Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 94 of 204
Found at i:29420859 original size:116 final size:115
Alignment explanation
Indices: 29420703--29421379 Score: 695
Period size: 116 Copynumber: 5.9 Consensus size: 115
29420693 TCGTTTATCA
* *
29420703 AAAACGCCACTAACACATAACCTTTTGCGGCGTTTTAGTCAAAATGCCACTAAAAATGCAGCTAC
1 AAAACGCCACTAACGCATAACCTTTTGCGGCGTTTTAGTCAAAATGCCACTAAAAATGCAGCTAA
* * * *
29420768 AAACGACGCCGTTTTGCAAATTGTTAATACATATTCGTGGCGTTTTTGGTG
66 AAAAGACACCGTTTTGCAAACT-TTAATACATATTCGCGGCGTTTTTGGTG
* * *
29420819 AAAACGCCACTAACGCATAACCTTTTGCGGCATTTTAGTCAAAACGCCACTAAAAGTGCAGCTAA
1 AAAACGCCACTAACGCATAACCTTTTGCGGCGTTTTAGTCAAAATGCCACTAAAAATGCAGCTAA
* * * * *
29420884 AAAGGGCACCGTTTTACAAAATTTTAAAACATATTCGCGGCGTTTTTGGTG
66 AAAAGACACCGTTTTGC-AAACTTTAATACATATTCGCGGCGTTTTTGGTG
* * * *
29420935 AAAATGCCACTAACGCATAACCTTTGATG-GG-GTTGTAGCCAAAACGCCACTAAAAATGCAGCT
1 AAAACGCCACTAACGCATAACCTTT--TGCGGCGTTTTAGTCAAAATGCCACTAAAAATGCAGCT
* * *
29420998 AAAAATGACACCATTTTGCAAACTATTAATACATATTCGCGGCGTTTTTGGTAA
64 AAAAAAGACACCGTTTTGCAAACT-TTAATACATATTCGCGGCGTTTTTGGT-G
** **
29421052 AAAACGCCACTAACGCATAACCTTTTATGGCGTTTTAGTCAAAATGCCACTAAAAACACAGCT-A
1 AAAACGCCACTAACGCATAACCTTTTGCGGCGTTTTAGTCAAAATGCCACTAAAAATGCAGCTAA
**
29421116 AAAAGTACACCGTTTTGCAAACTCTTAATACATATTCGCGGTATTTTTGGTG
66 AAAAG-ACACCGTTTTGCAAACT-TTAATACATATTCGCGGCGTTTTTGGTG
* * * *
29421168 AAAATGCCACTAATGCATAACCTTTTGCGGCGTTTTAGCCAAAATGCCACTAAAAA--C-GGT--
1 AAAACGCCACTAACGCATAACCTTTTGCGGCGTTTTAGTCAAAATGCCACTAAAAATGCAGCTAA
* * ** *
29421228 ----G---TCGTTTTTCAAACTCTTAATACATATTCGCACCATTTTTGGTG
66 AAAAGACACCGTTTTGCAAACT-TTAATACATATTCGCGGCGTTTTTGGTG
* * * * * **
29421272 AAAACGCCACTAA--CACAACCTTTTGCAGCGTTTTAGTCGAAACGCCGCTAAAAACACAGCTAA
1 AAAACGCCACTAACGCATAACCTTTTGCGGCGTTTTAGTCAAAATGCCACTAAAAATGCAGCTAA
* * * * * * *
29421335 AAACGACAACATTTTGCAATCTTTTAATATATATTTGCGGTGTTT
66 AAAAGACACCGTTTTGCAAAC-TTTAATACATATTCGCGGCGTTT
29421380 GGACAAAAAA
Statistics
Matches: 475, Mismatches: 65, Indels: 44
0.81 0.11 0.08
Matches are distributed among these distances:
102 35 0.07
104 51 0.11
105 2 0.00
108 1 0.00
111 1 0.00
113 2 0.00
114 26 0.05
115 6 0.01
116 250 0.53
117 99 0.21
118 2 0.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (115 bp):
AAAACGCCACTAACGCATAACCTTTTGCGGCGTTTTAGTCAAAATGCCACTAAAAATGCAGCTAA
AAAAGACACCGTTTTGCAAACTTTAATACATATTCGCGGCGTTTTTGGTG
Found at i:29421151 original size:233 final size:232
Alignment explanation
Indices: 29420703--29421223 Score: 740
Period size: 233 Copynumber: 2.2 Consensus size: 232
29420693 TCGTTTATCA
* * * *
29420703 AAAACGCCACTAACACATAACCTTTTGCGGCGTTTTAGTCAAAATGCCACTAAAAATGCAGCTAC
1 AAAATGCCACTAACGCATAACCTTTTGCGGCGTTTTAGCCAAAATGCCACTAAAAATGCAGCTAA
* * * * * *
29420768 AAACGACGCCGTTTTGCAAATTGTTAATACATATTCGTGGCGTTTTTGGTGAAAACGCCACTAAC
66 AAACGACACCATTTTGCAAACTATTAATACATATTCGCGGCGTTTTTGGTAAAAACGCCACTAAC
* *** *
29420833 GCATAACCTTTTGCGGCATTTTAGTCAAAACGCCACTAAAAGTGCAGCTAAAAAGGGCACCGTTT
131 GCATAACCTTTTACGGCATTTTAGTCAAAACGCCACTAAAAACACAGCTAAAAAGGACACCGTTT
* *
29420898 TACAAAATTTTAAAACATATTCGCGGCGTTTTTGGTG
196 TACAAAATCTTAAAACATATTCGCGGCATTTTTGGTG
* *
29420935 AAAATGCCACTAACGCATAACCTTTGATG-GG-GTTGTAGCCAAAACGCCACTAAAAATGCAGCT
1 AAAATGCCACTAACGCATAACCTTT--TGCGGCGTTTTAGCCAAAATGCCACTAAAAATGCAGCT
*
29420998 AAAAATGACACCATTTTGCAAACTATTAATACATATTCGCGGCGTTTTTGGTAAAAAACGCCACT
64 AAAAACGACACCATTTTGCAAACTATTAATACATATTCGCGGCGTTTTTGGT-AAAAACGCCACT
* * * *
29421063 AACGCATAACCTTTTATGGCGTTTTAGTCAAAATGCCACTAAAAACACAGCTAAAAAGTACACCG
128 AACGCATAACCTTTTACGGCATTTTAGTCAAAACGCCACTAAAAACACAGCTAAAAAGGACACCG
* * * *
29421128 TTTTGCAAACTCTTAATACATATTCGCGGTATTTTTGGTG
193 TTTTACAAAATCTTAAAACATATTCGCGGCATTTTTGGTG
*
29421168 AAAATGCCACTAATGCATAACCTTTTGCGGCGTTTTAGCCAAAATGCCACTAAAAA
1 AAAATGCCACTAACGCATAACCTTTTGCGGCGTTTTAGCCAAAATGCCACTAAAAA
29421224 CGGTGTCGTT
Statistics
Matches: 253, Mismatches: 31, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
231 2 0.01
232 99 0.39
233 150 0.59
234 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (232 bp):
AAAATGCCACTAACGCATAACCTTTTGCGGCGTTTTAGCCAAAATGCCACTAAAAATGCAGCTAA
AAACGACACCATTTTGCAAACTATTAATACATATTCGCGGCGTTTTTGGTAAAAACGCCACTAAC
GCATAACCTTTTACGGCATTTTAGTCAAAACGCCACTAAAAACACAGCTAAAAAGGACACCGTTT
TACAAAATCTTAAAACATATTCGCGGCATTTTTGGTG
Found at i:29421868 original size:7 final size:7
Alignment explanation
Indices: 29421856--29421917 Score: 70
Period size: 7 Copynumber: 8.6 Consensus size: 7
29421846 GAAATTTGTT
29421856 TTTAAGG
1 TTTAAGG
29421863 TTTAAGG
1 TTTAAGG
29421870 TTTTAAGG
1 -TTTAAGG
*
29421878 TTTATGG
1 TTTAAGG
*
29421885 TTTTAGG
1 TTTAAGG
*
29421892 TTTTAGGG
1 -TTTAAGG
29421900 TTTAAGG
1 TTTAAGG
*
29421907 TTTAGGG
1 TTTAAGG
29421914 TTTA
1 TTTA
29421918 GAGAAAGCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
7 34 0.74
8 12 0.26
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (7 bp):
TTTAAGG
Found at i:29421875 original size:15 final size:15
Alignment explanation
Indices: 29421855--29421916 Score: 81
Period size: 15 Copynumber: 4.2 Consensus size: 15
29421845 CGAAATTTGT
29421855 TTTTAAGGTTTAAGG
1 TTTTAAGGTTTAAGG
*
29421870 TTTTAAGGTTTATGG
1 TTTTAAGGTTTAAGG
*
29421885 TTTT-AGGTTTTAGG
1 TTTTAAGGTTTAAGG
* *
29421899 GTTTAAGGTTTAGGG
1 TTTTAAGGTTTAAGG
29421914 TTT
1 TTT
29421917 AGAGAAAGCC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
14 11 0.28
15 28 0.72
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (15 bp):
TTTTAAGGTTTAAGG
Found at i:29421886 original size:22 final size:22
Alignment explanation
Indices: 29421856--29421916 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
29421846 GAAATTTGTT
29421856 TTTAAGGTTTAAGGTTTTAAGG
1 TTTAAGGTTTAAGGTTTTAAGG
* * *
29421878 TTTATGGTTTTAGGTTTTAGGG
1 TTTAAGGTTTAAGGTTTTAAGG
*
29421900 TTTAAGGTTTAGGGTTT
1 TTTAAGGTTTAAGGTTT
29421917 AGAGAAAGCC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.51
Consensus pattern (22 bp):
TTTAAGGTTTAAGGTTTTAAGG
Found at i:29422769 original size:18 final size:18
Alignment explanation
Indices: 29422734--29422769 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
29422724 TCACATGCCA
*
29422734 AAGTGAAAAGTTATTTTT
1 AAGTGAAAAGTGATTTTT
29422752 AAGTGAAAAAGTGATTTT
1 AAGTG-AAAAGTGATTTT
29422770 GTGGTCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (18 bp):
AAGTGAAAAGTGATTTTT
Found at i:29422926 original size:47 final size:47
Alignment explanation
Indices: 29422816--29422929 Score: 149
Period size: 48 Copynumber: 2.4 Consensus size: 47
29422806 AGGTGGAATA
* *
29422816 ATGTGGCAGTTTATCTGCAAAAGTGGTGGCTTGTCCACAAATTTTATT
1 ATGTGGCAG-TTATCTACAAAAGTGGTGGCTTGTCCACAAATTTGATT
* * *
29422864 ATGTGGTAGTATATCTACAAAAGTGGTTGCTTGTCCA-TAATTTGATT
1 ATGTGGCAGT-TATCTACAAAAGTGGTGGCTTGTCCACAAATTTGATT
29422911 ATGTGGCAGCTTATCTACA
1 ATGTGGCAG-TTATCTACA
29422930 TTACAGTGAC
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
47 25 0.43
48 33 0.57
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (47 bp):
ATGTGGCAGTTATCTACAAAAGTGGTGGCTTGTCCACAAATTTGATT
Found at i:29427677 original size:15 final size:14
Alignment explanation
Indices: 29427657--29427690 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
29427647 CCACTTTTAT
*
29427657 TCCCTCATTCCCTCA
1 TCCCTCATT-CATCA
29427672 TCCCTCATTCATCA
1 TCCCTCATTCATCA
29427686 TCCCT
1 TCCCT
29427691 TTTCTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.15, C:0.50, G:0.00, T:0.35
Consensus pattern (14 bp):
TCCCTCATTCATCA
Found at i:29432079 original size:155 final size:155
Alignment explanation
Indices: 29431797--29432104 Score: 571
Period size: 155 Copynumber: 2.0 Consensus size: 155
29431787 TTTTCAACCC
* *
29431797 TTCATCAACAACATCACGAGAATTCGAAGACATCTTAACTACCACACATAAACATAGTTTAGCAA
1 TTCATCAACAACATCACGAGAATTCGAAGACATCTTAACTACCACACACAAACACAGTTTAGCAA
29431862 AACTATAAGAGGCTAGCAAAAAACATGTAACATGCATGTTGGGGCGTGACTCAACCTTTGGTCAT
66 AACTATAAGAGGCTAGCAAAAAACATGTAACATGCATGTTGGGGCGTGACTCAACCTTTGGTCAT
29431927 CCAAGAATCGGTTAAACCTAGGCCT
131 CCAAGAATCGGTTAAACCTAGGCCT
29431952 TTCATCAACAACATCACGAGAATTCGAAGACATCTTAACTACCACACACAAACACAGTTTAGCAA
1 TTCATCAACAACATCACGAGAATTCGAAGACATCTTAACTACCACACACAAACACAGTTTAGCAA
* *
29432017 AACTATAAGAGGCTAGCAAAAAACATGTAACGTGCATGTTGGGGTGTGACTCAACCTTTGGTCAT
66 AACTATAAGAGGCTAGCAAAAAACATGTAACATGCATGTTGGGGCGTGACTCAACCTTTGGTCAT
*
29432082 CCGAGAATCGGTTAAACCTAGGC
131 CCAAGAATCGGTTAAACCTAGGC
29432105 TCTGATATCA
Statistics
Matches: 148, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
155 148 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.23
Consensus pattern (155 bp):
TTCATCAACAACATCACGAGAATTCGAAGACATCTTAACTACCACACACAAACACAGTTTAGCAA
AACTATAAGAGGCTAGCAAAAAACATGTAACATGCATGTTGGGGCGTGACTCAACCTTTGGTCAT
CCAAGAATCGGTTAAACCTAGGCCT
Found at i:29433702 original size:27 final size:27
Alignment explanation
Indices: 29433672--29433732 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
29433662 AGAAAAGCCT
29433672 TTGTGGCAAAATAT-GAAAGGAATGCCC
1 TTGTGGCAAAAT-TCGAAAGGAATGCCC
* * *
29433699 TTGTGGAAAAATTCGTAAGGAATGCCT
1 TTGTGGCAAAATTCGAAAGGAATGCCC
29433726 TTGTGGC
1 TTGTGGC
29433733 GCACTCATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (27 bp):
TTGTGGCAAAATTCGAAAGGAATGCCC
Found at i:29441278 original size:27 final size:27
Alignment explanation
Indices: 29441240--29441364 Score: 119
Period size: 28 Copynumber: 4.6 Consensus size: 27
29441230 AAAATTTGTT
*
29441240 AAATTA-CTGAAATACTCTCGAAGGGTA
1 AAATTATC-GAAATACCCTCGAAGGGTA
29441267 AAATTATCGAAATACCCTCGAAGGGTA
1 AAATTATCGAAATACCCTCGAAGGGTA
** * *
29441294 AAATTATAAAAAAAACTCTCGAAGGGTA
1 AAATTAT-CGAAATACCCTCGAAGGGTA
* *
29441322 AAATTACCAAAATACCCCTCGAAGAGG-A
1 AAATTATCGAAATA-CCCTCGAAG-GGTA
* *
29441350 AAATGAACGAAATAC
1 AAATTATCGAAATAC
29441365 GCTCATGGGG
Statistics
Matches: 82, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
27 37 0.45
28 43 0.52
29 2 0.02
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.20
Consensus pattern (27 bp):
AAATTATCGAAATACCCTCGAAGGGTA
Found at i:29441342 original size:28 final size:27
Alignment explanation
Indices: 29441249--29441353 Score: 122
Period size: 28 Copynumber: 3.8 Consensus size: 27
29441239 TAAATTACTG
* *
29441249 AAATACTCTCGAAGGGTAAAATTATCG
1 AAATACCCTCGAAGGGTAAAATTATCA
*
29441276 AAATACCCTCGAAGGGTAAAATTATAAA
1 AAATACCCTCGAAGGGTAAAATTAT-CA
* * *
29441304 AAAAACTCTCGAAGGGTAAAATTACCA
1 AAATACCCTCGAAGGGTAAAATTATCA
29441331 AAATACCCCTCGAAGAGG-AAAAT
1 AAATA-CCCTCGAAG-GGTAAAAT
29441354 GAACGAAATA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
27 29 0.44
28 35 0.53
29 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.20
Consensus pattern (27 bp):
AAATACCCTCGAAGGGTAAAATTATCA
Found at i:29441582 original size:22 final size:22
Alignment explanation
Indices: 29441554--29441616 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
29441544 GGAAGTGTAT
29441554 GGCTTATAGTCGTTCTGTTCAA
1 GGCTTATAGTCGTTCTGTTCAA
* * * * *
29441576 GGCTTATTGTCTTTCTTTTTAT
1 GGCTTATAGTCGTTCTGTTCAA
* *
29441598 GGCTTTTAGCCGTTCTGTT
1 GGCTTATAGTCGTTCTGTT
29441617 AACTGGCAGC
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.11, C:0.17, G:0.21, T:0.51
Consensus pattern (22 bp):
GGCTTATAGTCGTTCTGTTCAA
Found at i:29446089 original size:45 final size:45
Alignment explanation
Indices: 29446040--29446125 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
29446030 ACCTATTTAC
*
29446040 CATGATGTCATAGCGTCTTTCAGCCATGGTCTTACTCATTTCTGT
1 CATGATGTCATAGCATCTTTCAGCCATGGTCTTACTCATTTCTGT
* *
29446085 CATGATGTGATAGCATCTTTCAGCTATGGTCTTACTCATTT
1 CATGATGTCATAGCATCTTTCAGCCATGGTCTTACTCATTT
29446126 TAGGCGTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (45 bp):
CATGATGTCATAGCATCTTTCAGCCATGGTCTTACTCATTTCTGT
Found at i:29447664 original size:34 final size:34
Alignment explanation
Indices: 29447626--29447789 Score: 150
Period size: 34 Copynumber: 4.7 Consensus size: 34
29447616 CTAACTTTGC
*
29447626 GCCCAGCGCTAGTCGGATAACTGACGATGGTTGT
1 GCCCAGCACTAGTCGGATAACTGACGATGGTTGT
* * *
29447660 GCCCAGCACTAGTCGGATAACCGACAATGGTTAT
1 GCCCAGCACTAGTCGGATAACTGACGATGGTTGT
* * ** * *
29447694 GCCCAGCACTAGTTGAACGAGTCGACGAT-GTTTT
1 GCCCAGCACTAGTCGGATAACT-GACGATGGTTGT
* * * *
29447728 GCACCCAGCGCTATTCGAATAACTGACGATAGTTGT
1 G--CCCAGCACTAGTCGGATAACTGACGATGGTTGT
*
29447764 GCCCAGCACTAGTCAGATAAACTGAC
1 GCCCAGCACTAGTCGGAT-AACTGAC
29447790 AAAAATTACG
Statistics
Matches: 102, Mismatches: 23, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
34 64 0.63
35 18 0.18
36 20 0.20
ACGTcount: A:0.27, C:0.26, G:0.25, T:0.23
Consensus pattern (34 bp):
GCCCAGCACTAGTCGGATAACTGACGATGGTTGT
Found at i:29448337 original size:50 final size:50
Alignment explanation
Indices: 29448278--29448381 Score: 208
Period size: 50 Copynumber: 2.1 Consensus size: 50
29448268 AAACATTTAA
29448278 CCCTTTAAACAAATTTCACATCTTTGCATTCAATATATATACCATTCAGT
1 CCCTTTAAACAAATTTCACATCTTTGCATTCAATATATATACCATTCAGT
29448328 CCCTTTAAACAAATTTCACATCTTTGCATTCAATATATATACCATTCAGT
1 CCCTTTAAACAAATTTCACATCTTTGCATTCAATATATATACCATTCAGT
29448378 CCCT
1 CCCT
29448382 AGAGATTAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.38
Consensus pattern (50 bp):
CCCTTTAAACAAATTTCACATCTTTGCATTCAATATATATACCATTCAGT
Found at i:29450816 original size:25 final size:25
Alignment explanation
Indices: 29450782--29450830 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
29450772 CTAACACAGA
29450782 GTAAGCATTTAAGCTTAGTAAGTTT
1 GTAAGCATTTAAGCTTAGTAAGTTT
29450807 GTAAGCATTTAAGCTTAGTAAGTT
1 GTAAGCATTTAAGCTTAGTAAGTT
29450831 CGTTTATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
GTAAGCATTTAAGCTTAGTAAGTTT
Found at i:29451254 original size:25 final size:24
Alignment explanation
Indices: 29451215--29451332 Score: 85
Period size: 25 Copynumber: 4.8 Consensus size: 24
29451205 TCCTAGACAT
* * *
29451215 GTATGGTCATACGAGCTATGAATCG
1 GTATGCTCACACGAGCTGT-AATCG
*
29451240 GTATGCTCACTCGAGCTGTAGATCG
1 GTATGCTCACACGAGCTGTA-ATCG
* *
29451265 GTATGCTCTCACGAGCTGTAAATCA
1 GTATGCTCACACGAGCTGT-AATCG
* * *
29451290 GTATGCCCTA-ACGACCTGTAAATCA
1 GTATGCTC-ACACGAGCTGT-AATCG
**
29451315 GTATGCTTTCACGAGCTG
1 GTATGCTCACACGAGCTG
29451333 CAGGTCAGAA
Statistics
Matches: 75, Mismatches: 14, Indels: 8
0.77 0.14 0.08
Matches are distributed among these distances:
24 1 0.01
25 73 0.97
26 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (24 bp):
GTATGCTCACACGAGCTGTAATCG
Found at i:29453442 original size:13 final size:13
Alignment explanation
Indices: 29453424--29453449 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29453414 TCTATCTGAT
29453424 GTGCTAAAATGCA
1 GTGCTAAAATGCA
29453437 GTGCTAAAATGCA
1 GTGCTAAAATGCA
29453450 ACCGCGTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
GTGCTAAAATGCA
Found at i:29460141 original size:25 final size:25
Alignment explanation
Indices: 29460113--29460173 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
29460103 GGATATAATA
*
29460113 GGGAACCTC-TTTCGAGCCATGTAAC
1 GGGAACCTCATGT-GAGCCATGTAAC
* *
29460138 GGGAAGCTCATGTGAGTCATGTAAC
1 GGGAACCTCATGTGAGCCATGTAAC
* *
29460163 GGAAAGCTCAT
1 GGGAACCTCAT
29460174 AAGAGTCATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 29 0.94
26 2 0.06
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (25 bp):
GGGAACCTCATGTGAGCCATGTAAC
Found at i:29460266 original size:25 final size:25
Alignment explanation
Indices: 29460137--29460268 Score: 103
Period size: 24 Copynumber: 5.4 Consensus size: 25
29460127 AGCCATGTAA
* * *
29460137 CGGGAAGCTCATGTGAGTCATGTAA
1 CGGGAAGCTCATGAGAGTCATATAT
* *
29460162 CGGAAAGCTCATAAGAGTCATAT-T
1 CGGGAAGCTCATGAGAGTCATATAT
* *
29460186 CGGGAAGCTTAT-ACGAGCCA-ATAT
1 CGGGAAGCTCATGA-GAGTCATATAT
* * *
29460210 CGGGAAGCTTC-GGAGAGCCAT-TAA
1 CGGGAAGC-TCATGAGAGTCATATAT
* *
29460234 CGGGAAGCTCATGACAGTCATTTAT
1 CGGGAAGCTCATGAGAGTCATATAT
29460259 CGGGAAGCTC
1 CGGGAAGCTC
29460269 CAAAGAGCCA
Statistics
Matches: 85, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
23 5 0.06
24 47 0.55
25 33 0.39
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (25 bp):
CGGGAAGCTCATGAGAGTCATATAT
Found at i:29460299 original size:25 final size:25
Alignment explanation
Indices: 29460126--29460300 Score: 121
Period size: 25 Copynumber: 7.1 Consensus size: 25
29460116 AACCTCTTTC
**
29460126 GAGCCATGTAA-CGGGAAGCTCATGT
1 GAGCCAT-TAATCGGGAAGCTCATAA
* *
29460151 GAGTCATGTAA-CGGAAAGCTCATAA
1 GAGCCAT-TAATCGGGAAGCTCATAA
* * * *
29460176 GAGTCA-TATTCGGGAAGCTTATAC
1 GAGCCATTAATCGGGAAGCTCATAA
* **
29460200 GAGCCAAT-ATCGGGAAGCTTC-GGA
1 GAGCCATTAATCGGGAAGC-TCATAA
*
29460224 GAGCCATTAA-CGGGAAGCTCATGA
1 GAGCCATTAATCGGGAAGCTCATAA
* * *
29460248 CAGTCATTTATCGGGAAGCTCCA-AA
1 GAGCCATTAATCGGGAAGCT-CATAA
*
29460273 GAGCCATTAATCGGGATGCTCATAA
1 GAGCCATTAATCGGGAAGCTCATAA
29460298 GAG
1 GAG
29460301 TTACGGTGTG
Statistics
Matches: 118, Mismatches: 24, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
23 4 0.03
24 51 0.43
25 61 0.52
26 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.21
Consensus pattern (25 bp):
GAGCCATTAATCGGGAAGCTCATAA
Found at i:29460374 original size:24 final size:25
Alignment explanation
Indices: 29460340--29460399 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
29460330 CACAACCAAT
* *
29460340 CAGGATGCTCATAAGAGCTAT-TAA
1 CAGGAAGCTCATAAGAGCCATCTAA
* * *
29460364 CGGGAAGCTCATGAGAGCCATCTAT
1 CAGGAAGCTCATAAGAGCCATCTAA
29460389 CAGGAAGCTCA
1 CAGGAAGCTCA
29460400 AGAGATCCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
24 17 0.59
25 12 0.41
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (25 bp):
CAGGAAGCTCATAAGAGCCATCTAA
Found at i:29462081 original size:50 final size:50
Alignment explanation
Indices: 29462026--29462135 Score: 170
Period size: 50 Copynumber: 2.2 Consensus size: 50
29462016 GTATGGTCAT
29462026 ACGAGCTGTAAATCGGTATG--CTCACTAGAGCTGTAGATCGGTATGCTCTC
1 ACGAGCTGTAAATCGGTATGCCCTCAC--GAGCTGTAGATCGGTATGCTCTC
*
29462076 ACGAGCTATAAATCGGTATGCCCTCACGAGCTGTAGATCGGTATGCTCTC
1 ACGAGCTGTAAATCGGTATGCCCTCACGAGCTGTAGATCGGTATGCTCTC
*
29462126 ATGAGCTGTA
1 ACGAGCTGTA
29462136 GGTCGAAACA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
50 50 0.91
52 5 0.09
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (50 bp):
ACGAGCTGTAAATCGGTATGCCCTCACGAGCTGTAGATCGGTATGCTCTC
Found at i:29462136 original size:25 final size:25
Alignment explanation
Indices: 29462026--29462136 Score: 152
Period size: 25 Copynumber: 4.4 Consensus size: 25
29462016 GTATGGTCAT
* *
29462026 ACGAGCTGTAAATCGGTATGCTCAC
1 ACGAGCTGTAGATCGGTATGCTCTC
29462051 TA-GAGCTGTAGATCGGTATGCTCTC
1 -ACGAGCTGTAGATCGGTATGCTCTC
* * *
29462076 ACGAGCTATAAATCGGTATGCCCTC
1 ACGAGCTGTAGATCGGTATGCTCTC
29462101 ACGAGCTGTAGATCGGTATGCTCTC
1 ACGAGCTGTAGATCGGTATGCTCTC
*
29462126 ATGAGCTGTAG
1 ACGAGCTGTAG
29462137 GTCGAAACAT
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
24 1 0.01
25 73 0.97
26 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (25 bp):
ACGAGCTGTAGATCGGTATGCTCTC
Found at i:29465587 original size:19 final size:19
Alignment explanation
Indices: 29465563--29465603 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
29465553 CTGCTAGTAG
29465563 ATTTTTACAATTAATTCAC
1 ATTTTTACAATTAATTCAC
29465582 ATTTTTACAATTAATTCAC
1 ATTTTTACAATTAATTCAC
29465601 ATT
1 ATT
29465604 GAACTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTTACAATTAATTCAC
Found at i:29468865 original size:22 final size:22
Alignment explanation
Indices: 29468821--29468866 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
29468811 AGAATATTAT
* *
29468821 AAAAAATTATTACAAACTGTAA
1 AAAAAATAATTACAAACTATAA
29468843 AAAAAATAATTA-AAAGCTATAA
1 AAAAAATAATTACAAA-CTATAA
29468865 AA
1 AA
29468867 TTATAAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.65, C:0.07, G:0.04, T:0.24
Consensus pattern (22 bp):
AAAAAATAATTACAAACTATAA
Found at i:29469246 original size:21 final size:21
Alignment explanation
Indices: 29469208--29469247 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29469198 ATTTGATTTT
*
29469208 TATATTATTAAATTATCATTA
1 TATATTATTAAATAATCATTA
* *
29469229 TATATTTTTATATAATCAT
1 TATATTATTAAATAATCAT
29469248 AAATTTAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TATATTATTAAATAATCATTA
Found at i:29470272 original size:17 final size:18
Alignment explanation
Indices: 29470252--29470286 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
29470242 ATTTTTTTTC
29470252 CTAAATTATATTT-TTAT
1 CTAAATTATATTTATTAT
*
29470269 CTAAATTCTATTTATTAT
1 CTAAATTATATTTATTAT
29470287 TATTTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (18 bp):
CTAAATTATATTTATTAT
Found at i:29476416 original size:29 final size:29
Alignment explanation
Indices: 29476383--29476453 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
29476373 AATCCTGAGA
*
29476383 TATTTTTTCAGAACCCATCTTGTCAAAAT
1 TATTTTTTCAGAACCCATCTCGTCAAAAT
* * *
29476412 TATTTTTTCAAAACTCATCTCGTCAAACT
1 TATTTTTTCAGAACCCATCTCGTCAAAAT
29476441 TATTTTTTCAGAA
1 TATTTTTTCAGAA
29476454 TCCCTAAACC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.44
Consensus pattern (29 bp):
TATTTTTTCAGAACCCATCTCGTCAAAAT
Found at i:29476797 original size:29 final size:28
Alignment explanation
Indices: 29476764--29476821 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
29476754 TTTGTATTTT
*
29476764 TAACCCATTTCTGTAATTTTCAACAAAAG
1 TAACCCATTTCCGTAATTTTCAA-AAAAG
*
29476793 TAACCCATTTCCGTAATTTTTAAAAAAG
1 TAACCCATTTCCGTAATTTTCAAAAAAG
29476821 T
1 T
29476822 GGATCTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (28 bp):
TAACCCATTTCCGTAATTTTCAAAAAAG
Found at i:29478516 original size:6 final size:6
Alignment explanation
Indices: 29478505--29478536 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
29478495 ATACTAATGC
29478505 TTTCTT TTTCTT TTTCTT TTTCTT TTT-TT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
29478537 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTCTT
Found at i:29482877 original size:24 final size:23
Alignment explanation
Indices: 29482850--29482896 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
29482840 TTGAATATTA
29482850 TTTAATT-TTTTTCATTTATATAAG
1 TTTAATTATTTTT-ATTT-TATAAG
29482874 TTTAATTAATTTTTATTTTATAA
1 TTTAATT-ATTTTTATTTTATAA
29482897 TTTTTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 12 0.57
25 4 0.19
26 5 0.24
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTAATTATTTTTATTTTATAAG
Found at i:29484421 original size:18 final size:18
Alignment explanation
Indices: 29484398--29484441 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
29484388 ATGCTAGGTG
*
29484398 TGTATCCTAGCCGTTATA
1 TGTATCCTAACCGTTATA
*
29484416 TGTATCCTAACCTTTATA
1 TGTATCCTAACCGTTATA
*
29484434 TGTTTCCT
1 TGTATCCT
29484442 GTTTCCAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.20, C:0.23, G:0.11, T:0.45
Consensus pattern (18 bp):
TGTATCCTAACCGTTATA
Found at i:29484949 original size:62 final size:60
Alignment explanation
Indices: 29484833--29484953 Score: 145
Period size: 62 Copynumber: 2.0 Consensus size: 60
29484823 ATTTGTACAA
* * ****
29484833 ATTTTTTATATTGTTTCATTTAATAAAATAAAAGTTTTTTTTAATATTTTAATAGTAAATT
1 ATTTTTTATATTGTCTCATTTAATAAAATAAAAGTTTTTTTGAATAAGACAATAG-AAATT
*
29484894 ATTTTTATATATTGTC-CTATTTAATAAAATAGAAGTTTTTTTGAATAAGACAATAGAAAT
1 ATTTTT-TATATTGTCTC-ATTTAATAAAATAAAAGTTTTTTTGAATAAGACAATAGAAAT
29484954 AATGCAACAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
61 11 0.22
62 40 0.78
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (60 bp):
ATTTTTTATATTGTCTCATTTAATAAAATAAAAGTTTTTTTGAATAAGACAATAGAAATT
Found at i:29488199 original size:114 final size:115
Alignment explanation
Indices: 29488055--29488279 Score: 353
Period size: 114 Copynumber: 2.0 Consensus size: 115
29488045 TTTCAAAACT
*
29488055 GTCTTCTCAAAATTATTTTTTTAGGAACTACTACAGAAAAAGAGCATCCACGTGGGAGCTTTTTT
1 GTCTTCTCAAAATTATTTTTTTAGAAACTACTACAGAAAAAGAGCATCCACGTGGGAGCTTTTTT
* * * *
29488120 CAGTACTTTTGCTGACAGTGCATCCTGCTTGAAGCATTTTTGACACAACC
66 CAGTACTTTTGCTGACAGTACACCCTGCTTAAAGAATTTTTGACACAACC
**
29488170 GTCTTCTCAAAATTA-TTTTTTAGAAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTT
1 GTCTTCTCAAAATTATTTTTTTAGAAACTACTACAGAAAAAGAGCATCCACGTGGGAGCTTTTTT
* * *
29488234 TAGTACTTTTGTTGATAGTACACCCTGCTTAAAGAATTTTTGACAC
66 CAGTACTTTTGCTGACAGTACACCCTGCTTAAAGAATTTTTGACAC
29488280 TATTTTTTTT
Statistics
Matches: 100, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
114 85 0.85
115 15 0.15
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (115 bp):
GTCTTCTCAAAATTATTTTTTTAGAAACTACTACAGAAAAAGAGCATCCACGTGGGAGCTTTTTT
CAGTACTTTTGCTGACAGTACACCCTGCTTAAAGAATTTTTGACACAACC
Found at i:29488466 original size:35 final size:32
Alignment explanation
Indices: 29488423--29488508 Score: 109
Period size: 35 Copynumber: 2.6 Consensus size: 32
29488413 ACAAAATTAT
* * *
29488423 TTTTAAAAATCCCCAAACCCTAATTTAATTTTTC
1 TTTTAAAAAACCCTAAACCCTAATTTAA--TTTA
*
29488457 TTTTAAAAAAACCTTAAACCCTAATTTAATTTA
1 TTTT-AAAAAACCCTAAACCCTAATTTAATTTA
29488490 TTTTAAAAAACCCTAAACC
1 TTTTAAAAAACCCTAAACC
29488509 TTAACCCCAC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 14 0.30
33 7 0.15
34 4 0.09
35 21 0.46
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (32 bp):
TTTTAAAAAACCCTAAACCCTAATTTAATTTA
Found at i:29488583 original size:16 final size:17
Alignment explanation
Indices: 29488552--29488585 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
29488542 ACAAAACCCT
29488552 AACCCTAAACCCCATAA
1 AACCCTAAACCCCATAA
29488569 AACCCTAAA-CCCATAA
1 AACCCTAAACCCCATAA
29488585 A
1 A
29488586 CGCTAGGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (17 bp):
AACCCTAAACCCCATAA
Found at i:29489809 original size:18 final size:18
Alignment explanation
Indices: 29489772--29489810 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
29489762 AATTGAAATT
*
29489772 TATTTTATAATAAGATAA
1 TATTTTATAATAAGAAAA
*
29489790 TATTTTATAATAATAAAA
1 TATTTTATAATAAGAAAA
29489808 TAT
1 TAT
29489811 CATATATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
TATTTTATAATAAGAAAA
Found at i:29490034 original size:25 final size:24
Alignment explanation
Indices: 29490006--29490072 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 24
29489996 TTGTAATTTG
29490006 TAATATATATTTATTAATAAAATAT
1 TAATATATATTT-TTAATAAAATAT
*
29490031 TAATATAAATATTTTTCAATAATATAT
1 TAATAT--ATATTTTT-AATAAAATAT
*
29490058 TAAGA-ATATTTTTAA
1 TAATATATATTTTTAA
29490073 AATTTAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
23 2 0.05
24 8 0.22
25 6 0.16
26 2 0.05
27 19 0.51
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (24 bp):
TAATATATATTTTTAATAAAATAT
Found at i:29490156 original size:22 final size:21
Alignment explanation
Indices: 29490094--29490158 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 21
29490084 ATTATGGTTA
29490094 AATT-TATTATTAAAAT-AA-
1 AATTATATTATTAAAATAAAT
* * *
29490112 AATTGTAATATT-AAATAATT
1 AATTATATTATTAAAATAAAT
29490132 AATTATATTATTAAATATAAAT
1 AATTATATTATTAAA-ATAAAT
29490154 AATTA
1 AATTA
29490159 AATAGGTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
18 8 0.22
19 7 0.19
20 10 0.27
21 2 0.05
22 10 0.27
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
AATTATATTATTAAAATAAAT
Found at i:29490836 original size:13 final size:15
Alignment explanation
Indices: 29490818--29490850 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
29490808 TGAGTGAAAA
29490818 AGAAGAAAAG-AA-G
1 AGAAGAAAAGTAAGG
29490831 AGAAGAAAAGTAAGG
1 AGAAGAAAAGTAAGG
29490846 AGAAG
1 AGAAG
29490851 GAGAGGGCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 2 0.11
15 6 0.33
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (15 bp):
AGAAGAAAAGTAAGG
Found at i:29490922 original size:18 final size:18
Alignment explanation
Indices: 29490892--29490929 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
29490882 AAAAAAAGAG
29490892 AAGGAGAAAAGAGAGAGGA
1 AAGGAGAAAAGAGA-AGGA
29490911 AAGGAG-AAAGAGAAGGA
1 AAGGAGAAAAGAGAAGGA
29490928 AA
1 AA
29490930 AAAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 7 0.37
19 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (18 bp):
AAGGAGAAAAGAGAAGGA
Found at i:29491832 original size:36 final size:37
Alignment explanation
Indices: 29491786--29491861 Score: 127
Period size: 38 Copynumber: 2.1 Consensus size: 37
29491776 TATGATGTGG
*
29491786 AAAAATTTGTTTGGTA-TTTTTTTTGTAATTAAAAGC
1 AAAAAATTGTTTGGTATTTTTTTTTGTAATTAAAAGC
29491822 AAAAAATTGTTTGGTATTTTTTTTTTGTAATTAAAAGC
1 AAAAAATTGTTTGGTA-TTTTTTTTTGTAATTAAAAGC
29491860 AA
1 AA
29491862 TATATAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
36 15 0.41
38 22 0.59
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.49
Consensus pattern (37 bp):
AAAAAATTGTTTGGTATTTTTTTTTGTAATTAAAAGC
Found at i:29499841 original size:27 final size:27
Alignment explanation
Indices: 29499800--29499877 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
29499790 ACTAGGTGTA
* *
29499800 CCGCCTATTAAATAGCCACCACTAGTG
1 CCGCCTATCAGATAGCCACCACTAGTG
* ** **
29499827 CCGCCTGTCAGATAGCCATAACCGGTG
1 CCGCCTATCAGATAGCCACCACTAGTG
29499854 CCGCCTATCAGATATG-CACCACTA
1 CCGCCTATCAGATA-GCCACCACTA
29499878 CTAAAATATT
Statistics
Matches: 38, Mismatches: 12, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
27 37 0.97
28 1 0.03
ACGTcount: A:0.27, C:0.35, G:0.18, T:0.21
Consensus pattern (27 bp):
CCGCCTATCAGATAGCCACCACTAGTG
Found at i:29500939 original size:66 final size:67
Alignment explanation
Indices: 29500778--29500955 Score: 216
Period size: 69 Copynumber: 2.6 Consensus size: 67
29500768 TGCTAATTTC
** * * * *
29500778 ATTAAAAAGTTAATTTTAATCTAACATTGGCTAGAGAATACTCTCGTAGCTCACTTCTAAACTAT
1 ATTAAAAAGTTAATTTTAATCCCATATTGGCTAGAGAATACTCCCATAGCCCACTTC--AACTAT
29500843 TTTT
64 TTTT
* *
29500847 CTTAAAAAGTTAATTTTAA-CCTCATATTGACTAGAGAATACTCCCATAGCCCACTTC-ACTATT
1 ATTAAAAAGTTAATTTTAATCC-CATATTGGCTAGAGAATACTCCCATAGCCCACTTCAACTATT
29500910 TTT
65 TTT
* * *
29500913 ATTAGAAAGTTAATTTTAATCCCATATTGGTTAGAGAACACTC
1 ATTAAAAAGTTAATTTTAATCCCATATTGGCTAGAGAATACTC
29500956 TCATGCTCAC
Statistics
Matches: 94, Mismatches: 13, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
66 44 0.47
67 2 0.02
68 1 0.01
69 47 0.50
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (67 bp):
ATTAAAAAGTTAATTTTAATCCCATATTGGCTAGAGAATACTCCCATAGCCCACTTCAACTATTT
TT
Found at i:29502126 original size:28 final size:29
Alignment explanation
Indices: 29502090--29502165 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 29
29502080 AAAAATAAAA
29502090 ATTTACCAAAATAT-TACAAC-TTTTTTTT
1 ATTTACCAAAATATATA-AACTTTTTTTTT
29502118 ATTTACCAAAATATATAAACTTTTTTTTT
1 ATTTACCAAAATATATAAACTTTTTTTTT
*
29502147 ATTTATCAAAATATATAAA
1 ATTTACCAAAATATATAAA
29502166 AAAACAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
28 17 0.38
29 28 0.62
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTTACCAAAATATATAAACTTTTTTTTT
Found at i:29502267 original size:27 final size:27
Alignment explanation
Indices: 29502237--29502303 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
29502227 CGCCAATGGT
29502237 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
* **
29502264 ATTGGCGGCACCAATGGTGCCAATGCC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
29502291 ATTGGCGGCACCA
1 ATTGGCGGCACCA
29502304 GTTGGTATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.28, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAACC
Found at i:29502354 original size:4 final size:4
Alignment explanation
Indices: 29502345--29502476 Score: 85
Period size: 4 Copynumber: 31.2 Consensus size: 4
29502335 CAGAAGGAGG
* *
29502345 GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA GAAA GGAGAG GAAA GAAA
1 GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA -GA-AA GAAA GAAA
*
29502393 GAAAA GGAAA GGAGAA GAAA -AAA -AAG GAAA GAAA G-AA G-AA GAAAA
1 G-AAA -GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA
*
29502438 GGAGAA GAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAA G
1 -GA-AA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
29502477 GGAAAGGAGA
Statistics
Matches: 107, Mismatches: 8, Indels: 26
0.76 0.06 0.18
Matches are distributed among these distances:
3 14 0.13
4 56 0.52
5 29 0.27
6 8 0.07
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:29502372 original size:14 final size:14
Alignment explanation
Indices: 29502344--29502476 Score: 79
Period size: 14 Copynumber: 9.7 Consensus size: 14
29502334 GCAGAAGGAG
29502344 GGAAAGAAAG-AAA
1 GGAAAGAAAGAAAA
* *
29502357 -GAAAGGAGAGGAAA
1 GGAAA-GAAAGAAAA
* *
29502371 -GAAAGAAAGGAGA
1 GGAAAGAAAGAAAA
29502384 GGAAAGAAAGAAAA
1 GGAAAGAAAGAAAA
29502398 GGAAAGGAGAAGAAAA
1 GGAAA-GA-AAGAAAA
*
29502414 -AAAAGGAAAG-AAA
1 GGAAA-GAAAGAAAA
29502427 -G-AAG-AAGAAAA
1 GGAAAGAAAGAAAA
29502438 GGAGAAGAGAAGAAAAA
1 GGA-AAGA-AAG-AAAA
*
29502455 AGAAAGAAAG--AA
1 GGAAAGAAAGAAAA
29502467 GGAAAGAAAG
1 GGAAAGAAAG
29502477 GGAAAGGAGA
Statistics
Matches: 99, Mismatches: 9, Indels: 25
0.74 0.07 0.19
Matches are distributed among these distances:
10 3 0.03
11 4 0.04
12 18 0.18
13 14 0.14
14 29 0.29
15 11 0.11
16 14 0.14
17 6 0.06
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
GGAAAGAAAGAAAA
Found at i:29502372 original size:18 final size:18
Alignment explanation
Indices: 29502349--29502429 Score: 107
Period size: 18 Copynumber: 4.6 Consensus size: 18
29502339 AGGAGGGAAA
29502349 GAAAGAAAGAAAGGAGAG
1 GAAAGAAAGAAAGGAGAG
29502367 GAAAGAAAGAAAGGAGAG
1 GAAAGAAAGAAAGGAGAG
*
29502385 GAAAGAAAGAAAAGGAAAG
1 GAAAGAAAG-AAAGGAGAG
29502404 GAGAAGAAA-AAA--A-AG
1 GA-AAGAAAGAAAGGAGAG
29502419 GAAAGAAAGAA
1 GAAAGAAAGAA
29502430 GAAGAAAAGG
Statistics
Matches: 59, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
14 6 0.10
15 6 0.10
16 1 0.02
18 30 0.51
19 10 0.17
20 6 0.10
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
GAAAGAAAGAAAGGAGAG
Found at i:29502392 original size:40 final size:38
Alignment explanation
Indices: 29502345--29502477 Score: 150
Period size: 38 Copynumber: 3.5 Consensus size: 38
29502335 CAGAAGGAGG
* *
29502345 GAAAGAAAGAAAGAAAGGAGAGGAAAGAAAGAAAGGAGAG
1 GAAAGAAAGAAAGAAAGGAGAAGAAAGAAA-AAAGGA-AA
29502385 GAAAGAAAGAAAAGGAAAGGAGAAG-AA-AAAAAAGGAAA
1 GAAAGAAAG-AAA-GAAAGGAGAAGAAAGAAAAAAGGAAA
29502423 GAAAG-AAG-AAGAAAAGGAGAAGAGAAGAAAAAA-GAAA
1 GAAAGAAAGAAAG-AAAGGAGAAGA-AAGAAAAAAGGAAA
*
29502460 GAAAGAAGGAAAGAAAGG
1 GAAAGAAAGAAAGAAAGG
29502478 GAAAGGAGAA
Statistics
Matches: 82, Mismatches: 3, Indels: 18
0.80 0.03 0.17
Matches are distributed among these distances:
34 1 0.01
35 12 0.15
37 14 0.17
38 19 0.23
39 9 0.11
40 12 0.15
41 5 0.06
42 10 0.12
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (38 bp):
GAAAGAAAGAAAGAAAGGAGAAGAAAGAAAAAAGGAAA
Found at i:29502423 original size:44 final size:44
Alignment explanation
Indices: 29502372--29502525 Score: 157
Period size: 44 Copynumber: 3.6 Consensus size: 44
29502362 GAGAGGAAAG
29502372 AAAGAAAGGAGAGGAAAGAAAGAAAAGGA-AAGGAGAAGAAAAAA
1 AAAGAAAGGAGAGGAAAGAAAGAAAAGGAGAA-GAGAAGAAAAAA
* *
29502416 AAGGAAA-GA-AAG-AAG-AAGAAAAGGAGAAGAGAAGAAAAAA
1 AAAGAAAGGAGAGGAAAGAAAGAAAAGGAGAAGAGAAGAAAAAA
*
29502456 GAAAGAAA-GA-AGGAAAGAAAGGGAAAGGAGAAGAGAA-AAAAAA
1 -AAAGAAAGGAGAGGAAAGAAA-GAAAAGGAGAAGAGAAGAAAAAA
29502499 AGAAGAAGAGGAG-GG-AAGAAAGGAAAA
1 A-AAGAA-AGGAGAGGAAAGAAA-GAAAA
29502526 AAAGGGAAAA
Statistics
Matches: 95, Mismatches: 6, Indels: 18
0.80 0.05 0.15
Matches are distributed among these distances:
40 22 0.23
41 15 0.16
42 6 0.06
43 15 0.16
44 33 0.35
45 4 0.04
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (44 bp):
AAAGAAAGGAGAGGAAAGAAAGAAAAGGAGAAGAGAAGAAAAAA
Found at i:29502508 original size:18 final size:18
Alignment explanation
Indices: 29502408--29502508 Score: 60
Period size: 18 Copynumber: 5.1 Consensus size: 18
29502398 GGAAAGGAGA
*
29502408 AGAAAAAAAAGGAAAGAA-
1 AGAAAAAAAAAG-AAGAAG
* *
29502426 AGAAGAAGAAAAGGAGAAG
1 AGAA-AAAAAAAGAAGAAG
*
29502445 AGAAGAAAAAAGAAAGAAAG
1 AGAAAAAAAAAG-AAG-AAG
*
29502465 AAGGAAAGAAAGGGAAAGGAGAAG
1 -A-GAAA-AAA---AAAGAAGAAG
29502489 AGAAAAAAAAAGAAGAAG
1 AGAAAAAAAAAGAAGAAG
29502507 AG
1 AG
29502509 GAGGGAAGAA
Statistics
Matches: 64, Mismatches: 9, Indels: 20
0.69 0.10 0.22
Matches are distributed among these distances:
18 25 0.39
19 12 0.19
20 3 0.05
21 4 0.06
22 7 0.11
23 4 0.06
24 3 0.05
25 2 0.03
26 4 0.06
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (18 bp):
AGAAAAAAAAAGAAGAAG
Found at i:29502533 original size:18 final size:18
Alignment explanation
Indices: 29502342--29502539 Score: 54
Period size: 18 Copynumber: 10.7 Consensus size: 18
29502332 GGGCAGAAGG
*
29502342 AGGGAAAGAAA-GAAAGAA
1 AGGG-AAGAAAGGAAAAAA
* *
29502360 AGGAGAGGAAA-GAAAGAA
1 AGG-GAAGAAAGGAAAAAA
*
29502378 AGGAGAGGAAA-GAAAGAAA
1 AGG-GAAGAAAGGAAA-AAA
* *
29502397 AGGAAAGGAGAAGAAAAAAA
1 AGGGAA-GA-AAGGAAAAAA
* *
29502417 AGGAAAGAAAGAAGAAGAAA
1 AGGGAAGAAAG--GAAAAAA
*
29502437 AGGAGAAGAGAAGAAAAAAGA
1 AGG-GAAGA-AAGGAAAAA-A
* * *
29502458 AAGAAAG-AAGGAAAGAA
1 AGGGAAGAAAGGAAAAAA
29502475 AGGGAAAGGAGAAGAGAAAAAA
1 AGGG-AA-GA-AAG-GAAAAAA
* **
29502497 A---AAG-AA-GAAGAGG
1 AGGGAAGAAAGGAAAAAA
29502510 AGGGAAGAAAGGAAAAAA
1 AGGGAAGAAAGGAAAAAA
*
29502528 AGGGAAAAAAGG
1 AGGGAAGAAAGG
29502540 TAATTTTATT
Statistics
Matches: 136, Mismatches: 24, Indels: 40
0.68 0.12 0.20
Matches are distributed among these distances:
13 5 0.04
15 2 0.01
16 3 0.02
17 6 0.04
18 60 0.44
19 11 0.08
20 26 0.19
21 13 0.10
22 10 0.07
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (18 bp):
AGGGAAGAAAGGAAAAAA
Found at i:29508843 original size:15 final size:12
Alignment explanation
Indices: 29508806--29508836 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29508796 AAAAAAATTT
*
29508806 ATACTCAAAATA
1 ATACACAAAATA
29508818 ATACACAAAATA
1 ATACACAAAATA
29508830 ATACACA
1 ATACACA
29508837 CTAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (12 bp):
ATACACAAAATA
Found at i:29508891 original size:23 final size:23
Alignment explanation
Indices: 29508834--29508891 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 23
29508824 AAAATAATAC
* *
29508834 ACACTAAA-ATTATTAATTTTAT
1 ACACAAAATATTAATAATTTTAT
29508856 ACTACGAATAATATTAATAATTTTAT
1 AC-AC-AA-AATATTAATAATTTTAT
29508882 ACACAAAATA
1 ACACAAAATA
29508892 ATACACACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
22 2 0.07
23 6 0.20
24 3 0.10
25 4 0.13
26 15 0.50
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (23 bp):
ACACAAAATATTAATAATTTTAT
Found at i:29508891 original size:26 final size:26
Alignment explanation
Indices: 29508842--29508894 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
29508832 ACACACTAAA
* *
29508842 ATTATTAATTTTATACTACGAATAAT
1 ATTAATAATTTTATACTACAAATAAT
29508868 ATTAATAATTTTATAC-ACAAAATAAT
1 ATTAATAATTTTATACTAC-AAATAAT
29508894 A
1 A
29508895 CACACTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.42
Consensus pattern (26 bp):
ATTAATAATTTTATACTACAAATAAT
Found at i:29509082 original size:3 final size:3
Alignment explanation
Indices: 29509074--29509108 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
29509064 TCTTCGTACT
29509074 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
29509109 TAATAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:29509202 original size:19 final size:21
Alignment explanation
Indices: 29509178--29509216 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
29509168 ACTAAAACAA
*
29509178 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
29509197 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
29509217 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:29509492 original size:27 final size:28
Alignment explanation
Indices: 29509457--29509526 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 28
29509447 GTTTTTTTTA
29509457 ATATATTTTGATAAATAAAAAAAGTT-T
1 ATATATTTTGATAAATAAAAAAAGTTGT
*
29509484 ATATATTTTGACAAATAAAAAAAGTTGT
1 ATATATTTTGATAAATAAAAAAAGTTGT
*
29509512 A-ATATTTTAATAAAT
1 ATATATTTTGATAAAT
29509527 TTTTATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
27 37 0.95
28 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.40
Consensus pattern (28 bp):
ATATATTTTGATAAATAAAAAAAGTTGT
Found at i:29520202 original size:24 final size:25
Alignment explanation
Indices: 29520139--29520204 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
29520129 AAGGGAATAG
*
29520139 GGGAAGGAA-ATGAGGAAAAATGGAA
1 GGGAATGAAGATGA-GAAAAATGGAA
29520164 GGGAATGAAGA-GAGAAAAATGAGAA
1 GGGAATGAAGATGAGAAAAATG-GAA
*
29520189 GTGAA-G-AGATGAGAAA
1 GGGAATGAAGATGAGAAA
29520205 GGTTGAGATG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
23 3 0.08
24 15 0.42
25 17 0.47
26 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.38, T:0.09
Consensus pattern (25 bp):
GGGAATGAAGATGAGAAAAATGGAA
Found at i:29521414 original size:2 final size:2
Alignment explanation
Indices: 29521407--29521440 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
29521397 CGCGTACGCG
*
29521407 CA CA CA CA CA GA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
29521441 ATGAACTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.47, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:29523676 original size:16 final size:16
Alignment explanation
Indices: 29523652--29523704 Score: 79
Period size: 16 Copynumber: 3.2 Consensus size: 16
29523642 GTTTTATCAA
*
29523652 TTTAGTCATTTGTTTAT
1 TTTA-TCATTTATTTAT
*
29523669 TTTATCATTTCTTTAT
1 TTTATCATTTATTTAT
29523685 TTTATCATTTATTTAT
1 TTTATCATTTATTTAT
29523701 TTTA
1 TTTA
29523705 ATTATTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
16 30 0.88
17 4 0.12
ACGTcount: A:0.21, C:0.08, G:0.04, T:0.68
Consensus pattern (16 bp):
TTTATCATTTATTTAT
Found at i:29530557 original size:35 final size:35
Alignment explanation
Indices: 29530525--29530639 Score: 101
Period size: 35 Copynumber: 3.3 Consensus size: 35
29530515 AGATTTATTC
*
29530525 GACTAGTGCAGCGCACACCTATCGCCAGTTTATCT
1 GACTAGTGCAGCGCACACCTATCGTCAGTTTATCT
* * * * *
29530560 GACTAGCACTG-GGCGCAAAAC-ATTGTCGGTTTAT-T
1 GACTAG---TGCAGCGCACACCTATCGTCAGTTTATCT
* *
29530595 CAACTAGTGCAGGGCACACCTATCGTCAGTTTATCT
1 -GACTAGTGCAGCGCACACCTATCGTCAGTTTATCT
29530631 GACTAGTGC
1 GACTAGTGC
29530640 TGGGCGCAAA
Statistics
Matches: 59, Mismatches: 14, Indels: 14
0.68 0.16 0.16
Matches are distributed among these distances:
33 2 0.03
34 6 0.10
35 26 0.44
36 16 0.27
37 7 0.12
38 2 0.03
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (35 bp):
GACTAGTGCAGCGCACACCTATCGTCAGTTTATCT
Found at i:29530593 original size:36 final size:36
Alignment explanation
Indices: 29530550--29530674 Score: 121
Period size: 36 Copynumber: 3.5 Consensus size: 36
29530540 CACCTATCGC
**
29530550 CAGTTTATCTGACTAGCACTGGGCGCAAAACATTGT
1 CAGTTTATCTGACTAGTGCTGGGCGCAAAACATTGT
* * * * * *
29530586 CGGTTTAT-TCAACTAGTGC-AGG-GCACACCTATCGT
1 CAGTTTATCT-GACTAGTGCTGGGCGCAAAAC-ATTGT
29530621 CAGTTTATCTGACTAGTGCTGGGCGCAAAACATTGT
1 CAGTTTATCTGACTAGTGCTGGGCGCAAAACATTGT
* *
29530657 CAATTTATCCGACTAGTG
1 CAGTTTATCTGACTAGTG
29530675 TAACCCATCA
Statistics
Matches: 68, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
34 5 0.07
35 22 0.32
36 36 0.53
37 5 0.07
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (36 bp):
CAGTTTATCTGACTAGTGCTGGGCGCAAAACATTGT
Found at i:29530606 original size:71 final size:71
Alignment explanation
Indices: 29530490--29530674 Score: 262
Period size: 71 Copynumber: 2.6 Consensus size: 71
29530480 GGTTCGTCCA
* * * *
29530490 ACTAGCGCTGGGTGCAAATCATTGTAGATTTATTCGACTAGTGCAGCGCACACCTATCGCCAGTT
1 ACTAGCGCTGGGCGCAAAACATTGTCGATTTATTCAACTAGTGCAGCGCACACCTATCGCCAGTT
29530555 TATCTG
66 TATCTG
* * * *
29530561 ACTAGCACTGGGCGCAAAACATTGTCGGTTTATTCAACTAGTGCAGGGCACACCTATCGTCAGTT
1 ACTAGCGCTGGGCGCAAAACATTGTCGATTTATTCAACTAGTGCAGCGCACACCTATCGCCAGTT
29530626 TATCTG
66 TATCTG
* * * *
29530632 ACTAGTGCTGGGCGCAAAACATTGTCAATTTATCCGACTAGTG
1 ACTAGCGCTGGGCGCAAAACATTGTCGATTTATTCAACTAGTG
29530675 TAACCCATCA
Statistics
Matches: 100, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 100 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (71 bp):
ACTAGCGCTGGGCGCAAAACATTGTCGATTTATTCAACTAGTGCAGCGCACACCTATCGCCAGTT
TATCTG
Found at i:29535929 original size:13 final size:13
Alignment explanation
Indices: 29535911--29535935 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29535901 CTTATTTAAA
29535911 TAAAATAAAATAG
1 TAAAATAAAATAG
29535924 TAAAATAAAATA
1 TAAAATAAAATA
29535936 AAAGTAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
TAAAATAAAATAG
Found at i:29537887 original size:29 final size:29
Alignment explanation
Indices: 29537855--29537928 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
29537845 TTGATGATTT
*
29537855 TTTCAACATTTTTAATTTATTTCAACTTA
1 TTTCAACATTTTTAATTTATTTAAACTTA
* * *
29537884 TTTCAATATTGTTAATTTATTTAAATTTA
1 TTTCAACATTTTTAATTTATTTAAACTTA
*
29537913 TTTTAACA-TTTTAATT
1 TTTCAACATTTTTAATT
29537929 GATATATTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 7 0.18
29 31 0.82
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.58
Consensus pattern (29 bp):
TTTCAACATTTTTAATTTATTTAAACTTA
Found at i:29540102 original size:21 final size:20
Alignment explanation
Indices: 29540056--29540102 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
29540046 ACGATATCCA
29540056 AGCAAAGGTTAGAAAAATAG
1 AGCAAAGGTTAGAAAAATAG
* * *
29540076 AACAAAGGTTGGAGAAATTAG
1 AGCAAAGGTTAGA-AAAATAG
29540097 AGCAAA
1 AGCAAA
29540103 TACAGATACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.53, C:0.06, G:0.26, T:0.15
Consensus pattern (20 bp):
AGCAAAGGTTAGAAAAATAG
Found at i:29542242 original size:14 final size:13
Alignment explanation
Indices: 29542190--29542242 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 13
29542180 ATCAAAAATG
29542190 AAAAG-AAAAGAAA
1 AAAAGAAAAAG-AA
*
29542203 AATAAGAAAAATAA
1 AA-AAGAAAAAGAA
29542217 AAAGAGAAAAAGAGA
1 AAA-AGAAAAAGA-A
29542232 AAAAGAAAAAG
1 AAAAGAAAAAG
29542243 GATAGGTCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
13 3 0.09
14 23 0.68
15 8 0.24
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (13 bp):
AAAAGAAAAAGAA
Found at i:29544199 original size:4 final size:4
Alignment explanation
Indices: 29544192--29544222 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
29544182 CATTCTCAAA
29544192 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
29544223 ATTCTGCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:29544821 original size:264 final size:264
Alignment explanation
Indices: 29544490--29545049 Score: 931
Period size: 264 Copynumber: 2.1 Consensus size: 264
29544480 GTAGATCGCA
* * * *
29544490 TCAGGTCTTACCTCCCTAAGGTTACAGTGGAGTAGGCAGAAGAATTTCAGATCTTATCTCCTTGA
1 TCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACAGAACAATTTCAGATCTTATCTCCTTGA
29544555 GGTTACAGTGGAGCAAATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGA
66 GGTTACAGTGGAGCAAATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGA
* *
29544620 AGACACTACCCTATCTCCCTGAAGTTATAGTAGAGCGGATTAAAATAAAGGATCTTATCTCTCTG
131 AGACACTACCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATAAAGGATCTTATCACTCTG
* ** *
29544685 AAGTTATAGTAGAGTAGATTGCATCAGGTCTTATCTCCCTGAGGTTACAGTAGAGTAGATCGAAG
196 AAGTTACAGTAGAGTAGATCCCATCAGGTCTTATCTCCCTGAGGTTACAGTAGAGTAGACCGAAG
29544750 AATT
261 AATT
* *
29544754 TCAGGTCTTATCTTCCTGAGGTTACAGTGGAGTAGACCGAACAATTTCAGATCTTATCTCCTTGA
1 TCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACAGAACAATTTCAGATCTTATCTCCTTGA
* *
29544819 GGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCTTGAGATTACAGCAGAGCAGATTGA
66 GGTTACAGTGGAGCAAATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGA
* * *
29544884 AGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGTATCTTATCACTCTG
131 AGACACTACCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATAAAGGATCTTATCACTCTG
* * *
29544949 AAGTTACAGTAGAGTAGATCCCATCAGGTCTTATCTCCCTGAGGTTATAGTGGAGTAGACCGATG
196 AAGTTACAGTAGAGTAGATCCCATCAGGTCTTATCTCCCTGAGGTTACAGTAGAGTAGACCGAAG
29545014 AATT
261 AATT
*
29545018 TCAGATCTTATCTCCCTGAGGTTACAGTGGAG
1 TCAGGTCTTATCTCCCTGAGGTTACAGTGGAG
29545050 CAGATTGAAG
Statistics
Matches: 274, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
264 274 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (264 bp):
TCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACAGAACAATTTCAGATCTTATCTCCTTGA
GGTTACAGTGGAGCAAATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGA
AGACACTACCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATAAAGGATCTTATCACTCTG
AAGTTACAGTAGAGTAGATCCCATCAGGTCTTATCTCCCTGAGGTTACAGTAGAGTAGACCGAAG
AATT
Found at i:29544956 original size:87 final size:86
Alignment explanation
Indices: 29544582--29544967 Score: 264
Period size: 87 Copynumber: 4.4 Consensus size: 86
29544572 TTGAAGCCAG
* * * * *
29544582 AGATCTTATCTCCCTG-AGATTACAGCAGAGCAGATTGAAGACACTACCCTATCTCCCTGAAGTT
1 AGATCTTATCTCTCTGAAG-TTACAGTAGAGTAGATTGAAGACACGATCCTATCTCCCTGAAGTT
* *
29544646 ATAGTAGAGCGGATTAAAATAA
65 ACAGTAGAGCAGATTAAAATAA
* * * * * *
29544668 AGGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATTGCA-TCA-GGTCTTATCTCCCTGAGGTT
1 A-GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATTGAAGACACGATCCTATCTCCCTGAAGTT
* * **
29544731 ACAGTAGAGTAGATCGAAGAATTTC
65 ACAGTAGAGCAGAT-TAA-AA-TAA
* * * ** * * *
29544756 AGGTCTTATCT-TCCTGAGGTTACAGTGGAGTAGACCGAACA-ATTTCAGATCTTATCTCCTTGA
1 AGATCTTATCTCT-CTGAAGTTACAGTAGAGTAGATTGAAGACA---C-GATCCTATCTCCCTGA
* * *** *
29544819 GGTTACAGTGGAGCAGATTGAAGCCAG
61 AGTTACAGTAGAGCAGATT-AAAATAA
* * *
29544846 AGATCTTATCTC-CTTG-AGATTACAGCAGAGCAGATTGAAGACACTATCCTATCTCCCTGAAGT
1 AGATCTTATCTCTC-TGAAG-TTACAGTAGAGTAGATTGAAGACACGATCCTATCTCCCTGAAGT
* *
29544909 TACAGTGGAGCGGATTAAAATAA
64 TACAGTAGAGCAGATTAAAATAA
*
29544932 AGTATCTTATCACTCTGAAGTTACAGTAGAGTAGAT
1 AG-ATCTTATCTCTCTGAAGTTACAGTAGAGTAGAT
29544968 CCCATCAGGT
Statistics
Matches: 225, Mismatches: 55, Indels: 39
0.71 0.17 0.12
Matches are distributed among these distances:
85 26 0.12
86 11 0.05
87 117 0.52
88 8 0.04
89 2 0.01
90 28 0.12
91 1 0.00
92 32 0.14
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (86 bp):
AGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATTGAAGACACGATCCTATCTCCCTGAAGTTA
CAGTAGAGCAGATTAAAATAA
Found at i:29544982 original size:218 final size:218
Alignment explanation
Indices: 29544754--29545419 Score: 901
Period size: 218 Copynumber: 3.1 Consensus size: 218
29544744 TCGAAGAATT
* * * *
29544754 TCAGGTCTTATCTTCCTGAGGTTACAGTGGAGTAGACCGAACAATTTCAGATCTTATCTCCTTGA
1 TCAGGTCTTATCTCCCTGAGGTTATAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGA
*
29544819 GGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCTTGAGATTACAGCAGAGCAGATTGA
66 GGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGA
*
29544884 AGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGTATCTTATCACTCTG
131 AGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCACTCTG
29544949 AAGTTACAGTAGAGTAGATCCCA
196 AAGTTACAGTAGAGTAGATCCCA
*
29544972 TCAGGTCTTATCTCCCTGAGGTTATAGTGGAGTAGACCGATGAATTTCAGATCTTATCTCCCTGA
1 TCAGGTCTTATCTCCCTGAGGTTATAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGA
*
29545037 GGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCTTGAGATTACAGCGGAACAGATTGA
66 GGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGA
* *
29545102 AGACACTATCCTATCTCCCTGAAGTTATAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTG
131 AGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCACTCTG
**
29545167 AAGTTACAGTAGAGTAGATTGCA
196 AAGTTACAGTAGAGTAGATCCCA
* * * *
29545190 TTAGGTCTTGTCTCCCTGAGGTTATAGTGGAGTAGACCGAAGAATTTTAGATCTTATCTCCCTAA
1 TCAGGTCTTATCTCCCTGAGGTTATAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGA
* * ** * * *
29545255 GCAG-T--AGTGGAGCAGATCGAGGATACCA-ATCTTATCTCCCTGAGATTATAGCGGAGCAGAT
66 G--GTTACAGTGGAGCAGATTGAAGCCA-GAGATCTTATCTCCTTGAGATTACAGCGGAGCAGAT
** * ** * * * * * * * *
29545316 AAAAGCCAGAAATCTTATTTCCCTGAAGTTGCAGTGGAGCGGATCAAAATGATGGATCTCATCCC
128 TGAAGACA-CTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCAC
* * *
29545381 TCTGAAGTTGCAGTAGAGCAGATCTCA
192 TCTGAAGTTACAGTAGAGTAGATCCCA
*
29545408 TCA-GACTTATCT
1 TCAGGTCTTATCT
29545420 TTAAAAGTTG
Statistics
Matches: 398, Mismatches: 46, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
217 58 0.15
218 338 0.85
219 1 0.00
220 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (218 bp):
TCAGGTCTTATCTCCCTGAGGTTATAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGA
GGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGA
AGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCACTCTG
AAGTTACAGTAGAGTAGATCCCA
Found at i:29545162 original size:44 final size:43
Alignment explanation
Indices: 29544413--29545221 Score: 309
Period size: 44 Copynumber: 18.6 Consensus size: 43
29544403 ATACCTATCC
* * * * *
29544413 TATCTCCCTAAAGTTATAGTAGAGCGGATTAAAATAAAGGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATT-AAATACAGGATCT
* * * * * ***
29544457 TATCTCTCTAAAGTTATAGTAGAGTAGATCGCAT-CAGG-TCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAATACAGGATCT
* ** * *
29544498 TACCTCCCT-AAGGTTACAGTGGAGTAGGCAGAAGAATTTCA-GATCT
1 TATCTCCCTGAA-GTTACAGT-G-G-A-GCAGATTAAATACAGGATCT
* * * * **
29544544 TATCTCCTTGAGGTTACAGTGGAGCAAATTGAAGCCAGAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAATACAG-GATCT
** * * ** * *
29544588 TATCTCCCTG-AGATTACAGCAGAGCAGATTGAAGACACTACCC
1 TATCTCCCTGAAG-TTACAGTGGAGCAGATTAAATACAGGATCT
* * * *
29544631 TATCTCCCTGAAGTTATAGTAGAGCGGATTAAAATAAAGGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATT-AAATACAGGATCT
* * * * **
29544675 TATCTCTCTGAAGTTATAGTAGAGTAGATTGCAT-CAGG-TCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAATACAGGATCT
* * * * *
29544716 TATCTCCCTGAGGTTACAGTAGAGTAGATCGAAGAATTTCAGG-TCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGAT--TA-AA-TACAGGATCT
* * * ** *
29544762 TATCTTCCTGAGGTTACAGTGGAGTAGACCGAACAATTTCA-GATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGA--TTA-AA-TACAGGATCT
* * * **
29544808 TATCTCCTTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAATACAG-GATCT
* ** * * ** *
29544852 TATCTCCTTG-AGATTACAGCAGAGCAGATTGAAGACACTATCC
1 TATCTCCCTGAAG-TTACAGTGGAGCAGATTAAATACAGGATCT
* * *
29544895 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGTATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATT-AAATACAGGATCT
* * * * ***
29544939 TATCACTCTGAAGTTACAGTAGAGTAGATCCCAT-CAGG-TCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAATACAGGATCT
* * * * * *
29544980 TATCTCCCTGAGGTTATAGTGGAGTAGACCGATGAATTTCA-GATCT
1 TATCTCCCTGAAGTTACAGT-G-G-AG-CAGATTAAATACAGGATCT
* * **
29545026 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAATACAG-GATCT
* * * * * ** *
29545070 TATCTCCTTG-AGATTACAGCGGAACAGATTGAAGACACTATCC
1 TATCTCCCTGAAG-TTACAGTGGAGCAGATTAAATACAGGATCT
* * *
29545113 TATCTCCCTGAAGTTATAGTGGAGCGGATTAAAATAAAGGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATT-AAATACAGGATCT
* * * ** *
29545157 TATCTCTCTGAAGTTACAGTAGAGTAGATTGCAT-TAGG-TCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAATACAGGATCT
* * *
29545198 TGTCTCCCTGAGGTTATAGTGGAG
1 TATCTCCCTGAAGTTACAGTGGAG
29545222 TAGACCGAAG
Statistics
Matches: 581, Mismatches: 147, Indels: 77
0.72 0.18 0.10
Matches are distributed among these distances:
40 2 0.00
41 87 0.15
42 27 0.05
43 95 0.16
44 240 0.41
45 15 0.03
46 114 0.20
47 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (43 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAATACAGGATCT
Found at i:29545684 original size:44 final size:44
Alignment explanation
Indices: 29545620--29545816 Score: 145
Period size: 44 Copynumber: 4.5 Consensus size: 44
29545610 CATCCAGTCT
* *
29545620 TATCTCCCTAAAGTTACAGTGGAGCAGACAGAAGAAACCAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCC
* ** ** * *
29545664 TATCTCCCTGAAGGTGCAGTGGAGTGGA-TTAA-AACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAAC-CA-ATCC
* * * * * * * *
29545708 TATCTCTCTGAAGTTACAAT--AG-AG-CAGATCGCATCCAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AGAAACCAATCC
*
29545749 TATCTCCCTGGAGTTGCAGTGGAGCAGACAGAAGAAACCAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCC
* *
29545793 TATCTCCCTGAAGGTGAAGTGGAG
1 TATCTCCCTGAAGTTGCAGTGGAG
29545817 TGCATTAAAA
Statistics
Matches: 112, Mismatches: 32, Indels: 18
0.69 0.20 0.11
Matches are distributed among these distances:
41 21 0.19
42 7 0.06
43 8 0.07
44 72 0.64
45 4 0.04
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCC
Found at i:29545692 original size:129 final size:129
Alignment explanation
Indices: 29545530--29545912 Score: 579
Period size: 129 Copynumber: 3.0 Consensus size: 129
29545520 ACAAAGCACA
* * *
29545530 AATCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAACCACAGATCTTATCTCTTTGAAGTTA
1 AATCCTATCTCCCTGAAGGTGAAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTA
* * *
29545595 CAGTAGAGCAGACCGCATCCAGTCTTATCTCCCTAAAGTTACAGTGGAGCAGACAGAAGAAACC
66 CAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACC
*
29545659 AATCCTATCTCCCTGAAGGTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTA
1 AATCCTATCTCCCTGAAGGTGAAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTA
* *
29545724 CAATAGAGCAGATCGCATCCAGTCTTATCTCCCTGGAGTTGCAGTGGAGCAGACAGAAGAAACC
66 CAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACC
* * * *
29545788 AATCCTATCTCCCTGAAGGTGAAGTGGAGTGCATTAAAATCATAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGGTGAAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTA
* * * * * *
29545853 CAGTAAAGTAGATCGCAT-CAGGTCTTATCCCCCTGAAGTTGCAGAGGGGCAGACTGAAGA
66 CAGTAGAGCAGATCGCATCCA-GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGA
29545913 TGGCGGATTT
Statistics
Matches: 232, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
128 2 0.01
129 230 0.99
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (129 bp):
AATCCTATCTCCCTGAAGGTGAAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTA
CAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACC
Found at i:29547889 original size:29 final size:28
Alignment explanation
Indices: 29547844--29547938 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 28
29547834 CTCTTTCAAA
* *
29547844 TATTTTAACATTTTTAATTTATTTCAACT
1 TATTTCAACA-TTTTAATTTATTTAAACT
* *
29547873 TATTTCAATATTGTTAATTTATTTAAATT
1 TATTTCAACATT-TTAATTTATTTAAACT
* *
29547902 TATTTTAACATTTTAATTGATATATTATACT
1 TATTTCAACATTTTAATT--TAT-TTAAACT
29547933 TATTTC
1 TATTTC
29547939 TTAAATTATG
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
28 8 0.15
29 32 0.60
30 3 0.06
31 10 0.19
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (28 bp):
TATTTCAACATTTTAATTTATTTAAACT
Found at i:29552337 original size:28 final size:28
Alignment explanation
Indices: 29552297--29552356 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
29552287 GTTTTGTGAT
* *
29552297 TGAAAGCGACTTGTGTATGGTTGACGGA
1 TGAAAGCGACTTGTGTATGATTGACGAA
29552325 TGAAAGCGACTTGTGTATGATTGACGAA
1 TGAAAGCGACTTGTGTATGATTGACGAA
29552353 TGAA
1 TGAA
29552357 GTAAGGTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.30, C:0.10, G:0.32, T:0.28
Consensus pattern (28 bp):
TGAAAGCGACTTGTGTATGATTGACGAA
Found at i:29560004 original size:18 final size:17
Alignment explanation
Indices: 29559975--29560017 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
29559965 TTTAAAAATT
*
29559975 TAAAATATAAAAGAATACA
1 TAAAA-ATAAAA-AACACA
*
29559994 TAAAAATAAAATACACA
1 TAAAAATAAAAAACACA
29560011 TAAAAAT
1 TAAAAAT
29560018 CTTAATTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 11 0.50
18 6 0.27
19 5 0.23
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.21
Consensus pattern (17 bp):
TAAAAATAAAAAACACA
Found at i:29560342 original size:19 final size:19
Alignment explanation
Indices: 29560309--29560361 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
29560299 TTCATAATAG
29560309 TAATTCATCAA-CATTTAAC
1 TAATT-ATCAATCATTTAAC
* *
29560328 TAA-TATCATATCATTTCAG
1 TAATTATCA-ATCATTTAAC
29560347 TAATTATCAATCATT
1 TAATTATCAATCATT
29560362 CATATTCGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 4 0.14
18 2 0.07
19 18 0.62
20 5 0.17
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.42
Consensus pattern (19 bp):
TAATTATCAATCATTTAAC
Found at i:29561276 original size:23 final size:26
Alignment explanation
Indices: 29561219--29561279 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 26
29561209 GAGCCATGAT
29561219 CGGTAAGCTCATTCCGAGCTAAATAA
1 CGGTAAGCTCATTCCGAGCTAAATAA
29561245 CGGTAAGCTC-TAT-CGAGCT-AA-AA
1 CGGTAAGCTCAT-TCCGAGCTAAATAA
*
29561268 TGGTAAGCTCAT
1 CGGTAAGCTCAT
29561280 AAGAGCTGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 11 0.34
24 3 0.09
25 7 0.22
26 11 0.34
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (26 bp):
CGGTAAGCTCATTCCGAGCTAAATAA
Found at i:29575491 original size:13 final size:14
Alignment explanation
Indices: 29575467--29575500 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
29575457 ATACAAATAT
29575467 CAGAATCAGATAAA
1 CAGAATCAGATAAA
*
29575481 CAGAA-CAGATAAT
1 CAGAATCAGATAAA
29575494 CAGAATC
1 CAGAATC
29575501 CTGCCCCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.53, C:0.18, G:0.15, T:0.15
Consensus pattern (14 bp):
CAGAATCAGATAAA
Found at i:29582970 original size:18 final size:18
Alignment explanation
Indices: 29582947--29583011 Score: 67
Period size: 18 Copynumber: 3.3 Consensus size: 18
29582937 TTAAATCGAT
29582947 ATCAACCTACCCAACACC
1 ATCAACCTACCCAACACC
* *
29582965 ATCAACGCCTACCTTAAATCAAC
1 ATCAA--CCTACC--CAA-CACC
29582988 ATCAACCTACCCAACACC
1 ATCAACCTACCCAACACC
29583006 ATCAAC
1 ATCAAC
29583012 TATCTTTACA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
18 14 0.37
19 2 0.05
20 6 0.16
21 6 0.16
22 2 0.05
23 8 0.21
ACGTcount: A:0.40, C:0.43, G:0.02, T:0.15
Consensus pattern (18 bp):
ATCAACCTACCCAACACC
Found at i:29582992 original size:41 final size:41
Alignment explanation
Indices: 29582930--29583011 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
29582920 ATTTGTCCTA
* *
29582930 GCCTACCTTAAATCGATATCAACCTACCCAACACCATCAAC
1 GCCTACCTTAAATCAACATCAACCTACCCAACACCATCAAC
29582971 GCCTACCTTAAATCAACATCAACCTACCCAACACCATCAAC
1 GCCTACCTTAAATCAACATCAACCTACCCAACACCATCAAC
29583012 TATCTTTACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.38, C:0.40, G:0.04, T:0.18
Consensus pattern (41 bp):
GCCTACCTTAAATCAACATCAACCTACCCAACACCATCAAC
Found at i:29582998 original size:21 final size:21
Alignment explanation
Indices: 29582931--29582998 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
29582921 TTTGTCCTAG
* *
29582931 CCTACCTTAAATCGATATCAA
1 CCTACCTTAAATCAACATCAA
* *
29582952 CCTACC--CAA-CACCATCAA
1 CCTACCTTAAATCAACATCAA
29582970 CGCCTACCTTAAATCAACATCAA
1 --CCTACCTTAAATCAACATCAA
29582993 CCTACC
1 CCTACC
29582999 CAACACCATC
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
18 6 0.17
19 2 0.06
20 6 0.17
21 12 0.33
22 2 0.06
23 8 0.22
ACGTcount: A:0.37, C:0.40, G:0.03, T:0.21
Consensus pattern (21 bp):
CCTACCTTAAATCAACATCAA
Found at i:29583852 original size:13 final size:12
Alignment explanation
Indices: 29583834--29583906 Score: 52
Period size: 12 Copynumber: 6.5 Consensus size: 12
29583824 TGTAAGCGAG
29583834 AAAAGAACATTGA
1 AAAAGAA-ATTGA
29583847 AAAAGAAATTG-
1 AAAAGAAATTGA
29583858 -AAAGAAA-TGA
1 AAAAGAAATTGA
*
29583868 AAAAGCAAA-AGA
1 AAAAG-AAATTGA
*
29583880 AGAA-AAA--GA
1 AAAAGAAATTGA
*
29583889 GAAAGAAATTGA
1 AAAAGAAATTGA
29583901 AAAAGA
1 AAAAGA
29583907 GAGTGAGACT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
9 6 0.12
10 13 0.27
11 4 0.08
12 19 0.39
13 7 0.14
ACGTcount: A:0.68, C:0.03, G:0.19, T:0.10
Consensus pattern (12 bp):
AAAAGAAATTGA
Found at i:29583870 original size:21 final size:21
Alignment explanation
Indices: 29583835--29583902 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 21
29583825 GTAAGCGAGA
29583835 AAAGAACATTGAAAAAGAAATTG
1 AAAGAA-A-TGAAAAAGAAATTG
*
29583858 AAAGAAATGAAAAAGCAAA-AG
1 AAAGAAATGAAAAAG-AAATTG
* *
29583879 -AAGAAAAAGAGAAAGAAATTG
1 AAAG-AAATGAAAAAGAAATTG
29583900 AAA
1 AAA
29583903 AAGAGAGTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
20 6 0.16
21 19 0.51
22 6 0.16
23 6 0.16
ACGTcount: A:0.68, C:0.03, G:0.19, T:0.10
Consensus pattern (21 bp):
AAAGAAATGAAAAAGAAATTG
Found at i:29591133 original size:49 final size:49
Alignment explanation
Indices: 29591068--29591687 Score: 1052
Period size: 47 Copynumber: 12.9 Consensus size: 49
29591058 TAGTATGGCG
*
29591068 TAATGGCTGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
*
29591117 TAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
29591166 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
*
29591215 TAATGGCCGATGTGATAAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
29591262 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
29591311 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
29591360 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
29591407 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
29591454 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
29591501 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
29591550 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
* *
29591597 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGACAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
* * * * *
29591644 GAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
29591688 TCCCGAAGGG
Statistics
Matches: 551, Mismatches: 14, Indels: 14
0.95 0.02 0.02
Matches are distributed among these distances:
47 282 0.51
48 1 0.00
49 268 0.49
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (49 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
Found at i:29591273 original size:96 final size:97
Alignment explanation
Indices: 29591068--29591687 Score: 1046
Period size: 96 Copynumber: 6.5 Consensus size: 97
29591058 TAGTATGGCG
* *
29591068 TAATGGCTGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
29591133 GAATGTGAAAGTGTATATATATGTGATAAGGCC
66 GAATGTGAAAGTG-ATATATATGTGATAAGGCC
29591166 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
29591231 AAATGTGAAAGTG-TATATATGTGATAAGGCC
66 GAATGTGAAAGTGATATATATGTGATAAGGCC
29591262 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
29591327 GAATGTGAAAGTGTATATATATGTGATAAGGCC
66 GAATGTGAAAGTG-ATATATATGTGATAAGGCC
29591360 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
29591423 GAATGTGAAAGTG-TATATATGTGATAAGGCC
66 GAATGTGAAAGTGATATATATGTGATAAGGCC
29591454 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
29591517 GAATGTGAAAGTGTATATATATGTGATAAGGCC
66 GAATGTGAAAGTG-ATATATATGTGATAAGGCC
29591550 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
* *
29591613 GAATGTGAAAGTG-TATATATGTGACAGGGCC
66 GAATGTGAAAGTGATATATATGTGATAAGGCC
* * * * *
29591644 GAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
29591688 TCCCGAAGGG
Statistics
Matches: 505, Mismatches: 11, Indels: 16
0.95 0.02 0.03
Matches are distributed among these distances:
94 144 0.29
95 1 0.00
96 238 0.47
98 122 0.24
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (97 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
GAATGTGAAAGTGATATATATGTGATAAGGCC
Found at i:29595314 original size:21 final size:21
Alignment explanation
Indices: 29595288--29595351 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
29595278 TTAGGGTGGA
29595288 TAAGCTCTTACGAGCTTCTGT
1 TAAGCTCTTACGAGCTTCTGT
29595309 TAAGCTCTTACGAGCTTCTGT
1 TAAGCTCTTACGAGCTTCTGT
* * *
29595330 TCAGCTCTTATGAGCTTTTGT
1 TAAGCTCTTACGAGCTTCTGT
29595351 T
1 T
29595352 GATGTGTTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (21 bp):
TAAGCTCTTACGAGCTTCTGT
Found at i:29597503 original size:29 final size:28
Alignment explanation
Indices: 29597411--29597528 Score: 98
Period size: 29 Copynumber: 4.1 Consensus size: 28
29597401 TTTAATTAAT
** * *
29597411 TTTTTAAAATTTAAAAATATTTTTTATAAT
1 TTTTTAATTTTTAAAAATA-ATTTTA-AAA
* **
29597441 TTTTTACTTTTTAAAAAATAATTTTAATG
1 TTTTTAATTTTT-AAAAATAATTTTAAAA
*
29597470 CTTTTAATTTTTAAAAATAATTTTAAAAA
1 TTTTTAATTTTTAAAAATAATTTT-AAAA
29597499 TTTTTGAA-TTTTAAAAAT--TTTTAAAA
1 TTTTT-AATTTTTAAAAATAATTTTAAAA
29597525 TTTT
1 TTTT
29597529 CAAAAGTTAA
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
26 8 0.11
27 4 0.05
28 12 0.16
29 27 0.36
30 16 0.22
31 7 0.09
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (28 bp):
TTTTTAATTTTTAAAAATAATTTTAAAA
Found at i:29597510 original size:17 final size:17
Alignment explanation
Indices: 29597488--29597520 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29597478 TTTTAAAAAT
29597488 AATTTTAAAAATTTTTG
1 AATTTTAAAAATTTTTG
29597505 AATTTTAAAAATTTTT
1 AATTTTAAAAATTTTT
29597521 AAAATTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AATTTTAAAAATTTTTG
Found at i:29598326 original size:20 final size:21
Alignment explanation
Indices: 29598303--29598345 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
29598293 AATTTGAAAA
*
29598303 TTAAAATATTTATTT-TAATT
1 TTAAAATATTAATTTCTAATT
*
29598323 TTAAATTATTAATTTCTAATT
1 TTAAAATATTAATTTCTAATT
29598344 TT
1 TT
29598346 TTTATGCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAAAATATTAATTTCTAATT
Found at i:29610075 original size:29 final size:29
Alignment explanation
Indices: 29610021--29610078 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
29610011 CTCCTGAACT
*
29610021 ATATTATTTTTCTCACTTTGACACTTAAA
1 ATATTATTTTTCTCACTTCGACACTTAAA
**
29610050 ATATT-TTTTTGCTCACTTCGGTACTTAAA
1 ATATTATTTTT-CTCACTTCGACACTTAAA
29610079 GTTTCATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (29 bp):
ATATTATTTTTCTCACTTCGACACTTAAA
Found at i:29610238 original size:18 final size:17
Alignment explanation
Indices: 29610215--29610248 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29610205 CCACATTGAT
29610215 TAAAATTATAAAAAATTC
1 TAAAATT-TAAAAAATTC
*
29610233 TAAAATTTCAAAAATT
1 TAAAATTTAAAAAATT
29610249 ATATAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAATTTAAAAAATTC
Found at i:29610371 original size:25 final size:24
Alignment explanation
Indices: 29610321--29610371 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
29610311 AATATATAAC
* * *
29610321 TTTTAAAAATTAAAGTTCAAATTA
1 TTTTAAAAATTAAAATTAAAAATA
*
29610345 TTTTAAAATTTTAAAATTAAAAATA
1 TTTTAAAA-ATTAAAATTAAAAATA
29610370 TT
1 TT
29610372 GTCATAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (24 bp):
TTTTAAAAATTAAAATTAAAAATA
Found at i:29618817 original size:3 final size:3
Alignment explanation
Indices: 29618746--29618797 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
29618736 AACCATGCTG
29618746 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29618793 ATA AT
1 ATA AT
29618798 GCAAAGAACA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:29619741 original size:27 final size:28
Alignment explanation
Indices: 29619692--29619747 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
29619682 AAAATTTTCA
*
29619692 AAAAAATTATAATATTATTTTAAAAATT
1 AAAAAATTATAATATTATCTTAAAAATT
29619720 AAAAAATATATAA-ATT-TCTTAAAAATT
1 AAAAAAT-TATAATATTATCTTAAAAATT
29619747 A
1 A
29619748 TATTAAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 11 0.42
28 10 0.38
29 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (28 bp):
AAAAAATTATAATATTATCTTAAAAATT
Found at i:29621081 original size:7 final size:7
Alignment explanation
Indices: 29621067--29621101 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
29621057 GTTACATTTG
29621067 AAATATA
1 AAATATA
*
29621074 ATATATA
1 AAATATA
29621081 AAA-ATA
1 AAATATA
29621087 AAATATA
1 AAATATA
29621094 AAATATA
1 AAATATA
29621101 A
1 A
29621102 GTGTTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAATATA
Found at i:29621092 original size:13 final size:14
Alignment explanation
Indices: 29621067--29621101 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
29621057 GTTACATTTG
*
29621067 AAATATAATATATA
1 AAATATAAAATATA
29621081 AAA-ATAAAATATA
1 AAATATAAAATATA
29621094 AAATATAA
1 AAATATAA
29621102 GTGTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATATAAAATATA
Found at i:29622245 original size:20 final size:19
Alignment explanation
Indices: 29622222--29622288 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 19
29622212 GTCAAAACTA
29622222 TATAAAATAATATAAAATTT
1 TATAAAATAA-ATAAAATTT
29622242 TATATTAAA-AAATAAAA-TT
1 TATA--AAATAAATAAAATTT
*
29622261 TATGAAATAAAT--AATTT
1 TATAAAATAAATAAAATTT
*
29622278 TTTAAAATAAA
1 TATAAAATAAA
29622289 AATTTATTAC
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
16 2 0.05
17 14 0.35
18 4 0.10
19 5 0.12
20 10 0.25
21 2 0.05
22 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (19 bp):
TATAAAATAAATAAAATTT
Found at i:29622245 original size:22 final size:20
Alignment explanation
Indices: 29622220--29622261 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
29622210 TAGTCAAAAC
29622220 TATATAAAATAATATAAAATTT
1 TATATAAAA-AA-ATAAAATTT
*
29622242 TATATTAAAAAATAAAATTT
1 TATATAAAAAAATAAAATTT
29622262 ATGAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TATATAAAAAAATAAAATTT
Found at i:29630330 original size:11 final size:11
Alignment explanation
Indices: 29630310--29630359 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
29630300 TTTTGTAGAT
29630310 TTTTGGTGTTG
1 TTTTGGTGTTG
*
29630321 TTTTGATGTTG
1 TTTTGGTGTTG
* **
29630332 TTTTGCTACTG
1 TTTTGGTGTTG
29630343 TTGTTGGTGTTG
1 TT-TTGGTGTTG
29630355 TTTTG
1 TTTTG
29630360 CTACTTTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
11 23 0.74
12 8 0.26
ACGTcount: A:0.04, C:0.04, G:0.30, T:0.62
Consensus pattern (11 bp):
TTTTGGTGTTG
Found at i:29630353 original size:23 final size:22
Alignment explanation
Indices: 29630319--29630370 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
29630309 TTTTTGGTGT
29630319 TGTTTTGATGTTGTTTTGCTAC
1 TGTTTTGATGTTGTTTTGCTAC
*
29630341 TGTTGTTGGTGTTGTTTTGCTAC
1 TGTT-TTGATGTTGTTTTGCTAC
*
29630364 TTTTTTG
1 TGTTTTG
29630371 TGCTATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.06, C:0.08, G:0.25, T:0.62
Consensus pattern (22 bp):
TGTTTTGATGTTGTTTTGCTAC
Found at i:29632798 original size:27 final size:27
Alignment explanation
Indices: 29632722--29632801 Score: 124
Period size: 27 Copynumber: 3.0 Consensus size: 27
29632712 ACACGCCATA
29632722 AAAGAAAAGCCTTTGCGGTGAATTATG
1 AAAGAAAAGCCTTTGCGGTGAATTATG
* *
29632749 AAAGAAAAGTCTTCGCGGTGAATTATG
1 AAAGAAAAGCCTTTGCGGTGAATTATG
* *
29632776 AAAGAAAAGCCTTTGTGGCGAATTAT
1 AAAGAAAAGCCTTTGCGGTGAATTAT
29632802 TGAAGGATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.26
Consensus pattern (27 bp):
AAAGAAAAGCCTTTGCGGTGAATTATG
Found at i:29636431 original size:25 final size:26
Alignment explanation
Indices: 29636390--29636440 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
29636380 ATAATATAAC
* *
29636390 TTTTAATATAAATATAGTATTAATAT
1 TTTTAATATAAATATAGAATAAATAT
29636416 TTTTAAT-TATAA-ATAGAATAAATAT
1 TTTTAATATA-AATATAGAATAAATAT
29636441 AAATATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (26 bp):
TTTTAATATAAATATAGAATAAATAT
Found at i:29637702 original size:48 final size:48
Alignment explanation
Indices: 29637620--29637713 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
29637610 TTTCTTGGCT
* * *
29637620 TAAAAGCGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
*
29637668 TAAAAACGCCTAAGTCAG-CTCAAC-TCGTAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
29637714 AGAATTCCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 4 0.10
48 36 0.90
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:29640218 original size:48 final size:48
Alignment explanation
Indices: 29640136--29640229 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
29640126 TTTCTTGGCT
* * *
29640136 TAAAAGCGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
29640184 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
29640230 AGAATTCCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 4 0.10
48 37 0.90
ACGTcount: A:0.39, C:0.28, G:0.14, T:0.19
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:29643271 original size:17 final size:18
Alignment explanation
Indices: 29643249--29643282 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
29643239 CGATCGTGTC
29643249 AAACGCGA-CGCGACCGA
1 AAACGCGACCGCGACCGA
29643266 AAACGCGACCGCGACCG
1 AAACGCGACCGCGACCG
29643283 CAATTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.32, C:0.38, G:0.29, T:0.00
Consensus pattern (18 bp):
AAACGCGACCGCGACCGA
Found at i:29657256 original size:44 final size:44
Alignment explanation
Indices: 29657146--29657258 Score: 154
Period size: 44 Copynumber: 2.6 Consensus size: 44
29657136 ACTACTGCTT
* *
29657146 AGGGAGATAGGATCTACAATCTTCAACCTATTCCACTGCAGTCC
1 AGGGAGATAGGATTTACAATCTTCAACCTATTCCACTGCAGCCC
* * **
29657190 AGGGAGATAGGACTTACAATCTTTAACCTATTCCACTGTTGCCC
1 AGGGAGATAGGATTTACAATCTTCAACCTATTCCACTGCAGCCC
* *
29657234 AGGGAGATAGGATTTGCTATCTTCA
1 AGGGAGATAGGATTTACAATCTTCA
29657259 CCGATCTCTA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (44 bp):
AGGGAGATAGGATTTACAATCTTCAACCTATTCCACTGCAGCCC
Found at i:29666422 original size:55 final size:55
Alignment explanation
Indices: 29666344--29666456 Score: 217
Period size: 55 Copynumber: 2.1 Consensus size: 55
29666334 CTTTCGATTT
*
29666344 TTTGACAAGCTCCTCTCTAAAGCCTCGTTTCGTACTTGAACTTCTTGGAATTTTC
1 TTTGACAAGCTCCTCTCTAAAGCCTCGTTTCGTACTTGAACTTCCTGGAATTTTC
29666399 TTTGACAAGCTCCTCTCTAAAGCCTCGTTTCGTACTTGAACTTCCTGGAATTTTC
1 TTTGACAAGCTCCTCTCTAAAGCCTCGTTTCGTACTTGAACTTCCTGGAATTTTC
29666454 TTT
1 TTT
29666457 CCCACCTATC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.19, C:0.26, G:0.14, T:0.41
Consensus pattern (55 bp):
TTTGACAAGCTCCTCTCTAAAGCCTCGTTTCGTACTTGAACTTCCTGGAATTTTC
Found at i:29673435 original size:17 final size:17
Alignment explanation
Indices: 29673407--29673457 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
29673397 ACTTTCAAGA
*
29673407 AAATGATTTACGAAAAC
1 AAATGTTTTACGAAAAC
*
29673424 AACA-GTTTTACGTAAAC
1 AA-ATGTTTTACGAAAAC
29673441 AAATGTTTT-CGAAAAC
1 AAATGTTTTACGAAAAC
29673457 A
1 A
29673458 CAAGTTCGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 8 0.28
17 20 0.69
18 1 0.03
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (17 bp):
AAATGTTTTACGAAAAC
Found at i:29674040 original size:19 final size:19
Alignment explanation
Indices: 29673995--29674045 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
29673985 ACTGAAACTG
29673995 ATGCATAAAA--TTTTATA
1 ATGCATAAAAGTTTTTATA
*
29674012 ATGTAGATAAAAGTTTTTATA
1 ATG--CATAAAAGTTTTTATA
29674033 ATGCATAAAAGTT
1 ATGCATAAAAGTT
29674046 GTTTTGATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 3 0.11
19 15 0.54
21 10 0.36
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.39
Consensus pattern (19 bp):
ATGCATAAAAGTTTTTATA
Found at i:29680764 original size:27 final size:28
Alignment explanation
Indices: 29680727--29680780 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
29680717 CTAAACTTTA
29680727 AGGTTCAAGGTTTAG-GTTTAGGGTTTT
1 AGGTTCAAGGTTTAGAGTTTAGGGTTTT
* * *
29680754 AGGTTCGAGGTTTGGAGTTTATGGTTT
1 AGGTTCAAGGTTTAGAGTTTAGGGTTT
29680781 GCAGTTACGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.17, C:0.04, G:0.35, T:0.44
Consensus pattern (28 bp):
AGGTTCAAGGTTTAGAGTTTAGGGTTTT
Found at i:29687243 original size:24 final size:24
Alignment explanation
Indices: 29687215--29687266 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
29687205 AATAAAAAAT
*
29687215 AAAAAGTAGTCCAAAATCAACAGA
1 AAAAAGTAGTCCAAAAGCAACAGA
* *
29687239 AAAAAGTTGTCCAAAAGCAATAGA
1 AAAAAGTAGTCCAAAAGCAACAGA
29687263 AAAA
1 AAAA
29687267 TATGAAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.60, C:0.13, G:0.13, T:0.13
Consensus pattern (24 bp):
AAAAAGTAGTCCAAAAGCAACAGA
Found at i:29687748 original size:8 final size:7
Alignment explanation
Indices: 29687738--29687762 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29687728 AGGATTTTGT
29687738 TTTTTTA
1 TTTTTTA
29687745 TTTTTTA
1 TTTTTTA
29687752 TTTTTTA
1 TTTTTTA
29687759 TTTT
1 TTTT
29687763 ACCTTACAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:29688443 original size:7 final size:7
Alignment explanation
Indices: 29688431--29688455 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29688421 TTGTTGTTTT
29688431 TAAAAAA
1 TAAAAAA
29688438 TAAAAAA
1 TAAAAAA
29688445 TAAAAAA
1 TAAAAAA
29688452 TAAA
1 TAAA
29688456 TTATGCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:29693389 original size:24 final size:25
Alignment explanation
Indices: 29693325--29693403 Score: 69
Period size: 24 Copynumber: 3.3 Consensus size: 25
29693315 CAAAAGAGCG
*
29693325 TCCCGATATTA-GCTCTCTC-TAGCT
1 TCCCGATAATATGCTCT-TCGTAGCT
* *
29693349 TCCCG-TTATATGGTCTTGCG-AGCT
1 TCCCGATAATATGCTCTT-CGTAGCT
*
29693373 TCCCGATAATAT-CTCTTCGTAGCA
1 TCCCGATAATATGCTCTTCGTAGCT
29693397 TCCCGAT
1 TCCCGAT
29693404 TGGTTGTGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
23 6 0.14
24 33 0.75
25 5 0.11
ACGTcount: A:0.18, C:0.30, G:0.16, T:0.35
Consensus pattern (25 bp):
TCCCGATAATATGCTCTTCGTAGCT
Done.