Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013095.1 Kokia drynarioides strain JFW-HI SEQ_128113, whole genome shotgun sequence
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: 427744
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 263 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:4578 original size:3 final size:3
Alignment explanation
Indices: 4570--4594 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4560 TTATGACGTG
4570 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
4595 AGGATGCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5880 original size:22 final size:22
Alignment explanation
Indices: 5855--5898 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5845 AAGCTTTGAT
5855 TTTAAAATTAGGTTTAAATTTA
1 TTTAAAATTAGGTTTAAATTTA
* **
5877 TTTAAATTTATTTTTAAATTTA
1 TTTAAAATTAGGTTTAAATTTA
5899 AATTTATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TTTAAAATTAGGTTTAAATTTA
Found at i:5885 original size:6 final size:6
Alignment explanation
Indices: 5867--5939 Score: 73
Period size: 6 Copynumber: 12.8 Consensus size: 6
5857 TAAAATTAGG
** *
5867 TTTAAA TTT--A TTTAAA TTTATT TTTAAA TTTAAA TTTATA -TTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
**
5912 TTTAAA TTT-GC TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
5940 TCAAATTTGA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
4 4 0.08
5 7 0.13
6 42 0.79
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:5898 original size:28 final size:31
Alignment explanation
Indices: 5867--5947 Score: 96
Period size: 34 Copynumber: 2.6 Consensus size: 31
5857 TAAAATTAGG
5867 TTTAAATTTATTTAAATTT-A-TT-TTTAAA
1 TTTAAATTTATTTAAATTTAATTTCTTTAAA
5895 TTTAAATTTATATTAAATTTAAATTTGCTTTAAA
1 TTTAAATTTAT-TTAAATTT-AATTT-CTTTAAA
* *
5929 TTTAAATTTAATCAAATTT
1 TTTAAATTTATTTAAATTT
5948 GAATGGATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
28 11 0.24
29 8 0.18
31 1 0.02
32 2 0.04
33 7 0.16
34 16 0.36
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (31 bp):
TTTAAATTTATTTAAATTTAATTTCTTTAAA
Found at i:5912 original size:17 final size:17
Alignment explanation
Indices: 5876--5947 Score: 85
Period size: 17 Copynumber: 4.2 Consensus size: 17
5866 GTTTAAATTT
*
5876 ATTTAAATTTATTTTTAA
1 ATTTAAATTTA-TATTAA
5894 ATTTAAATTTATATTAA
1 ATTTAAATTTATATTAA
*
5911 ATTTAAATTTGCT-TTAA
1 ATTTAAATTT-ATATTAA
*
5928 ATTTAAATTTA-ATCAA
1 ATTTAAATTTATATTAA
5944 ATTT
1 ATTT
5948 GAATGGATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
16 7 0.15
17 29 0.60
18 12 0.25
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (17 bp):
ATTTAAATTTATATTAA
Found at i:5990 original size:13 final size:13
Alignment explanation
Indices: 5974--6007 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5964 TTAATATTTA
5974 AAATTAAAAGCCC
1 AAATTAAAAGCCC
*
5987 AAATTAAAAGTCC
1 AAATTAAAAGCCC
*
6000 AAAATAAA
1 AAATTAAA
6008 TACAAAATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.62, C:0.15, G:0.06, T:0.18
Consensus pattern (13 bp):
AAATTAAAAGCCC
Found at i:6674 original size:21 final size:21
Alignment explanation
Indices: 6641--6680 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6631 ATGTTTTTAA
* * *
6641 TAATATTATTAATTATATTGG
1 TAATAATAATAATAATATTGG
6662 TAATAATAATAATAATATT
1 TAATAATAATAATAATATT
6681 ACTAATATCA
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:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
TAATAATAATAATAATATTGG
Found at i:7853 original size:30 final size:30
Alignment explanation
Indices: 7820--8199 Score: 304
Period size: 30 Copynumber: 12.7 Consensus size: 30
7810 TTACCCCCCG
* * * *
7820 AACTTCTAAAGATCCCATTTTTGACCCTCG
1 AACTTCAAAAAATACCATTTTTGACCCTCA
7850 AACTTCAAAAAAT-CTCATTTTTGA-CCTCAA
1 AACTTCAAAAAATAC-CATTTTTGACCCTC-A
* *
7880 AACTTCTAAAAATTACCATTTAAT-ACCCTCA
1 AACTTC-AAAAAATACCATTT-TTGACCCTCA
* *
7911 AACTTCCAAAAATTCCATTTTTGA-CCTCAA
1 AACTTCAAAAAATACCATTTTTGACCCTC-A
* * * *
7941 AACTTCCAAAAATAACA-TTTTAACCC-CG
1 AACTTCAAAAAATACCATTTTTGACCCTCA
*
7969 AACTTCCAAAAAAT-CTCATTTTTGACCCTAA
1 AACTT-CAAAAAATAC-CATTTTTGACCCTCA
* *
8000 AACTTCCAAAAAATACCA-TTTT-ACCCCCG
1 AACTT-CAAAAAATACCATTTTTGACCCTCA
* * *
8029 AACTTCCAAAAATTCCATTTTTGACCCTAA
1 AACTTCAAAAAATACCATTTTTGACCCTCA
*
8059 AACTTCAAAAAATTACCA-TTTTAACCC-CA
1 AACTTCAAAAAA-TACCATTTTTGACCCTCA
*
8088 AACTTACAAAAAATCCCATTTTTGA-CCTCGA
1 AACTT-CAAAAAATACCATTTTTGACCCTC-A
* *
8119 AACTTCCAAAAATTACCA-TTTT-ACCCCCA
1 AACTT-CAAAAAATACCATTTTTGACCCTCA
* *
8148 AACTTCCAAAAATCCCATTTTTGACCC-CGA
1 AACTTCAAAAAATACCATTTTTGACCCTC-A
*
8178 AACTTCCAAAAATTACCATTTT
1 AACTT-CAAAAAATACCATTTT
8200 ACTCTCGGAT
Statistics
Matches: 282, Mismatches: 42, Indels: 51
0.75 0.11 0.14
Matches are distributed among these distances:
28 24 0.09
29 62 0.22
30 121 0.43
31 68 0.24
32 7 0.02
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.30
Consensus pattern (30 bp):
AACTTCAAAAAATACCATTTTTGACCCTCA
Found at i:8137 original size:119 final size:118
Alignment explanation
Indices: 7850--8200 Score: 519
Period size: 119 Copynumber: 2.9 Consensus size: 118
7840 TTGACCCTCG
* *
7850 AACTTCAAAAAATCTCATTTTTGACCTCAAAACTTCTAAAAATTACCATTTAATACCCTCAAACT
1 AACTTCAAAAAATCTCATTTTTGACCTCAAAACTTCCAAAAATTACCATTT--TACCCCCAAACT
* *
7915 TCCAAAAATTCCATTTTTGA-CCTCAAAACTTCCAAAAA-TAACATTTTAACCCCG
64 TCCAAAAATTCCATTTTTGACCCT-AAAACTTCCAAAAATTACCATTTTAACCCCA
* *
7969 AACTTCCAAAAAATCTCATTTTTGACC-CTAAAACTTCCAAAAAATACCATTTTACCCCCGAACT
1 AACTT-CAAAAAATCTCATTTTTGACCTC-AAAACTTCCAAAAATTACCATTTTACCCCCAAACT
*
8033 TCCAAAAATTCCATTTTTGACCCTAAAACTTCAAAAAATTACCATTTTAACCCCA
64 TCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACCATTTTAACCCCA
* *
8088 AACTTACAAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTACCCCCAAACTT
1 AACTT-CAAAAAATCTCATTTTTGACCTCAAAACTTCCAAAAATTACCATTTTACCCCCAAACTT
* **
8153 CCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTACCATTTTA
65 CCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACCATTTTA
8201 CTCTCGGATG
Statistics
Matches: 211, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
118 43 0.20
119 125 0.59
120 43 0.20
ACGTcount: A:0.39, C:0.28, G:0.03, T:0.30
Consensus pattern (118 bp):
AACTTCAAAAAATCTCATTTTTGACCTCAAAACTTCCAAAAATTACCATTTTACCCCCAAACTTC
CAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACCATTTTAACCCCA
Found at i:8201 original size:59 final size:59
Alignment explanation
Indices: 7850--8201 Score: 463
Period size: 59 Copynumber: 5.9 Consensus size: 59
7840 TTGACCCTCG
* * * * *
7850 AACTTCAAAAAATCTCATTTTTGACCTCAAAACTTCTAAAAATTACCATTTAATACCCTCA
1 AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTACCATTT--TACCCCCA
* * * * *
7911 AACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAA-TAACATTTTAACCCCG
1 AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCCCA
* * * *
7969 AACTTCCAAAAAATCTCATTTTTGACCCTAAAACTTCCAAAAAATACCATTTTACCCCCG
1 AACTTCC-AAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCCCA
* * * *
8029 AACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCAAAAAATTACCATTTTAACCCCA
1 AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCCCA
* * *
8088 AACTTACAAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTACCCCCA
1 AACTT-CCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCCCA
*
8148 AACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTACCATTTTAC
1 AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTAC
8202 TCTCGGATGT
Statistics
Matches: 259, Mismatches: 29, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
58 12 0.05
59 129 0.50
60 80 0.31
61 38 0.15
ACGTcount: A:0.39, C:0.28, G:0.03, T:0.30
Consensus pattern (59 bp):
AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCCCA
Found at i:11241 original size:17 final size:17
Alignment explanation
Indices: 11219--11300 Score: 85
Period size: 17 Copynumber: 4.8 Consensus size: 17
11209 CAAACTCATT
11219 TTAAATTTATTTTAAGA
1 TTAAATTTATTTTAAGA
* *
11236 TTAAATTTGTTTTAAAA
1 TTAAATTTATTTTAAGA
*
11253 TTTAAATTTATTTTTAA-T
1 -TTAAATTTA-TTTTAAGA
* * *
11271 TTAAATTTAATTTGAGT
1 TTAAATTTATTTTAAGA
11288 TTAAATTTATTTT
1 TTAAATTTATTTT
11301 TATCCATTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
16 4 0.07
17 37 0.67
18 8 0.15
19 6 0.11
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
TTAAATTTATTTTAAGA
Found at i:18077 original size:4 final size:4
Alignment explanation
Indices: 18068--18099 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
18058 TAACAAAAGG
18068 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
18100 CTTTAAGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:18629 original size:15 final size:15
Alignment explanation
Indices: 18609--18797 Score: 99
Period size: 15 Copynumber: 12.2 Consensus size: 15
18599 TTATCGTTCG
*
18609 CATTTGGTACCGCAA
1 CATTTGGTACAGCAA
* *
18624 CATTTGGTGTAAAAGCAG
1 CATTT-G-GT-ACAGCAA
* **
18642 CATTTGGAACCCCAA
1 CATTTGGTACAGCAA
* *
18657 AATTTGGTACAGCAG
1 CATTTGGTACAGCAA
* *
18672 CATCTAGTGTAACAGCAG
1 CAT-TTG-GT-ACAGCAA
* ** *
18690 CATTTGGAACCCCAG
1 CATTTGGTACAGCAA
* *
18705 CATTTGGCACAACAA
1 CATTTGGTACAGCAA
*
18720 CATTTGGTACAGCAG
1 CATTTGGTACAGCAA
**
18735 CATTTGGTACCCCAA
1 CATTTGGTACAGCAA
*
18750 CATTTGGCACAGCAA
1 CATTTGGTACAGCAA
* * * *
18765 CATTCGATATAGCAG
1 CATTTGGTACAGCAA
*
18780 CATTTGGTACAGCGA
1 CATTTGGTACAGCAA
18795 CAT
1 CAT
18798 AGGGCAGCGG
Statistics
Matches: 126, Mismatches: 42, Indels: 12
0.70 0.23 0.07
Matches are distributed among these distances:
15 95 0.75
16 5 0.04
17 7 0.06
18 19 0.15
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (15 bp):
CATTTGGTACAGCAA
Found at i:18666 original size:48 final size:47
Alignment explanation
Indices: 18609--18768 Score: 198
Period size: 48 Copynumber: 3.4 Consensus size: 47
18599 TTATCGTTCG
* * *
18609 CATTTGGTACCGCAACATTTGGTGTAAAAGCAGCATTTGGAACCCCAA
1 CATTTGGCACAGCAACATTT-GTGTAACAGCAGCATTTGGAACCCCAA
* * * * *
18657 AATTTGGTACAGCAGCATCTAGTGTAACAGCAGCATTTGGAACCCCAG
1 CATTTGGCACAGCAACAT-TTGTGTAACAGCAGCATTTGGAACCCCAA
* *
18705 CATTTGGCACAACAACATTTG-GT-ACAGCAGCATTTGGTACCCCAA
1 CATTTGGCACAGCAACATTTGTGTAACAGCAGCATTTGGAACCCCAA
18750 CATTTGGCACAGCAACATT
1 CATTTGGCACAGCAACATT
18769 CGATATAGCA
Statistics
Matches: 97, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
45 38 0.39
46 2 0.02
47 2 0.02
48 54 0.56
49 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (47 bp):
CATTTGGCACAGCAACATTTGTGTAACAGCAGCATTTGGAACCCCAA
Found at i:18673 original size:30 final size:30
Alignment explanation
Indices: 18637--18768 Score: 111
Period size: 30 Copynumber: 4.3 Consensus size: 30
18627 TTGGTGTAAA
* *
18637 AGCAGCATTTGGAACCCCAAAATTTGGTAC
1 AGCAGCATTTGGAACACCAACATTTGGTAC
* * * *
18667 AGCAGCATCTAGTGTAACAGCAGCATTTGGAAC
1 AGCAGCAT-T--TGGAACACCAACATTTGGTAC
** * *
18700 CCCAGCATTTGGCACAACAACATTTGGTAC
1 AGCAGCATTTGGAACACCAACATTTGGTAC
* * *
18730 AGCAGCATTTGGTACCCCAACATTTGGCAC
1 AGCAGCATTTGGAACACCAACATTTGGTAC
*
18760 AGCAACATT
1 AGCAGCATT
18769 CGATATAGCA
Statistics
Matches: 79, Mismatches: 20, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
30 56 0.71
31 1 0.01
32 1 0.01
33 21 0.27
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.23
Consensus pattern (30 bp):
AGCAGCATTTGGAACACCAACATTTGGTAC
Found at i:18789 original size:45 final size:45
Alignment explanation
Indices: 18637--18786 Score: 183
Period size: 45 Copynumber: 3.3 Consensus size: 45
18627 TTGGTGTAAA
* * *
18637 AGCAGCATTTGGAACCCCAAAATTTGGTACAGCAGCATCTAGTGTAAC
1 AGCAGCATTTGGAACCCCAACATTTGGCACAGCAACAT-TAG-GT-AC
* * *
18685 AGCAGCATTTGGAACCCCAGCATTTGGCACAACAACATTTGGTAC
1 AGCAGCATTTGGAACCCCAACATTTGGCACAGCAACATTAGGTAC
* * * *
18730 AGCAGCATTTGGTACCCCAACATTTGGCACAGCAACATTCGATAT
1 AGCAGCATTTGGAACCCCAACATTTGGCACAGCAACATTAGGTAC
18775 AGCAGCATTTGG
1 AGCAGCATTTGG
18787 TACAGCGACA
Statistics
Matches: 90, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
45 53 0.59
46 2 0.02
47 2 0.02
48 33 0.37
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (45 bp):
AGCAGCATTTGGAACCCCAACATTTGGCACAGCAACATTAGGTAC
Found at i:21013 original size:20 final size:19
Alignment explanation
Indices: 20998--21053 Score: 85
Period size: 20 Copynumber: 2.9 Consensus size: 19
20988 TCAAAACAAT
20998 AACCAAAATAGTAAAAAAA
1 AACCAAAATAGTAAAAAAA
* *
21017 ATACCAAAACAGTAAAAAAC
1 A-ACCAAAATAGTAAAAAAA
21037 AACCAAAATAGTAAAAA
1 AACCAAAATAGTAAAAA
21054 GAAGCACCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.70, C:0.14, G:0.05, T:0.11
Consensus pattern (19 bp):
AACCAAAATAGTAAAAAAA
Found at i:21035 original size:19 final size:18
Alignment explanation
Indices: 20998--21067 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 18
20988 TCAAAACAAT
*
20998 AACCAAAATAGTAAAAAAA
1 AACCAAAACAGT-AAAAAA
21017 ATACCAAAACAGTAAAAAA
1 A-ACCAAAACAGTAAAAAA
*
21036 CAACCAAAATAGTAAAAAGA
1 -AACCAAAACAGTAAAAA-A
21056 AGCACCAAAACA
1 A--ACCAAAACA
21068 AGAATATGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
19 23 0.53
20 12 0.28
21 8 0.19
ACGTcount: A:0.67, C:0.17, G:0.07, T:0.09
Consensus pattern (18 bp):
AACCAAAACAGTAAAAAA
Found at i:21041 original size:39 final size:39
Alignment explanation
Indices: 20955--21067 Score: 117
Period size: 39 Copynumber: 2.9 Consensus size: 39
20945 AAATAACAGT
* *
20955 AAAACAACAAAAATAG-AAACAAAAATA--ACAACATCAA
1 AAAACAACCAAAATAGTAAA-AAAAATACCAAAACATCAA
*
20992 AACAATAACCAAAATAGTAAAAAAAATACCAAAACAGT-AA
1 AA-AACAACCAAAATAGTAAAAAAAATACCAAAACA-TCAA
**
21032 AAAACAACCAAAATAGTAAAAAGAAGCACCAAAACA
1 AAAACAACCAAAATAGTAAAAA-AAATACCAAAACA
21068 AGAATATGAT
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
37 2 0.03
38 19 0.30
39 22 0.34
40 20 0.31
41 1 0.02
ACGTcount: A:0.69, C:0.17, G:0.05, T:0.09
Consensus pattern (39 bp):
AAAACAACCAAAATAGTAAAAAAAATACCAAAACATCAA
Found at i:22024 original size:24 final size:23
Alignment explanation
Indices: 21997--22062 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
21987 AATGATTTTA
*
21997 GGTCGAGTTCGATCTACGAGTTCG
1 GGTC-AGTTCGATCAACGAGTTCG
* *
22021 GGTCAGCTTAGATCAACGGGTTCG
1 GGTCAG-TTCGATCAACGAGTTCG
*
22045 GATCAGGTTCGATCAACG
1 GGTCA-GTTCGATCAACG
22063 TATTCAAGTC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 2 0.06
24 32 0.91
25 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (23 bp):
GGTCAGTTCGATCAACGAGTTCG
Found at i:22127 original size:27 final size:27
Alignment explanation
Indices: 22087--22144 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
22077 TCAATCAACG
* *
22087 GGTTCAATTGGTTTGGGTGTTGGGCTT
1 GGTTCAATTAGTTTGGGTGTTAGGCTT
*
22114 GGTTCACTTAGTTTGGGTGTTAGGCTT
1 GGTTCAATTAGTTTGGGTGTTAGGCTT
22141 GGTT
1 GGTT
22145 TGGATCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.09, C:0.09, G:0.38, T:0.45
Consensus pattern (27 bp):
GGTTCAATTAGTTTGGGTGTTAGGCTT
Found at i:29878 original size:20 final size:19
Alignment explanation
Indices: 29863--29918 Score: 85
Period size: 20 Copynumber: 2.9 Consensus size: 19
29853 TCAAAACAAT
29863 AACCAAAATAGTAAAAAAA
1 AACCAAAATAGTAAAAAAA
* *
29882 ATACCAAAACAGTAAAAAAC
1 A-ACCAAAATAGTAAAAAAA
29902 AACCAAAATAGTAAAAA
1 AACCAAAATAGTAAAAA
29919 GAAGCACCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.70, C:0.14, G:0.05, T:0.11
Consensus pattern (19 bp):
AACCAAAATAGTAAAAAAA
Found at i:29900 original size:19 final size:18
Alignment explanation
Indices: 29863--29932 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 18
29853 TCAAAACAAT
*
29863 AACCAAAATAGTAAAAAAA
1 AACCAAAACAGT-AAAAAA
29882 ATACCAAAACAGTAAAAAA
1 A-ACCAAAACAGTAAAAAA
*
29901 CAACCAAAATAGTAAAAAGA
1 -AACCAAAACAGTAAAAA-A
29921 AGCACCAAAACA
1 A--ACCAAAACA
29933 AGAATATGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
19 23 0.53
20 12 0.28
21 8 0.19
ACGTcount: A:0.67, C:0.17, G:0.07, T:0.09
Consensus pattern (18 bp):
AACCAAAACAGTAAAAAA
Found at i:29906 original size:39 final size:39
Alignment explanation
Indices: 29820--29932 Score: 117
Period size: 39 Copynumber: 2.9 Consensus size: 39
29810 AAATAACAGT
* *
29820 AAAACAACAAAAATAG-AAACAAAAATA--ACAACATCAA
1 AAAACAACCAAAATAGTAAA-AAAAATACCAAAACATCAA
*
29857 AACAATAACCAAAATAGTAAAAAAAATACCAAAACAGT-AA
1 AA-AACAACCAAAATAGTAAAAAAAATACCAAAACA-TCAA
**
29897 AAAACAACCAAAATAGTAAAAAGAAGCACCAAAACA
1 AAAACAACCAAAATAGTAAAAA-AAATACCAAAACA
29933 AGAATATGAT
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
37 2 0.03
38 19 0.30
39 22 0.34
40 20 0.31
41 1 0.02
ACGTcount: A:0.69, C:0.17, G:0.05, T:0.09
Consensus pattern (39 bp):
AAAACAACCAAAATAGTAAAAAAAATACCAAAACATCAA
Found at i:30889 original size:24 final size:23
Alignment explanation
Indices: 30862--30927 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
30852 AATGATTTTA
*
30862 GGTCGAGTTCGATCTACGAGTTCG
1 GGTC-AGTTCGATCAACGAGTTCG
* *
30886 GGTCAGCTTAGATCAACGGGTTCG
1 GGTCAG-TTCGATCAACGAGTTCG
*
30910 GATCAGGTTCGATCAACG
1 GGTCA-GTTCGATCAACG
30928 TATTCAAGTC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 2 0.06
24 32 0.91
25 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (23 bp):
GGTCAGTTCGATCAACGAGTTCG
Found at i:30992 original size:27 final size:27
Alignment explanation
Indices: 30952--31009 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
30942 TCAATCAACG
* *
30952 GGTTCAATTGGTTTGGGTGTTGGGCTT
1 GGTTCAATTAGTTTGGGTGTTAGGCTT
*
30979 GGTTCACTTAGTTTGGGTGTTAGGCTT
1 GGTTCAATTAGTTTGGGTGTTAGGCTT
31006 GGTT
1 GGTT
31010 TGGATCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.09, C:0.09, G:0.38, T:0.45
Consensus pattern (27 bp):
GGTTCAATTAGTTTGGGTGTTAGGCTT
Found at i:36933 original size:79 final size:79
Alignment explanation
Indices: 36802--37007 Score: 385
Period size: 79 Copynumber: 2.6 Consensus size: 79
36792 AGTTTAACTG
* * *
36802 ACTAGAGTTGGGCTCACATTTGCGGTTTATCCGCTAGGCATTGGGTACCAGGATTTGACGGATAT
1 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCATTGGGTGCCAGGATTTGACGGATAT
36867 TGTTGGTTAATCCA
66 TGTTGGTTAATCCA
36881 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCATTGGGTGCCAGGATTTGACGGATAT
1 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCATTGGGTGCCAGGATTTGACGGATAT
36946 TGTTGGTTAATCCA
66 TGTTGGTTAATCCA
36960 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCATTGGGTGC
1 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCATTGGGTGC
37008 TACAATCGTC
Statistics
Matches: 124, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 124 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (79 bp):
ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCATTGGGTGCCAGGATTTGACGGATAT
TGTTGGTTAATCCA
Found at i:38443 original size:30 final size:30
Alignment explanation
Indices: 38385--38443 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
38375 TGTCATATTT
* *
38385 GGAACCCCAGCATTTGGCACAGCTGCATTC
1 GGAACCCCAACATTTGGCACAGATGCATTC
38415 GGAACCCCAACATTTGGCACA-ATAGCATT
1 GGAACCCCAACATTTGGCACAGAT-GCATT
38444 TGATATAGCA
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:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (30 bp):
GGAACCCCAACATTTGGCACAGATGCATTC
Found at i:39283 original size:130 final size:130
Alignment explanation
Indices: 39050--39312 Score: 508
Period size: 130 Copynumber: 2.0 Consensus size: 130
39040 ATGAATTACA
39050 ATAACAGGGCAAAGGCTGAACAGCTAACGCAATTAGTGCGACTCGAATCCAAGACACATTTGAAA
1 ATAACAGGGCAAAGGCTGAACAGCTAACGCAATTAGTGCGACTCGAATCCAAGACACATTTGAAA
*
39115 CGGTGAACACCCTTGACCATCAGACTATAATTTTATGTGTTTTATTATAAATCATGTAAATCACC
66 CGGTGAACACCCTTGACCATCAAACTATAATTTTATGTGTTTTATTATAAATCATGTAAATCACC
*
39180 ATAACAGGGCAAAGGCTGAACAGCTAACGCAATTAGTGCGACTCGAATCCAGGACACATTTGAAA
1 ATAACAGGGCAAAGGCTGAACAGCTAACGCAATTAGTGCGACTCGAATCCAAGACACATTTGAAA
39245 CGGTGAACACCCTTGACCATCAAACTATAATTTTATGTGTTTTATTATAAATCATGTAAATCACC
66 CGGTGAACACCCTTGACCATCAAACTATAATTTTATGTGTTTTATTATAAATCATGTAAATCACC
39310 ATA
1 ATA
39313 TTTATATAAT
Statistics
Matches: 131, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 131 1.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.26
Consensus pattern (130 bp):
ATAACAGGGCAAAGGCTGAACAGCTAACGCAATTAGTGCGACTCGAATCCAAGACACATTTGAAA
CGGTGAACACCCTTGACCATCAAACTATAATTTTATGTGTTTTATTATAAATCATGTAAATCACC
Found at i:39731 original size:20 final size:20
Alignment explanation
Indices: 39701--39739 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
39691 ATACTTTTTC
39701 CTTCTTTTGTTGT-TTGCTT
1 CTTCTTTTGTTGTATTGCTT
39720 CTTCTATTTGTTGTATTGCT
1 CTTCT-TTTGTTGTATTGCT
39740 GTATGCTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 8 0.44
21 5 0.28
ACGTcount: A:0.05, C:0.15, G:0.15, T:0.64
Consensus pattern (20 bp):
CTTCTTTTGTTGTATTGCTT
Found at i:45153 original size:24 final size:24
Alignment explanation
Indices: 45120--45165 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
45110 CATTCAAGTT
* *
45120 TATAATATAAATTTTTATAATTTG
1 TATAAAATAAATTTTTAAAATTTG
*
45144 TATAAAATAATTTTTTAAAATT
1 TATAAAATAAATTTTTAAAATT
45166 AGATTTGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TATAAAATAAATTTTTAAAATTTG
Found at i:45299 original size:20 final size:20
Alignment explanation
Indices: 45274--45311 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
45264 AATTACACGC
45274 AATTACAACCAAATTCAAGT
1 AATTACAACCAAATTCAAGT
45294 AATTACAACCAAATTCAA
1 AATTACAACCAAATTCAA
45312 TTATTAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.21, G:0.03, T:0.24
Consensus pattern (20 bp):
AATTACAACCAAATTCAAGT
Found at i:47071 original size:33 final size:35
Alignment explanation
Indices: 47015--47094 Score: 101
Period size: 33 Copynumber: 2.3 Consensus size: 35
47005 AAAATAAATA
*
47015 TATGTAATGACAATGAGTGACTAAAATGACAAAAG
1 TATGTAATGACAATGAGTGACTAAAACGACAAAAG
* *
47050 TATGTAATGA-TA-GAGTGACTAAAACGATAAAAG
1 TATGTAATGACAATGAGTGACTAAAACGACAAAAG
* *
47083 TATATAACGACA
1 TATGTAATGACA
47095 GTACCTAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
33 27 0.71
34 1 0.03
35 10 0.26
ACGTcount: A:0.49, C:0.09, G:0.19, T:0.24
Consensus pattern (35 bp):
TATGTAATGACAATGAGTGACTAAAACGACAAAAG
Found at i:48353 original size:24 final size:24
Alignment explanation
Indices: 48298--48362 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
48288 AGATTACTTT
*
48298 ATATTTTATATATAATTATATTAA
1 ATATTTTATATATCATTATATTAA
*
48322 ATATTTTATGTATCATTATATTAA
1 ATATTTTATATATCATTATATTAA
*
48346 AT-TATTTAAATATCATT
1 ATAT-TTTATATATCATT
48363 TATCATTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 1 0.03
24 35 0.97
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.54
Consensus pattern (24 bp):
ATATTTTATATATCATTATATTAA
Found at i:48370 original size:31 final size:30
Alignment explanation
Indices: 48332--48416 Score: 107
Period size: 31 Copynumber: 2.8 Consensus size: 30
48322 ATATTTTATG
48332 TATCATTATATTAAATTATTTAAATATCATT
1 TATCATTATATTAAATT-TTTAAATATCATT
* * *
48363 TATCATTATAGTAAATTGTTTAAATCTTATT
1 TATCATTATATTAAATT-TTTAAATATCATT
* *
48394 TATTATTATATTTAATTTTTAAA
1 TATCATTATATTAAATTTTTAAA
48417 AATATTTCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 6 0.13
31 41 0.87
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (30 bp):
TATCATTATATTAAATTTTTAAATATCATT
Found at i:48837 original size:2 final size:2
Alignment explanation
Indices: 48830--48858 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
48820 AGCGCTCTTT
48830 TA TA 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 TA TA T
48859 TAAAATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48993 original size:25 final size:27
Alignment explanation
Indices: 48948--49001 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
48938 ACAACTTAGC
48948 ATATATTTATATTTATATTATAATATA
1 ATATATTTATATTTATATTATAATATA
* *
48975 ATATATTTA-ATTT-TCTTATCATATA
1 ATATATTTATATTTATATTATAATATA
49000 AT
1 AT
49002 TTACATATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 12 0.48
26 4 0.16
27 9 0.36
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (27 bp):
ATATATTTATATTTATATTATAATATA
Found at i:60974 original size:31 final size:31
Alignment explanation
Indices: 60939--61004 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 31
60929 ATAATTAAAT
*
60939 TATTCTAAAAT-TTTCATTTAAGTCACT-GAAC
1 TATTCAAAAATATTT-ATTTAAGTCACTAG-AC
60970 TATTCAAAAATATTTATTTAAGTCACTAGAC
1 TATTCAAAAATATTTATTTAAGTCACTAGAC
61001 TATT
1 TATT
61005 ACATTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (31 bp):
TATTCAAAAATATTTATTTAAGTCACTAGAC
Found at i:69844 original size:2 final size:2
Alignment explanation
Indices: 69837--69869 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
69827 ATAAAAGTAG
69837 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
69870 TTGCTTTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:77337 original size:32 final size:31
Alignment explanation
Indices: 77273--77338 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
77263 AGTTTTGGAT
* ***
77273 CCCTTAAAAGTTGGAGAAATTTTTTTTAGGC
1 CCCTTAAAAGTTGGAAAAAAAATTTTTAGGC
*
77304 CCCTTAAAAGTTGGTAAAAAAAATTTTTGGGC
1 CCCTTAAAAGTTGG-AAAAAAAATTTTTAGGC
77336 CCC
1 CCC
77339 AAACTGAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 14 0.48
32 15 0.52
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (31 bp):
CCCTTAAAAGTTGGAAAAAAAATTTTTAGGC
Found at i:79058 original size:60 final size:60
Alignment explanation
Indices: 78936--79074 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 60
78926 ACTTAAATGA
* * * * * *
78936 AAACTTTCAAATAGTTTAGTGACTATTTTGTAATTTTTTGAAGTTGAGTGATAAAAATGT
1 AAACTTACAAATAGTTTAGTAACTATTTTGTAACTTTTTAAAATTGAGTGATAAAAACGT
* * * * * *
78996 AAATTTACTAATAGTTTAGTAATTATTTTGTAACTTTTTAAAATTTATTGATCAAAACGT
1 AAACTTACAAATAGTTTAGTAACTATTTTGTAACTTTTTAAAATTGAGTGATAAAAACGT
*
79056 AAACTTACAAATAATTTAG
1 AAACTTACAAATAGTTTAG
79075 AGACATTTGA
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (60 bp):
AAACTTACAAATAGTTTAGTAACTATTTTGTAACTTTTTAAAATTGAGTGATAAAAACGT
Found at i:80497 original size:124 final size:124
Alignment explanation
Indices: 80269--80519 Score: 432
Period size: 124 Copynumber: 2.0 Consensus size: 124
80259 TATAAAAAAA
* *
80269 AAAAAGGATAATTTAAATATAAGCAAACCATACACAGAAGACGTGGACATCATGTTTCCATCAAT
1 AAAAAGGATAATTTAAAGATAAACAAACCATACACAGAAGACGTGGACATCATGTTTCCATCAAT
80334 TTTAAACAGATAGATCATATCACTCTTCAAGCGTCAAATCTTATATTTCCAACCCACAC
66 TTTAAACAGATAGATCATATCACTCTTCAAGCGTCAAATCTTATATTTCCAACCCACAC
*
80393 AAAATGGATAATTTAAAGATAAACAAACCATACACAGAAGACGTGGACATCATGTTTCCATCAAT
1 AAAAAGGATAATTTAAAGATAAACAAACCATACACAGAAGACGTGGACATCATGTTTCCATCAAT
* * *
80458 TTTAAACAGATAGATCATATCACTCTTTATA-CGTGAAATCTTATATTTCCAACCTACAC
66 TTTAAACAGATAGATCATATCACTCTTCA-AGCGTCAAATCTTATATTTCCAACCCACAC
80517 AAA
1 AAA
80520 CAACATATAT
Statistics
Matches: 120, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
124 119 0.99
125 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.27
Consensus pattern (124 bp):
AAAAAGGATAATTTAAAGATAAACAAACCATACACAGAAGACGTGGACATCATGTTTCCATCAAT
TTTAAACAGATAGATCATATCACTCTTCAAGCGTCAAATCTTATATTTCCAACCCACAC
Found at i:82571 original size:3 final size:3
Alignment explanation
Indices: 82563--82606 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
82553 GTTGGGATAG
82563 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
82607 TTATATTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:83417 original size:30 final size:28
Alignment explanation
Indices: 83383--83438 Score: 67
Period size: 30 Copynumber: 1.9 Consensus size: 28
83373 AGTTGAAATC
* *
83383 TAAAAGTAGAAAGATTAAAATTCTTAAAAA
1 TAAAAATAGAAAGACT-AAATT-TTAAAAA
*
83413 TAAAAATATAAAGACTAAATTTTAAA
1 TAAAAATAGAAAGACTAAATTTTAAA
83439 CTTGTGAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.22
29 5 0.22
30 13 0.57
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.29
Consensus pattern (28 bp):
TAAAAATAGAAAGACTAAATTTTAAAAA
Found at i:89928 original size:20 final size:20
Alignment explanation
Indices: 89889--89928 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
89879 TAAATAAAAT
*
89889 ATAAACTTAATGATACTTTA
1 ATAAACTTAATGATAATTTA
* *
89909 ATAACCTTAATTATAATTTA
1 ATAAACTTAATGATAATTTA
89929 TCCTTAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (20 bp):
ATAAACTTAATGATAATTTA
Found at i:90111 original size:46 final size:47
Alignment explanation
Indices: 90037--90137 Score: 159
Period size: 50 Copynumber: 2.1 Consensus size: 47
90027 TGGGACTTGG
90037 CCAAACGGCTGCCAAAAAT-AAAATAAAAAAGTCAAAATACTAAGAA
1 CCAAACGGCTGCCAAAAATAAAAATAAAAAAGTCAAAATACTAAGAA
*
90083 CCAAACGGCTGCCAAAAATATAAAAAAAAAAAAAGTCAAAATACTAAGAA
1 CCAAACGGCTGCC-AAAA-AT-AAAAATAAAAAAGTCAAAATACTAAGAA
90133 CCAAA
1 CCAAA
90138 ATAGTAAATA
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
46 13 0.26
47 4 0.08
48 2 0.04
50 31 0.62
ACGTcount: A:0.60, C:0.18, G:0.10, T:0.12
Consensus pattern (47 bp):
CCAAACGGCTGCCAAAAATAAAAATAAAAAAGTCAAAATACTAAGAA
Found at i:90138 original size:24 final size:24
Alignment explanation
Indices: 90061--90138 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
90051 AAAATAAAAT
90061 AAAAAAGTCAAAATACTAAGAACC
1 AAAAAAGTCAAAATACTAAGAACC
** * **
90085 -AAACGGCTGCCAAAAATA-TAAAAAAA
1 AAAAAAG-T--C-AAAATACTAAGAACC
90111 AAAAAAGTCAAAATACTAAGAACC
1 AAAAAAGTCAAAATACTAAGAACC
90135 AAAA
1 AAAA
90139 TAGTAAATAT
Statistics
Matches: 38, Mismatches: 10, Indels: 12
0.63 0.17 0.20
Matches are distributed among these distances:
23 10 0.26
24 11 0.29
26 7 0.18
27 10 0.26
ACGTcount: A:0.64, C:0.15, G:0.09, T:0.12
Consensus pattern (24 bp):
AAAAAAGTCAAAATACTAAGAACC
Found at i:99280 original size:96 final size:96
Alignment explanation
Indices: 99101--99282 Score: 226
Period size: 96 Copynumber: 1.9 Consensus size: 96
99091 AAGGATGTTC
** *
99101 GATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATTGAAGA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGAAGA
* **
99166 TAAGGAAACATTGTCTCGATTAAGGGTATTG
66 TAAAGAAACATTACCTCGATTAAGGGTATTG
* * *
99197 GATTATTTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTC-GAAACTCGAA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAG-AA-TCGAA
*
99261 -ATAAA-AGAATATTACCTCGATT
64 GATAAAGA-AACATTACCTCGATT
99283 TTAAAGTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
95 2 0.03
96 67 0.92
97 4 0.05
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGAAGA
TAAAGAAACATTACCTCGATTAAGGGTATTG
Found at i:99676 original size:60 final size:59
Alignment explanation
Indices: 99578--99740 Score: 199
Period size: 59 Copynumber: 2.8 Consensus size: 59
99568 TTTTGGGGTT
* *
99578 AAAAATGGAA-TTTTAGACATCCGAGGGTAAAACGGTAATTTTTAGAAAAAATCG-AGATC
1 AAAAATGGAATTTTTAGACATTCGAGGGTAAAATGGTAATTTTT-GAAAAAATCGAAGA-C
* * ***
99637 AAAAACGGAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGAAGAC
1 AAAAATGGAATTTTTAGACATTCGAGGGTAAAATGGTAATTTTTGAAAAAATCGAAGAC
99696 AAAAATGGAATTTTTAGA-AGTTCGAGGGTAAAAAT-GTAATTTTTG
1 AAAAATGGAATTTTTAGACA-TTCGAGGGT-AAAATGGTAATTTTTG
99741 GAAGTTTGGG
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
58 1 0.01
59 52 0.57
60 38 0.42
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.30
Consensus pattern (59 bp):
AAAAATGGAATTTTTAGACATTCGAGGGTAAAATGGTAATTTTTGAAAAAATCGAAGAC
Found at i:99681 original size:29 final size:30
Alignment explanation
Indices: 99519--99826 Score: 143
Period size: 29 Copynumber: 10.5 Consensus size: 30
99509 GCCTGGGGGC
* * *
99519 AAAATGGTAA-TTTTGGACTCTCGGGGGT-
1 AAAATGGTAATTTTTGGAATTTCGAGGGTA
*
99547 AAAATGGTAA-TTTTGGTAATTTTTTG-GGGTTA
1 AAAATGGTAATTTTTGG-AA--TTTCGAGGG-TA
* *
99579 AAAATGG-AA-TTTTAGACA-TCCGAGGGT-
1 AAAATGGTAATTTTTGGA-ATTTCGAGGGTA
* * ** *
99606 AAAACGGTAATTTTTAGAAAAAATCGA-GATCA
1 AAAATGGTAATTTTT-G-GAATTTCGAGGGT-A
*
99638 AAAACGG-AATTTTTGGACA-TTCGAGGGT-
1 AAAATGGTAATTTTTGGA-ATTTCGAGGGTA
* * **
99666 AAAATGGTAATTTTTGAAAGTTTCGAAGACA
1 AAAATGGTAATTTTTGGAA-TTTCGAGGGTA
* *
99697 AAAATGG-AATTTTTAGAAGTTCGAGGGTA
1 AAAATGGTAATTTTTGGAATTTCGAGGGTA
*
99726 AAAAT-GTAATTTTTGGAAGTTT-GGGGGTA
1 AAAATGGTAATTTTTGGAA-TTTCGAGGGTA
* *
99755 AAAAT-GTAATTTTTGGAAGTTT-TAGGGTT
1 AAAATGGTAATTTTTGGAA-TTTCGAGGGTA
* * *
99784 AAAATAG-AATTTTTAGAAGTTTAG-GGGTA
1 AAAATGGTAATTTTTGGAA-TTTCGAGGGTA
99813 AAAAT-GTAATTTTT
1 AAAATGGTAATTTTT
99827 CAGACATTTT
Statistics
Matches: 220, Mismatches: 35, Indels: 49
0.72 0.12 0.16
Matches are distributed among these distances:
27 6 0.03
28 30 0.14
29 111 0.50
30 29 0.13
31 30 0.14
32 14 0.06
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAATTTCGAGGGTA
Found at i:99746 original size:59 final size:59
Alignment explanation
Indices: 99578--99834 Score: 179
Period size: 58 Copynumber: 4.4 Consensus size: 59
99568 TTTTGGGGTT
* ** ***
99578 AAAAATGGAA-TTTTAGACATCCGAGGGT-AAAACGGTAATTTTTAGAAAAAATCGAGATC
1 AAAAATGGAATTTTTAGACATTCGAGGGTAAAAATAGTAATTTTT-GAAAGTTTCGAGA-C
* * *
99637 AAAAACGGAATTTTTGGACATTCGAGGGT-AAAATGGTAATTTTTGAAAGTTTCGAAGAC
1 AAAAATGGAATTTTTAGACATTCGAGGGTAAAAATAGTAATTTTTGAAAGTTTCG-AGAC
* * * **
99696 AAAAATGGAATTTTTAGA-AGTTCGAGGGTAAAAAT-GTAATTTTTGGAAGTTTGGGGGT
1 AAAAATGGAATTTTTAGACA-TTCGAGGGTAAAAATAGTAATTTTTGAAAGTTTCGAGAC
* * ** * * * **
99754 AAAAATGTAATTTTTGGA-AGTTTTAGGGTTAAAATAG-AATTTTT-AGAAGTTTAGGGGT
1 AAAAATGGAATTTTTAGACA-TTCGAGGGTAAAAATAGTAATTTTTGA-AAGTTTCGAGAC
*
99812 AAAAATGTAATTTTTCAGACATT
1 AAAAATGGAATTTTT-AGACATT
99835 TTAGGGACCT
Statistics
Matches: 168, Mismatches: 22, Indels: 16
0.82 0.11 0.08
Matches are distributed among these distances:
58 65 0.39
59 64 0.38
60 39 0.23
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (59 bp):
AAAAATGGAATTTTTAGACATTCGAGGGTAAAAATAGTAATTTTTGAAAGTTTCGAGAC
Found at i:99788 original size:58 final size:59
Alignment explanation
Indices: 99657--99826 Score: 193
Period size: 58 Copynumber: 2.9 Consensus size: 59
99647 TTTTTGGACA
* * ** ** *
99657 TTCGAGGG-TAAAATGGTAATTTTTGAAAGTTTCGAAGACAAAAATGGAATTTTTAGAAG
1 TTCGAGGGTTAAAATAGTAATTTTTGGAAGTTT-GGGGGTAAAAATGTAATTTTTAGAAG
* *
99716 TTCGAGGGTAAAAAT-GTAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGGAAG
1 TTCGAGGGTTAAAATAGTAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTAGAAG
** * *
99774 TTTTAGGGTTAAAATAG-AATTTTTAGAAGTTTAGGGGTAAAAATGTAATTTTT
1 TTCGAGGGTTAAAATAGTAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTT
99827 CAGACATTTT
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
58 66 0.69
59 25 0.26
60 5 0.05
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (59 bp):
TTCGAGGGTTAAAATAGTAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTAGAAG
Found at i:113130 original size:22 final size:23
Alignment explanation
Indices: 113104--113149 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
113094 ATTTTTTAAG
**
113104 TTAATATGTAATTTTAT-AATTA
1 TTAATATAAAATTTTATCAATTA
*
113126 TTAATTTAAAATTTTATCAATTA
1 TTAATATAAAATTTTATCAATTA
113149 T
1 T
113150 AAAAAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
TTAATATAAAATTTTATCAATTA
Found at i:117525 original size:30 final size:31
Alignment explanation
Indices: 117478--117542 Score: 114
Period size: 30 Copynumber: 2.1 Consensus size: 31
117468 AAATGCTCAT
117478 TGAACTATTCGAAAGTTTTCATTTAAGTCAC
1 TGAACTATTCGAAAGTTTTCATTTAAGTCAC
*
117509 TGAACTATTC-AAAGTTTTTATTTAAGTCAC
1 TGAACTATTCGAAAGTTTTCATTTAAGTCAC
117539 TGAA
1 TGAA
117543 TTGTTAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 23 0.70
31 10 0.30
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (31 bp):
TGAACTATTCGAAAGTTTTCATTTAAGTCAC
Found at i:117557 original size:30 final size:29
Alignment explanation
Indices: 117478--117555 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 29
117468 AAATGCTCAT
*
117478 TGAACTATTCGAAAGTTTTCATTTAAGTCAC
1 TGAACTATT--AAAGTTTTTATTTAAGTCAC
117509 TGAACTATTCAAAGTTTTTATTTAAGTCAC
1 TGAACTATT-AAAGTTTTTATTTAAGTCAC
* *
117539 TGAATTGTT-AAGTTTTT
1 TGAACTATTAAAGTTTTT
117556 TTTTTTAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.45
Consensus pattern (29 bp):
TGAACTATTAAAGTTTTTATTTAAGTCAC
Found at i:119109 original size:30 final size:31
Alignment explanation
Indices: 119062--119190 Score: 115
Period size: 30 Copynumber: 4.3 Consensus size: 31
119052 AAAATATTAA
* **
119062 GTACCAACTTAAGAAAAAGTGTTGAGTTTAG
1 GTACCAAATTAAGAAAAAGTGTCAAGTTTAG
119093 GTACCAAATT-AGAAAAAGTGTCAAGTTTAG
1 GTACCAAATTAAGAAAAAGTGTCAAGTTTAG
* **
119123 GTACCAAATT-GGACAAAA---AAAAGTTTAG
1 GTACCAAATTAAGA-AAAAGTGTCAAGTTTAG
* * * *
119151 ATATCAAATTAAGAAAAAGTATCAAGTTTGG
1 GTACCAAATTAAGAAAAAGTGTCAAGTTTAG
*
119182 GTGCCAAAT
1 GTACCAAAT
119191 GTTATATTAA
Statistics
Matches: 78, Mismatches: 15, Indels: 10
0.76 0.15 0.10
Matches are distributed among these distances:
28 20 0.26
29 2 0.03
30 30 0.38
31 26 0.33
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.26
Consensus pattern (31 bp):
GTACCAAATTAAGAAAAAGTGTCAAGTTTAG
Found at i:119179 original size:89 final size:89
Alignment explanation
Indices: 119016--119190 Score: 201
Period size: 89 Copynumber: 2.0 Consensus size: 89
119006 GAGAAAAAAA
*** *
119016 AAAAAGAGTCAAGTTTAGGTACCAAATAGAACCCCAAAAATATTAAGTACCAACTTAAGAAAAAG
1 AAAAAGAGTCAAGTTTAGGTACCAAATAGAACAAAAAAAATATTAAGTACCAAATTAAGAAAAAG
* **
119081 TGTTGAGTTTAGGTACCAAATTAG
66 TATCAAGTTTAGGTACCAAATTAG
* * * *
119105 AAAAAGTGTCAAGTTTAGGTACCAAATTGGACAAAAAAAAGT-TT-AGATATCAAATTAAGAAAA
1 AAAAAGAGTCAAGTTTAGGTACCAAATAGAACAAAAAAAA-TATTAAG-TACCAAATTAAGAAAA
* *
119168 AGTATCAAGTTTGGGTGCCAAAT
64 AGTATCAAGTTTAGGTACCAAAT
119191 GTTATATTAA
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
88 2 0.03
89 68 0.96
90 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (89 bp):
AAAAAGAGTCAAGTTTAGGTACCAAATAGAACAAAAAAAATATTAAGTACCAAATTAAGAAAAAG
TATCAAGTTTAGGTACCAAATTAG
Found at i:119610 original size:29 final size:28
Alignment explanation
Indices: 119576--119663 Score: 72
Period size: 28 Copynumber: 3.0 Consensus size: 28
119566 AAACTTCAAT
* *
119576 TTTTAAATTAAAAAAATTGAGGACTAAA
1 TTTTAAATTAAAAAAATTAAGAACTAAA
*
119604 TTCTTAAAAGT-AAAAAA-TAAGAACTAAA
1 TT-TT-AAATTAAAAAAATTAAGAACTAAA
* *
119632 TTTTAAATATATAAAAATATAAAAACTTAAA
1 TTTTAAAT-TAAAAAAAT-TAAGAAC-TAAA
119663 T
1 T
119664 CATACTGTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
26 3 0.06
27 3 0.06
28 18 0.38
29 8 0.17
30 10 0.21
31 5 0.11
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.32
Consensus pattern (28 bp):
TTTTAAATTAAAAAAATTAAGAACTAAA
Found at i:119647 original size:28 final size:27
Alignment explanation
Indices: 119576--119650 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
119566 AAACTTCAAT
* *
119576 TTTTAAAT-TAAAAAAATTGAGGACTAAA
1 TTTTAAATAT-AAAAAA-TAAGAACTAAA
119604 TTCTTAAA-AGTAAAAAATAAGAACTAAA
1 TT-TTAAATA-TAAAAAATAAGAACTAAA
119632 TTTTAAATATATAAAAATA
1 TTTTAAATATA-AAAAATA
119651 TAAAAACTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
27 7 0.17
28 21 0.52
29 11 0.28
30 1 0.03
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (27 bp):
TTTTAAATATAAAAAATAAGAACTAAA
Found at i:124111 original size:21 final size:22
Alignment explanation
Indices: 124070--124119 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
124060 GCAATATGAT
124070 AGCAAAATGGAAGCAAAACAAC
1 AGCAAAATGGAAGCAAAACAAC
*
124092 ATCAAAATGGCAA-C-AAACAAC
1 AGCAAAATGG-AAGCAAAACAAC
124113 AGCAAAA
1 AGCAAAA
124120 CAGCAGTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 13 0.52
22 10 0.40
23 2 0.08
ACGTcount: A:0.60, C:0.20, G:0.14, T:0.06
Consensus pattern (22 bp):
AGCAAAATGGAAGCAAAACAAC
Found at i:143630 original size:68 final size:68
Alignment explanation
Indices: 143504--143631 Score: 163
Period size: 69 Copynumber: 1.9 Consensus size: 68
143494 GAAGCAACAT
* **
143504 AAGCTTGATTTAGTTCCACACATTCTTCCACCTCATATTCTCTCTACCTCCGTCGTTCCCTTTTA
1 AAGCTTGATTTAGTTCCACACATTCTTCCACCCCATATTCTCTCTACCTCCGAAGTTCCCTTTTA
143569 TAA
66 TAA
* *
143572 AAGCTTGATTTAGTTCTCACTA-ATTCTTCCGCCCCATGTTCTCTC-ATCCTCC-AAGTTCCC
1 AAGCTTGATTTAGTTC-CAC-ACATTCTTCCACCCCATATTCTCTCTA-CCTCCGAAGTTCCC
143632 ACTCATTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
68 23 0.44
69 28 0.54
70 1 0.02
ACGTcount: A:0.20, C:0.34, G:0.09, T:0.38
Consensus pattern (68 bp):
AAGCTTGATTTAGTTCCACACATTCTTCCACCCCATATTCTCTCTACCTCCGAAGTTCCCTTTTA
TAA
Found at i:153806 original size:18 final size:17
Alignment explanation
Indices: 153755--153806 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
153745 GCCCGACCCG
153755 TTTTTA-ATT-TATAAT
1 TTTTTATATTATATAAT
* * *
153770 ATTTTATATTATGTTAT
1 TTTTTATATTATATAAT
153787 TTTTATATATTATATAAT
1 TTTT-TATATTATATAAT
153805 TT
1 TT
153807 CGAATACATT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 5 0.18
16 3 0.11
17 7 0.25
18 13 0.46
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTTATATTATATAAT
Found at i:153957 original size:22 final size:23
Alignment explanation
Indices: 153919--153963 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
153909 ATAAAATTAT
153919 TAAATATTAAAATAAAA-TAAAA
1 TAAATATTAAAATAAAATTAAAA
*
153941 TAAATATTTTAAA-AAAATTAAAA
1 TAAATA-TTAAAATAAAATTAAAA
153964 ATAACATGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
TAAATATTAAAATAAAATTAAAA
Found at i:162481 original size:11 final size:11
Alignment explanation
Indices: 162459--162489 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
162449 GTATCTTACA
162459 ATTTTG-TATT
1 ATTTTGTTATT
162469 ATTTTGTTATT
1 ATTTTGTTATT
162480 ATTTTGTTAT
1 ATTTTGTTAT
162490 AAAGTGATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (11 bp):
ATTTTGTTATT
Found at i:175788 original size:7 final size:7
Alignment explanation
Indices: 175776--175814 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
175766 ATCAATCAAT
175776 CAAGGGA
1 CAAGGGA
175783 CAAGGGA
1 CAAGGGA
175790 CAAGGGA
1 CAAGGGA
175797 CAAGGGA
1 CAAGGGA
*
175804 CAAGGGC
1 CAAGGGA
175811 CAAG
1 CAAG
175815 CCAAAGGAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.41, C:0.18, G:0.41, T:0.00
Consensus pattern (7 bp):
CAAGGGA
Found at i:177420 original size:2 final size:2
Alignment explanation
Indices: 177403--177438 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
177393 ATGAATTTAG
177403 AT AT A- AT AT A- 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
177439 TTTTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:188908 original size:23 final size:21
Alignment explanation
Indices: 188874--188924 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
188864 AATTTTAATA
*
188874 TTTTTTA-ATTAAAATCTTAG
1 TTTTTTATTTTAAAATCTTAG
*
188894 ATTCTTTTATTTTAAAATTTTAG
1 -TT-TTTTATTTTAAAATCTTAG
188917 TTTTTTAT
1 TTTTTTAT
188925 GGAAATTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 8 0.31
22 7 0.27
23 11 0.42
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (21 bp):
TTTTTTATTTTAAAATCTTAG
Found at i:194081 original size:26 final size:26
Alignment explanation
Indices: 194015--194083 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 26
194005 CTAAATACAT
*
194015 AAAACTAA-AATTTT-ATATTTTTAAA
1 AAAATTAATAATTTTAATATTTTT-AA
194040 AAAATTAATAA-TTTAATATTTCTT-A
1 AAAATTAATAATTTTAATATTT-TTAA
194065 AAAATTAATAATTTTAATA
1 AAAATTAATAATTTTAATA
194084 AATGAAAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
25 22 0.56
26 15 0.38
27 2 0.05
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (26 bp):
AAAATTAATAATTTTAATATTTTTAA
Found at i:194086 original size:17 final size:18
Alignment explanation
Indices: 194044--194086 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
194034 TTTAAAAAAA
* *
194044 TTAATAATTTAATATTTC
1 TTAATAAATTAATAATTC
194062 TTAA-AAATTAATAATT-
1 TTAATAAATTAATAATTC
194078 TTAATAAAT
1 TTAATAAAT
194087 GAAAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 4 0.18
17 14 0.64
18 4 0.18
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAATAAATTAATAATTC
Found at i:199696 original size:24 final size:25
Alignment explanation
Indices: 199669--199716 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
199659 TACCAATATA
* *
199669 CTAAAATTCTTAAT-TTTTTTTCAT
1 CTAAAATTATTAATAGTTTTTTCAT
199693 CTAAAATTATTAATAGTTTTTTCA
1 CTAAAATTATTAATAGTTTTTTCA
199717 AAAGTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.54
Consensus pattern (25 bp):
CTAAAATTATTAATAGTTTTTTCAT
Found at i:208416 original size:26 final size:26
Alignment explanation
Indices: 208361--208422 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
208351 AAAATGTTTT
* * *
208361 ATAATAATACTTAATTTATTATAAAT
1 ATAATAATAATTAATTTATCATAAAG
*
208387 ATAATTAATAATTAA-TTATCATTAAG
1 ATAA-TAATAATTAATTTATCATAAAG
208413 ATAAATAATA
1 AT-AATAATA
208423 TTTATCTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 19 0.63
27 11 0.37
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (26 bp):
ATAATAATAATTAATTTATCATAAAG
Found at i:210627 original size:18 final size:19
Alignment explanation
Indices: 210606--210644 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
210596 AAATTGAAAT
*
210606 TTTTATAAAT-ATTTTGAA
1 TTTTAAAAATCATTTTGAA
*
210624 TTTTAAAAATCATTTTTAA
1 TTTTAAAAATCATTTTGAA
210643 TT
1 TT
210645 ATTTTGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATCATTTTGAA
Found at i:213863 original size:19 final size:22
Alignment explanation
Indices: 213823--213865 Score: 65
Period size: 19 Copynumber: 2.1 Consensus size: 22
213813 ATAATTATTT
213823 TAAATATTGTATTATAAAATAA
1 TAAATATTGTATTATAAAATAA
213845 TAAATA-TGTATT-T-AAATAA
1 TAAATATTGTATTATAAAATAA
213864 TA
1 TA
213866 TTTAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.38
20 1 0.05
21 6 0.29
22 6 0.29
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (22 bp):
TAAATATTGTATTATAAAATAA
Found at i:214040 original size:18 final size:18
Alignment explanation
Indices: 213983--214040 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
213973 ATTAATTATT
213983 TATAAAATCTAATTAAAA
1 TATAAAATCTAATTAAAA
**
214001 TATATAAA-CTATATTTTTAA
1 TATA-AAATCTA-A-TTAAAA
*
214021 TATAAAATCTAATTAGAA
1 TATAAAATCTAATTAAAA
214039 TA
1 TA
214041 AGGTTGTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 13 0.41
19 8 0.25
20 11 0.34
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (18 bp):
TATAAAATCTAATTAAAA
Found at i:222926 original size:5 final size:6
Alignment explanation
Indices: 222910--222935 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
222900 GAAACAAACA
222910 AGGGGG AGGGGG AGGGGG AGGGGG AG
1 AGGGGG AGGGGG AGGGGG AGGGGG AG
222936 AGAATGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.81, T:0.00
Consensus pattern (6 bp):
AGGGGG
Found at i:230926 original size:43 final size:43
Alignment explanation
Indices: 230815--230926 Score: 134
Period size: 43 Copynumber: 2.6 Consensus size: 43
230805 TATACTTTGG
* * * * ** *
230815 TTTAGCCGATGATGCATTATGTGTGCCAGTATTTTTGCTTCGA
1 TTTATCCGATGATGCACTATGTGTGTCAATACATTTGCTTCAA
*
230858 TTTATCCGATGATGCGCTATGTGTGTCAATACATTTGCTTCAA
1 TTTATCCGATGATGCACTATGTGTGTCAATACATTTGCTTCAA
* *
230901 TTTATTCGATAATGCACTATGTGTGT
1 TTTATCCGATGATGCACTATGTGTGT
230927 TAGTATGATT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (43 bp):
TTTATCCGATGATGCACTATGTGTGTCAATACATTTGCTTCAA
Found at i:230932 original size:86 final size:86
Alignment explanation
Indices: 230821--231046 Score: 233
Period size: 86 Copynumber: 2.6 Consensus size: 86
230811 TTGGTTTAGC
* * * ** * *
230821 CGATGATGCATTATGTGTGCCAGTATTTTTGCTTCGATTTATCCGATGATGCGCTATGTGTGTCA
1 CGATAATGCACTATGTGTGCTAGTATAATTGTTTCGATTTATCCGATGATGCACTATGTGTGT-A
* *
230886 ATACAT-TTGCTTCAATTTAT-T
65 AGA-ATATTGATTCAATTTATAT
* * * ** * *
230907 CGATAATGCACTATGTGTGTTAGTATGATTGTTTTGATTTATCTAATGATGCACTGTGTGTGTTA
1 CGATAATGCACTATGTGTGCTAGTATAATTGTTTCGATTTATCCGATGATGCACTATGTGTGTAA
*
230972 GAATGATTGATTCAGTTTATAT
66 GAAT-ATTGATTCAATTTATAT
* *
230994 -GATAATGCACTATGTGTGCTAATATAATTGTTTCGATTCATCCGATGATGCAC
1 CGATAATGCACTATGTGTGCTAGTATAATTGTTTCGATTTATCCGATGATGCAC
231047 CTCTTGTGCC
Statistics
Matches: 114, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
84 2 0.02
85 2 0.02
86 109 0.96
87 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.42
Consensus pattern (86 bp):
CGATAATGCACTATGTGTGCTAGTATAATTGTTTCGATTTATCCGATGATGCACTATGTGTGTAA
GAATATTGATTCAATTTATAT
Found at i:230947 original size:43 final size:43
Alignment explanation
Indices: 230900--231046 Score: 129
Period size: 43 Copynumber: 3.4 Consensus size: 43
230890 ATTTGCTTCA
230900 ATTTATTCGATAATGCACTATGTGTGTTAGTATGATTGTTTTG
1 ATTTATTCGATAATGCACTATGTGTGTTAGTATGATTGTTTTG
* * * * * *
230943 ATTTA-TCTAATGATGCACTGTGTGTGTTAGAATGATTG-ATTC
1 ATTTATTC-GATAATGCACTATGTGTGTTAGTATGATTGTTTTG
* * * *
230985 AGTTTATAT-GATAATGCACTATGTGTGCTAATATAATTGTTTCG
1 A-TTTAT-TCGATAATGCACTATGTGTGTTAGTATGATTGTTTTG
* * *
231029 ATTCATCCGATGATGCAC
1 ATTTATTCGATAATGCAC
231047 CTCTTGTGCC
Statistics
Matches: 79, Mismatches: 19, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
42 5 0.06
43 71 0.90
44 2 0.03
45 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.43
Consensus pattern (43 bp):
ATTTATTCGATAATGCACTATGTGTGTTAGTATGATTGTTTTG
Found at i:233581 original size:24 final size:24
Alignment explanation
Indices: 233553--233615 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
233543 AAAAATAATC
233553 TTTCAGTTAAACTCTATTTAATTG
1 TTTCAGTTAAACTCTATTTAATTG
* * *
233577 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTATTTAATTG
* *
233601 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
233616 TATTAGTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTAATTG
Found at i:238471 original size:16 final size:16
Alignment explanation
Indices: 238450--238486 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
238440 TAATCTTCTC
238450 TATAATAACTATTTT-T
1 TATAATAA-TATTTTGT
238466 TATAATAATATTTTGT
1 TATAATAATATTTTGT
238482 TATAA
1 TATAA
238487 CAATTAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (16 bp):
TATAATAATATTTTGT
Found at i:242064 original size:6 final size:6
Alignment explanation
Indices: 242043--242098 Score: 57
Period size: 6 Copynumber: 9.8 Consensus size: 6
242033 TTTAATTTAT
* *
242043 TTTAAA TTT-GA TTTAAA TTTAAT TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
242089 -TTAAA TTTAA
1 TTTAAA TTTAA
242099 TTTCAAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
4 2 0.05
5 11 0.27
6 25 0.61
7 3 0.07
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:242069 original size:23 final size:23
Alignment explanation
Indices: 242036--242101 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
242026 GGCTCTTTTT
*
242036 AATTT-ATTTTAAATTTGATTTA
1 AATTTAATTTTAAATTTAATTTA
242058 AATTTAATTTTAAA-TTAATCTTA
1 AATTTAATTTTAAATTTAAT-TTA
*
242081 AATTTAA-ATTAAATTTAATTT
1 AATTTAATTTTAAATTTAATTT
242102 CAAAATTAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 16 0.41
23 23 0.59
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
AATTTAATTTTAAATTTAATTTA
Found at i:242075 original size:17 final size:17
Alignment explanation
Indices: 242055--242101 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
242045 TAAATTTGAT
242055 TTAAATTTAATTTTAAA
1 TTAAATTTAATTTTAAA
*
242072 TT-AATCTTAAATTTAAA
1 TTAAAT-TTAATTTTAAA
242089 TTAAATTTAATTT
1 TTAAATTTAATTT
242102 CAAAATTAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 3 0.12
17 20 0.77
18 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAATTTAATTTTAAA
Found at i:242098 original size:11 final size:12
Alignment explanation
Indices: 242031--242101 Score: 78
Period size: 11 Copynumber: 6.2 Consensus size: 12
242021 GACTGGGCTC
*
242031 TTTTTAATTT-A
1 TTTTAAATTTAA
*
242042 TTTTAAATTTGA
1 TTTTAAATTTAA
242054 -TTTAAATTTAA
1 TTTTAAATTTAA
242065 TTTTAAA-TTAA
1 TTTTAAATTTAA
*
242076 TCTTAAATTTAA
1 TTTTAAATTTAA
*
242088 -ATTAAATTTAA
1 TTTTAAATTTAA
242099 TTT
1 TTT
242102 CAAAATTAGC
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
11 39 0.76
12 12 0.24
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (12 bp):
TTTTAAATTTAA
Found at i:242729 original size:12 final size:12
Alignment explanation
Indices: 242708--242756 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
242698 ATATTTCGAA
*
242708 AATATCATTAAT
1 AATATTATTAAT
242720 AATATTATTAAT
1 AATATTATTAAT
* ***
242732 TATATTGGCAAT
1 AATATTATTAAT
242744 AATATTATTAAT
1 AATATTATTAAT
242756 A
1 A
242757 TCATTAACAG
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (12 bp):
AATATTATTAAT
Found at i:242788 original size:15 final size:15
Alignment explanation
Indices: 242770--242803 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
242760 TTAACAGTAT
242770 TAATGACAACAATAA
1 TAATGACAACAATAA
*
242785 TAATGACATCAATAA
1 TAATGACAACAATAA
242800 TAAT
1 TAAT
242804 ATTTAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (15 bp):
TAATGACAACAATAA
Found at i:243028 original size:21 final size:22
Alignment explanation
Indices: 242999--243040 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
242989 AAATATTAGT
* *
242999 TTTTTAAAAAAACGA-AAAGGG
1 TTTTAAAAAAAAAGAGAAAGGG
243020 TTTTAAAAAAAAAGAGAAAGG
1 TTTTAAAAAAAAAGAGAAAGG
243041 AAAATAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.57, C:0.02, G:0.19, T:0.21
Consensus pattern (22 bp):
TTTTAAAAAAAAAGAGAAAGGG
Found at i:243888 original size:29 final size:29
Alignment explanation
Indices: 243851--244185 Score: 220
Period size: 29 Copynumber: 11.4 Consensus size: 29
243841 GAGGTCCCTA
*
243851 AACTATCCAAAAATTACAATTTTACCCTCG
1 AACT-TCCAAAAATTACAATTTTACCCCCG
** * **
243881 AACTTCCAAAAATCCCATTTTTGACCCCAA
1 AACTTCCAAAAATTACAATTTT-ACCCCCG
**
243911 AACTTTTAAAAATTATC-ATTTTACCCCCG
1 AACTTCCAAAAATTA-CAATTTTACCCCCG
*
243940 AACTTCCAAAAATCT-CATTTTTGA--CCCG
1 AACTTCCAAAAAT-TACAATTTT-ACCCCCG
* * *
243968 AACCTT-CTAAAATTACCATTTTCCCCCCG
1 AA-CTTCCAAAAATTACAATTTTACCCCCG
** * **
243997 AACTTCCAAAAATCCCATTTTTAACCCCAA
1 AACTTCCAAAAATTACAATTTT-ACCCCCG
* * *
244027 AACTT-CTAAAATTACCATTTTACCCTCG
1 AACTTCCAAAAATTACAATTTTACCCCCG
* *
244055 AACTTCCAAAAATCT-CATTTTTGA-CCTCG
1 AACTTCCAAAAAT-TACAATTTT-ACCCCCG
* *
244084 AAACTTCTAAAAATTACCATTTTACCCCCG
1 -AACTTCCAAAAATTACAATTTTACCCCCG
* ** *
244114 AACTCCCAAAAATCCCAATTTTGA-CCTCG
1 AACTTCCAAAAATTACAATTTT-ACCCCCG
* * *
244143 AAACTTCTAAAAATTACCATTTTACCCCCA
1 -AACTTCCAAAAATTACAATTTTACCCCCG
244173 AACTTCCAAAAAT
1 AACTTCCAAAAAT
244186 CCTATTTTTG
Statistics
Matches: 228, Mismatches: 57, Indels: 41
0.70 0.17 0.13
Matches are distributed among these distances:
27 1 0.00
28 30 0.13
29 118 0.52
30 78 0.34
31 1 0.00
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (29 bp):
AACTTCCAAAAATTACAATTTTACCCCCG
Found at i:244225 original size:59 final size:59
Alignment explanation
Indices: 243850--244205 Score: 511
Period size: 59 Copynumber: 6.1 Consensus size: 59
243840 GGAGGTCCCT
* * * *
243850 AAACTATCCAAAAATTACAATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACT-TCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
243910 AAACTTTTAAAAATTATCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGA-CCCG
1 AAACTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * *
243968 AACCTTCT-AAAATTACCATTTTCCCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
244026 AAACTTCT-AAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCTCG
1 AAACTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
244084 AAACTTCTAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCAATTTTGACCTCG
1 AAACTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* *
244143 AAACTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCTATTTTTGACCCCG
1 AAACTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
244202 AAAC
1 AAAC
244206 ATCCAATGAT
Statistics
Matches: 264, Mismatches: 30, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
57 41 0.16
58 71 0.27
59 147 0.56
60 5 0.02
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.30
Consensus pattern (59 bp):
AAACTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:246212 original size:5 final size:5
Alignment explanation
Indices: 246176--246209 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
246166 TCTGAATGGT
*
246176 TGAAA TGAAA TGAAA TGAAA TGAAA TGAAG TGAA
1 TGAAA TGAAA TGAAA TGAAA TGAAA TGAAA TGAA
246210 GTGGGCTATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.21
Consensus pattern (5 bp):
TGAAA
Found at i:254287 original size:15 final size:15
Alignment explanation
Indices: 254284--254470 Score: 161
Period size: 15 Copynumber: 12.3 Consensus size: 15
254274 GGAGCCACAA
254284 GAGCCACAGGAGCAG
1 GAGCCACAGGAGCAG
254299 GAGCCAC---A--A-
1 GAGCCACAGGAGCAG
254308 GAGCCACAGGAGCAG
1 GAGCCACAGGAGCAG
*
254323 GAGCCACAAGAGCCACGG
1 GAGCCACAGGAG-CA--G
*
254341 GAGCCGCAGGAGCAG
1 GAGCCACAGGAGCAG
* *
254356 GAGCTACAAGAGCCACAG
1 GAGCCACAGGAG---CAG
*
254374 GAGCCGCAGGAGCAG
1 GAGCCACAGGAGCAG
* *
254389 GAGCTACAAGAGCTACAG
1 GAGCCACAGGAG---CAG
*
254407 GAGCCGCAGGAGCAG
1 GAGCCACAGGAGCAG
*
254422 GAGCCGCAGGAGCAG
1 GAGCCACAGGAGCAG
254437 GAGCCACAGGAGCAG
1 GAGCCACAGGAGCAG
*
254452 GAGCCGCAGGAGCAG
1 GAGCCACAGGAGCAG
254467 GAGC
1 GAGC
254471 AGCAGCCGGA
Statistics
Matches: 140, Mismatches: 17, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
9 7 0.05
10 1 0.01
12 2 0.01
14 1 0.01
15 90 0.64
16 2 0.01
17 2 0.01
18 35 0.25
ACGTcount: A:0.32, C:0.27, G:0.39, T:0.02
Consensus pattern (15 bp):
GAGCCACAGGAGCAG
Found at i:254289 original size:9 final size:9
Alignment explanation
Indices: 254272--254449 Score: 113
Period size: 9 Copynumber: 21.8 Consensus size: 9
254262 GGAGAAGGAG
254272 CAGGAGCCA
1 CAGGAGCCA
*
254281 CAAGAGCCA
1 CAGGAGCCA
254290 CAGGAG---
1 CAGGAGCCA
254296 CAGGAGCCA
1 CAGGAGCCA
*
254305 CAAGAGCCA
1 CAGGAGCCA
254314 CAGGAG---
1 CAGGAGCCA
254320 CAGGAGCCA
1 CAGGAGCCA
*
254329 CAAGAGCCA
1 CAGGAGCCA
* *
254338 CGGGAGCCG
1 CAGGAGCCA
254347 CAGGAG---
1 CAGGAGCCA
*
254353 CAGGAGCTA
1 CAGGAGCCA
*
254362 CAAGAGCCA
1 CAGGAGCCA
*
254371 CAGGAGCCG
1 CAGGAGCCA
254380 CAGGAG---
1 CAGGAGCCA
*
254386 CAGGAGCTA
1 CAGGAGCCA
* *
254395 CAAGAGCTA
1 CAGGAGCCA
*
254404 CAGGAGCCG
1 CAGGAGCCA
254413 CAGGAG---
1 CAGGAGCCA
*
254419 CAGGAGCCG
1 CAGGAGCCA
254428 CAGGAG---
1 CAGGAGCCA
254434 CAGGAGCCA
1 CAGGAGCCA
254443 CAGGAGC
1 CAGGAGC
254450 AGGAGCCGCA
Statistics
Matches: 134, Mismatches: 17, Indels: 36
0.72 0.09 0.19
Matches are distributed among these distances:
6 36 0.27
9 98 0.73
ACGTcount: A:0.33, C:0.28, G:0.37, T:0.02
Consensus pattern (9 bp):
CAGGAGCCA
Found at i:254294 original size:24 final size:24
Alignment explanation
Indices: 254267--254344 Score: 147
Period size: 24 Copynumber: 3.2 Consensus size: 24
254257 CAGCAGGAGA
254267 AGGAGCAGGAGCCACAAGAGCCAC
1 AGGAGCAGGAGCCACAAGAGCCAC
254291 AGGAGCAGGAGCCACAAGAGCCAC
1 AGGAGCAGGAGCCACAAGAGCCAC
254315 AGGAGCAGGAGCCACAAGAGCCAC
1 AGGAGCAGGAGCCACAAGAGCCAC
*
254339 GGGAGC
1 AGGAGC
254345 CGCAGGAGCA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.36, C:0.28, G:0.36, T:0.00
Consensus pattern (24 bp):
AGGAGCAGGAGCCACAAGAGCCAC
Found at i:254336 original size:33 final size:33
Alignment explanation
Indices: 254299--254456 Score: 214
Period size: 33 Copynumber: 4.9 Consensus size: 33
254289 ACAGGAGCAG
* *
254299 GAGCCACAAGAGCCACAGGAGCAGGAGCCACAA
1 GAGCCACAGGAGCCGCAGGAGCAGGAGCCACAA
* *
254332 GAGCCACGGGAGCCGCAGGAGCAGGAGCTACAA
1 GAGCCACAGGAGCCGCAGGAGCAGGAGCCACAA
*
254365 GAGCCACAGGAGCCGCAGGAGCAGGAGCTACAA
1 GAGCCACAGGAGCCGCAGGAGCAGGAGCCACAA
* * *
254398 GAGCTACAGGAGCCGCAGGAGCAGGAGCCGCAG
1 GAGCCACAGGAGCCGCAGGAGCAGGAGCCACAA
*
254431 GAG---CAGGAGCCACAGGAGCAGGAGCC
1 GAGCCACAGGAGCCGCAGGAGCAGGAGCC
254457 GCAGGAGCAG
Statistics
Matches: 115, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
30 22 0.19
33 93 0.81
ACGTcount: A:0.32, C:0.28, G:0.38, T:0.02
Consensus pattern (33 bp):
GAGCCACAGGAGCCGCAGGAGCAGGAGCCACAA
Found at i:254460 original size:9 final size:9
Alignment explanation
Indices: 254319--254464 Score: 61
Period size: 9 Copynumber: 17.9 Consensus size: 9
254309 AGCCACAGGA
254319 GCAGGAGCC
1 GCAGGAGCC
* *
254328 ACAAGAGCC
1 GCAGGAGCC
* *
254337 ACGGGAGCC
1 GCAGGAGCC
254346 GCAGGA---
1 GCAGGAGCC
*
254352 GCAGGAGCT
1 GCAGGAGCC
* *
254361 ACAAGAGCC
1 GCAGGAGCC
*
254370 ACAGGAGCC
1 GCAGGAGCC
254379 GCAGGA---
1 GCAGGAGCC
*
254385 GCAGGAGCT
1 GCAGGAGCC
* * *
254394 ACAAGAGCT
1 GCAGGAGCC
*
254403 ACAGGAGCC
1 GCAGGAGCC
254412 GCAGGA---
1 GCAGGAGCC
254418 GCAGGAGCC
1 GCAGGAGCC
254427 GCAGGA---
1 GCAGGAGCC
254433 GCAGGAGCC
1 GCAGGAGCC
*
254442 ACAGGA---
1 GCAGGAGCC
254448 GCAGGAGCC
1 GCAGGAGCC
254457 GCAGGAGC
1 GCAGGAGC
254465 AGGAGCAGCA
Statistics
Matches: 104, Mismatches: 18, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
6 29 0.28
9 75 0.72
ACGTcount: A:0.31, C:0.27, G:0.40, T:0.02
Consensus pattern (9 bp):
GCAGGAGCC
Found at i:254460 original size:24 final size:24
Alignment explanation
Indices: 254267--254475 Score: 108
Period size: 24 Copynumber: 8.7 Consensus size: 24
254257 CAGCAGGAGA
* *
254267 AGGAGCAGGAGCCACAAGAGCCAC
1 AGGAGCAGGAGCCGCAGGAGCCAC
* *
254291 AGGAGCAGGAGCCACAAGAGCCAC
1 AGGAGCAGGAGCCGCAGGAGCCAC
* *
254315 AGGAGCAGGAGCCACAAGAGCCAC
1 AGGAGCAGGAGCCGCAGGAGCCAC
* * * ** *
254339 GGGAGCCGCAGGAGCAGGAGCTAC
1 AGGAGCAGGAGCCGCAGGAGCCAC
*
254363 AAGAGCCACAGGAGCCGCAGGAG---C
1 AGGAG---CAGGAGCCGCAGGAGCCAC
* ** *
254387 AGGAGCTACAAGAGCTACAGGAGCCGC
1 AGGAG---CAGGAGCCGCAGGAGCCAC
254414 AGGAGCAGGAGCCGCAGGAG---C
1 AGGAGCAGGAGCCGCAGGAGCCAC
* ** *
254435 AGGAGCCA-CAGGAGCAGGAGCCGC
1 AGGAG-CAGGAGCCGCAGGAGCCAC
*
254459 AGGAGCAGGAGCAGCAG
1 AGGAGCAGGAGCCGCAG
254476 CCGGAGCCAG
Statistics
Matches: 147, Mismatches: 27, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
21 15 0.10
22 2 0.01
23 2 0.01
24 111 0.76
27 17 0.12
ACGTcount: A:0.33, C:0.27, G:0.39, T:0.01
Consensus pattern (24 bp):
AGGAGCAGGAGCCGCAGGAGCCAC
Found at i:259391 original size:19 final size:19
Alignment explanation
Indices: 259367--259405 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
259357 TTTTTTGGTG
* *
259367 TATGATGGTTTCATCCCTA
1 TATGATAGTTTCAACCCTA
259386 TATGATAGTTTCAACCCTA
1 TATGATAGTTTCAACCCTA
259405 T
1 T
259406 CTTTTGCAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.41
Consensus pattern (19 bp):
TATGATAGTTTCAACCCTA
Found at i:261207 original size:162 final size:160
Alignment explanation
Indices: 260940--261740 Score: 808
Period size: 162 Copynumber: 5.0 Consensus size: 160
260930 CATCATTTAG
* * * * * *
260940 GATTTGTTTTCATTGTTAAAACAGTAGTGTGCA-TAAGTGGTAAATTACATAAGCATTTTACCAG
1 GATTTGTATTCATTGTTAAAACAGTAGTGGGCAGTAA-TGGTTAATTGCATAAGCATTTTAACAC
* * * *
261004 GTCTTGCTTGTTTATAAAAATTTAAAATTGTTACTTTATCTCTTCTTTTTGAGTTAATTGCAAGT
65 GTCTTGCTTGTTTAT-AAGATTTAAAATTGTAACTTTATCTCTTCTTTTTAAGTTAATTGTAAGT
* * *
261069 TAATATTATAAAAGTGTAAGCGACTCTCTTTAA
129 CAATATTATGAAAGTGTAAGTGACTCTC-TTAA
*
261102 GATTTGTATTCATTGTTAAAACAGTTGTGGGCAGTAATGGTTAATTGCATAAGCATTTTAACACG
1 GATTTGTATTCATTGTTAAAACAGTAGTGGGCAGTAATGGTTAATTGCATAAGCATTTTAACACG
* * * *
261167 TCGTGCTTGTTTATAAGATTATAACATTGTAACTTTATCTCTTCTTCTTAAATTAATTGTAAGTC
66 TCTTGCTTGTTTATAAGATT-TAAAATTGTAACTTTATCTCTTCTTTTTAAGTTAATTGTAAGTC
261232 AATATTATGAAAGTGTAAGTGACTCTCTTAA
130 AATATTATGAAAGTGTAAGTGACTCTCTTAA
* * * * *
261263 TATTTATATTCATTGTTAAAACAATAGT-GGCAGTACTGGCTAATTGCATAAGCATTTTAACACA
1 GATTTGTATTCATTGTTAAAACAGTAGTGGGCAGTAATGGTTAATTGCATAAGCATTTT-A-ACA
* * * * *
261327 CGTCTTGTTTGTTTATAAGAATCTAAAATTATAATTTTATCTCTTCTTTTTAAGTTAATTGTAAA
64 CGTCTTGCTTGTTTATAAG-ATTTAAAATTGTAACTTTATCTCTTCTTTTTAAGTTAATTGTAAG
* *
261392 TCAATATTATGAAAGTGTAAGTGATTCTCTTAG
128 TCAATATTATGAAAGTGTAAGTGACTCTCTTAA
261425 GATTTGTATTCATTGTTAAAACAGTAGT-----G--A---TT-ATTGCATAAGCATTTTAACACA
1 GATTTGTATTCATTGTTAAAACAGTAGTGGGCAGTAATGGTTAATTGCATAAGCATTTT-A-ACA
* * * * * * * *
261479 CATCTTGTTTGTTTGTTTATAATAAGAATCTAAAATTGTTATTTTATCTATTATTTTTAAGCTAA
64 CGTC----TTGCTTG-TT-T-ATAAG-ATTTAAAATTGTAACTTTATCTCTTCTTTTTAAGTTAA
* * * *
261544 TTGTAACTCAATATTATGAAAGTATAAATGACTCTCTTAG
121 TTGTAAGTCAATATTATGAAAGTGTAAGTGACTCTCTTAA
* * * * * *
261584 GATTTATATTCATTGTTAAAACAATAATGGGTAGTAGTGGTTAATTGCAAAAGCATTTTAACACA
1 GATTTGTATTCATTGTTAAAACAGTAGTGGGCAGTAATGGTTAATTGCATAAGCATTTT-A-ACA
* * *
261649 CGTCTTG-TGTGTTTATAAGATTCTAAAATCTTTACCTGTT-T-T-TTCTTTTTAAGCTAATTGT
64 CGTCTTGCT-TGTTTATAAGATT-TAAAAT-TGTAACT-TTATCTCTTCTTTTTAAGTTAATTGT
*
261710 AAGTCAGTATTATGAAAGTGTAAGTGACTCT
125 AAGTCAATATTATGAAAGTGTAAGTGACTCT
261741 TTTGACAATT
Statistics
Matches: 546, Mismatches: 66, Indels: 54
0.82 0.10 0.08
Matches are distributed among these distances:
152 25 0.05
153 1 0.00
156 7 0.01
157 2 0.00
158 2 0.00
159 100 0.18
160 28 0.05
161 34 0.06
162 288 0.53
163 17 0.03
164 6 0.01
165 5 0.01
166 5 0.01
169 2 0.00
170 24 0.04
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.42
Consensus pattern (160 bp):
GATTTGTATTCATTGTTAAAACAGTAGTGGGCAGTAATGGTTAATTGCATAAGCATTTTAACACG
TCTTGCTTGTTTATAAGATTTAAAATTGTAACTTTATCTCTTCTTTTTAAGTTAATTGTAAGTCA
ATATTATGAAAGTGTAAGTGACTCTCTTAA
Found at i:261601 original size:321 final size:316
Alignment explanation
Indices: 260936--261740 Score: 885
Period size: 321 Copynumber: 2.5 Consensus size: 316
260926 CATACATCAT
* * * *
260936 TTAGGATTTGTTTTCATTGTTAAAACAGTAGTGTGCA-TAAGTGGTAAATTACATAAGCATTTT-
1 TTAGGATTTATATTCATTGTTAAAACAATAGTG-GCAGT-AGTGGT-AATTGCATAAGCATTTTA
* * * * * * * *
260999 AC-CAGGTCTTGCTTGTTTATAAAAATTTAAAATTGTTACTTTATCTCTTCTTTTTGAGTTAATT
63 ACACACGTCTTGTTTGTTTATAAGAATCTAAAATTATAATTTTATCTCTTCTTTTTAAGTTAATT
* * * *
261063 GCAAGTTAATATTATAAAAGTGTAAGCGACTCTCTTTAAGATTTGTATTCATTGTTAAAACAGTT
128 GTAAGTCAATATTATGAAAGTGTAAGTGACTCTCTTTAAGATTTGTATTCATTGTTAAAACA--T
* * * *
261128 GTGGGCAGTAATGGTTAATTGCATAAGCATTTTAACACGTCGTGCTTGTTTATAAGATTATAACA
191 GT--G-AG--ATGATTAATTGCATAAGCATTTTAACACATCGTGCTTGTTTATAAGAATATAAAA
* * * * * *
261193 TTGTAACTTTATCTCTTCTTCTTAAATTAATTGTAAGTCAATATTATGAAAGTGTAAGTGACTCT
251 TTGTAACTTTATCTATTATTCTTAAACTAATTGTAACTCAATATTATGAAAGTATAAATGACTCT
261258 C
316 C
** *
261259 TTAATATTTATATTCATTGTTAAAACAATAGTGGCAGTACTGGCTAATTGCATAAGCATTTTAAC
1 TTAGGATTTATATTCATTGTTAAAACAATAGTGGCAGTAGTGG-TAATTGCATAAGCATTTTAAC
261324 ACACGTCTTGTTTGTTTATAAGAATCTAAAATTATAATTTTATCTCTTCTTTTTAAGTTAATTGT
65 ACACGTCTTGTTTGTTTATAAGAATCTAAAATTATAATTTTATCTCTTCTTTTTAAGTTAATTGT
* * *
261389 AAATCAATATTATGAAAGTGTAAGTGATTCTC-TTAGGATTTGTATTCATTGTTAAAACA-GT-A
130 AAGTCAATATTATGAAAGTGTAAGTGACTCTCTTTAAGATTTGTATTCATTGTTAAAACATGTGA
* *
261451 G-TGATT-ATTGCATAAGCATTTTAACACACATCTTGTTTGTTTGTTTATAATAAGAATCTAAAA
195 GATGATTAATTGCATAAGCATTTT-A-ACACATC--G--TGCTTG-TT-T-ATAAGAATATAAAA
* * * *
261514 TTGTTATTTTATCTATTATTTTTAAGCTAATTGTAACTCAATATTATGAAAGTATAAATGACTCT
251 TTGTAACTTTATCTATTATTCTTAAACTAATTGTAACTCAATATTATGAAAGTATAAATGACTCT
261579 C
316 C
* * *
261580 TTAGGATTTATATTCATTGTTAAAACAATAATGGGTAGTAGTGGTTAATTGCAAAAGCATTTTAA
1 TTAGGATTTATATTCATTGTTAAAACAATAGT-GGCAGTAGTGG-TAATTGCATAAGCATTTTAA
* * * * * *
261645 CACACGTCTTGTGTGTTTATAAGATTCTAAAATCTTTACCTGTT-T-T-TTCTTTTTAAGCTAAT
64 CACACGTCTTGTTTGTTTATAAGAATCTAAAAT-TATA-ATTTTATCTCTTCTTTTTAAGTTAAT
*
261707 TGTAAGTCAGTATTATGAAAGTGTAAGTGACTCT
127 TGTAAGTCAATATTATGAAAGTGTAAGTGACTCT
261741 TTTGACAATT
Statistics
Matches: 412, Mismatches: 54, Indels: 34
0.82 0.11 0.07
Matches are distributed among these distances:
312 16 0.04
313 5 0.01
314 6 0.01
316 3 0.01
318 5 0.01
319 2 0.00
320 3 0.01
321 142 0.34
322 83 0.20
323 62 0.15
324 85 0.21
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (316 bp):
TTAGGATTTATATTCATTGTTAAAACAATAGTGGCAGTAGTGGTAATTGCATAAGCATTTTAACA
CACGTCTTGTTTGTTTATAAGAATCTAAAATTATAATTTTATCTCTTCTTTTTAAGTTAATTGTA
AGTCAATATTATGAAAGTGTAAGTGACTCTCTTTAAGATTTGTATTCATTGTTAAAACATGTGAG
ATGATTAATTGCATAAGCATTTTAACACATCGTGCTTGTTTATAAGAATATAAAATTGTAACTTT
ATCTATTATTCTTAAACTAATTGTAACTCAATATTATGAAAGTATAAATGACTCTC
Found at i:262275 original size:2 final size:2
Alignment explanation
Indices: 262268--262293 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
262258 CATGTCAATC
262268 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
262294 AATAAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:265334 original size:2 final size:2
Alignment explanation
Indices: 265327--265368 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
265317 CTATCAGCAA
265327 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
265369 GCTATCAGTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:269781 original size:21 final size:21
Alignment explanation
Indices: 269742--269781 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
269732 AAATTCTCAA
* *
269742 TTCTTTTCTTCTGGTTTTTCC
1 TTCTTTTCTTCAGGGTTTTCC
269763 TTCTTTTCTTCAGGGTTTT
1 TTCTTTTCTTCAGGGTTTT
269782 ATAGTTAGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.03, C:0.20, G:0.12, T:0.65
Consensus pattern (21 bp):
TTCTTTTCTTCAGGGTTTTCC
Found at i:296033 original size:60 final size:60
Alignment explanation
Indices: 295940--296187 Score: 390
Period size: 60 Copynumber: 4.2 Consensus size: 60
295930 ATACTTTCGT
* *
295940 TAATATTTTCAAGATTGTCTATTTTCATCACTAAACTTTAAAAAGTTACAATTTGGTCAC
1 TAATATTTTCAAGATTGTCTATTTTGATCACTAAACTTTAAAAAGTTACAATTTGCTCAC
*
296000 TAATATTTTCAAGATTGTCTATTTTGATCACTAAACTTTAAAAAGTTATAATTTGCTCAC
1 TAATATTTTCAAGATTGTCTATTTTGATCACTAAACTTTAAAAAGTTACAATTTGCTCAC
* * * *
296060 AAATATTTTCAAGATTGTCTGTTTTGATCATTAAACTTTAAAAAATTACAATTTGCTCAC
1 TAATATTTTCAAGATTGTCTATTTTGATCACTAAACTTTAAAAAGTTACAATTTGCTCAC
* * * *
296120 TAACATTTTCAAGATTATCTATTTTGATCACTAAA-TTTAAAAAGTTATAATTTGATCAC
1 TAATATTTTCAAGATTGTCTATTTTGATCACTAAACTTTAAAAAGTTACAATTTGCTCAC
296179 TAATATTTT
1 TAATATTTT
296188 TAAAATGATT
Statistics
Matches: 171, Mismatches: 17, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
59 29 0.17
60 142 0.83
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (60 bp):
TAATATTTTCAAGATTGTCTATTTTGATCACTAAACTTTAAAAAGTTACAATTTGCTCAC
Found at i:296059 original size:29 final size:29
Alignment explanation
Indices: 295966--296181 Score: 130
Period size: 30 Copynumber: 7.3 Consensus size: 29
295956 GTCTATTTTC
*
295966 ATCACTAAACTTTAAAAAGTTACAATTTG
1 ATCACTAAACTTTAAAAAGTTATAATTTG
* * * * * * *
295995 GTCACTAATATTTTCAAGATTGTCTATTTTG
1 ATCACTAA-ACTTTAAAAAGT-TATAATTTG
296026 ATCACTAAACTTTAAAAAGTTATAATTTG
1 ATCACTAAACTTTAAAAAGTTATAATTTG
* * * * * * * **
296055 CTCACAAATATTTTCAAGATTGTCTGTTTTG
1 ATCACTAA-ACTTTAAAAAGT-TATAATTTG
* * *
296086 ATCATTAAACTTTAAAAAATTACAATTTG
1 ATCACTAAACTTTAAAAAGTTATAATTTG
* * * * *
296115 CTCACTAACATTTTCAAGA-TTATCTATTTTG
1 ATCACTAA-ACTTTAAAAAGTTA--TAATTTG
296146 ATCACTAAA-TTTAAAAAGTTATAATTTG
1 ATCACTAAACTTTAAAAAGTTATAATTTG
296174 ATCACTAA
1 ATCACTAA
296182 TATTTTTAAA
Statistics
Matches: 133, Mismatches: 46, Indels: 17
0.68 0.23 0.09
Matches are distributed among these distances:
28 14 0.11
29 40 0.30
30 43 0.32
31 36 0.27
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (29 bp):
ATCACTAAACTTTAAAAAGTTATAATTTG
Found at i:300243 original size:4 final size:4
Alignment explanation
Indices: 300236--300264 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
300226 TAGAGAGGAT
300236 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
300265 AGGATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:305079 original size:8 final size:8
Alignment explanation
Indices: 305066--305092 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
305056 TAGGAATAGT
305066 GATGTAAG
1 GATGTAAG
305074 GATGTAAG
1 GATGTAAG
305082 GATGTAAG
1 GATGTAAG
305090 GAT
1 GAT
305093 TGAAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.26
Consensus pattern (8 bp):
GATGTAAG
Found at i:305691 original size:8 final size:8
Alignment explanation
Indices: 305678--305704 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
305668 GAAGAATATA
305678 TTGAATCT
1 TTGAATCT
305686 TTGAATCT
1 TTGAATCT
305694 TTGAATCT
1 TTGAATCT
305702 TTG
1 TTG
305705 GGTTAATGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.52
Consensus pattern (8 bp):
TTGAATCT
Found at i:307041 original size:16 final size:17
Alignment explanation
Indices: 307001--307041 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
306991 TGACTTTAAT
307001 TAATATTTAATATATAC
1 TAATATTTAATATATAC
307018 TAAT-TTTAATAT-TA-
1 TAATATTTAATATATAC
307032 TAATTATTTA
1 TAA-TATTTA
307042 TTTAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.14
15 3 0.14
16 12 0.55
17 4 0.18
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
TAATATTTAATATATAC
Found at i:307522 original size:80 final size:80
Alignment explanation
Indices: 307389--307549 Score: 322
Period size: 80 Copynumber: 2.0 Consensus size: 80
307379 AGTTCACTTG
307389 TCACTACATAGGCGAATCCCCGTCGCCCAAACACGTGTTAAGTCTAGAGTGCATGAAACCTATCT
1 TCACTACATAGGCGAATCCCCGTCGCCCAAACACGTGTTAAGTCTAGAGTGCATGAAACCTATCT
307454 AAAATATCACATCAA
66 AAAATATCACATCAA
307469 TCACTACATAGGCGAATCCCCGTCGCCCAAACACGTGTTAAGTCTAGAGTGCATGAAACCTATCT
1 TCACTACATAGGCGAATCCCCGTCGCCCAAACACGTGTTAAGTCTAGAGTGCATGAAACCTATCT
307534 AAAATATCACATCAA
66 AAAATATCACATCAA
307549 T
1 T
307550 AATAATAATC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (80 bp):
TCACTACATAGGCGAATCCCCGTCGCCCAAACACGTGTTAAGTCTAGAGTGCATGAAACCTATCT
AAAATATCACATCAA
Found at i:314334 original size:30 final size:31
Alignment explanation
Indices: 314266--314346 Score: 114
Period size: 31 Copynumber: 2.6 Consensus size: 31
314256 GAGACATTTG
314266 CAATTGTAGTTGCTGCA-TGTAAGAATGATCA
1 CAATTGTAGTTGCTG-ATTGTAAGAATGATCA
*
314297 CAATTGTATTTGCTGATTGTAAGAAT-ATC-
1 CAATTGTAGTTGCTGATTGTAAGAATGATCA
314326 CGAATTGTAGTTGCTGATTGT
1 C-AATTGTAGTTGCTGATTGT
314347 TGACCAAGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
29 1 0.02
30 22 0.48
31 23 0.50
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.38
Consensus pattern (31 bp):
CAATTGTAGTTGCTGATTGTAAGAATGATCA
Found at i:315812 original size:25 final size:25
Alignment explanation
Indices: 315778--315829 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
315768 CCAGAATTAC
315778 TTAATTTAGTAATTATTTTTGGTTA
1 TTAATTTAGTAATTATTTTTGGTTA
315803 TTAATTTAGTAATTATTTTTGGTTA
1 TTAATTTAGTAATTATTTTTGGTTA
315828 TT
1 TT
315830 CTTTTGTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.62
Consensus pattern (25 bp):
TTAATTTAGTAATTATTTTTGGTTA
Found at i:331700 original size:4 final size:4
Alignment explanation
Indices: 331691--331715 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
331681 AAGATTCCAA
331691 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
331716 TATGTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:331732 original size:18 final size:18
Alignment explanation
Indices: 331709--331746 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
331699 ACATACATAC
331709 ATACATATATGTATATAT
1 ATACATATATGTATATAT
*
331727 ATACATATATGTATGTAT
1 ATACATATATGTATATAT
331745 AT
1 AT
331747 GATGACAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (18 bp):
ATACATATATGTATATAT
Found at i:338945 original size:15 final size:15
Alignment explanation
Indices: 338925--338976 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 15
338915 ATAAGAAGCT
338925 ATAAATTATATAAAC
1 ATAAATTATATAAAC
338940 ATAAATTATATTATTAAAAC
1 ATAAA-T-TA-TA-T-AAAC
338960 ATAAATTATATAAAC
1 ATAAATTATATAAAC
338975 AT
1 AT
338977 TTAAAATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 11 0.34
16 2 0.06
17 4 0.12
18 4 0.12
19 2 0.06
20 9 0.28
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAAATTATATAAAC
Found at i:348464 original size:30 final size:30
Alignment explanation
Indices: 348428--348501 Score: 148
Period size: 30 Copynumber: 2.5 Consensus size: 30
348418 GTGAACTATG
348428 TTGCTCACACAAGCCAAAATTACATCAAGA
1 TTGCTCACACAAGCCAAAATTACATCAAGA
348458 TTGCTCACACAAGCCAAAATTACATCAAGA
1 TTGCTCACACAAGCCAAAATTACATCAAGA
348488 TTGCTCACACAAGC
1 TTGCTCACACAAGC
348502 TGCATTTATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.41, C:0.28, G:0.11, T:0.20
Consensus pattern (30 bp):
TTGCTCACACAAGCCAAAATTACATCAAGA
Found at i:352411 original size:24 final size:25
Alignment explanation
Indices: 352370--352419 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
352360 AATTTAAGTA
352370 AATCTATATTTTATAGTTAAATTTT
1 AATCTATATTTTATAGTTAAATTTT
352395 AATCTATA-TTTATAGTTAAATTTT
1 AATCTATATTTTATAGTTAAATTTT
352419 A
1 A
352420 TTAGGGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (25 bp):
AATCTATATTTTATAGTTAAATTTT
Found at i:357281 original size:137 final size:139
Alignment explanation
Indices: 357130--357400 Score: 456
Period size: 142 Copynumber: 1.9 Consensus size: 139
357120 GGGACAAATC
* *
357130 TTTTTGACCTGAGTCCAGAGTGGGGAAAACAATTTACAGACAACACAAACCACATTT-CA-TATA
1 TTTTTGACATGAGTCCAAAGTGGGGAAAACAATTTACAGACAACACAAACCACATTTACATTATA
** *
357193 ATGCACAGCAAACATTCGTCTTTCCTTTGAGAAAGAGAGAGCAAGAGAGAAGAATAGACAGAAGA
66 ATGCACAGCAAACATTCGTAATTCCTTTGAGAAAGAGAGAGCAAGAAAGAAGAATAGACAGAAGA
357258 CAAATCTTT
131 CAAATCTTT
357267 TTTTTGACATGAGTCCAAAGTGGGGAAAACAATTTACAGACAACACAAACCACATTTCACATGTT
1 TTTTTGACATGAGTCCAAAGTGGGGAAAACAATTTACAGACAACACAAACCACATTT-ACA--TT
357332 ATAATGCACAGCAAACATTCGTAATTCCTTTGAGAAAGAGAGAGCAAGAAAGAAGAATAGACAGA
63 ATAATGCACAGCAAACATTCGTAATTCCTTTGAGAAAGAGAGAGCAAGAAAGAAGAATAGACAGA
357397 AGAC
128 AGAC
357401 GCAAGATAAG
Statistics
Matches: 124, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
137 55 0.44
139 2 0.02
142 67 0.54
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.22
Consensus pattern (139 bp):
TTTTTGACATGAGTCCAAAGTGGGGAAAACAATTTACAGACAACACAAACCACATTTACATTATA
ATGCACAGCAAACATTCGTAATTCCTTTGAGAAAGAGAGAGCAAGAAAGAAGAATAGACAGAAGA
CAAATCTTT
Found at i:360913 original size:56 final size:56
Alignment explanation
Indices: 360846--360957 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
360836 AATGGCAAAA
360846 GCTTCAACAATGGAATGACTAAAATAAGCATAAATAAAATCAGAAAAAATTTTAAG
1 GCTTCAACAATGGAATGACTAAAATAAGCATAAATAAAATCAGAAAAAATTTTAAG
360902 GCTTCAACAATGGAATGACTAAAATAAGCATAAATAAAATCAGAAAAAATTTTAAG
1 GCTTCAACAATGGAATGACTAAAATAAGCATAAATAAAATCAGAAAAAATTTTAAG
360958 CACATAGCCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.54, C:0.11, G:0.12, T:0.23
Consensus pattern (56 bp):
GCTTCAACAATGGAATGACTAAAATAAGCATAAATAAAATCAGAAAAAATTTTAAG
Found at i:380358 original size:14 final size:14
Alignment explanation
Indices: 380339--380376 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
380329 TTGGTTTGGT
380339 TTTTTCTTTTTTTC
1 TTTTTCTTTTTTTC
*
380353 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTC
*
380367 TTTTTGTTTT
1 TTTTTCTTTT
380377 GGTTTAGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (14 bp):
TTTTTCTTTTTTTC
Found at i:382218 original size:23 final size:22
Alignment explanation
Indices: 382173--382223 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
382163 AAATCATTTA
* *
382173 TATTTT-TATAATATAGAATAT
1 TATTTTATATAATATAAAAAAT
*
382194 TAATTTTATATTATATAAAAAAT
1 T-ATTTTATATAATATAAAAAAT
382217 TATTTTA
1 TATTTTA
382224 AAAATTCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 11 0.44
23 13 0.52
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TATTTTATATAATATAAAAAAT
Done.