Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007087.1 Kokia drynarioides strain JFW-HI SEQ_121696, 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: 23124
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1420 original size:17 final size:17
Alignment explanation
Indices: 1398--1447 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
1388 CTACAAGATA
*
1398 AATATTAAATTAAATTT
1 AATATTAAATTAAATGT
*
1415 AATATTAAAATAATAACTGT
1 AATATT-AAAT--TAAATGT
1435 AATATTAAATTAA
1 AATATTAAATTAA
1448 TAAAATACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 9 0.32
18 4 0.14
19 4 0.14
20 11 0.39
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
AATATTAAATTAAATGT
Found at i:5081 original size:26 final size:26
Alignment explanation
Indices: 5052--5102 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
5042 AAAACTCTAA
5052 AGCTTCCAATGGAACTGAACTATTAT
1 AGCTTCCAATGGAACTGAACTATTAT
*
5078 AGCTTCCAGTGGAACTGAACTATTA
1 AGCTTCCAATGGAACTGAACTATTA
5103 CAACAAGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (26 bp):
AGCTTCCAATGGAACTGAACTATTAT
Found at i:11670 original size:20 final size:20
Alignment explanation
Indices: 11633--11670 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11623 TTCAAAGTAT
*
11633 ACATGAAATTCATTGAAACA
1 ACATGAAATTCATAGAAACA
11653 ACATGAGAATTCA-AGAAA
1 ACATGA-AATTCATAGAAA
11671 ACAAGTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.21
Consensus pattern (20 bp):
ACATGAAATTCATAGAAACA
Found at i:14644 original size:23 final size:23
Alignment explanation
Indices: 14618--14696 Score: 122
Period size: 23 Copynumber: 3.4 Consensus size: 23
14608 GAACACTAGC
14618 GTGCTTACTGTTTCGCACTTCGT
1 GTGCTTACTGTTTCGCACTTCGT
14641 GTGCTTACTGTTTCGCACTTCGT
1 GTGCTTACTGTTTCGCACTTCGT
* * *
14664 GTGCTTATTGTTTCACACCTCGT
1 GTGCTTACTGTTTCGCACTTCGT
*
14687 GTGCCTACTG
1 GTGCTTACTG
14697 ATTTGCGCTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.10, C:0.27, G:0.22, T:0.42
Consensus pattern (23 bp):
GTGCTTACTGTTTCGCACTTCGT
Found at i:14716 original size:46 final size:46
Alignment explanation
Indices: 14620--14718 Score: 112
Period size: 46 Copynumber: 2.2 Consensus size: 46
14610 ACACTAGCGT
* * * *
14620 GCTTACTGTTTCGCACTTCGTGTGCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCACACCTCGTGTGCCTACTGTTTCGCACTTCGTGC
* *
14666 GCTTATTGTTTCACACCTCGTGTGCCTACTGATTT-GCGCTAT-GTGC
1 GCTTACTGTTTCACACCTCGTGTGCCTACTG-TTTCGCACT-TCGTGC
14712 GCTTACT
1 GCTTACT
14719 AATTGCACTG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
46 40 0.91
47 4 0.09
ACGTcount: A:0.11, C:0.26, G:0.21, T:0.41
Consensus pattern (46 bp):
GCTTACTGTTTCACACCTCGTGTGCCTACTGTTTCGCACTTCGTGC
Found at i:14737 original size:22 final size:23
Alignment explanation
Indices: 14712--14761 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
14702 CGCTATGTGC
*
14712 GCTTACT-AATTGCACTGTGTTT
1 GCTTACTGAATTGCACTGTGTCT
*
14734 GCTTACTGGATTGCACTGTGTCT
1 GCTTACTGAATTGCACTGTGTCT
14757 GCTTA
1 GCTTA
14762 TTGTTTCCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (23 bp):
GCTTACTGAATTGCACTGTGTCT
Found at i:18360 original size:31 final size:31
Alignment explanation
Indices: 18322--18385 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
18312 GGTAAGGAAT
18322 TTGTGACTTATAGTGATGCTTCTTACAATGG
1 TTGTGACTTATAGTGATGCTTCTTACAATGG
18353 TTGTGACTTATAGTGATGCTTCTTACAATGG
1 TTGTGACTTATAGTGATGCTTCTTACAATGG
18384 TT
1 TT
18386 TGGGTTGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.44
Consensus pattern (31 bp):
TTGTGACTTATAGTGATGCTTCTTACAATGG
Found at i:21830 original size:23 final size:22
Alignment explanation
Indices: 21798--21965 Score: 126
Period size: 22 Copynumber: 7.5 Consensus size: 22
21788 AACGCTAGCA
* *
21798 CTTACAGTTTCGCACTTTGTGTG
1 CTTACTGTTT-GCACTGTGTGTG
*
21821 CTTACTGTTTCGCACCT-CGTGTG
1 CTTACTGTTT-GCA-CTGTGTGTG
* * * * *
21844 CCTATTGATTTGCGCTATGTGCG
1 CTTACTG-TTTGCACTGTGTGTG
* *
21867 CCTACTGATTGCACTGTGTGTG
1 CTTACTGTTTGCACTGTGTGTG
* *
21889 CTTACAGGATTGC-CTGTGTGTG
1 CTTAC-TGTTTGCACTGTGTGTG
* *
21911 CTTACAGGATTGC-CTGTGTGTG
1 CTTAC-TGTTTGCACTGTGTGTG
21933 CTTACTGTATTGCACTGTGTGTG
1 CTTACTGT-TTGCACTGTGTGTG
21956 CTTACTGTTT
1 CTTACTGTTT
21966 CCCCAATACT
Statistics
Matches: 123, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
21 1 0.01
22 59 0.48
23 58 0.47
24 5 0.04
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.40
Consensus pattern (22 bp):
CTTACTGTTTGCACTGTGTGTG
Found at i:21922 original size:45 final size:45
Alignment explanation
Indices: 21873--21960 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 45
21863 TGCGCCTACT
21873 GATTGCACTGTGTGTGCTTACAGGATTGC-CTGTGTGTGCTTACAG
1 GATTGC-CTGTGTGTGCTTACAGGATTGCACTGTGTGTGCTTACAG
* *
21918 GATTGCCTGTGTGTGCTTACTGTATTGCACTGTGTGTGCTTAC
1 GATTGCCTGTGTGTGCTTACAGGATTGCACTGTGTGTGCTTAC
21961 TGTTTCCCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 20 0.50
45 20 0.50
ACGTcount: A:0.14, C:0.18, G:0.30, T:0.39
Consensus pattern (45 bp):
GATTGCCTGTGTGTGCTTACAGGATTGCACTGTGTGTGCTTACAG
Done.