Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013972.1 Kokia drynarioides strain JFW-HI SEQ_129003, 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: 113305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 90 characters in sequence are not A, C, G, or T
Found at i:74 original size:11 final size:11
Alignment explanation
Indices: 60--106 Score: 67
Period size: 11 Copynumber: 4.2 Consensus size: 11
50 GAAAATAATT
*
60 TTAAACTTAAA
1 TTAAATTTAAA
71 TTAAATTTAAA
1 TTAAATTTAAA
82 TTTAAATTTAAA
1 -TTAAATTTAAA
*
94 ATAAATTTAAA
1 TTAAATTTAAA
105 TT
1 TT
107 TTTAAGCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
11 21 0.66
12 11 0.34
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:80 original size:6 final size:6
Alignment explanation
Indices: 34--107 Score: 73
Period size: 6 Copynumber: 12.5 Consensus size: 6
24 TTCTATTTAT
* * *
34 TTTAAA CTTTAAA TTTGAAA -ATAAT TTTAAA CTTAAA -TTAAA TTTAAA
1 TTTAAA -TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
82 TTTAAA TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
108 TTAAGCAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
5 11 0.20
6 36 0.64
7 9 0.16
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:81 original size:17 final size:17
Alignment explanation
Indices: 35--106 Score: 74
Period size: 17 Copynumber: 4.1 Consensus size: 17
25 TCTATTTATT
35 TTAAACTTTAAATTTGAAA
1 TTAAA-TTTAAATTT-AAA
* * *
54 ATAATTTTAAACTTAAA
1 TTAAATTTAAATTTAAA
71 TTAAATTTAAATTTAAA
1 TTAAATTTAAATTTAAA
*
88 TTTAAA-ATAAATTTAAA
1 -TTAAATTTAAATTTAAA
105 TT
1 TT
107 TTTAAGCAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
16 2 0.04
17 27 0.60
18 13 0.29
19 3 0.07
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
TTAAATTTAAATTTAAA
Found at i:92 original size:23 final size:23
Alignment explanation
Indices: 59--107 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
49 TGAAAATAAT
*
59 TTTAAACTTAAATTAAATTTAAA
1 TTTAAACTTAAAATAAATTTAAA
*
82 TTTAAATTTAAAATAAATTTAAA
1 TTTAAACTTAAAATAAATTTAAA
105 TTT
1 TTT
108 TTAAGCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTAAACTTAAAATAAATTTAAA
Found at i:135 original size:18 final size:18
Alignment explanation
Indices: 78--139 Score: 74
Period size: 18 Copynumber: 3.5 Consensus size: 18
68 AAATTAAATT
*
78 TAAATTTAA-ATTTAAAA
1 TAAATTTAATTTTTAAAA
*
95 TAAATTTAAATTTTT-AAG
1 TAAATTT-AATTTTTAAAA
*
113 CAAATTTAATTTTTAAAA
1 TAAATTTAATTTTTAAAA
131 TAAATTTAA
1 TAAATTTAA
140 AGGGAGTATG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
17 14 0.38
18 20 0.54
19 3 0.08
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
TAAATTTAATTTTTAAAA
Found at i:4208 original size:16 final size:17
Alignment explanation
Indices: 4187--4219 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4177 TTGAGTTGAG
4187 AAAATT-ATTTAATTAA
1 AAAATTAATTTAATTAA
*
4203 AAAATTAATTTAGTTAA
1 AAAATTAATTTAATTAA
4220 TGTAATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
AAAATTAATTTAATTAA
Found at i:13335 original size:13 final size:13
Alignment explanation
Indices: 13297--13337 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
13287 AATAATCCAA
*
13297 GAAGCATTATTAA
1 GAAGCATTATTAT
13310 GAAGCATTATTAT
1 GAAGCATTATTAT
13323 GAAGCATTATTAT
1 GAAGCATTATTAT
13336 GA
1 GA
13338 TATGTCAGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (13 bp):
GAAGCATTATTAT
Found at i:18731 original size:23 final size:22
Alignment explanation
Indices: 18701--18777 Score: 75
Period size: 23 Copynumber: 3.4 Consensus size: 22
18691 ACGCTAGCGC
18701 GCTTACTGTTCAGCACTAT-GTGT
1 GCTTACTGTTC-GCACT-TCGTGT
18724 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTG-TTCGCACTTCGTGT
* * *
18747 TCTTACTGTTTCGTACCTCGTGT
1 GCTTACTG-TTCGCACTTCGTGT
*
18770 GCCTACTG
1 GCTTACTG
18778 ATTTGCGCTA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 1 0.02
23 43 0.91
24 3 0.06
ACGTcount: A:0.12, C:0.26, G:0.21, T:0.42
Consensus pattern (22 bp):
GCTTACTGTTCGCACTTCGTGT
Found at i:18832 original size:23 final size:22
Alignment explanation
Indices: 18766--18833 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 22
18756 TTCGTACCTC
* *
18766 GTGTGCCTACTGATTTGCGCTAT
1 GTGTGCCTACTGA-TTGCACTGT
* *
18789 GTGCGCCTACTGATTGTACTGT
1 GTGTGCCTACTGATTGCACTGT
18811 GTGTGCCTACTGGATTGCACTGT
1 GTGTGCCTACT-GATTGCACTGT
18834 ATGCTTACTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 16 0.42
23 22 0.58
ACGTcount: A:0.13, C:0.22, G:0.28, T:0.37
Consensus pattern (22 bp):
GTGTGCCTACTGATTGCACTGT
Found at i:21155 original size:13 final size:13
Alignment explanation
Indices: 21117--21157 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
21107 AATAATCCAA
*
21117 GAAGCATTATTAA
1 GAAGCATTATTAT
21130 GAAGCATTATTAT
1 GAAGCATTATTAT
21143 GAAGCATTATTAT
1 GAAGCATTATTAT
21156 GA
1 GA
21158 TATGTCAGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (13 bp):
GAAGCATTATTAT
Found at i:26551 original size:23 final size:22
Alignment explanation
Indices: 26521--26597 Score: 75
Period size: 23 Copynumber: 3.4 Consensus size: 22
26511 ACGCTAGCGC
26521 GCTTACTGTTCAGCACTAT-GTGT
1 GCTTACTGTTC-GCACT-TCGTGT
26544 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTG-TTCGCACTTCGTGT
* * *
26567 TCTTACTGTTTCGTACCTCGTGT
1 GCTTACTG-TTCGCACTTCGTGT
*
26590 GCCTACTG
1 GCTTACTG
26598 ATTTGCGCTA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 1 0.02
23 43 0.91
24 3 0.06
ACGTcount: A:0.12, C:0.26, G:0.21, T:0.42
Consensus pattern (22 bp):
GCTTACTGTTCGCACTTCGTGT
Found at i:26652 original size:23 final size:22
Alignment explanation
Indices: 26586--26653 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 22
26576 TTCGTACCTC
* *
26586 GTGTGCCTACTGATTTGCGCTAT
1 GTGTGCCTACTGA-TTGCACTGT
* *
26609 GTGCGCCTACTGATTGTACTGT
1 GTGTGCCTACTGATTGCACTGT
26631 GTGTGCCTACTGGATTGCACTGT
1 GTGTGCCTACT-GATTGCACTGT
26654 ATGCTTACTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 16 0.42
23 22 0.58
ACGTcount: A:0.13, C:0.22, G:0.28, T:0.37
Consensus pattern (22 bp):
GTGTGCCTACTGATTGCACTGT
Found at i:27126 original size:84 final size:84
Alignment explanation
Indices: 27017--27186 Score: 340
Period size: 84 Copynumber: 2.0 Consensus size: 84
27007 GTGAAAAATA
27017 TAGATTTTATATAATAAATATTCATACGTTTATTAAAATGAGTTAATAAAAAATTTAGAATTGAT
1 TAGATTTTATATAATAAATATTCATACGTTTATTAAAATGAGTTAATAAAAAATTTAGAATTGAT
27082 TAATTATTCTTGTAGTACT
66 TAATTATTCTTGTAGTACT
27101 TAGATTTTATATAATAAATATTCATACGTTTATTAAAATGAGTTAATAAAAAATTTAGAATTGAT
1 TAGATTTTATATAATAAATATTCATACGTTTATTAAAATGAGTTAATAAAAAATTTAGAATTGAT
27166 TAATTATTCTTGTAGTACT
66 TAATTATTCTTGTAGTACT
27185 TA
1 TA
27187 CTAAGCATTC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (84 bp):
TAGATTTTATATAATAAATATTCATACGTTTATTAAAATGAGTTAATAAAAAATTTAGAATTGAT
TAATTATTCTTGTAGTACT
Found at i:31385 original size:22 final size:22
Alignment explanation
Indices: 31336--31388 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
31326 TACAATTTTA
* * *
31336 AAAATGTTAAAGGGTTTAAATT
1 AAAATTTTAAAAGATTTAAATT
31358 AAAATTTTAAAAGATTTAAATT
1 AAAATTTTAAAAGATTTAAATT
31380 AAAATTTTA
1 AAAATTTTA
31389 TCTTTCAGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (22 bp):
AAAATTTTAAAAGATTTAAATT
Found at i:32321 original size:11 final size:12
Alignment explanation
Indices: 32294--32326 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
32284 AAAGTTGAAG
32294 ATTAAAATGATA
1 ATTAAAATGATA
*
32306 ATTAAAATTA-A
1 ATTAAAATGATA
32317 ATTAAAATGA
1 ATTAAAATGA
32327 ACCCTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (12 bp):
ATTAAAATGATA
Found at i:36861 original size:24 final size:23
Alignment explanation
Indices: 36838--36895 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 23
36828 TATAATTTTA
36838 ATATTTTTAATATTTATATATTT
1 ATATTTTTAATATTTATATATTT
*
36861 ATATATTTATATATTTATATATTT
1 ATATTTTTA-ATATTTATATATTT
36885 ATAATTTTTAA
1 AT-ATTTTTAA
36896 ATTATTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 8 0.26
24 17 0.55
25 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
ATATTTTTAATATTTATATATTT
Found at i:36866 original size:16 final size:16
Alignment explanation
Indices: 36838--36891 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
36828 TATAATTTTA
*
36838 ATATTTTTA-ATATTT
1 ATATATTTATATATTT
36853 ATATATTTATATATTT
1 ATATATTTATATATTT
36869 ATATATTTATATATTT
1 ATATATTTATATATTT
36885 ATA-ATTT
1 ATATATTT
36892 TTAAATTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
15 12 0.32
16 25 0.68
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATATATTTATATATTT
Found at i:36898 original size:8 final size:8
Alignment explanation
Indices: 36832--36897 Score: 51
Period size: 8 Copynumber: 8.0 Consensus size: 8
36822 TAAAAATATA
*
36832 ATTTTAAT
1 ATTTAAAT
*
36840 ATTTTTAAT
1 A-TTTAAAT
*
36849 ATTTATAT
1 ATTTAAAT
*
36857 ATTTATAT
1 ATTTAAAT
*
36865 ATTTATAT
1 ATTTAAAT
*
36873 ATTTATAT
1 ATTTAAAT
36881 ATTTATAAT
1 ATTTA-AAT
*
36890 TTTTAAAT
1 ATTTAAAT
36898 TATTAAATCA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
8 38 0.73
9 14 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTTAAAT
Found at i:37989 original size:30 final size:30
Alignment explanation
Indices: 37955--38080 Score: 130
Period size: 30 Copynumber: 4.3 Consensus size: 30
37945 CATTAAAACT
* * *
37955 GGGTCAAGTTTGAATTTTTTGAAAGTTCAA
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
* *
37985 GGGTCAAACTTGAATTTTTGGAAAGTTTGA
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
* *
38015 GGGTCAAATTT-AAATTTTGGAAAGTTTAG
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
** * * *
38044 GGGTCAAATTCAAATTTTTGAAAAATTT-G
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
38073 GGGTCAAA
1 GGGTCAAA
38081 CATAATTTTA
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
29 34 0.41
30 48 0.59
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (30 bp):
GGGTCAAATTTGAATTTTTGGAAAGTTTAA
Found at i:38049 original size:59 final size:59
Alignment explanation
Indices: 37955--38080 Score: 148
Period size: 59 Copynumber: 2.1 Consensus size: 59
37945 CATTAAAACT
* * * * * *
37955 GGGTCAAGTTTGAATTTTTTGAAAGTTCAAGGGTCAAACTT-GAATTTTTGGAAAGTTTG
1 GGGTCAAATTTGAAATTTTGGAAAGTTCAAGGGTCAAA-TTCAAATTTTTGAAAAATTTG
* *
38014 AGGGTCAAATTT-AAATTTTGGAAAGTTTAGGGGTCAAATTCAAATTTTTGAAAAATTTG
1 -GGGTCAAATTTGAAATTTTGGAAAGTTCAAGGGTCAAATTCAAATTTTTGAAAAATTTG
38073 GGGTCAAA
1 GGGTCAAA
38081 CATAATTTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
58 10 0.18
59 37 0.65
60 10 0.18
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (59 bp):
GGGTCAAATTTGAAATTTTGGAAAGTTCAAGGGTCAAATTCAAATTTTTGAAAAATTTG
Found at i:39912 original size:24 final size:24
Alignment explanation
Indices: 39804--39927 Score: 185
Period size: 24 Copynumber: 5.2 Consensus size: 24
39794 TAGCCCACAT
*
39804 GAGCCCAAAATGATTAGCTCTTAC
1 GAGCCCAAAATGGTTAGCTCTTAC
39828 GAGCCCAAAATGGTTAGCTCTTAC
1 GAGCCCAAAATGGTTAGCTCTTAC
* * * *
39852 AAGCCTAGAATGATTAGCTCTTAC
1 GAGCCCAAAATGGTTAGCTCTTAC
39876 GAGCCCAAAATGGTTAGCTCTTAC
1 GAGCCCAAAATGGTTAGCTCTTAC
* *
39900 GAGCCCAGAATGGCTAGCTCTTAC
1 GAGCCCAAAATGGTTAGCTCTTAC
39924 GAGC
1 GAGC
39928 TCAGACAGAG
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 89 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (24 bp):
GAGCCCAAAATGGTTAGCTCTTAC
Found at i:42013 original size:4 final size:4
Alignment explanation
Indices: 42002--42050 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
41992 GTATTTATTC
* *
42002 AAAT -AAT AAAT AGAT AAAT AAAT -AA- AAAT AAAAG AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT
42048 AAA
1 AAA
42051 GTTAAAAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 7 0.19
4 27 0.73
5 3 0.08
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:42790 original size:39 final size:39
Alignment explanation
Indices: 42747--42875 Score: 120
Period size: 39 Copynumber: 3.3 Consensus size: 39
42737 CTCTGATTAG
* *
42747 GGTAAAAGATTAAATTGCTTCAGTTTGCCCCATGGTCAA
1 GGTAAAAGATTAGATTGCTTCAATTTGCCCCATGGTCAA
* * *
42786 GGTAAAAGATTGGA-TGATCTTCAATCTT-CCCCACT-CTCAG
1 GGTAAAAGATTAGATTG--CTTCAAT-TTGCCCCA-TGGTCAA
* * * *
42826 GGTAAAATATTAGATTGCTTCAATCTGCTCCATGGTCGA
1 GGTAAAAGATTAGATTGCTTCAATTTGCCCCATGGTCAA
42865 GGTAAAAGATT
1 GGTAAAAGATT
42876 GGATGTTGTG
Statistics
Matches: 70, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
38 4 0.06
39 35 0.50
40 26 0.37
41 5 0.07
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (39 bp):
GGTAAAAGATTAGATTGCTTCAATTTGCCCCATGGTCAA
Found at i:53164 original size:4 final size:4
Alignment explanation
Indices: 53157--53197 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
53147 TCAAATAATT
*
53157 AATA AATA AAT- AA-A AATAA AAGA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AAT-A AATA AATA AATA AATA AATA AA
53198 GTTAAAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 4 0.12
4 25 0.78
5 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (4 bp):
AATA
Found at i:68661 original size:14 final size:14
Alignment explanation
Indices: 68642--68675 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
68632 GTTGGTGGCT
68642 AAAGGATTTAGGCA
1 AAAGGATTTAGGCA
68656 AAAGGATTTAGGCA
1 AAAGGATTTAGGCA
68670 AAAGGA
1 AAAGGA
68676 AGGTCTAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.47, C:0.06, G:0.29, T:0.18
Consensus pattern (14 bp):
AAAGGATTTAGGCA
Found at i:73912 original size:17 final size:18
Alignment explanation
Indices: 73876--73913 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
73866 ATTGCTTTTC
* *
73876 AAAAATATTTTTGGATTA
1 AAAAATACTTTTGGAGTA
73894 AAAAATACTTTTGG-GTA
1 AAAAATACTTTTGGAGTA
73911 AAA
1 AAA
73914 CTCAACCGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (18 bp):
AAAAATACTTTTGGAGTA
Found at i:75436 original size:7 final size:7
Alignment explanation
Indices: 75424--75449 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
75414 TTAAGGTTAG
75424 TGGATTA
1 TGGATTA
75431 TGGATTA
1 TGGATTA
75438 TGGATTA
1 TGGATTA
75445 TGGAT
1 TGGAT
75450 AATAGAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (7 bp):
TGGATTA
Found at i:88278 original size:92 final size:92
Alignment explanation
Indices: 88117--88302 Score: 345
Period size: 92 Copynumber: 2.0 Consensus size: 92
88107 ATCAACCACA
88117 TAGTTCGACTACTCACCGAGTTATTGAATAAAAATGCCTCGGAATGAAGTCCAACTAGTGCAGCG
1 TAGTTCGACTACTCACCGAGTTATTGAATAAAAATGCCTCGGAATGAAGTCCAACTAGTGCAGCG
*
88182 CGTTTAGCAATCTTAAACCTTGAACTT
66 CGTTTAGCAATCTTAAACCCTGAACTT
* *
88209 TAGTTCGACTACTCACCGAGTTGTTGAATAAAAATGCCTCGGAATGAAGTCCAACTAGTGCAGCT
1 TAGTTCGACTACTCACCGAGTTATTGAATAAAAATGCCTCGGAATGAAGTCCAACTAGTGCAGCG
88274 CGTTTAGCAATCTTAAACCCTGAACTT
66 CGTTTAGCAATCTTAAACCCTGAACTT
88301 TA
1 TA
88303 AAACACTGAA
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.28
Consensus pattern (92 bp):
TAGTTCGACTACTCACCGAGTTATTGAATAAAAATGCCTCGGAATGAAGTCCAACTAGTGCAGCG
CGTTTAGCAATCTTAAACCCTGAACTT
Found at i:96591 original size:16 final size:18
Alignment explanation
Indices: 96558--96593 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
96548 TAAACTATTG
96558 AATTATTGAACATTAATT
1 AATTATTGAACATTAATT
96576 AATTATT-AAC-TTAATT
1 AATTATTGAACATTAATT
96592 AA
1 AA
96594 CACAGTTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 3 0.17
18 7 0.39
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (18 bp):
AATTATTGAACATTAATT
Found at i:98548 original size:19 final size:18
Alignment explanation
Indices: 98516--98551 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
98506 TTTAAAAAAT
98516 ATAAAATTTAGAATTTTC
1 ATAAAATTTAGAATTTTC
*
98534 ATAAATATTTTGAATTTT
1 ATAAA-ATTTAGAATTTT
98552 AAAAATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (18 bp):
ATAAAATTTAGAATTTTC
Found at i:98564 original size:19 final size:19
Alignment explanation
Indices: 98520--98591 Score: 65
Period size: 20 Copynumber: 3.7 Consensus size: 19
98510 AAAAATATAA
*
98520 AATTTAGAATTTTCATAAA-T
1 AATTT-GAATTTT-AAAAATT
*
98540 ATTTTGAATTTTAAAAATT
1 AATTTGAATTTTAAAAATT
* *
98559 AATTTGATGTTTTGAAAATT
1 AATTTGA-ATTTTAAAAATT
*
98579 AATTTGATTTTTA
1 AATTTGAATTTTA
98592 TTTTTTTTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
18 4 0.09
19 18 0.42
20 21 0.49
ACGTcount: A:0.39, C:0.01, G:0.08, T:0.51
Consensus pattern (19 bp):
AATTTGAATTTTAAAAATT
Found at i:98571 original size:20 final size:19
Alignment explanation
Indices: 98542--98591 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 19
98532 TCATAAATAT
*
98542 TTTGAATTTTAAAAATTAA
1 TTTGATTTTTAAAAATTAA
*
98561 TTTGATGTTTTGAAAATTAA
1 TTTGAT-TTTTAAAAATTAA
98581 TTTGATTTTTA
1 TTTGATTTTTA
98592 TTTTTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (19 bp):
TTTGATTTTTAAAAATTAA
Found at i:107776 original size:2 final size:2
Alignment explanation
Indices: 107769--107795 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
107759 CATTTCTATT
107769 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 T
107796 TTTATTTATT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:109915 original size:22 final size:23
Alignment explanation
Indices: 109853--109916 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
109843 TAAATTTTTA
109853 AAAATTATAAAAATATAAACTATT
1 AAAATTATAAAAATAT-AACTATT
* * *
109877 AAAATAATAAAATTATAA-TTTT
1 AAAATTATAAAAATATAACTATT
**
109899 ACTATTATAAAAATATAA
1 AAAATTATAAAAATATAA
109917 GATTTAATTC
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
22 17 0.52
23 2 0.06
24 14 0.42
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATTATAAAAATATAACTATT
Found at i:112854 original size:23 final size:23
Alignment explanation
Indices: 112828--112873 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
112818 TTAATCATTA
112828 CATTAGGAAACAAATCTAGAAGT
1 CATTAGGAAACAAATCTAGAAGT
112851 CATTAGGAAACAAATCTAGAAGT
1 CATTAGGAAACAAATCTAGAAGT
112874 TATATGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.22
Consensus pattern (23 bp):
CATTAGGAAACAAATCTAGAAGT
Done.