTAAAGAGAAAA
Found at i:42474760 original size:20 final size:20
Alignment explanation
Indices: 42474690--42474760 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
42474680 CATTCATAAA
42474690 AAAGGGAGG-AAATCAGTGT
1 AAAGGGAGGAAAATCAGTGT
*
42474709 AAAGTG-GGAAAATCAGTGT
1 AAAGGGAGGAAAATCAGTGT
* **
42474728 AAAGAGAAAAAAATCAGTGT
1 AAAGGGAGGAAAATCAGTGT
42474748 AAAGGGAGGAAAA
1 AAAGGGAGGAAAA
42474761 AAGAAATCAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 2 0.05
19 20 0.47
20 21 0.49
ACGTcount: A:0.51, C:0.04, G:0.31, T:0.14
Consensus pattern (20 bp):
AAAGGGAGGAAAATCAGTGT
Found at i:42475588 original size:24 final size:24
Alignment explanation
Indices: 42475559--42475808 Score: 155
Period size: 24 Copynumber: 10.7 Consensus size: 24
42475549 GTTTATTGTA
*
42475559 TATTATTATTTTAGATTTATCATG
1 TATTATTATTTTAAATTTATCATG
* *
42475583 TTTTATTATTTGT-AATTTATCA-A
1 TATTATTATTT-TAAATTTATCATG
* *
42475606 TATTATTATTTTAAATTCATCGT-
1 TATTATTATTTTAAATTTATCATG
**
42475629 TAACATTATTTTAAATTTATCATG
1 TATTATTATTTTAAATTTATCATG
*
42475653 TA-TATTTATTTCAAATTTATCAT-
1 TATTA-TTATTTTAAATTTATCATG
* * *
42475676 TAATA-T-TTTTAAATTTATTATA
1 TATTATTATTTTAAATTTATCATG
* ** *
42475698 TACTATTATTTTGGATTTATCACG
1 TATTATTATTTTAAATTTATCATG
* *
42475722 TATGATTATTCTAGAA-TTATCAT-
1 TATTATTATTTTA-AATTTATCATG
* * *
42475745 CA-AAAT-TTTTAAATTTTAT-ATG
1 TATTATTATTTTAAA-TTTATCATG
* * *
42475767 TATTATTATTTCAAATTTATTATA
1 TATTATTATTTTAAATTTATCATG
*
42475791 TATTATTTATTGTAAATT
1 TATTA-TTATTTTAAATT
42475809 ATTCAATTCA
Statistics
Matches: 172, Mismatches: 37, Indels: 33
0.71 0.15 0.14
Matches are distributed among these distances:
20 2 0.01
21 19 0.11
22 13 0.08
23 48 0.28
24 78 0.45
25 12 0.07
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (24 bp):
TATTATTATTTTAAATTTATCATG
Found at i:42475731 original size:69 final size:69
Alignment explanation
Indices: 42475525--42475798 Score: 199
Period size: 69 Copynumber: 4.0 Consensus size: 69
42475515 TATTATCATT
* * * * * *
42475525 AAATTAATCATTAATATTATCTAAGTTTAT-TGTATATTATTATTTTAGATTTATCATGTTTTAT
1 AAATTTATCATTAATATT-TTTAAATTTATATATATACTATTATTTTAGATTTATCATG-TATAT
*
42475589 TATTTG
64 TATTTC
* * * * * *
42475595 TAATTTATCAATATTATTATTTTAAATTCATCGT-TA-AC-ATTATTTTAAATTTATCATGTATA
1 AAATTTATCATTAATA-T-TTTTAAATTTAT-ATATATACTATTATTTTAGATTTATCATGTATA
42475657 TTTATTTC
63 -TTATTTC
* *
42475665 AAATTTATCATTAATATTTTTAAATTTAT-TATATACTATTATTTTGGATTTATCACGTATGATT
1 AAATTTATCATTAATATTTTTAAATTTATATATATACTATTATTTTAGATTTATCATGTAT-ATT
42475729 A-TTC
65 ATTTC
* * * * * * *
42475733 TAGAA-TTATCATCAAAATTTTTAAATTT-TATATGTATTATTATTTCAAATTTAT--TATATAT
1 -A-AATTTATCATTAATATTTTTAAATTTATATATATACTATTATTTTAGATTTATCATGTATAT
42475794 TATTT
64 TATTT
42475799 ATTGTAAATT
Statistics
Matches: 164, Mismatches: 27, Indels: 29
0.75 0.12 0.13
Matches are distributed among these distances:
66 5 0.03
67 7 0.04
68 17 0.10
69 68 0.41
70 53 0.32
71 10 0.06
72 3 0.02
73 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.54
Consensus pattern (69 bp):
AAATTTATCATTAATATTTTTAAATTTATATATATACTATTATTTTAGATTTATCATGTATATTA
TTTC
Found at i:42475932 original size:23 final size:25
Alignment explanation
Indices: 42475906--42475956 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
42475896 ACTTCATCCA
*
42475906 TATACATACTATTTA-TTTTG-AAT
1 TATACATACTAATTATTTTTGTAAT
*
42475929 TATACATATTAATTATTTTTGTAAT
1 TATACATACTAATTATTTTTGTAAT
42475954 TAT
1 TAT
42475957 TTTTTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 13 0.54
24 5 0.21
25 6 0.25
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (25 bp):
TATACATACTAATTATTTTTGTAAT
Found at i:42475955 original size:12 final size:11
Alignment explanation
Indices: 42475937--42475972 Score: 56
Period size: 12 Copynumber: 3.3 Consensus size: 11
42475927 ATTATACATA
42475937 TTAATTATTTT
1 TTAATTATTTT
42475948 TGTAATTATTTT
1 T-TAATTATTTT
42475960 TT-ATTATTTT
1 TTAATTATTTT
42475970 TTA
1 TTA
42475973 TATAATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.43
11 2 0.09
12 11 0.48
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (11 bp):
TTAATTATTTT
Found at i:42475967 original size:10 final size:10
Alignment explanation
Indices: 42475940--42475973 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
42475930 ATACATATTA
42475940 ATTATTTTTGT
1 ATTATTTTT-T
42475951 AATTATTTTTT
1 -ATTATTTTTT
42475962 ATTATTTTTT
1 ATTATTTTTT
42475972 AT
1 AT
42475974 ATAATGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 1 0.05
12 9 0.41
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (10 bp):
ATTATTTTTT
Found at i:42486949 original size:5 final size:5
Alignment explanation
Indices: 42486939--42486964 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42486929 TGAGCATTCG
42486939 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
42486965 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:42487759 original size:9 final size:9
Alignment explanation
Indices: 42487745--42487781 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
42487735 TATAGTTTGA
42487745 TATTCGAAT
1 TATTCGAAT
42487754 TATTCGAAT
1 TATTCGAAT
*
42487763 TATTCGAGT
1 TATTCGAAT
42487772 TATTCGAAT
1 TATTCGAAT
42487781 T
1 T
42487782 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:42487851 original size:9 final size:9
Alignment explanation
Indices: 42487834--42487864 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
42487824 TCGAGTTGAT
42487834 TCGAATAAC
1 TCGAATAAC
*
42487843 TCGATTAAC
1 TCGAATAAC
42487852 TCGAATAAC
1 TCGAATAAC
42487861 TCGA
1 TCGA
42487865 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:42488756 original size:24 final size:23
Alignment explanation
Indices: 42488704--42488761 Score: 55
Period size: 24 Copynumber: 2.4 Consensus size: 23
42488694 AGTAGAATAC
*
42488704 AAAGATGAAAGGTGAAGAGTTAA
1 AAAGAAGAAAGGTGAAGAGTTAA
*
42488727 AGAAGAAGAAATGTGAA-AGGTTAA
1 A-AAGAAGAAAGGTGAAGA-GTTAA
42488751 TAAAGATAGAA
1 -AAAGA-AGAA
42488762 GGTTGAACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 2 0.07
24 22 0.76
25 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.28, T:0.17
Consensus pattern (23 bp):
AAAGAAGAAAGGTGAAGAGTTAA
Found at i:42489987 original size:32 final size:31
Alignment explanation
Indices: 42489948--42490038 Score: 80
Period size: 30 Copynumber: 2.9 Consensus size: 31
42489938 ATTGAAATAA
42489948 TAATTAAGGTGATTGGATTTATTTATTAGCAT
1 TAATTAAGGTGATT-GATTTATTTATTAGCAT
* * * *
42489980 TAATTAA-G-GATT-TTTTTTTTATTGAAACTT
1 TAATTAAGGTGATTGATTTATTTATT--AGCAT
*
42490010 TAGTTAAGGTGATTGAATTTATTTATTAG
1 TAATTAAGGTGATTG-ATTTATTTATTAG
42490039 TACTAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
28 9 0.20
30 13 0.29
31 2 0.04
32 12 0.27
34 9 0.20
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (31 bp):
TAATTAAGGTGATTGATTTATTTATTAGCAT
Done.