Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015287.1 Corchorus olitorius cultivar O-4 contig15320, 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: 206952
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1416 original size:28 final size:27
Alignment explanation
Indices: 1375--1475 Score: 107
Period size: 27 Copynumber: 3.7 Consensus size: 27
1365 TGTGAACTTA
*
1375 AAATGACCACAATGCCCCTTGAGTATGC
1 AAATGACCAAAATGCCCCTTGAGTAT-C
*
1403 AAATGACCAAAATGCCCCTGGACGT-TC
1 AAATGACCAAAATGCCCCTTGA-GTATC
* * * *
1430 AAATGACTAAAATG-TCCTTGAATATAA
1 AAATGACCAAAATGCCCCTTGAGTAT-C
1457 AAATGACCAAAATGCCCCT
1 AAATGACCAAAATGCCCCT
1476 AGATGACCCT
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
25 1 0.02
26 6 0.10
27 27 0.45
28 24 0.40
29 2 0.03
ACGTcount: A:0.39, C:0.25, G:0.15, T:0.22
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTTGAGTATC
Found at i:1779 original size:18 final size:18
Alignment explanation
Indices: 1756--1906 Score: 117
Period size: 18 Copynumber: 8.1 Consensus size: 18
1746 TTAATTAAGG
1756 TTAATTAGTGTTAATTAC
1 TTAATTAGTGTTAATTAC
*
1774 TTAATTAGTGTTAACTAC
1 TTAATTAGTGTTAATTAC
* * **
1792 TGTTAATTAACTAATTTGTTA-
1 --TTAATT-AGT-GTTAATTAC
1813 TTAATTAGTGTTAATTAC
1 TTAATTAGTGTTAATTAC
*
1831 TTAATTAGTGTTAACTAC
1 TTAATTAGTGTTAATTAC
* * **
1849 TGTTAATTAACTAATTTGTTA-
1 --TTAATT-AGT-GTTAATTAC
1870 TTAATTAGTGTTAATTAC
1 TTAATTAGTGTTAATTAC
*
1888 TTAATTAGTGTTAACTAC
1 TTAATTAGTGTTAATTAC
1906 T
1 T
1907 GTTAATTAAC
Statistics
Matches: 102, Mismatches: 21, Indels: 20
0.71 0.15 0.14
Matches are distributed among these distances:
17 10 0.10
18 56 0.55
19 12 0.12
20 12 0.12
21 4 0.04
22 8 0.08
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAATTAGTGTTAATTAC
Found at i:1779 original size:28 final size:28
Alignment explanation
Indices: 1746--1943 Score: 197
Period size: 28 Copynumber: 7.0 Consensus size: 28
1736 ATTGTTAAAT
1746 TTAATTAAG-GTTAATTAGTGTTAATTAC
1 TTAATT-AGTGTTAATTAGTGTTAATTAC
* *
1774 TTAATTAGTGTTAACTACTGTTAATTAAC
1 TTAATTAGTGTTAATTAGTGTTAATT-AC
* *
1803 -TAATTTGTTATTAATTAGTGTTAATTAC
1 TTAATTAG-TGTTAATTAGTGTTAATTAC
* *
1831 TTAATTAGTGTTAACTACTGTTAATTAAC
1 TTAATTAGTGTTAATTAGTGTTAATT-AC
* *
1860 -TAATTTGTTATTAATTAGTGTTAATTAC
1 TTAATTAG-TGTTAATTAGTGTTAATTAC
* *
1888 TTAATTAGTGTTAACTACTGTTAATTAAC
1 TTAATTAGTGTTAATTAGTGTTAATT-AC
* *
1917 -TAATTTGTTATTAATTAGTGTTAATTA
1 TTAATTAG-TGTTAATTAGTGTTAATTA
1944 GTGTTAATTA
Statistics
Matches: 139, Mismatches: 22, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
27 2 0.01
28 74 0.53
29 63 0.45
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (28 bp):
TTAATTAGTGTTAATTAGTGTTAATTAC
Found at i:1818 original size:57 final size:57
Alignment explanation
Indices: 1756--1943 Score: 376
Period size: 57 Copynumber: 3.3 Consensus size: 57
1746 TTAATTAAGG
1756 TTAATTAGTGTTAATTACTTAATTAGTGTTAACTACTGTTAATTAACTAATTTGTTA
1 TTAATTAGTGTTAATTACTTAATTAGTGTTAACTACTGTTAATTAACTAATTTGTTA
1813 TTAATTAGTGTTAATTACTTAATTAGTGTTAACTACTGTTAATTAACTAATTTGTTA
1 TTAATTAGTGTTAATTACTTAATTAGTGTTAACTACTGTTAATTAACTAATTTGTTA
1870 TTAATTAGTGTTAATTACTTAATTAGTGTTAACTACTGTTAATTAACTAATTTGTTA
1 TTAATTAGTGTTAATTACTTAATTAGTGTTAACTACTGTTAATTAACTAATTTGTTA
1927 TTAATTAGTGTTAATTA
1 TTAATTAGTGTTAATTA
1944 GTGTTAATTA
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 131 1.00
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (57 bp):
TTAATTAGTGTTAATTACTTAATTAGTGTTAACTACTGTTAATTAACTAATTTGTTA
Found at i:1933 original size:39 final size:38
Alignment explanation
Indices: 1888--1975 Score: 131
Period size: 39 Copynumber: 2.3 Consensus size: 38
1878 TGTTAATTAC
*
1888 TTAATTAGTGTTAACTACTGTTAATTAACTAATTTGTTA
1 TTAATTAGTGTTAACTACTGTTAATTAACTAATTAG-TA
* * *
1927 TTAATTAGTGTTAATTAGTGTTAATTAACTAATTAGTG
1 TTAATTAGTGTTAACTACTGTTAATTAACTAATTAGTA
1965 TTAATTAGTGT
1 TTAATTAGTGT
1976 ATTAATTAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 12 0.27
39 33 0.73
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (38 bp):
TTAATTAGTGTTAACTACTGTTAATTAACTAATTAGTA
Found at i:1967 original size:114 final size:113
Alignment explanation
Indices: 1756--1971 Score: 353
Period size: 114 Copynumber: 1.9 Consensus size: 113
1746 TTAATTAAGG
1756 TTAATTAGTGTTAATTACTTAATTAGTGTTAACTACTGTTAATTAACTAATTTGTTATTAATTAG
1 TTAATTAGTGTTAATTACTTAATTAGTGTTAACTACTGTTAATTAACTAATTTGTTATTAATTAG
**
1821 TGTTAATTACTTAATTAGTGTTAACTACTGTTAATTAACTAATTTGTTA
66 TGTTAATTACTTAATTAG-ACTAACTACTGTTAATTAACTAATTTGTTA
1870 TTAATTAGTGTTAATTACTTAATTAGTGTTAACTACTGTTAATTAACTAATTTGTTATTAATTAG
1 TTAATTAGTGTTAATTACTTAATTAGTGTTAACTACTGTTAATTAACTAATTTGTTATTAATTAG
* * *
1935 TGTTAATTAGTGTTAATTA-ACTAATTAGTGTTAATTA
66 TGTTAATTA--CTTAATTAGACTAACTACTGTTAATTA
1972 GTGTATTAAT
Statistics
Matches: 95, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
114 88 0.93
116 7 0.07
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (113 bp):
TTAATTAGTGTTAATTACTTAATTAGTGTTAACTACTGTTAATTAACTAATTTGTTATTAATTAG
TGTTAATTACTTAATTAGACTAACTACTGTTAATTAACTAATTTGTTA
Found at i:1979 original size:8 final size:10
Alignment explanation
Indices: 1746--1975 Score: 112
Period size: 10 Copynumber: 24.1 Consensus size: 10
1736 ATTGTTAAAT
1746 TTAATTAAG-G
1 TTAATT-AGTG
1756 TTAATTAGTG
1 TTAATTAGTG
*
1766 TTAATTA--C
1 TTAATTAGTG
1774 TTAATTAGTG
1 TTAATTAGTG
* *
1784 TTAACTACTG
1 TTAATTAGTG
*
1794 TTAATTA--A
1 TTAATTAGTG
* * *
1802 CTAATTTGTTA
1 TTAATTAG-TG
1813 TTAATTAGTG
1 TTAATTAGTG
*
1823 TTAATTA--C
1 TTAATTAGTG
1831 TTAATTAGTG
1 TTAATTAGTG
* *
1841 TTAACTACTG
1 TTAATTAGTG
*
1851 TTAATTA--A
1 TTAATTAGTG
* * *
1859 CTAATTTGTTA
1 TTAATTAG-TG
1870 TTAATTAGTG
1 TTAATTAGTG
*
1880 TTAATTA--C
1 TTAATTAGTG
1888 TTAATTAGTG
1 TTAATTAGTG
* *
1898 TTAACTACTG
1 TTAATTAGTG
*
1908 TTAATTA--A
1 TTAATTAGTG
* * *
1916 CTAATTTGTTA
1 TTAATTAG-TG
1927 TTAATTAGTG
1 TTAATTAGTG
1937 TTAATTAGTG
1 TTAATTAGTG
*
1947 TTAATTA--A
1 TTAATTAGTG
*
1955 CTAATTAGTG
1 TTAATTAGTG
1965 TTAATTAGTG
1 TTAATTAGTG
1975 T
1 T
1976 ATTAATTAGC
Statistics
Matches: 165, Mismatches: 37, Indels: 36
0.69 0.16 0.15
Matches are distributed among these distances:
8 42 0.25
9 2 0.01
10 100 0.61
11 21 0.13
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.49
Consensus pattern (10 bp):
TTAATTAGTG
Found at i:1979 original size:18 final size:18
Alignment explanation
Indices: 1927--1979 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
1917 TAATTTGTTA
1927 TTAATTAGTGTTAATTAGTG
1 TTAATTAGTG-T-ATTAGTG
* *
1947 TTAATTAACT-AATTAGTG
1 TTAATT-AGTGTATTAGTG
1965 TTAATTAGTGTATTA
1 TTAATTAGTGTATTA
1980 ATTAGCTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
17 2 0.07
18 17 0.63
20 6 0.22
21 2 0.07
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (18 bp):
TTAATTAGTGTATTAGTG
Found at i:1982 original size:12 final size:12
Alignment explanation
Indices: 1956--2014 Score: 54
Period size: 12 Copynumber: 5.1 Consensus size: 12
1946 GTTAATTAAC
1956 TAATTAGTG--T
1 TAATTAGTGTAT
1966 TAATTAGTGTAT
1 TAATTAGTGTAT
*
1978 TAATTAGCT-TTT
1 TAATTAG-TGTAT
*
1990 TAATTAAT-TAAT
1 TAATTAGTGT-AT
2002 TAATTAGTGTAT
1 TAATTAGTGTAT
2014 T
1 T
2015 TAATAGTTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
10 9 0.22
11 2 0.05
12 27 0.68
13 2 0.05
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.53
Consensus pattern (12 bp):
TAATTAGTGTAT
Found at i:6689 original size:35 final size:35
Alignment explanation
Indices: 6636--6723 Score: 108
Period size: 35 Copynumber: 2.5 Consensus size: 35
6626 AAAATGGCAT
* *
6636 AATTATAAATA-TACATAATAAATTATACTAATATC
1 AATTATAACTACTA-ATAATAAATAATACTAATATC
* *
6671 GATTATAACTACTAATAATAAATAATACTAATATT
1 AATTATAACTACTAATAATAAATAATACTAATATC
*
6706 AATAATAAC-ACTAATAAT
1 AATTATAACTACTAATAAT
6724 CATAAAATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
34 9 0.20
35 35 0.76
36 2 0.04
ACGTcount: A:0.55, C:0.09, G:0.01, T:0.35
Consensus pattern (35 bp):
AATTATAACTACTAATAATAAATAATACTAATATC
Found at i:6718 original size:18 final size:19
Alignment explanation
Indices: 6686--6721 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
6676 TAACTACTAA
*
6686 TAATAAATAATACTAATAT
1 TAATAAATAACACTAATAT
6705 TAAT-AATAACACTAATA
1 TAATAAATAACACTAATA
6722 ATCATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAAATAACACTAATAT
Found at i:7280 original size:13 final size:15
Alignment explanation
Indices: 7247--7286 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 15
7237 AACTGTAAAG
7247 TTTAAACAATATATCA
1 TTTAAA-AATATATCA
7263 TTTAAAAA-ATAT-A
1 TTTAAAAATATATCA
7276 TTTAAAAATAT
1 TTTAAAAATAT
7287 TCTAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.39
14 6 0.26
15 2 0.09
16 6 0.26
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTAAAAATATATCA
Found at i:7586 original size:21 final size:21
Alignment explanation
Indices: 7560--7672 Score: 158
Period size: 21 Copynumber: 5.4 Consensus size: 21
7550 TGCTAGAAGT
7560 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
7581 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
7602 TCATTGGAGCAGGTTCCAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
7623 TCATTGGAG-AAGGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
*
7644 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
7665 TCATTGGA
1 TCATTGGA
7673 AATGCCTAAG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
20 1 0.01
21 84 0.99
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Found at i:8871 original size:33 final size:33
Alignment explanation
Indices: 8816--9375 Score: 546
Period size: 33 Copynumber: 15.9 Consensus size: 33
8806 CTATTGATTA
*
8816 TCTTTTTACTTATTAATTACCAAATACCATTTTAC
1 TCTTTTTAC-T-TTAATTACCAAATTCCATTTTAC
* *
8851 TCTTTTTACTCTAATTACCAAATTTCATTTTAC
1 TCTTTTTACTTTAATTACCAAATTCCATTTTAC
* *
8884 TCTTTTTA-TTCAAACTACCAAATTCCATTTTAC
1 TCTTTTTACTT-TAATTACCAAATTCCATTTTAC
* *
8917 TCTTTTTACTTTAATTAGCATATTCCATTTTTAC
1 TCTTTTTACTTTAATTACCAAATTCCA-TTTTAC
*
8951 TCTTTTTACTTATTAATTACCAAATACCATTTTAC
1 TCTTTTTAC-T-TTAATTACCAAATTCCATTTTAC
*
8986 TCTTTTTAAATACTTTAATTACCACATTCCATTTTTAC
1 TC-TTTT---TACTTTAATTACCAAATTCCA-TTTTAC
* * *
9024 TCGTTTTACTCTAATTACCGAATTCCATTTTAC
1 TCTTTTTACTTTAATTACCAAATTCCATTTTAC
* *
9057 TCTTTTTACTCTAATTACCAAATTTCATTTTAC
1 TCTTTTTACTTTAATTACCAAATTCCATTTTAC
* * *
9090 TCTTTTTAAATACTTTAATCACCATATTCTATTTTTAC
1 TC-TTTT---TACTTTAATTACCAAATTCCA-TTTTAC
* * *
9128 TCTTTTTACTTATTAATTAGCATATTCTATTTTTAC
1 TCTTTTTAC-T-TTAATTACCAAATTCCA-TTTTAC
*
9164 TCTTTTTACTTATCAATTACCAAATACCATTTTAC
1 TCTTTTTACTT-T-AATTACCAAATTCCATTTTAC
*
9199 TCTTTTTAAATACTTTAATTACCATATTCCATTTTTAC
1 TC-TTTT---TACTTTAATTACCAAATTCCA-TTTTAC
*
9237 TCTTTTTACTTATTAATTACCAAATACCATTTTAC
1 TCTTTTTAC-T-TTAATTACCAAATTCCATTTTAC
* *
9272 TCTTTTTACTTTAATTACCATATTCTATTTTTAC
1 TCTTTTTACTTTAATTACCAAATTCCA-TTTTAC
* *
9306 TCTCTTTACTTATTAATTACCAAATACCATTTTAC
1 TCTTTTTAC-T-TTAATTACCAAATTCCATTTTAC
*
9341 TCTTTTTAAATACTTTAATTACCATATTCCATTTT
1 TC-TTTT---TACTTTAATTACCAAATTCCATTTT
9376 TACTGATTAC
Statistics
Matches: 444, Mismatches: 48, Indels: 64
0.80 0.09 0.12
Matches are distributed among these distances:
32 1 0.00
33 119 0.27
34 62 0.14
35 54 0.12
36 96 0.22
37 74 0.17
38 27 0.06
39 11 0.02
ACGTcount: A:0.28, C:0.20, G:0.01, T:0.51
Consensus pattern (33 bp):
TCTTTTTACTTTAATTACCAAATTCCATTTTAC
Found at i:9024 original size:73 final size:69
Alignment explanation
Indices: 8816--9379 Score: 692
Period size: 73 Copynumber: 8.0 Consensus size: 69
8806 CTATTGATTA
* * *
8816 TCTTTTTACTTATTAATTACCAAATACCATTTTACTCTTTTTACTCTAATTACCAAATTTCA-TT
1 TCTTTTTACTTATTAATTACCAAATACCATTTTACTCTTTTTACTTTAATTACCATATTCCATTT
8880 TTAC
66 TTAC
* * *
8884 TCTTTTTA-TTCA--AACTACCAAATTCCATTTTACTCTTTTTACTTTAATTAGCATATTCCATT
1 TCTTTTTACTT-ATTAATTACCAAATACCATTTTACTCTTTTTACTTTAATTACCATATTCCATT
8946 TTTAC
65 TTTAC
*
8951 TCTTTTTACTTATTAATTACCAAATACCATTTTACTCTTTTTAAATACTTTAATTACCACATTCC
1 TCTTTTTACTTATTAATTACCAAATACCATTTTACTC-TTTT---TACTTTAATTACCATATTCC
9016 ATTTTTAC
62 ATTTTTAC
* * * * * * *
9024 TCGTTTTAC-T-CTAATTACCGAATTCCATTTTACTCTTTTTACTCTAATTACCAAATTTCA-TT
1 TCTTTTTACTTATTAATTACCAAATACCATTTTACTCTTTTTACTTTAATTACCATATTCCATTT
9086 TTAC
66 TTAC
** * * * * *
9090 TCTTTTTAAATACTTTAATCACCATATTCTATTTTTACTCTTTTTACTTATTAATTAGCATATTC
1 TCTTTTTACTTA--TTAATTACCAAATACCA-TTTTACTCTTTTTAC-T-TTAATTACCATATTC
*
9155 TATTTTTAC
61 CATTTTTAC
*
9164 TCTTTTTACTTATCAATTACCAAATACCATTTTACTCTTTTTAAATACTTTAATTACCATATTCC
1 TCTTTTTACTTATTAATTACCAAATACCATTTTACTC-TTTT---TACTTTAATTACCATATTCC
9229 ATTTTTAC
62 ATTTTTAC
*
9237 TCTTTTTACTTATTAATTACCAAATACCATTTTACTCTTTTTACTTTAATTACCATATTCTATTT
1 TCTTTTTACTTATTAATTACCAAATACCATTTTACTCTTTTTACTTTAATTACCATATTCCATTT
9302 TTAC
66 TTAC
*
9306 TCTCTTTACTTATTAATTACCAAATACCATTTTACTCTTTTTAAATACTTTAATTACCATATTCC
1 TCTTTTTACTTATTAATTACCAAATACCATTTTACTC-TTTT---TACTTTAATTACCATATTCC
9371 ATTTTTAC
62 ATTTTTAC
9379 T
1 T
9380 GATTACTCTT
Statistics
Matches: 429, Mismatches: 42, Indels: 45
0.83 0.08 0.09
Matches are distributed among these distances:
66 55 0.13
67 36 0.08
68 11 0.03
69 84 0.20
70 24 0.06
71 45 0.10
72 22 0.05
73 132 0.31
74 17 0.04
75 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.01, T:0.51
Consensus pattern (69 bp):
TCTTTTTACTTATTAATTACCAAATACCATTTTACTCTTTTTACTTTAATTACCATATTCCATTT
TTAC
Found at i:14933 original size:20 final size:21
Alignment explanation
Indices: 14891--14938 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
14881 ATAGTTTAGA
*
14891 TTTAATTTACTTTGTTTA-TT
1 TTTAATTTACATTGTTTATTT
*
14911 TTTAATTTA-ATTGTTTTTCTT
1 TTTAATTTACATTGTTTAT-TT
14932 TTTAATT
1 TTTAATT
14939 GTTATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (21 bp):
TTTAATTTACATTGTTTATTT
Found at i:20045 original size:2 final size:2
Alignment explanation
Indices: 20034--20071 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
20024 AACTGTGTCT
*
20034 CA CA -A CA CA CA CA CA CA CA CA CA CA CA CA CA TA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
20072 TTGTTTACCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:23809 original size:20 final size:21
Alignment explanation
Indices: 23784--23824 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
23774 TACAACTTGT
*
23784 AAGAACAAGGGTGAT-AAAAA
1 AAGAACAAGGATGATGAAAAA
23804 AAGAACAAGGATGATGAAAAA
1 AAGAACAAGGATGATGAAAAA
23825 TAAAAGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.61, C:0.05, G:0.24, T:0.10
Consensus pattern (21 bp):
AAGAACAAGGATGATGAAAAA
Found at i:24931 original size:19 final size:18
Alignment explanation
Indices: 24907--24946 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
24897 TTGAAGACTT
*
24907 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
24926 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
24944 ATT
1 ATT
24947 ATTTCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:30321 original size:18 final size:19
Alignment explanation
Indices: 30287--30324 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
30277 GTCCATCGTT
*
30287 ATCTCCATGGTCTCCATGC
1 ATCTCCATGGCCTCCATGC
30306 ATCTCCAT-GCCTCCATGC
1 ATCTCCATGGCCTCCATGC
30324 A
1 A
30325 ACCCATGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.18, C:0.39, G:0.13, T:0.29
Consensus pattern (19 bp):
ATCTCCATGGCCTCCATGC
Found at i:30404 original size:30 final size:30
Alignment explanation
Indices: 30368--30424 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
30358 CATCTTCAAG
* *
30368 TCCATGATAAGTCTTTGGCGCATCATTCCC
1 TCCATGATAAGCCTTGGGCGCATCATTCCC
30398 TCCATGATAAGCCTTGGGCGCATCATT
1 TCCATGATAAGCCTTGGGCGCATCATT
30425 GAAGACATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCGCATCATTCCC
Found at i:32573 original size:22 final size:21
Alignment explanation
Indices: 32528--32569 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
32518 TTACAACTTG
*
32528 TAAGAACAAGGGTGATGAAAA
1 TAAGAACAAGGGTGACGAAAA
32549 TAAGAACAAGGGTGACGAAAA
1 TAAGAACAAGGGTGACGAAAA
32570 ATAAATGACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.07, G:0.29, T:0.12
Consensus pattern (21 bp):
TAAGAACAAGGGTGACGAAAA
Found at i:34902 original size:19 final size:18
Alignment explanation
Indices: 34869--34904 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
34859 TTGAAATTAT
*
34869 TCTTCAATGATCTTCAAA
1 TCTTCAATCATCTTCAAA
34887 TCTTCAAATCATCTTCAA
1 TCTTC-AATCATCTTCAA
34905 TGAGTCTTCA
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:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAATCATCTTCAAA
Found at i:34912 original size:11 final size:10
Alignment explanation
Indices: 34869--34915 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
34859 TTGAAATTAT
34869 TCTTCAATGA
1 TCTTCAATGA
34879 TCTTCAA--A
1 TCTTCAATGA
*
34887 TCTTCAAATCA
1 TCTTC-AATGA
34898 TCTTCAATGA
1 TCTTCAATGA
34908 GTCTTCAA
1 -TCTTCAA
34916 ACATGAACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 11 0.34
11 13 0.41
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.38
Consensus pattern (10 bp):
TCTTCAATGA
Found at i:39382 original size:53 final size:53
Alignment explanation
Indices: 39297--39433 Score: 202
Period size: 53 Copynumber: 2.6 Consensus size: 53
39287 TGCCATAAGA
* * *
39297 AAGATCGAGCATCCCTCGGTCGCATTATCTATTGGGCATCCCCCACGAACAAT
1 AAGATCGAGCATCCCTCGGTCGCACTACCTATTAGGCATCCCCCACGAACAAT
* * *
39350 AAGATCGAGCATCCCTCGGTCACACTACCTATTAGGCATCCCGCACGAGCAAT
1 AAGATCGAGCATCCCTCGGTCGCACTACCTATTAGGCATCCCCCACGAACAAT
* *
39403 AAAATCGAGCACCCCTCGGTCGCACTACCTA
1 AAGATCGAGCATCCCTCGGTCGCACTACCTA
39434 AAATGGGTAT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 75 1.00
ACGTcount: A:0.28, C:0.34, G:0.18, T:0.20
Consensus pattern (53 bp):
AAGATCGAGCATCCCTCGGTCGCACTACCTATTAGGCATCCCCCACGAACAAT
Found at i:40167 original size:28 final size:28
Alignment explanation
Indices: 40128--40190 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
40118 TCCCAAGGAA
**
40128 AAAGCGGTGGTATGCCCTCAAGGATCGC
1 AAAGCGGTGGTACACCCTCAAGGATCGC
* *
40156 AAAGTGGTGGTACACCCTCAAGTATCGC
1 AAAGCGGTGGTACACCCTCAAGGATCGC
40184 AAAGCGG
1 AAAGCGG
40191 CAGTACGGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.24, G:0.30, T:0.17
Consensus pattern (28 bp):
AAAGCGGTGGTACACCCTCAAGGATCGC
Found at i:40196 original size:28 final size:28
Alignment explanation
Indices: 40142--40196 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
40132 CGGTGGTATG
* **
40142 CCCTCAAGGATCGCAAAGTGGTGGTACA
1 CCCTCAAGGATCGCAAAGCGGCAGTACA
*
40170 CCCTCAAGTATCGCAAAGCGGCAGTAC
1 CCCTCAAGGATCGCAAAGCGGCAGTAC
40197 GGTCTCGAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.16
Consensus pattern (28 bp):
CCCTCAAGGATCGCAAAGCGGCAGTACA
Found at i:40362 original size:24 final size:24
Alignment explanation
Indices: 40317--40363 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
40307 GATCGAAAAC
* *
40317 GGTCGCGCGCCCATCATCAGAAGA
1 GGTCGCACGCCCACCATCAGAAGA
* *
40341 GGTCGCACGTCCACCATTAGAAG
1 GGTCGCACGCCCACCATCAGAAG
40364 CGGTAGCGCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.15
Consensus pattern (24 bp):
GGTCGCACGCCCACCATCAGAAGA
Found at i:40429 original size:22 final size:22
Alignment explanation
Indices: 40403--40444 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
40393 AGAAAGTGGG
*
40403 AGATCA-CTAACCATTGAAGATA
1 AGATCACCT-ACCATTAAAGATA
40425 AGATCACCTACCATTAAAGA
1 AGATCACCTACCATTAAAGA
40445 CAGTAGACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.21
Consensus pattern (22 bp):
AGATCACCTACCATTAAAGATA
Found at i:41034 original size:2 final size:2
Alignment explanation
Indices: 41027--41056 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
41017 AGGGAAATCG
*
41027 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41057 TTACAAGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:50485 original size:1 final size:1
Alignment explanation
Indices: 50479--50505 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
50469 AGTCTTTAGT
50479 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
50506 GCTGTAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:52774 original size:17 final size:18
Alignment explanation
Indices: 52752--52790 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
52742 GGGTATTTTT
*
52752 GGGTTCGGTCTCAGG-TA
1 GGGTTCGGGCTCAGGCTA
*
52769 GGGTTCGGGCTCGGGCTA
1 GGGTTCGGGCTCAGGCTA
52787 GGGT
1 GGGT
52791 CGAGTTCGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.08, C:0.18, G:0.49, T:0.26
Consensus pattern (18 bp):
GGGTTCGGGCTCAGGCTA
Found at i:53259 original size:31 final size:31
Alignment explanation
Indices: 53215--53296 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 31
53205 TAATCAATCA
* * *
53215 TAAATTATTACAAATTAAAACAAAT-TAAGTAT
1 TAAATTA-AACAAATTAAAA-AAATGAAAGCAT
* *
53247 TAAATTAAACAAA-TAATTAAAATGAAAGCCT
1 TAAATTAAACAAATTAA-AAAAATGAAAGCAT
53278 TAAATTAAACAAATTAAAA
1 TAAATTAAACAAATTAAAA
53297 GCTGATAGAC
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
30 7 0.17
31 24 0.59
32 10 0.24
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (31 bp):
TAAATTAAACAAATTAAAAAAATGAAAGCAT
Found at i:53758 original size:23 final size:23
Alignment explanation
Indices: 53726--53776 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
53716 TCAAATTATT
*
53726 TCGGGATCGAGCTCGGGTCGGGA
1 TCGGGATCGAGCTCGGATCGGGA
* * * *
53749 TCGGGCTCGATCTTGGATCGGGT
1 TCGGGATCGAGCTCGGATCGGGA
53772 TCGGG
1 TCGGG
53777 TATTTTCGGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.10, C:0.22, G:0.45, T:0.24
Consensus pattern (23 bp):
TCGGGATCGAGCTCGGATCGGGA
Found at i:58303 original size:6 final size:6
Alignment explanation
Indices: 58292--58318 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
58282 GTGTGGAGTT
58292 CATCTC CATCTC CATCTC CATCTC CAT
1 CATCTC CATCTC CATCTC CATCTC CAT
58319 ACTCATGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.48, G:0.00, T:0.33
Consensus pattern (6 bp):
CATCTC
Found at i:64392 original size:22 final size:22
Alignment explanation
Indices: 64362--64566 Score: 154
Period size: 22 Copynumber: 9.4 Consensus size: 22
64352 TCCAACGTAG
*
64362 AAATATTGATAACTACACTGTGA
1 AAAT-TTGATAACTACACTATGA
*
64385 AAATTTGATAACCT-CATTATG-
1 AAATTTGATAA-CTACACTATGA
*
64406 AAATTTCGATAACCTTC-CTATGA
1 AAATTT-GATAA-CTACACTATGA
* *
64429 AAATTTGATAACCACACTGTGA
1 AAATTTGATAACTACACTATGA
* *
64451 AATTTTGATAACCACACTATGA
1 AAATTTGATAACTACACTATGA
* * * *
64473 AATTTTGATAACTTCAGTGTGA
1 AAATTTGATAACTACACTATGA
* *
64495 AATTTTGATAATCTTC-CTATGA
1 AAATTTGATAA-CTACACTATGA
* *
64517 AATTTTGATAA-TCACATTAT-A
1 AAATTTGATAACT-ACACTATGA
*
64538 AAA-TTGGTAACTACACTATGA
1 AAATTTGATAACTACACTATGA
*
64559 AAAATTGA
1 AAATTTGA
64567 AAATTTTGAT
Statistics
Matches: 151, Mismatches: 20, Indels: 23
0.78 0.10 0.12
Matches are distributed among these distances:
20 13 0.09
21 17 0.11
22 104 0.69
23 17 0.11
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (22 bp):
AAATTTGATAACTACACTATGA
Found at i:64430 original size:44 final size:44
Alignment explanation
Indices: 64382--64542 Score: 180
Period size: 44 Copynumber: 3.7 Consensus size: 44
64372 AACTACACTG
* *
64382 TGAAAATTTGATAACCTCATTATGAAATTTCGATAACCTTCCTA
1 TGAAAATTTGATAACCACATTATGAAATTTTGATAACCTTCCTA
* * *
64426 TGAAAATTTGATAACCACACTGTGAAATTTTGATAACC-ACACTA
1 TGAAAATTTGATAACCACATTATGAAATTTTGATAACCTTC-CTA
* ** * * *
64470 TGAAATTTTGATAACTTCAGTGTGAAATTTTGATAATCTTCCTA
1 TGAAAATTTGATAACCACATTATGAAATTTTGATAACCTTCCTA
* * *
64514 TGAAATTTTGATAATCACATTATAAAATT
1 TGAAAATTTGATAACCACATTATGAAATT
64543 GGTAACTACA
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
43 1 0.01
44 96 0.98
45 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (44 bp):
TGAAAATTTGATAACCACATTATGAAATTTTGATAACCTTCCTA
Found at i:64473 original size:66 final size:66
Alignment explanation
Indices: 64362--64566 Score: 220
Period size: 66 Copynumber: 3.1 Consensus size: 66
64352 TCCAACGTAG
* *
64362 AAATATTGATAACTACACTGTGAAAATTTGATAACCTCATTATGAAATTTCGATAACCTTC-CTA
1 AAAT-TTGATAACTACACTGTGAAATTTTGATAACCACATTATGAAATTTCGATAA-CTTCACTA
64426 TGA
64 TGA
* * * * *
64429 AAATTTGATAACCACACTGTGAAATTTTGATAACCACACTATGAAATTTTGATAACTTCAGTGTG
1 AAATTTGATAACTACACTGTGAAATTTTGATAACCACATTATGAAATTTCGATAACTTCACTATG
64494 A
66 A
* * * * * * *
64495 AATTTTGATAATCTTC-CTATGAAATTTTGATAATCACATTAT-AAAATT-GGTAACTACACTAT
1 AAATTTGATAA-CTACACTGTGAAATTTTGATAACCACATTATGAAATTTCGATAACTTCACTAT
64557 GA
65 GA
*
64559 AAAATTGA
1 AAATTTGA
64567 AAATTTTGAT
Statistics
Matches: 116, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
64 18 0.16
65 9 0.08
66 83 0.72
67 6 0.05
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (66 bp):
AAATTTGATAACTACACTGTGAAATTTTGATAACCACATTATGAAATTTCGATAACTTCACTATG
A
Found at i:64641 original size:73 final size:73
Alignment explanation
Indices: 64494--64633 Score: 167
Period size: 73 Copynumber: 1.9 Consensus size: 73
64484 CTTCAGTGTG
* ** *
64494 AAATTTTGATAATCTTCCTATGAAATTTTGATAATCACATTATAAAATTGGTAACTACACTATGA
1 AAATTTTGATAATCTTCCTATAAAATTTTGATAATCACACCATAAAATTGATAACTACACTATGA
64559 AAAATTGA
66 AAAATTGA
** *
64567 AAATTTTGATAA-CTTTTTTATAAAATTTTGATAATCACACCATAAGATCTCGATAACCT-CACT
1 AAATTTTGATAATC-TTCCTATAAAATTTTGATAATCACACCATAAAAT-T-GATAA-CTACACT
64630 ATGA
62 ATGA
64634 GAATGAAACT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
72 1 0.02
73 40 0.71
74 1 0.02
75 12 0.21
76 2 0.04
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.37
Consensus pattern (73 bp):
AAATTTTGATAATCTTCCTATAAAATTTTGATAATCACACCATAAAATTGATAACTACACTATGA
AAAATTGA
Found at i:64676 original size:22 final size:22
Alignment explanation
Indices: 64636--64918 Score: 159
Period size: 22 Copynumber: 12.8 Consensus size: 22
64626 CACTATGAGA
* * *
64636 ATGAAACTGTGATACCCTCTCT
1 ATGAAATTTTGATAACCTCTCT
* * *
64658 ATGTAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCTCTCT
* * *
64680 ATAAAATTTTCATAACCTCCCTAT
1 ATGAAATTTTGATAACCT--CTCT
* * *
64704 ATGAAATTTTGTTAACTTCCCT
1 ATGAAATTTTGATAACCTCTCT
64726 A-GAAATTTTGATAACCTCCCTTCCT
1 ATGAAATTTTGATAACCT--C-T-CT
* *
64751 ATGAACTTTTGTTAACCT-TCTT
1 ATGAAATTTTGATAACCTCTC-T
* *
64773 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCTCTCT
* * *
64795 ATAAAATTTCGGTAACCT-TCGT
1 ATGAAATTTTGATAACCTCTC-T
** * *
64817 ATGAAATTTTTTTAACCCCCCT
1 ATGAAATTTTGATAACCTCTCT
* *
64839 AAGAAATTTTGAT-A---CACT
1 ATGAAATTTTGATAACCTCTCT
*
64857 ATGAAGTTTTGATAACCTC-CAT
1 ATGAAATTTTGATAACCTCTC-T
* * *
64879 ATGAAATTTTGGTAACCACACT
1 ATGAAATTTTGATAACCTCTCT
*
64901 ATGAAGTTTTGATAACCT
1 ATGAAATTTTGATAACCT
64919 TCATGTGTAA
Statistics
Matches: 194, Mismatches: 50, Indels: 34
0.70 0.18 0.12
Matches are distributed among these distances:
18 14 0.07
19 1 0.01
21 18 0.09
22 125 0.64
23 4 0.02
24 15 0.08
25 3 0.02
26 14 0.07
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCTCT
Found at i:64909 original size:44 final size:44
Alignment explanation
Indices: 64852--64935 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
64842 AAATTTTGAT
64852 ACACTATGAAGTTTTGATAACCTCCATATGAAATTTTGGTAACC
1 ACACTATGAAGTTTTGATAACCTCCATATGAAATTTTGGTAACC
* * *
64896 ACACTATGAAGTTTTGATAACCTTCATGTGTAATTTTGGT
1 ACACTATGAAGTTTTGATAACCTCCATATGAAATTTTGGT
64936 TTGATTGTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (44 bp):
ACACTATGAAGTTTTGATAACCTCCATATGAAATTTTGGTAACC
Found at i:64932 original size:22 final size:21
Alignment explanation
Indices: 64851--64933 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 21
64841 GAAATTTTGA
64851 TACACTATGAAGTTTTGATAACC
1 TACA-TATGAA-TTTTGATAACC
* *
64874 TCCATATGAAATTTTGGTAACC
1 TACATATG-AATTTTGATAACC
64896 -ACACTATGAAGTTTTGATAACC
1 TACA-TATGAA-TTTTGATAACC
* *
64918 TTCATGTGTAATTTTG
1 TACATATG-AATTTTG
64934 GTTTGATTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
21 4 0.08
22 36 0.73
23 9 0.18
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (21 bp):
TACATATGAATTTTGATAACC
Found at i:66114 original size:5 final size:5
Alignment explanation
Indices: 66104--66130 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
66094 TAATACGTAG
66104 TAAGA TAAGA TAAGA TAAGA TAAGA TA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TA
66131 TGCAATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (5 bp):
TAAGA
Found at i:71032 original size:14 final size:14
Alignment explanation
Indices: 71013--71040 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
71003 AAGAACCCTA
71013 ACACACTAATGAAG
1 ACACACTAATGAAG
71027 ACACACTAATGAAG
1 ACACACTAATGAAG
71041 CTTGGTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.14, T:0.14
Consensus pattern (14 bp):
ACACACTAATGAAG
Found at i:71952 original size:29 final size:29
Alignment explanation
Indices: 71910--71966 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
71900 AATTTCTTTT
*
71910 TTTTGTTGCCCTAATTTCTTACAAACTTG
1 TTTTCTTGCCCTAATTTCTTACAAACTTG
*
71939 TTTTCTTGCCCTAATTTCTTATAAACTT
1 TTTTCTTGCCCTAATTTCTTACAAACTT
71967 CGTAGTGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.51
Consensus pattern (29 bp):
TTTTCTTGCCCTAATTTCTTACAAACTTG
Found at i:77044 original size:178 final size:178
Alignment explanation
Indices: 76674--77059 Score: 490
Period size: 178 Copynumber: 2.2 Consensus size: 178
76664 ATTCACCATA
* * * * * * * *
76674 AGCACAAATTATGTAATATTAAGTAGACCGTCTATTTCCGTTAATCGAAACAACTAATTCTTTGT
1 AGCAAAAATTATATAATATTAAGTAGACCGTCTATTCCCATTAACCGAAACAACAAATTCTTCGG
* * * *
76739 AATCATTTTTTATATCTTGAACATTAAATTTAGTTTTTGAGTCCTTCATGAAAGTTGTAGATCAT
66 AAGCATTTTTGATATCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATAAT
* * * * * *
76804 GGAACAACCTTTCAAGAGACACTTGAATCATCTTAATCAGACATCTGG
131 GGAACAACATTTCAAGAGACACTTAAATCACCCTAATCAGACAACCGG
*
76852 AGCAAAAGTTATATAATATTAAGTAGACCGTCTATTCCCATTAACCGAAACAACAAATAT-TTCG
1 AGCAAAAATTATATAATATTAAGTAGACCGTCTATTCCCATTAACCGAAACAACAAAT-TCTTCG
76916 GAAGCATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATA
65 GAAGCATTTTTGATATCTTG-AACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATA
* * * * *
76980 ATGGAACAATATTTTAATAGACACTTAAATCACCCTAATCGGATAACCGG
129 ATGGAACAACATTTCAAGAGACACTTAAATCACCCTAATCAGACAACCGG
* *
77030 AG-AGAAAATTATATAATGTTAAATAGACCG
1 AGCA-AAAATTATATAATATTAAGTAGACCG
77060 CTTAGTCAAA
Statistics
Matches: 178, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
177 5 0.03
178 172 0.97
179 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (178 bp):
AGCAAAAATTATATAATATTAAGTAGACCGTCTATTCCCATTAACCGAAACAACAAATTCTTCGG
AAGCATTTTTGATATCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATAAT
GGAACAACATTTCAAGAGACACTTAAATCACCCTAATCAGACAACCGG
Found at i:77713 original size:21 final size:21
Alignment explanation
Indices: 77658--77714 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
77648 GTGCTCCCGT
*
77658 TGTGATGCACCCACTTCTCAA
1 TGTGATGCACCCATTTCTCAA
*
77679 TGTGATGCTCCCATTTCTCAA
1 TGTGATGCACCCATTTCTCAA
77700 TGTGATGCACCCATT
1 TGTGATGCACCCATT
77715 GAATTCTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (21 bp):
TGTGATGCACCCATTTCTCAA
Found at i:80179 original size:30 final size:30
Alignment explanation
Indices: 80140--80210 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
80130 TAAGTCTCTC
80140 AACTTTTATTT-CAATC-AAATAAGCTCTTTA
1 AACTTTTATTTGCAA-CGAAATAAGC-CTTTA
* *
80170 AATTTTTATTTGTAACGAAATAAGCCTTTA
1 AACTTTTATTTGCAACGAAATAAGCCTTTA
*
80200 AACTTTGATTT
1 AACTTTTATTT
80211 ATACCCAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
30 25 0.71
31 10 0.29
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (30 bp):
AACTTTTATTTGCAACGAAATAAGCCTTTA
Found at i:99695 original size:21 final size:21
Alignment explanation
Indices: 99671--99710 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
99661 CACATGGTTG
99671 GCCTGAGCACCCAGGTCTTAA
1 GCCTGAGCACCCAGGTCTTAA
* *
99692 GCCTGATCACCCATGTCTT
1 GCCTGAGCACCCAGGTCTT
99711 CCTGATGACT
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:0.20, C:0.35, G:0.20, T:0.25
Consensus pattern (21 bp):
GCCTGAGCACCCAGGTCTTAA
Found at i:100496 original size:292 final size:291
Alignment explanation
Indices: 99973--100556 Score: 1105
Period size: 292 Copynumber: 2.0 Consensus size: 291
99963 TTATTTAGCG
99973 AAACGCCGCTATTTGATTCGCTTAAATTGAAGATAGCGGCGTTTCTTCCAAAAAACGCCACTAAA
1 AAACGCCGCTATTTGATTCGCTTAAATTGAAGATAGCGGCGTTTCTTCCAAAAAACGCCACTAAA
100038 TTGCGGCGTTTCGTAGCACAAACGCCGATATATGCAAAAAGAAGTGCGGGAAAATATCTCCGCGC
66 TTGCGGCGTTTCGTAGCACAAACGCCGATATATGCAAAAAGAAGTGCGGGAAAATATCTCCGCGC
* *
100103 GACTAATTTAAGCGAAAATTACATTTCTAAATACAATAGCGGCGTTTCTCACAAAAGACGCCGCT
131 GACTAATTTAAACGAAAATTACATTTCTAAATACAATAGCGGCGTTTCTCAAAAAAGACGCCGCT
100168 AAATAGTGGCATTTCTAGAGTAAACGCCGCGATATATAATCTTATCCAAAGAATAGAAATTCGGT
196 AAATAGTGGCATTTCTAGAGTAAACGCCGCGATATATAATCTTATCCAAAGAATAGAAATTCGGT
100233 GAAACTAAAAACATTATTTCTTGTTGGGAAT
261 GAAACTAAAAACATTATTTCTTGTTGGGAAT
100264 AAACGCCGCTATTTGATTCGCTTAAATTGAAGATAGCGGCGTTTCTTCCAAAAAAACGCCACTAA
1 AAACGCCGCTATTTGATTCGCTTAAATTGAAGATAGCGGCGTTTCTTCC-AAAAAACGCCACTAA
* *
100329 ATTGCGGCGTTTCGTAGCACAAACGCCGGTATATGCAAAAAGAAGTGCTGGAAAATATCTCCGCG
65 ATTGCGGCGTTTCGTAGCACAAACGCCGATATATGCAAAAAGAAGTGCGGGAAAATATCTCCGCG
100394 CGACTAATTTAAACGAAAATTACATTTCTAAATACAATAGCGGCGTTTCTCAAAAAAGACGCCGC
130 CGACTAATTTAAACGAAAATTACATTTCTAAATACAATAGCGGCGTTTCTCAAAAAAGACGCCGC
* *
100459 TAAATAGTGGCGTTTCTAGAGTAAAGGCCGCGATATATAATCTTATCCAAAGAATAGAAATTCGG
195 TAAATAGTGGCATTTCTAGAGTAAACGCCGCGATATATAATCTTATCCAAAGAATAGAAATTCGG
100524 TGAAACTAAAAACATTATTTCTTGTTGGGAAT
260 TGAAACTAAAAACATTATTTCTTGTTGGGAAT
100556 A
1 A
100557 GTGGCGTTTC
Statistics
Matches: 286, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
291 49 0.17
292 237 0.83
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (291 bp):
AAACGCCGCTATTTGATTCGCTTAAATTGAAGATAGCGGCGTTTCTTCCAAAAAACGCCACTAAA
TTGCGGCGTTTCGTAGCACAAACGCCGATATATGCAAAAAGAAGTGCGGGAAAATATCTCCGCGC
GACTAATTTAAACGAAAATTACATTTCTAAATACAATAGCGGCGTTTCTCAAAAAAGACGCCGCT
AAATAGTGGCATTTCTAGAGTAAACGCCGCGATATATAATCTTATCCAAAGAATAGAAATTCGGT
GAAACTAAAAACATTATTTCTTGTTGGGAAT
Found at i:100716 original size:127 final size:125
Alignment explanation
Indices: 100553--100889 Score: 428
Period size: 124 Copynumber: 2.7 Consensus size: 125
100543 TCTTGTTGGG
* *
100553 AATAGTGGCGTTTCTTGAGTAAACGCCGCTATATATAATCTTATCCAAAGAGTAGAAATATGGTG
1 AATAGTGGCGTTTCTAGAGTAAACGCCGCTATATATAATCTTATCCAAAGAATAGAAATATGGTG
* *
100618 CAATTGATAAAAACACCATTTCTTGATGGGAATAGCGGCGTTTCTC-C-TATGAAACGCCGCTA
66 CAA-T-ATAAAAACACCATTTCTTGATGGGAATAGCGGCGTTTCTCACAAAT--AACGCCACTA
* * *
100680 AATAGTGGCGTTTCTAGAGTAAATGCCGCTATATATAATCTTATTCGAAGAATAGAAATATGGTG
1 AATAGTGGCGTTTCTAGAGTAAACGCCGCTATATATAATCTTATCCAAAGAATAGAAATATGGTG
* ** * *
100745 CAA-CTAAAAACATTATTTCTTGTTGGGAATAGTGGCGTTTCTCACAAATAACGCCACTA
66 CAATATAAAAACACCATTTCTTGATGGGAATAGCGGCGTTTCTCACAAATAACGCCACTA
* * * * * *
100804 AATTGTGGCATTTCTAAAGTAAACGCCGTTATATATAATCTTATCCAAAGAATAGAAATTTTGTG
1 AATAGTGGCGTTTCTAGAGTAAACGCCGCTATATATAATCTTATCCAAAGAATAGAAATATGGTG
*
100869 AAACTAGTAAAAACACCATTT
66 CAA-TA-TAAAAACACCATTT
100890 ATAAATCATA
Statistics
Matches: 180, Mismatches: 25, Indels: 10
0.84 0.12 0.05
Matches are distributed among these distances:
124 102 0.57
125 1 0.01
126 2 0.01
127 75 0.42
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (125 bp):
AATAGTGGCGTTTCTAGAGTAAACGCCGCTATATATAATCTTATCCAAAGAATAGAAATATGGTG
CAATATAAAAACACCATTTCTTGATGGGAATAGCGGCGTTTCTCACAAATAACGCCACTA
Found at i:102036 original size:38 final size:38
Alignment explanation
Indices: 101985--102060 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
101975 GATATGTTTT
101985 ATTTAGATCTGATGAAAATGATTTCGAAATGACACTCA
1 ATTTAGATCTGATGAAAATGATTTCGAAATGACACTCA
102023 ATTTAGATCTGATGAAAATGATTTCGAAATGACACTCA
1 ATTTAGATCTGATGAAAATGATTTCGAAATGACACTCA
102061 TTTCATCTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (38 bp):
ATTTAGATCTGATGAAAATGATTTCGAAATGACACTCA
Found at i:104041 original size:33 final size:33
Alignment explanation
Indices: 104004--104093 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 33
103994 CATCTAATGT
*
104004 TAATGTTAACATTTACAGAAATCTTCCATCACC
1 TAATGTTAACATTTACAGAAATCTACCATCACC
* * *
104037 TAATGATAACATTTCCAGAAATCTACTATCACC
1 TAATGTTAACATTTACAGAAATCTACCATCACC
* * **
104070 TAATTTTTACATTTGTAGAAATCT
1 TAATGTTAACATTTACAGAAATCT
104094 GCATTTCCAA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (33 bp):
TAATGTTAACATTTACAGAAATCTACCATCACC
Found at i:104582 original size:30 final size:30
Alignment explanation
Indices: 104548--104646 Score: 139
Period size: 30 Copynumber: 3.3 Consensus size: 30
104538 CCTCCTTGGT
*
104548 GGACCTTTGCTTGGTGCAGTGGCTTGGGCA
1 GGACCTTTGCTTGGTGCAGTGGCTTGTGCA
* *
104578 GGACCTTTAG-TTCGTGCAGTGGAGTT-TGCA
1 GGACCTTT-GCTTGGTGCAGTGG-CTTGTGCA
104608 GGACCTTTGCTTGGTGCAGTGGCTTGTGCA
1 GGACCTTTGCTTGGTGCAGTGGCTTGTGCA
104638 GGACCTTTG
1 GGACCTTTG
104647 GTTGCTTGAT
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
29 3 0.05
30 54 0.90
31 3 0.05
ACGTcount: A:0.12, C:0.19, G:0.36, T:0.32
Consensus pattern (30 bp):
GGACCTTTGCTTGGTGCAGTGGCTTGTGCA
Found at i:110415 original size:2 final size:2
Alignment explanation
Indices: 110408--110434 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
110398 TTCAGGCAAT
110408 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 T
110435 TCTAATTCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:110785 original size:2 final size:2
Alignment explanation
Indices: 110780--110835 Score: 71
Period size: 2 Copynumber: 28.0 Consensus size: 2
110770 TTATAGTTCC
*
110780 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA GT- TCC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA T-A TA
110822 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
110836 GCTTCTTGTA
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
1 2 0.04
2 45 0.92
3 2 0.04
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:113014 original size:59 final size:60
Alignment explanation
Indices: 112900--113016 Score: 200
Period size: 60 Copynumber: 2.0 Consensus size: 60
112890 CTTAAATATA
*
112900 TAAACGCCGCTATATTTAATTTGAGATTTAATTTAAAATATCCTTAAATATAGCGGCGTT
1 TAAACGCCGCTATATTTAATTTGAGATTTAATTTAAAATACCCTTAAATATAGCGGCGTT
* *
112960 TAAACGCCGCTATATTTAATTTGATATTT-TTTTAAAATACCCTTAAATATAGCGGCG
1 TAAACGCCGCTATATTTAATTTGAGATTTAATTTAAAATACCCTTAAATATAGCGGCG
113017 CCGAAACGCC
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
59 26 0.48
60 28 0.52
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (60 bp):
TAAACGCCGCTATATTTAATTTGAGATTTAATTTAAAATACCCTTAAATATAGCGGCGTT
Found at i:113024 original size:59 final size:60
Alignment explanation
Indices: 112901--113028 Score: 195
Period size: 59 Copynumber: 2.1 Consensus size: 60
112891 TTAAATATAT
* ***
112901 AAACGCCGCTATATTTAATTTGAGATTTAATTTAAAATATCCTTAAATATAGCGGCGTTT
1 AAACGCCGCTATATTTAATTTGAGATTTAATTTAAAATACCCTTAAATATAGCGGCGCCG
* *
112961 AAACGCCGCTATATTTAATTTGATATTT-TTTTAAAATACCCTTAAATATAGCGGCGCCG
1 AAACGCCGCTATATTTAATTTGAGATTTAATTTAAAATACCCTTAAATATAGCGGCGCCG
113020 AAACGCCGC
1 AAACGCCGC
113029 AATTCCTAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
59 35 0.56
60 27 0.44
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (60 bp):
AAACGCCGCTATATTTAATTTGAGATTTAATTTAAAATACCCTTAAATATAGCGGCGCCG
Found at i:115241 original size:19 final size:19
Alignment explanation
Indices: 115217--115254 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
115207 AACGTGTCAC
115217 GTCTTTATGAAATTAATTA
1 GTCTTTATGAAATTAATTA
115236 GTCTTTATGAAATTAATTA
1 GTCTTTATGAAATTAATTA
115255 ATTGGCAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (19 bp):
GTCTTTATGAAATTAATTA
Found at i:116027 original size:7 final size:7
Alignment explanation
Indices: 116015--116039 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
116005 ACAATACCCT
116015 TTTGGAG
1 TTTGGAG
116022 TTTGGAG
1 TTTGGAG
116029 TTTGGAG
1 TTTGGAG
116036 TTTG
1 TTTG
116040 AACAGTTTCC
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:0.40, T:0.48
Consensus pattern (7 bp):
TTTGGAG
Found at i:118472 original size:24 final size:24
Alignment explanation
Indices: 118443--118490 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
118433 TCTTACCACC
118443 CTTCTCTATTAAATTTACCATTCT
1 CTTCTCTATTAAATTTACCATTCT
118467 CTTCTCTATTAAATTTACCATTCT
1 CTTCTCTATTAAATTTACCATTCT
118491 AATGCATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (24 bp):
CTTCTCTATTAAATTTACCATTCT
Found at i:120581 original size:42 final size:42
Alignment explanation
Indices: 120522--120602 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
120512 TAAGGATCGG
*
120522 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTCAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
120564 GATTTCAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTCAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
120603 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.47
Consensus pattern (42 bp):
GATTTCAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:125284 original size:41 final size:41
Alignment explanation
Indices: 125227--125317 Score: 182
Period size: 41 Copynumber: 2.2 Consensus size: 41
125217 GACTGAGAAA
125227 ACCTTTCAACCCCATGTCTCTCTCGCGTGCCCCAGAATACG
1 ACCTTTCAACCCCATGTCTCTCTCGCGTGCCCCAGAATACG
125268 ACCTTTCAACCCCATGTCTCTCTCGCGTGCCCCAGAATACG
1 ACCTTTCAACCCCATGTCTCTCTCGCGTGCCCCAGAATACG
125309 ACCTTTCAA
1 ACCTTTCAA
125318 TTCCCCCACC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.21, C:0.41, G:0.13, T:0.25
Consensus pattern (41 bp):
ACCTTTCAACCCCATGTCTCTCTCGCGTGCCCCAGAATACG
Found at i:134246 original size:15 final size:15
Alignment explanation
Indices: 134228--134261 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
134218 TGATTATTCA
134228 CACCATTATTATTTG
1 CACCATTATTATTTG
* *
134243 CACCATTGTTGTTTG
1 CACCATTATTATTTG
134258 CACC
1 CACC
134262 GTTCACCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.41
Consensus pattern (15 bp):
CACCATTATTATTTG
Found at i:145910 original size:25 final size:25
Alignment explanation
Indices: 145876--145924 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
145866 CCGAACAATC
145876 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
145901 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
145925 CAAACCAATC
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:0.12, C:0.33, G:0.20, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:146799 original size:25 final size:25
Alignment explanation
Indices: 146765--146813 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
146755 CCGAACAATC
146765 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
146790 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
146814 CAAACCAATC
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:0.12, C:0.33, G:0.20, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:146839 original size:21 final size:21
Alignment explanation
Indices: 146810--146851 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
146800 TCGCTCGGTC
*
146810 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
146830 TCTACCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
146852 CACACACACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.17
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Found at i:149290 original size:22 final size:24
Alignment explanation
Indices: 149257--149308 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
149247 CTTAAATTTC
149257 TATTTTTAATTT-GTTCT-ATCTTT
1 TATTTTTAATTTCGTT-TAATCTTT
149280 TATTTTT-ATTTCGTTTAATCTTT
1 TATTTTTAATTTCGTTTAATCTTT
*
149303 TCTTTT
1 TATTTT
149309 CTTTGATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.15, C:0.10, G:0.04, T:0.71
Consensus pattern (24 bp):
TATTTTTAATTTCGTTTAATCTTT
Found at i:156565 original size:22 final size:22
Alignment explanation
Indices: 156540--156582 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
156530 ATTGATATGA
156540 AAGAGGATAAGATTAATCAAAT
1 AAGAGGATAAGATTAATCAAAT
156562 AAGAGGATAAGATTAATCAAA
1 AAGAGGATAAGATTAATCAAA
156583 GTTCAATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.56, C:0.05, G:0.19, T:0.21
Consensus pattern (22 bp):
AAGAGGATAAGATTAATCAAAT
Found at i:164970 original size:21 final size:21
Alignment explanation
Indices: 164941--164980 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
164931 CAGACATGCA
164941 ACTTCTTCAGTGAGTGATTCT
1 ACTTCTTCAGTGAGTGATTCT
*
164962 ACTTTTTCAGTGAGTGATT
1 ACTTCTTCAGTGAGTGATT
164981 GCACATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (21 bp):
ACTTCTTCAGTGAGTGATTCT
Found at i:164989 original size:21 final size:21
Alignment explanation
Indices: 164946--164990 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
164936 ATGCAACTTC
*
164946 TTCAGTGAGTGATTCTACTTT
1 TTCAGTGAGTGATTCTACATT
164967 TTCAGTGAGTGATTGC-ACATT
1 TTCAGTGAGTGATT-CTACATT
164988 TTC
1 TTC
164991 TTGTAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.44
Consensus pattern (21 bp):
TTCAGTGAGTGATTCTACATT
Found at i:168497 original size:29 final size:29
Alignment explanation
Indices: 168455--168510 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
168445 TGTCACCAAA
168455 AGTTACCTATGGTTCCAATTCCTTGGAAG
1 AGTTACCTATGGTTCCAATTCCTTGGAAG
**
168484 AGTTACCTATGGTTCTGATTCCTTGGA
1 AGTTACCTATGGTTCCAATTCCTTGGA
168511 TGGATCCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (29 bp):
AGTTACCTATGGTTCCAATTCCTTGGAAG
Found at i:168546 original size:11 final size:11
Alignment explanation
Indices: 168530--168562 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
168520 TGGAGAAGAG
168530 TTAGAAGAGTT
1 TTAGAAGAGTT
*
168541 TTAGAAGACTT
1 TTAGAAGAGTT
168552 TTAGAAGAGTT
1 TTAGAAGAGTT
168563 ACCTATGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.36
Consensus pattern (11 bp):
TTAGAAGAGTT
Found at i:168602 original size:41 final size:41
Alignment explanation
Indices: 168545--168624 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
168535 AGAGTTTTAG
168545 AAGACTTTTAGAAGAGTTACCTATGGTTCCAATTCCTTGAT
1 AAGACTTTTAGAAGAGTTACCTATGGTTCCAATTCCTTGAT
168586 AAGACTTTTAGAAGAGTTACCTATGGTTCCAATTCCTTG
1 AAGACTTTTAGAAGAGTTACCTATGGTTCCAATTCCTTG
168625 GATGGATCCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (41 bp):
AAGACTTTTAGAAGAGTTACCTATGGTTCCAATTCCTTGAT
Found at i:188757 original size:18 final size:18
Alignment explanation
Indices: 188734--188768 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
188724 GTCGTTGAAT
188734 GAATGTCATGATTAAAAG
1 GAATGTCATGATTAAAAG
188752 GAATGTCATGATTAAAA
1 GAATGTCATGATTAAAA
188769 CCCAACTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.29
Consensus pattern (18 bp):
GAATGTCATGATTAAAAG
Found at i:201925 original size:45 final size:45
Alignment explanation
Indices: 201860--201986 Score: 211
Period size: 45 Copynumber: 2.8 Consensus size: 45
201850 ACGCAAAAAT
* *
201860 TAATATTAGGTTTATTTTGATGAATTACTTAGAGATGGAGGAGTAG
1 TAATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGT-G
201906 -AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTG
1 TAATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTG
*
201950 TAATATTATCTTTATTTTGATGAATTACCTAGAGATG
1 TAATATTAGCTTTATTTTGATGAATTACCTAGAGATG
201987 AAGTAGAATT
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
44 1 0.01
45 76 0.99
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.40
Consensus pattern (45 bp):
TAATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTG
Found at i:203449 original size:2 final size:2
Alignment explanation
Indices: 203442--203481 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
203432 AATCTTTGAT
*
203442 TC TC TC TC TC TC TC TC TC TC TC TG TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
203482 ATTTAATGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
TC
Found at i:206614 original size:29 final size:30
Alignment explanation
Indices: 206554--206633 Score: 117
Period size: 29 Copynumber: 2.7 Consensus size: 30
206544 GCTAAATACC
* *
206554 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTTCGGGA
206585 CAAAATAATCCCTTATGTTTT-TTTCGGGA
1 CAAAATAATCCCTTATGTTTTCTTTCGGGA
*
206614 CAAATTAATCCCTTATGTTT
1 CAAAATAATCCCTTATGTTT
206634 CAAAAATGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 26 0.57
31 20 0.43
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTCGGGA
Found at i:206825 original size:31 final size:31
Alignment explanation
Indices: 206787--206867 Score: 119
Period size: 30 Copynumber: 2.6 Consensus size: 31
206777 TTTGTCCCAA
206787 AAAAACATAAGGGATTTTTTTGTCCCAAAAG
1 AAAAACATAAGGGATTTTTTTGTCCCAAAAG
* *
206818 AAAAACATGAGAGA-TTTTTTGTCCCAAAAG
1 AAAAACATAAGGGATTTTTTTGTCCCAAAAG
* *
206848 AAAAATATTAGGGATTTTTT
1 AAAAACATAAGGGATTTTTT
206868 AGTATTTAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 27 0.61
31 17 0.39
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (31 bp):
AAAAACATAAGGGATTTTTTTGTCCCAAAAG
Done.